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Laminin Reduces Expression of the Human 6 Integrin Subunit Gene by Altering the Level of the Transcription Factors Sp1 and Sp3

Manon Gaudreault,¹ Franois Vigneault,¹ Steeve Leclerc,¹ and Sylvain L. Guérin^1,2

¹From the Oncology and Molecular Endocrinology Research Center and the ²Unit of Ophthalmology, CHUL, Centre Hospitalier Universitaire de Québec and Laval University, Québec, QC, Canada.

	Abstract

Top Abstract Materials and Methods Results Discussion References

 
PURPOSE. Damage to the corneal epithelium results in the massive secretion of fibronectin (FN) shortly after corneal injury, which is later replaced by the secretion of laminin (LM). Laminin is recognized by receptors (6ß1 and 6ß4) that belong to the integrin family. The authors characterized the regulatory influence exerted by laminin on the Sp1/Sp3-mediated 6 gene promoter function.

METHODS. Recombinant plasmids bearing the CAT reporter gene, fused to various segments from the 6 promoter, were transfected into rabbit corneal epithelial cells (RCECs) grown on untreated or on LM-coated culture plates or into Sp1-deficient Drosophila Schneider cells. Expression and DNA binding of Sp1/Sp3 was monitored with the use of Western blot and electrophoretic mobility shift assays (EMSAs), respectively. DNA target sites for Sp1/Sp3 in the 6 gene promoter were identified in vitro by DNAse I footprinting. Binding of Sp1 and of a few other transcription factors was also examined in vivo by chromatin immunoprecipitation (ChIP) assays. Expression of the 6 mRNA in RCECs grown on LM-coated culture plates was also assessed by Northern blot and RT-PCR analyses.

RESULTS. Transfection experiments provided evidence that both Sp1 and Sp3 positively influence 6 promoter activity in Sp1/Sp3-deficient SL2 Schneider cells. Two GC-rich target sites for Sp1/Sp3 (a proximal and a distal site) were identified in the 6 promoter by DNAse I footprinting. Binding of Sp1/Sp3 was further validated in vivo by ChIP. Transfections conducted into RCECs grown on LM-coated culture plates resulted in repression of the activity directed by the 6 promoter. This LM-mediated negative regulatory influence also translated into a similar reduction in the expression of the endogenous 6 mRNA as revealed by both RT-PCR and Northern blot analyses. Most of all, results from EMSA and Western blot analyses suggested that the LM-mediated repression of the 6 promoter activity results in part from the proteolytic cleavage of Sp1/Sp3.

CONCLUSIONS. Unlike FN, which functions as an activator of 5 gene transcription, LM repressed transcription, directed by the 6 gene promoter, by altering the nuclear levels of Sp1 and Sp3. Reappearance of LM in the basement membrane after repair of the corneal damage is therefore expected to substantially contribute to the final steps of this process by influencing the degree to which genes that encode protein products requested for cell adhesion and migration, such as integrin genes, are expressed during corneal wound healing.

Integrins are widely expressed, glycosylated, heterodimeric transmembrane adhesion receptors made up of noncovalently bound - and ß-subunits that link the extracellular matrix (ECM) to the cell’s cytoskeleton. They mediate bidirectional transfer of information through diverse signal transduction pathways (for reviews, see Plow et al.¹² and van der Flier and Sonnenberg¹³ ). In a recent survey of the human genome, 24 - and 9 ß-integrin subunits have been identified,¹⁴ which implies 6 novel - and 1 novel ß-subunits relative to the previously recognized 18 - and 8 ß-subunits reported to form 24 different heterodimers.^{12 15 16 17} However, the existence of these new integrin subunits remains to be firmly established. The 6ß1 and the 6ß4 integrins recognize LM as their ligand.^{18 19} The integrin 6ß4 is a component of the hemidesmosomes (HDs) and is therefore located to the basal side of the basal epithelial cells.^{20 21 22 23} HDs are specialized junctional complexes that contribute to the attachment of epithelial cells to the BM²⁴ and are implicated in signal transduction through 6ß4.²⁵ The pattern of integrins expressed by the basal cells of the corneal epithelium is considerably altered as the leading edge progresses toward the wounded corneal surface.^{4 20 26 27} A few studies reported dynamic changes in the distribution of the 6 subunit during corneal wound healing in vivo.^{20 28} In response to wounding, HDs are disassembled, and the expression of 6²² and ß4²⁷ increases during migration of the epithelial cells in vivo. Stepp et al.²⁷ suggested that the increased ß4 expression must play a role in cell-cell or cell-substrate adhesion mechanisms that are required during the corneal wounding or in the preparation of cells for the restratification process.

Although FN deposition can be observed as early as 3 hours after damage to the corneal epithelium, no staining of LM occurs beneath the leading edge of migrating epithelial cells until 24 hours after the injury.²⁹ Interestingly, FN has been shown to influence the transcriptional activity not only of the 5 subunit gene³⁰ but also that of the LM binding 6 integrin subunit ²² in in vitro cultures of rabbit corneal epithelial cells (RCECs). These results suggest that while corneal epithelial cells start migrating over the newly synthesized temporary FN matrix, expression of the 5 and 6 integrin subunit genes is turned on, ensuring early expression of the 6 subunit well before LM accumulates beneath the leading edge. As a consequence, the signal transduction pathway activated on binding of the 6ß1 and 6ß4 integrins to their ligand LM might trigger regulatory signals distinct from those resulting from the binding of FN to the 5ß1 integrin. Activation of the MAPK pathway through the binding of FN to its 5ß1 integrin was recently reported to result in the transcriptional activation of the 5 gene through a modification in the phosphorylation state of Sp1.³⁰ Both the promoter and the 5'-flanking region of the human 6 subunit gene have recently been cloned.^{31 32 33} Although multiple target sites for Sp1 were identified along the 6 proximal promoter sequence by DNAse I footprinting,³² only the most proximal Sp1 site (position –48 to –43) was assessed for its regulatory influence through site-directed mutagenesis.³¹ In addition, all 6 promoter transfection experiments conducted to date were performed in cancer cell lines of various origins. Nontransformed primary cultured cells are much closer to their in vivo counterparts than are transformed cells or cell lines; consequently, they are attractive as a source of cellular material for gene expression studies^{34 35 36} (also see Gaudreault et al.³⁷ ). Considering that cancer cell lines and nontransformed primary cultured cells of similar tissue origin often behave differently, regulatory elements with negligible regulatory influence in transformed cells may be required for gene transcription in nontransformed cells.

The purpose of this study was to investigate in more detail the role exerted by the positive transcription factors Sp1 and Sp3 on the transcriptional activity directed by the 6 promoter in primary cultured and established tissue-cultured cells and to evaluate whether LM may alter the regulatory influence mediated by these nuclear proteins. DNAse I footprinting analyses identified two specific target sites for Sp1 (a proximal and a distal site) along the 6 promoter sequence. Binding of Sp1 to the 6 promoter was also demonstrated in vivo through ChIP assays. Site-directed mutational analyses provided evidence that different cells use either Sp1 target site, proximal or distal, with varying efficiency. Most of all, the activity directed by the 6 promoter was found to be downregulated when RCECs were grown on LM-coated culture plates. The reduced 6 promoter activity was shown to rely, at least in part, on a reduced level of expression of Sp1 and Sp3 in corneal epithelial cells (RCECs and HCECs) when they are grown on LM.

	Materials and Methods

Top Abstract Materials and Methods Results Discussion References

 
All experiments were conducted in voluntary compliance with the ARVO Statement for the Use of Animals in Ophthalmic and Vision Research, and all procedures were approved by the Laval University Animal Care and Use Committee.

Cell Culture and Media
HCECs were isolated from the limbal area of normal eyes from a 44-year-old donor and were obtained through the Eye Bank from the CHUL Research Center in accordance with a procedure we previously described.^{37 38} RCECs were obtained from the central area of freshly dissected rabbit corneas and were grown into SHEM medium (fetal bovine serum, 15% wt/vol), as recently described.³⁹ Human skin keratinocytes (HSKs) were obtained from normal newborn foreskin specimens from a 17-day-old donor and were cultured with a feeder layer, as recently described.⁴⁰ Human skin fibroblasts (HSFs) were isolated from skin biopsy specimens of healthy male donors and underwent primary culture in Dulbecco modified Eagle medium (DMEM, Gibco BRL, Burlington, ON, Canada) supplemented with 10% fetal bovine serum (FBS; Gibco BRL). Human epithelioid carcinoma HeLa (ATCC CCL 2) cells were grown in DMEM supplemented with 10% fetal bovine serum (FBS). Human colon adenocarcinoma Caco2/15, a derivative of the Caco2 cell line (ATCC HTB-37; Rockville, MD) characterized by Beaulieu and Quaroni,⁴¹ was grown in DMEM high glucose, 10% FBS, HEPES 20 mM, and glutamine 10 mM. ARPE-19 cells were purchased from the ATCC (CRL-2302) (Manassas, VA) and grown in DMEM/F12 growth medium (Canadian Life Technologies, Burlington, ON, Canada) with 3 mM glutamine (Sigma, Oakville, ON, Canada) and supplemented with 10% fetal bovine serum (Hyclone, Logan, UT). SL2 Drosophila Schneider cells (ATCC CRL-1963) were cultured at 28°C without CO₂ in Schneider insect medium (Sigma) supplemented with 10% FBS and 20 µg/mL gentamicin. All cells were grown under 5% CO₂ at 37°C, and gentamicin was added to all media at a final concentration of 15 µg/mL.

Flow Cytometric Analysis
RCECs, HeLa, HSFs, HSKs, and ARPE-19 cells were grown as described and removed from the culture dishes (Sarstedt, Montréal, QC, Canada) with PBS/citrate/EDTA solution and were washed twice with serum-free medium containing 1% BSA and fixed with 1% paraformaldehyde-PBS (1% PFA/PBS) for 20 minutes. Aliquots of fixed cells (1 x 10⁶) were washed twice and resuspended in PBS (pH 7.2) containing 1% BSA. One microgram of a primary antibody directed against the 6 integrin subunit (MA6; Chemicon, Temecula, CA) was added to cell suspensions for 60 minutes at room temperature and agitated on a rotator. After 1 hour, cells were washed twice, and a dilution of 1:100 of fluorescein isothiocyanate-conjugated (FITC) human anti-rat IgG suspended in PBS-1% BSA was added to cells and incubated for 30 minutes on a rotator at room temperature. Finally, cells were resuspended in 1% PFA/PBS and analyzed with a flow cytometer (Epics XL; Beckman Coulter, Miami, FL).

Laminin and Fibronectin Coating
Skin keratinocytes (2.5 x 10⁴/cm²) known for their ability to secrete large amounts of LM-5⁴² and obtained from an adult skin donor (kindly provided by Lucie Germain, Laboratoire d’Organogénèse Expérimentale [LOEX], Hôpital du Saint-Sacrement du CHA, Québec, QC, Canada) were plated on an irradiated 3T3 feeder layer (2 x 10⁴ 3T3/cm²) on tissue culture plates. Keratinocytes were cultured in Dulbecco-Vogt modified Eagle medium (Life Technologies, Grand Island, NY), supplemented with 10% fetal calf serum (FCS; Hyclone-PDI Bioscience, Aurora, ON, Canada), 100 IU/mL penicillin, and 25 µg/mL gentamicin (Sigma, St. Louis, MO) until they reached 30%, 70%, or 100% cell density for various periods of time (1, 3, 5, and 10 days) and then were completely removed from the plates by incubation in 20 mM NH₄OH for 5 to 10 minutes. The plates on which LM was deposited were then washed with PBS and reseeded either with RCECs (2.5 x 10⁴/cm²) or HCECs (5 x 10⁴/cm²) grown to midconfluence before transfection. A similar approach was used with Caco2/15 cells, which are known for their ability to secrete LM-10⁴³ and LM-1. ⁴⁴ When indicated, coating of tissue-culture plates with commercially purified LM (LM-1, 0.5–8 µg/cm²; Sigma) before RCECs were added, as described.³⁰ Human plasma FN (obtained as previously described⁴⁵ ) was coated for 18 hours at 37°C on the culture dishes at 8 µg/cm². Coated petri dishes were washed twice with PBS and blocked at 37°C with 2% BSA in PBS. Cells were then seeded and grown as described.

Plasmids and Oligonucleotides
Recombinant plasmids 6–84, 6–141, 6–181, 6–352, 6–430, and 6–590—all of which bore the chloramphenicol acetyltransferase (CAT) reporter gene fused to DNA fragments from the human 6 gene upstream regulatory sequence extending to 5' positions –84, –141, –181, –352, –430, and –590 but shared a common 3' end located at position +76—were constructed. The PGEM-3Z f(+) AvaI/6 plasmid that bears the human 6 gene promoter from position –930 to +76 relative to the 6 mRNA start site (generously provided by Schei Kitazawa, Kobe University School of Medicine, Kusunoki-Cho, Chuo-Ku, Kobe, Japan) was linearized at its unique KpnI site (5' end) and was treated with the nuclease Bal31 before it was blunted. The 5'-digested 6 promoter fragments generated were then digested with HindIII (3' end at 6 position +76) before they were ligated into the unique SmaI/HindIII sites of the plasmid PGL3 to produce the PGL3/6–590 vector. The PGL3/6–590 construct was digested with NheI and blunt-ended with Klenow (which then preserved the 6–590 5' end), before it was second-digested with XbaI (which preserved the 6 +76 3' end). The resultant 6 promoter-bearing DNA fragment was ligated upstream of the CAT reporter gene from the pCATBasic vector (Promega, Madison, WI), which was first digested with PstI (5' end), blunt-ended with Klenow, and second digested with XbaI (3' end) before its dephosphorylation with alkaline phosphatase (to yield pCATBasic/6–590). Removal of the 6 promoter fragments from the common SphI site (located upstream from 6 promoter position –590 in the multiple cloning site of the parental plasmid pCATBasic) to the internal restriction sites SacII (at 6 position –84), KpnI (at –141), SacI (at –181), NsiI (at –352), and AccI (at position –430) yielded, after blunt-ending with Klenow and ligation, the plasmids 6–84, 6–141, 6–181, 6–352, and 6–430, respectively.

The plasmid derivatives 6–84/mSp1p, 6–141/mSp1p, and 6–352/mSp1p (which bear mutations into the proximal Sp1 site), 6–352/mSp1d (which bear mutations into the distal Sp1 site), and 6–352/mSp1pd (which bear mutations into the proximal and the distal Sp1 sites) were all produced by PCR with a site-directed mutagenesis kit (QuickChange; Stratagene, La Jolla, CA) according to the manufacturer’s instructions. Parental plasmids 6–84, 6–141, and 6–352 were used as templates. Double-stranded oligonucleotides used to introduce mutations in the Sp1 sites (mutations are shown in bold) contained the following sequences: proximal Sp1 site (top strand, 5'-GGGGCGAGAGGGTGGGGAGGATCGCGGCCGGCGTCCTCGTC-3'; bottom strand, 5'-GACGAGGACGCCGGCCGCGATCCTCCCCACCCTCTCGCCCC-3'); distal Sp1 site (top strand, 5'-GTCCACAGAGATCGCCGCAGTGGGGCTGCTTCGCCG-3'; bottom strand, 5'-CGGCGAAGCAGCCCCACTGCGGCGATCTCTGTGGAC-3'). Sp1 and Sp3 expression plasmids pPacSp1 and pPacSp3, respectively, were obtained from Guntram Suske (Institute für Molecularbiology und Tumorforschung, Philipps Universität, Marburg, Germany). Double-stranded oligonucleotides used for competition assays in the EMSAs contained the following DNA sequences: proximal (5'-GAGGGTGGGGAGGGGCGGGGCCGGCGTCCTCGTCA-3') and distal (5'-TTCTGTCCACAGAGGGCGGCGCAGTGGGGCTGCTT-3'); Sp1 sites identified in this study in the 6 gene promoter and in the alternative Sp1p_a site (5'-GGGCGCGCAAGGAGGGGCGAGAGGGTGGGGAGGGG-3'); the high-affinity binding sites for the transcription factors Sp1 (5'-GATCATATCTGCGGGGCGGGGCAGACACAG-3')⁴⁶ and NFI (5'-TTATTTTGGATTGAAGCCAATATGAG-3')⁴⁷ ; the consensus sequence for the transcription factor E2F1 (5'-CAGAGCCGTTTCGCGCGGTGCGGGCGGTGC-3'); and the AP-1 site identified in the promoter of the human 5 integrin subunit gene (5'-GATCCCCGCGTTGAGTCATTCGCCTC-3').⁴⁸ All oligonucleotides used in the present study were chemically synthesized (Biosearch 8700 apparatus; Millipore, Beford, MA).

DNAse I Footprinting
DNAse I footprinting was performed in DNAse I buffer⁴⁹ by incubating 3 x 10⁴ cpm labeled probe with increasing amounts (1–10 µL) of recombinant Sp1 protein (GST-Sp1–8xHis protein; kindly provided by Claude Labrie, Oncology and Molecular Endocrinology Research Center, CHUL). The recombinant GST-Sp1–8xHis protein was overexpressed in Escherichia coli BL21 CodonPlus R1L cells with the pGEX-Sp1–8xHis plasmid before purification, as described.⁵⁰ The 217-bp HindIII-XbaI DNA fragment from the 6 promoter extending from positions –141 to +76 and the 430-bp fragment spanning 6 promoter sequences from –352 to +76 were used as labeled probes in these assays. DNAse I digestion and further analysis of the digestion products onto polyacrylamide sequencing gels were performed as described.⁴⁹

Chromatin Immunoprecipitation Assays
ChIP analyses were conducted as previously described.⁵¹ Briefly, HCECs were grown on 150-mm tissue culture dishes to approximately 75% confluence in complete medium. Cells were then cross-linked with 1% formaldehyde for 10 minutes, harvested, and chromatin immunoprecipitated with 1 µg polyclonal antibodies directed against the Sp1 (sc-59; Santa Cruz Biotechnology, Inc., Santa Cruz, CA), Sp3 (sc-644; Santa Cruz Biotechnology), and NFI (SC-5567; Santa Cruz Biotechnology) and E2F1 (sc-193x; Santa Cruz Biotechnology) transcription factors. The resultant DNA was analyzed by PCR using a pair of primers (ITGA6-U,5'CTATCAAGGTGTGCGCTGTG-3'; ITGA6-L,5'CAGAATTGTGGTTGCCGAGTA-3') spanning the entire ITGA6 gene-promoter area. As a negative control, each ChIP sample was also subjected to PCR using primers (p21-U [5'AATTCCTCTGAAAGCTGACTGCC3'] and p21-L [5'OAGGTTTACCTGGGGTCTTTA-GA-3']) specific to a region located approximately 2 kbp upstream of the human p21 promoter. Standard deviation is provided and has been calculated from three separate experiments.

Transient Transfections and CAT Assays
HCECs and RCECs were grown to midconfluence (near 80% coverage) into six-well (35-mm) tissue culture plates and transiently transfected using a polycationic detergent reagent (Lipofectamine; Gibco BRL) according to a procedure we previously described.^{30 52} Each reagent (Lipofectamine)-transfected plate received 1 µg 6-CAT test plasmid and 0.5 µg human growth hormone (hGH)-encoding plasmid pXGH5.⁵³ Primary cultured HSFs, established tissue culture HeLa cells, and Drosophila SL2 Schneider cells were transfected according to the calcium phosphate precipitation procedure^{49 54} at a density of 5 x 10⁵ HSF, 4 x 10⁵ HeLa, or 1 x 10⁶ SL2 cells per 60-mm culture plate. Levels of CAT activity for all transfected cells were determined as described⁵⁴ and were normalized to either ß-galactosidase or the amount of hGH secreted into the culture media and were assayed using a kit for quantitative measurement of hGH (Immunocorp, Montréal, QC, Canada). The value presented for each individual test plasmid transfected corresponded to the mean of at least three separate transfections performed in triplicate. To be considered significant, each value had to be at least three times over the background level caused by the reaction buffer used (usually corresponding to 0.15% chloramphenicol conversion). Student’s t-test was performed for comparison of the groups. Differences were considered statistically significant at P < 0.05. All data are expressed as mean ± SD.

Nuclear Extracts, Electrophoretic Mobility Shift Assays, and Supershift Experiments
Crude nuclear extracts were prepared from midconfluent RCECs (5 x 10⁴ cells/cm² cultured for 72 hours usually yields almost 70% coverage of the culture flasks) grown either on BSA- (2% BSA in PBS) or LM-coated culture dishes, as detailed previously.⁵⁵ Electrophoretic mobility shift assays (EMSAs) were conducted as described³⁰ by using the Sp1 oligomer as a probe and 5 µg nuclear proteins. When indicated, unlabeled oligomers bearing the sequence of various target sites for known transcription factors (SP1p, Sp1d, Sp1p_a, Sp1, NFI, AP-1) were added as unlabeled competitors (50-, 100-, 125- and 500-fold molar excesses) during the assay. DNA-protein complexes were then separated by gel electrophoresis through 6% native polyacrylamide gels run against Tris-glycine buffer.⁵⁶ Supershift experiments in EMSA were conducted by incubation of 5 µg nuclear proteins from RCECs in the presence of no or 2 µL polyclonal antibodies raised against the transcription factors Sp1 and Sp3 (Santa Cruz Biotechnology, Inc.).

SDS-PAGE and Western Blot
Approximately 30 µg protein was added to 1 vol sample buffer (6 M urea, 63 mM Tris [pH 6.8], 10% [vol/vol] glycerol, 1% SDS, 0.00125% [wt/vol] bromophenol blue, 300 mM ß-mercaptoethanol) and was size-fractionated on a 10% SDS-polyacrylamide minigel before transfer to a nitrocellulose filter. The blot was then washed in TS and TSM buffers, as described.³⁰ A 1:5000 dilution of a rabbit polyclonal antibody raised against Sp1 or Sp3 was added, and incubation proceeded for 2 hours at 22°C. The blot was then washed and incubated with a 1:1000 dilution of a peroxidase-conjugated goat anti-rabbit immunoglobulin G (Jackson ImmunoResearch Laboratories, Inc., Bar Harbor, ME), and immunoreactive complexes were revealed with the use of Western blot chemiluminescence reagents (Amersham Biosciences, Arlington Heights, IL), as recently described.³⁰

RT-PCR and Northern Blot Analyses
Total RNA was isolated from midconfluent RCECs grown on BSA or on LM-coated culture plates using a reagent (Tri Reagent; Molecular Research Center, Inc., Cincinnati, OH) and was reverse transcribed using a transcriptase kit (Superscript II; Gibco-BRL), as recently detailed.⁵² The resultant newly synthesized first-strand cDNAs were column purified (QIAquick nucleotide removal kit; Qiagen, Santa Clarita, CA) and used for PCR amplification of the 6 integrin subunit transcript and the 18S ribosomal RNA. The DNA sequence of both the 5' and the 3' template primers for 6 (5' primer, CAAGATGGCTACCCAGATAT-bp; 3' primer, CTGAATCTGAGAGGGAACCA-bp; PCR product, 210 bp) was derived from the corresponding human 6 integrin gene (GenBank accession no., NM 000210). Oligonucleotide primers for the amplification of the 18S ribosomal RNA were provided (Quantum RNA 18S Internal Standards kit; Ambion Inc., Austin, TX). Taq polymerase (Pharmacia-LKB, Uppsala, Sweden) was selected for PCR amplification. Cycle parameters were the same for all primers used (denaturation 94°C, 30 seconds; annealing 58°C, 30 seconds; extension 72°C, 30 seconds) with an identical number of cycles (24, 26, 28, 30, 32, and 34 cycles) for both sets of primers. PCR-amplified DNAs were fractionated on a 2% agarose gel, and their positions were revealed by ethidium bromide staining. The gel photograph was scanned (Visage 110S Bioimage analyzer; Millipore) to quantify the alterations in the amount of the 6 and the 18S PCR-amplified fragments.

Northern blot analyses were conducted on total RNA isolated from midconfluent RCECs grown on BSA- or LM-coated culture plates, as detailed. Total RNA was size-fractionated on a 1.2% formaldehyde-agarose gel and blotted onto a Hybond-N+ membrane (Amersham Canada, Oakville, ON, Canada), as described elsewhere. The membrane was then hybridized at 65°C in buffer (PerfectHybrid Plus Hybridization; Sigma). Blots were washed once at 25°C in 2x SSC-0.1% SDS (1x SSC is 150 mM NaCl; 15 mM sodium citrate) and twice at 50°C in 0.2x SSC-0.1% SDS. The labeled probe used for hybridization consisted of a 665-bp EcoRI–EcoRI restriction fragment derived from the 6 cDNA. Membranes were autoradiographed at –80°C for 18 hours before development.

	Results

Top Abstract Materials and Methods Results Discussion References

 
DNAse I Footprinting of the Sp1 Binding Sites along the Promoter of the 6 Integrin Gene Subunit
To determine precisely where Sp1 binds along the 6 integrin subunit gene promoter, in vitro DNAse I footprinting was performed using a recombinant preparation of Sp1. The DNA sequence, located between positions +76 to –352 and constituting the entire 6 promoter, was examined on both strands for Sp1 binding. Two distinct target sites for Sp1 were identified along the 6 promoter sequence: a proximal site, located between positions –38 to –62 (Sp1p; Fig. 1A and also depicted on Fig. 1C ), and a more distal site, located between positions –195 and –215 (Sp1d; Fig. 1B and also depicted on Fig. 1C ). No binding site for Sp1 except Sp1p and Sp1d could be identified on the 6 promoter under the experimental conditions used.

View larger version (43K): [in this window] [in a new window]   FIGURE 1. DNAse I footprinting of Sp1 binding to the 6 gene promoter. (A) A preparation of recombinant Sp1 (1–10 µL) was incubated with a 217-bp 6 probe labeled on either the top (Top) or the bottom strand (Bottom) and subjected to DNAse I digestion. The digestion products were then analyzed by gel electrophoresis through an 8% sequencing gel. The position of a promoter proximal Sp1 protected site (Sp1p) is indicated for both the top and bottom strands. G, Maxam and Gilbert G sequencing ladder; C, labeled probe incubated with DNAse I but without recombinant Sp1. (B) Same as in (A) except that the labeled probe consisted of a 430-bp HindIII-KpnI DNA fragment from the 6 promoter 5' end-labeled on either its bottom or top strand. The position of a promoter distal Sp1 protected site (Sp1d) is indicated for both the bottom and top strands. (C) Positioning of the DNAse I footprinted Sp1 sites along the 6 promoter sequence. The positions of proximal (Sp1p) and distal (Sp1d) Sp1 target sites (boxes) relative to the 6 mRNA start site (identified as +1) are provided, along with the 6 promoter 5' end point from the recombinant constructs 6–84, 6–141, 6–181, and 6–352.

Regulatory Influence Played by Both the Sp1p and the Sp1d Sites on 6 Promoter Activity

View larger version (12K): [in this window] [in a new window]   FIGURE 2. FACS analysis of integrin 6 expression in primary cultured and established tissue culture cells. Expression of the 6 integrin subunit was monitored by FACS analyses in primary cultures of RCEC, HSK, and HSF cells and in established HeLa and ARPE19 cells. Results are expressed as low (+) to very strong (++++) expression of 6 (bottom right table). Typical histograms of ++++ (RCECs), ++ (HeLa), and + (HSFs) are also provided. Values presented are from four individual measurements from two different batches of cells.

View larger version (23K): [in this window] [in a new window]   FIGURE 3. Transfection analyses in primary and established tissue culture cells. (A) Schematic representation of the recombinant 6/CAT constructs used in this study. Positions of proximal (Sp1p) and distal (Sp1d) Sp1 target sites identified by DNAse I footprinting are indicated along with the 5' end of each of the 6 promoter segment contained on the recombinant construct. Mutations that disrupt binding of Sp1 to proximal or distal Sp1 sites (in plasmids 6–84/mSp1p, 6–352/mSp1p, and 6–352/mSp1d), or both (in 6–352/mSp1pd), are indicated by the removal of the corresponding Sp1 box. (B–F) Site-directed mutational analysis of Sp1p and Sp1d. Wild-type constructs 6–84 and 6–352, and their derivatives bearing mutations into either Sp1p (6–84/mSp1p and 6–352/mSp1p) or Sp1d (6–352/mSp1d), or both Sp1 sites (6–352/mSp1pd), were transfected into primary cultured cells (RCECs, B; HSKs, C; HSFs, F) or established tissue culture cells (HeLa, D; ARPE19, E). Cells were then harvested, and CAT activity was determined and normalized to secreted hGH. SD is provided.

To evaluate the respective contribution of Sp1 and Sp3 on the activity directed by the 6 Sp1p and the Sp1d sites, cotransfection experiments were conducted into Drosophila SL2 Schneider cells. These cells have been reported to be deficient in producing these transcription factors and many others expressed in higher eukaryotes, making them an ideal system for studying gene expression or transcription factors function (for a review, see Suske⁵⁷ ). The plasmids 6–141 or 6–352 or their derivatives—which bear mutations into Sp1p (6–141/mSp1p and 6–352/mSp1p), Sp1d (6–352/mSp1d), or both sites (6–352/mSp1pd)—were cotransfected into Schneider cells alone or with recombinant plasmids (pPacSp1 and pPacSp3) containing Sp1 or Sp3 cDNA under the control of the Drosophila actin gene promoter, therefore ensuring high levels of both these proteins in Schneider cells. Preliminary transfection experiments indicated that neither 6–141 nor 6–352 could sustain basal promoter activity when individually transfected into Schneider cells in the absence of Sp1 and Sp3. However, when cotransfected along with pPacSp1, 38- and 68-fold increases in promoter activity were observed with the plasmids 6–141 and 6–352, respectively (Fig. 4) . Mutations that eliminated the Sp1p site did not completely abolish Sp1 responsiveness because the 6 promoter preserved 29% of its activity with the 6–141/mSp1p construct and approximately 75% with 6–352/mSp1p. On the other hand, responsiveness toward Sp3 was much lower than that observed with Sp1 (sevenfold and threefold increases in CAT activity when pPacSp3 was cotransfected along with 6–141 and 6–352, respectively). Mutating the Sp1p site into both constructs entirely abolished promoter activity in SL2 cells, whereas disrupting Sp1d had no influence at all on the Sp3 responsiveness of the 6 promoter (Fig. 4) . Surprisingly, mutations that disrupt the Sp1d site in the 6–352/mSp1d construct did not suppress, but rather stimulated, 6 promoter function when cotransfected with pPacSp1 in SL2 cells. No such effect was observed with Sp3. Cotransfection of pPacSp1 and pPacSp3, together with the 6 promoter constructs, provided evidence that Sp1 and Sp3 do not function synergistically to modulate the transcriptional activity directed by the 6 promoter. At the most, a weak additive effect is observed when the 6–352 construct is cotransfected along with both the Sp1 and Sp3 expression vectors.

View larger version (29K): [in this window] [in a new window]   FIGURE 4. Transfections in Drosophila SL2 Schneider cells. Both the recombinant plasmids 6–141 (which bears only the Sp1p site) and 6–352 (which bears both the Sp1p and the Sp1d sites) and their Sp1-mutated derivatives (6–141/mSp1p, 6–352/mSp1p, 6–352/mSp1d, and 6–352/mSp1pd) were transfected alone or with pPacSp1 (Sp1), pPacSp3 (Sp3), or both (Sp1/Sp3) into Drosophila SL2 Schneider cells. Cells were harvested 48 hours later, and CAT activities (expressed as fold activity relative to the level directed by the 6–141 or the 6–352 promoter constructs alone) was determined and normalized to ß-gal. SD is also provided.

View larger version (42K): [in this window] [in a new window]   FIGURE 5. DNAse I footprinting of an Sp1 alternative target site on the Sp1p-mutated 6 promoter. Recombinant Sp1 (2, 5, or 10 µL) was incubated with the 217-bp 6 probe used in Figure 1A , which bears either an intact (wt) or a mutated (mutant) Sp1p site and 5' end-labeled on either the top (A) or the bottom strand (B). DNA-protein complexes were then subjected to DNAse I digestion, and the products were analyzed by gel electrophoresis through an 8% sequencing gel. The position of the promoter proximal Sp1 protected site (Sp1p) identified on the wild-type promoter fragment (wt) is indicated, along with that of an alternative Sp1 target site (Sp1pa) identified on the labeled probe bearing mutations in the Sp1p site (mutant). G, Maxam and Gilbert G sequencing ladder; C, labeled probe incubated with DNAse I but without recombinant Sp1. (C) Same as in Figure 1C except that the position of the alternative Sp1 site (Sp1pa) is indicated relative to the 6 mRNA start site (identified as +1).

View larger version (83K): [in this window] [in a new window]   FIGURE 6. EMSA analysis of Sp1 binding to the Sp1 sites from the 6 promoter. (A) DNA sequence of the various Sp1 oligonucleotides used in the EMSA. (B) Crude nuclear proteins (5 µg) from RCECs grown on BSA were incubated with the Sp1-labeled probe either alone (C) or in the presence of double-stranded oligonucleotides bearing the sequence of either the Sp1p or Sp1d sites identified in the 6 promoter, or that of the alternative Sp1pa site, as unlabeled competitors. Oligonucleotides bearing the high-affinity binding sites for the unrelated transcription factors NFI and E2F1 were also used as negative controls for the competition experiment. Formation of the DNA-protein complexes was then monitored by EMSA. The position of the Sp1 and Sp3 complexes is shown. P, labeled probe alone; U, unbound fraction of the probe.

Influence of Laminin on the Activity Directed by the 6 Gene Promoter

Interestingly, transfection of the 6–181 plasmid into RCECs grown on LM-coated culture plates resulted in repression of the 6 promoter activity; maximum (eightfold) repression was reached when skin keratinocytes were maintained at after confluence for 5 days before their removal, though this result cannot be considered statistically different from the other conditions used (Fig. 7A) . On the contrary, transfection of 6–181 in RCECs that have been grown on FN-coated culture plates resulted not in a reduction but rather in a nearly threefold increase in 6 promoter activity (Fig. 7A) . To test whether other types of LM will trigger different regulatory responses on the 6 promoter activity, we substituted skin keratinocytes with human colon adenocarcinoma Caco-2 cells because these cells were reported to secrete primarily LM-10.⁴³ As shown on Figure 7B , growing RCECs on LM-10 also resulted in weaker, but significant, repression of 6 promoter function. However, this repression was dependent on the seeding density of RCECs because no repression was observed when cells were seeded at 2.5 x 10⁴ RCECs/cm², whereas a 40% reduction was observed at 7.5 x 10⁴ RCECs/cm². Although skin keratinocytes and Caco-2 cells were shown primarily to secrete LM-5 and LM-10, respectively, in the cell environment, we could not exclude the possibility that they may also secrete other components from the ECM. To validate the results obtained with the keratinocyte- and Caco-2-secreted LMs, RCECs were also grown on culture plates coated with increasing concentrations of a commercial preparation of LM type-1 (LM-1) as a control. As shown on Figure 7C , LM-1 could also downregulate, though to a much lower level than with LM from skin keratinocytes, the expression directed by the 6 promoter contained on the 6–181 construct, validating the use of keratinocyte-mediated secretion of LM as a suitable model for the remaining experiments. Extending the 6 promoter 5' further from position –181 did not result in any further LM-mediated repression (Fig. 7D) . In addition, deletion of the 6 promoter segment located from position –181 to –84 (in plasmid 6–84) had no influence on the repression by LM, suggesting that LM-responsive sequences are located somewhere between the 6 mRNA start site and position –84.

View larger version (22K): [in this window] [in a new window]   FIGURE 7. Transfection of the 6 promoter in RCECs and HCECs grown in the presence of LM. LM-producing dermal keratinocytes (A) or colon carcinoma Caco-2 cells (B) were grown to 30%, 70%, or 100% cell density for 1, 3, 5, and 10 days (for skin keratinocytes) or to 100% confluence for 25 days (for Caco-2). Keratinocytes and Caco-2 cells were then completely removed, and the culture plates were immediately reseeded with RCECs (2.5 x 104/cm2 on LM from skin keratinocytes and 2.5 x 104, 5 x 104, and 7.5 x 104/cm2 on LM from Caco-2 cells) that were grown to midconfluence before transfection with the recombinant plasmid 6–181. Negative controls (–LM) correspond to RCECs seeded on culture plates coated with BSA. CAT activities were measured and expressed relative to the level directed by 6–181 transfected in cells grown without LM. SD is also provided. (C) RCECs were plated on culture plates coated with BSA (used as a negative control; –LM) or with varying concentrations of a commercial preparation of LM type 1 (0.5–8 µg/cm2) before transfection with the plasmid 6–181, as in panel (A). (D) Dermal keratinocytes were grown on culture plates until they reached 100% confluence for 5 days and then were completely removed. Culture plates were reseeded with RCECs before they were transfected with the recombinant plasmids 6–84, 6–141, 6–181, 6–352, 6–430, and 6–590. CAT activities were measured and normalized as in Figure 2 and are expressed relative to the level directed when transfected in RCECs without LM. (E) Same as in panel (D), except that LM-coated plates were reseeded with RCECs (as a control) and HCECs at P2 or P3 before transfection with the 6–181 recombinant construct. As negative controls, RCECs and HCECs were also seeded on BSA before transfection with 6–181 (–LM).

Laminin Alters the Nuclear Level of Sp1 and Sp3 in RCECs
After we established that Sp1 and Sp3 contribute to the transcription of the 6 gene by interacting with proximal and distal Sp1p and Sp1d sites, respectively, we reasoned that LM may exert its repressive influence by altering the nuclear level of each transcription factor. Crude nuclear extracts were obtained from RCECs grown to midconfluence (near 80% coverage of the plate) on culture plates coated with BSA (which is used as a negative control) or with LM and were examined in EMSA for their ability to sustain the binding of both Sp1 and Sp3 to a labeled probe bearing a high-affinity target site for these transcription factors. As shown on Figure 8A , shifted DNA-protein complexes with electrophoretic mobilities identical to those reported for Sp1 and Sp3 could easily be observed in the nuclear extract from RCECs grown solely on BSA (–LM). Specificity of the formation of these complexes was further confirmed through competition experiments in EMSA. Indeed, only the unlabeled Sp1 oligonucleotide, but not the oligomers bearing the target sites for the unrelated transcription factor NFI or AP-1, could compete for the formation of the Sp1/Sp3 complexes (Fig. 8A , right). The identity of the nuclear proteins yielding these complexes as Sp1 and Sp3 was further verified by supershift experiments in EMSA. As shown on Figure 8B (left, –LM), adding a polyclonal antibody directed against Sp1 dramatically reduced the formation of the slowest shifted complex on gel without altering that of the faster migrating complex. On the other hand, adding an Sp3 polyclonal antibody reduced the formation of the slow-migrating complex but totally prevented the formation of the faster one. Both antibodies generated slow-migrating, supershifted complexes (SCs) that corresponded to the recognition of the Sp1 or the Sp3 protein component from the DNA-protein complexes detected on the gel by the Sp1 and Sp3 antibodies, respectively. These results suggest that Sp1 and Sp3 are constituents of the more intense, slow-migrating complex seen in EMSA, whereas the less intense, faster migrating complex is exclusively constituted of Sp3 bound to the labeled probe. Both the slow- and the fast-migrating complexes disappeared when incubated along with both the Sp1 and the Sp3 antibodies (Sp1/Sp3Abs; Fig. 8B , left).

View larger version (74K): [in this window] [in a new window]   FIGURE 8. Expression of Sp1 and Sp3 in RCECs grown on LM and FN. (A) EMSA analysis of Sp1 binding in RCECs cultured on LM-coated plates. Crude nuclear proteins (5 µg) from RCECs grown on BSA (–LM) or LM-coated culture plates (precultured with skin keratinocytes for 5 days before removal; +LM) were incubated with the Sp1-labeled probe (left). Where indicated, double-stranded oligonucleotides bearing high-affinity binding sites for the transcription factors Sp1, NFI, and AP-1 were added as unlabeled competitors (right). Formation of the DNA-protein complexes was then monitored by EMSA. The position of the Sp1 and Sp3 complexes is shown. P, labeled probe alone; U, unbound fraction of the probe. (B) Supershift analysis in EMSA. Nuclear proteins from RCECs grown on BSA (–LM) or on LM (+LM) were incubated with the Sp1-labeled probe in the presence of antibodies directed against Sp1 or Sp3, either individually (Sp1Ab, Sp3Ab) or in combination (Sp1/Sp3Abs). Positions of the Sp1 and Sp3 DNA-protein complexes were then revealed by EMSA, as in panel (A). SC, supershifted complexes of low electrophoretic mobility that correspond to the binding of the Sp-antibodies to the Sp1- and Sp3-DNA complexes; C, positive control in which the labeled probe was incubated with proteins but without antibodies. (C) Comparative influence of the ECM components LM and FN on the DNA-binding properties of Sp1/Sp3. Nuclear proteins (5 µg) from RCECs grown on BSA (–FN or –LM) or on culture plates coated with either LM (+LM) or FN (+FN) were incubated with the Sp1-labeled probe before analysis of the complexes formed by EMSA. (D) Approximately 30 µg nuclear proteins from the extracts used in (C) were examined in Western blot analyses using the Sp1 and Sp3 antisera. Positions of the molecular mass markers are shown.

To determine whether the LM-mediated repression of the 6 promoter also translated to similar alterations in the expression of the endogenous 6 mRNA transcript, semiquantitative RT-PCR analyses were conducted. To eliminate the possibility that saturation of the PCR reaction is reached, amplifications were performed at 24, 26, 28, 30, 32, and 34 cycles. The specific 6 PCR product became detectable on gel after 24 cycles of amplification. Its formation happened to be nonlinear at 30 cycles and reached complete saturation after 32 cycles. PCR amplification of the 6 product remained fairly linear from 26 to 30 cycles of amplification (data not shown). As shown on Figure 9A , PCR amplification using both 6 primers yielded a single 6 DNA fragment of the correct size (210 bp) when total RNA was extracted from RCECs grown on BSA (only the result at 28 cycles of PCR amplification is shown). However, a significant reduction was observed when total RNA was obtained from cells grown on LM-coated culture plates. We then isolated total RNA from RCECs grown on either BSA or LM and examined the 6 mRNA transcript by Northern blot analysis. As shown on Figure 9B , a single mRNA species of approximately 5.5 kb that perfectly matched the size previously reported for the major 6 mRNA transcript²² was observed just below the 18S rRNA. As with RT-PCR, expression of the 6 transcript was considerably reduced when RNA was isolated from RCECs grown on LM, on normalization to GAPDH.

View larger version (25K): [in this window] [in a new window]   FIGURE 9. Influence of LM on the expression of the 6 mRNA transcript. (A) Total RNAs extracted from RCECs grown on BSA (–LM) or on LM-coated culture plates (+LM) were reverse transcribed and PCR amplified using synthetic, oligonucleotide primers specific to both the 6 and 18S ribosomal RNAs. Positions of the amplified 210-bp 6 (6) and the 489-bp 18S fragments (18S) is indicated along with that of the most relevant markers (left). (B) Total RNA preparations used in (A) were subjected to analyses by Northern blot. Positions of the 6 5.5-kb mRNA is indicated, along with that of the 28S ribosomal RNA. As a control, the membrane was also hybridized with a 548-bp HindIII-XbaI fragment digested from the human glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) cDNA and used as a labeled probe for normalization of the 6 mRNA signal to that corresponding to GAPDH (1.2 kb).

View larger version (18K): [in this window] [in a new window]   FIGURE 10. In vivo ChIP analysis on the 6 promoter. (A) ChIP assays were performed on HCECs grown on either BSA or LM. Chromatin was isolated and immunoprecipitated with antibodies directed against the transcription factors Sp1, Sp3, NFI, and E2F1. PCR of the 6 (ITGA6) gene promoter was then carried out on the ChIP samples, along with a "no antibody" control (No Ab) that contains chromatin but no antibody, an "input" sample corresponding to 0.2% of the total input chromatin, and a "mock" sample that does not contain chromatin. PCR amplification of a gene segment located approximately 2000 bp upstream of the p21 promoter was also conducted on the same sample as a negative control for all immunoprecipitates. (B) Graph representing the amount of specific PCR products expressed as the percentage of antibody binding versus the amount of PCR product obtained using a standardized aliquot of input chromatin. The signal in the no-antibody lane corresponds to the nonspecific binding background and was subtracted from each sample.

	Discussion

Top Abstract Materials and Methods Results Discussion References

Sp1 is the founding member of a Zn-finger family of transcription factors, the Sp family, which now includes nine Sp genes (Sp1-Sp9; for a review, see Zhao and Meng⁶⁴ ). Sp1 is of a particular interest as its GC-rich target site is found in a very large number of eukaryotic genes, including many integrin subunit genes (for further details, see Zaniolo et al.⁶⁵ ). Consequently, Sp1 is likely to mediate some, if not most, of the regulatory influences the many ECM components exert on the transcription of the integrin subunit genes. By exploiting in vitro DNAse I footprinting, two target sites for Sp1 and Sp3 were identified along the human 6 promoter; a proximal site (Sp1p, centered at position –50) located near the mRNA start site and a more distant site (Sp1d, centered at position –205). The position of the proximal Sp1 site identified in this study (–38 to –62) is consistent with that previously reported for this transcription factor,³¹ unlike the distal site, which has never before been reported. However, the affinity of Sp1 for this more distantly located target site proved to be eightfold lower than that of the proximal site, and its mutation alone had little influence on the basal promoter function in most types of transfected cells. On the other hand, when the Sp1p site was mutated in the shorter 6 promoter-bearing construct 6–84, dramatic reductions in basal promoter activity were observed in all types of cells. However, its mutation had marginal influence considering the longer construct that included an intact Sp1d site (in 6–352). It was only when both Sp1 sites were mutated that a substantial reduction in 6 promoter activity was observed in all types of cells, indicating that both Sp1 sites are redundant with each other. Yet, despite the mutation of both Sp1 sites, basal 6 promoter activity remained relatively high in most types of cells. Remarkably, when the proximal site was mutated, Sp1 was found to bind with a lower affinity to an alternative target site located immediately 5' of Sp1p. Examination of this sequence revealed that it contains a GA- and a GT-rich sequence. Sp1 and Sp3 have been reported to bind to GC-, GT-, or GA-rich target sites with nearly the same affinity⁶⁶ and are therefore likely to bind the alternative Sp1p_a GT- or GA-rich Sp1 sites identified in the 6 basal promoter. Use of an alternative degenerated site by Sp1 may explain the residual promoter activity observed despite that both the Sp1p and the Sp1d sites were mutated in the 6–352 construct. This constitutes a noteworthy evolutionary advantage for Sp1. Its ability to bind and use alternative low-affinity binding sites would ensure the maintenance of a minimal promoter activity when high-affinity sites are lost during the course of evolution.

Dramatic differences were observed in the level of 6 expression (evaluated by FACS analyses) and 6 promoter activity between primary cultured RCECs and HSKs, both of which expressed 6 to high levels, and HSFs, which barely directed any promoter activity at all (5755- and 5025-fold lower than in RCECs and HSKs, respectively, with the 6–352 construct). These results are consistent with basal corneal epithelial cells and skin keratinocytes, two epithelial-type cells, expressing high levels of the 6 integrin subunit while stromal fibroblasts from the cornea do not.^{9 23 38 60 67 68 69 70 71} By exploiting primary RCEC cultures to study the influence played by the ECM on the expression of integrin subunit genes, we previously reported dramatic increases in the activity directed by the promoter of the 4 and 5 integrins when these cells are grown in the presence of FN.^{30 72} In addition to 4 and 5, FN considerably increased (by approximately fivefold) the activity of the 6 promoter in in vitro cultures of RCECs (Fig. 7A) , consistent with the results reported by Grushkin-Lerner et al.²² Interestingly, human LM did not increase but rather reduced to various degrees the expression of the 6 promoter (and that of the 4 and 5 integrin gene promoters⁷² ), irrespective of whether corneal epithelial cells were primary cultured from rabbit or human eyes. Differences in the strength of LM repression between keratinocyte-secreted LM and commercially produced LM-1 may reside in the fact that skin keratinocytes primarily secrete type 5 LM, which is also the major LM isoform secreted during corneal wound healing. Binding of Sp1 and Sp3 to the 6 promoter primarily accounts for its transcription in the many types of cells transfected in the present study. Surprisingly, culturing RCECs in the presence of LM resulted in a reduction in Sp1 binding caused by a corresponding decrease in its expression at the protein level. The appearance of faster migrating DNA-protein complexes in EMSA (Figs. 8A 8B 8C , +LM) and much smaller protein products in Western blot (Fig. 8D , +LM), when cells are grown on LM but not on FN or BSA, indicate that both factors must be subjected to protein degradation by a yet unknown protease(s) that may become activated by the signal transduction pathway activated by the binding of LM to its integrin receptor subunit 6. Similar degradation of Sp1/Sp3 was demonstrated when RCECs reached quiescence at a high cell density.⁵² Interestingly, Sp1 expression has been shown to predominate during the G1 phase of the cell cycle and is then subjected to proteasome-dependent degradation before the S phase, a process thought to be dependent on the level of Sp1 phosphorylation.⁷³ Consequently, LM, by reducing the level to which Sp1 and Sp3 are expressed in RCECs in vitro, also contributes to the reduction in the transcription directed by the 6 promoter when cells are grown on this ECM component.

Although the amount of intact Sp1 clearly decreases when corneal epithelial cells are grown on LM, only marginal reduction of 6 promoter occupation by Sp1 is observed in ChIP. However, ChIP is by no mean a reliable quantitative method. At the most, one may consider ChIP semiquantitative when repeated experiments yield reproducible results on normalization to the input DNA, as has been the case for Sp3 and E2F1 in the present study. We have shown previously that many of the Sp1/Sp3 cleavage products retain their ability to bind Sp1 target sites despite the truncations they bear in their N-terminal domain^{49 52} (see also Figs. 8B 8C , which show the appearance of fast-migrating DNA-protein complexes as Sp1 and Sp3 disappear when cells grow on LM). Therefore, one may assume that such Sp1/Sp3 degradation products will also bind the 6 promoter in vivo when examined by ChIP assays. Without the combined use of EMSA and Western blotting, ChIP would have failed to recognize these 6 promoter-bound proteins as degradation products of Sp1/Sp3 because it does not discriminate for changes in the molecular mass of these proteins. ChIP only requires that the epitope recognized by the antibody used for the immunoprecipitation step be preserved in the truncated proteins, which is precisely the case for Sp1 and Sp3; some of their corresponding degradation products are easily recognized by the Sp1 and Sp3 Abs in Western blot^{49 52} (also see Fig. 8D ). We must therefore consider ChIP for what it truly is: a qualitative method that tells us whether any given transcription factor binds in vivo to a particular gene regulatory area with a resolution range between 300 and 500 bp (which corresponds to the average size of the sonicated, cross-linked DNA used for the assay).

The finding that NFI binds the 6 promoter in ChIP assays, irrespective of whether HCECs are grown on LM, suggests that members from this family of transcription factors, which comprises four proteins—NFI-A, NFI-B, NFI-C, and NFI-X—may contribute to the extinction of 6 gene expression under this culture condition. Interestingly, members of the NFI family are reported to be as efficient as repressors^{74 75 76} as they are as activators^{77 78} of gene transcription. Through interactions with weak binding sites, NFI may regulate gene expression by its ability to cooperate or to compete with many transcription factors.^{74 79} NFI was reported to interact with and antagonize Sp1, resulting in the downregulation of platelet-derived growth factor (PDGF)-A gene expression.⁷⁹ We recently reported that similar interference of Sp1 action by NFI might also account for the transcriptional repression of the PARP-1^{74 80} and p21 genes.⁸¹ A search using computer databases for the identification of transcription factors target sites failed to identify any intact, prototypical NFI binding site in the proximal promoter of the 6 gene but did find a number of putative half-canonical target sites for this transcription factor (data not shown). Therefore, the possibility remains that NFI might bind these degenerated target sites because this transcription factor has been reported to bind half its canonical sequence⁸² in the basal promoter of many genes, including those from surfactant protein-C (SP-C⁸³ ), 3ß-hydroxysteroid/dihydrodiol dehydrogenase (3ß-HSD/DD, AKR1C9⁸⁴ ), and metallothionein-I (MT-I⁸⁵ ).

In addition to NFI and Sp1, the in vivo ChIP analyses evidenced the binding of E2F1 to the 6 promoter. Most interestingly, of all the transcription factors tested, E2F1 was the one whose binding to the 6 promoter was most diminished by the presence of LM on the culture plates. Members of the E2F family play a crucial role in the transactivation of G1/S transition-specific genes⁸⁶ and are thereby required to ensure proper cell proliferation. By conducting a representational difference analysis to identify genes differentially expressed in E2F1^–/– versus wild-type undifferentiated primary keratinocytes, D’Souza et al.⁶¹ identified four integrin gene products (5, 6, ß1, ß4) of 11 distinct genes downregulated in E2F1-deficient cells, suggesting that their transcription is clearly modulated by E2F1. E2F1^–/– knockout mice had a considerably reduced wound healing response after partial tail amputation, suggesting that the 5 and 6 integrin subunits must contribute to this process.⁶¹ D’Souza et al.⁶¹ were unable to reveal the existence of E2F-binding elements in the 5'-flanking sequence of this integrin gene. However, the need for a perfect prototypical E2F1 site (TTTSSCGC, in which S = C or G)⁸⁷ in the 6 promoter is not an absolute requirement because only 12% of the E2F1 target sites occupied by this transcription factor in the human genome have the canonical binding motif, as recently revealed by high-density oligonucleotide tiling arrays.⁸⁸ Other studies have shown the importance of preserving the central SSCGC for E2F binding,⁸⁹ whereas binding can still be retained with a single mismatch in the three Ts.⁸⁷ Therefore, we searched for E2F1 target sites in the 6 promoter that might have diverged from the consensus by one of the three Ts. Three such sites could be identified from positions –191 to –184 on the top strand (5'-TTcGCCGC-3') and from –113 to –106 (5'-GCGGGtAA-3') and –79 to –72 (5'-GCGCGcAA-3') on the bottom strand. Their true functional significance remains to be established.

Considering the results presented in this study, the binding of the 6ß4 integrin to its ligand LM is expected to trigger growth-regulatory signals (probably negative ones) completely distinct from those resulting from the binding of FN to the 5ß1 integrin. Although the positive influence of FN and collagen on cell migration is well documented, that of LM remains controversial because it has been reported to promote or to suppress cell adhesion and migration. Evidence points, however, toward a major role for LM in the suppression of cell growth and migration. Indeed, the overexpression of ß4 in a cell that lacks this integrin subunit slows down the migration of that cell.⁹⁰ LM-5 densely deposited under the cell is suggested to contribute to the stabilization of the 6ß4 integrin binding to this ECM ligand. Retroviral-mediated siRNA suppression of LM-5 in an established oral squamous cell carcinoma (OSCC) cell line substantially enhanced the migratory, tumorigenic, and invasive properties of these cancer cells.⁹¹ Several breakdown products of LM-5, which is composed of three subunits (3ß32), have been reported to exert different influences that may explain, at least in part, the paradoxical action of LM on cell migration. For instance, the proteolytic processing of the 3 chain of LM-5 by plasmin produces an LM-5 molecule that induces the assembly of hemidesmosomes and impedes cell migration.⁹² On the contrary, proteolytic processing of the 2 chain is related to the induction of cell migration.⁹³ Therefore, the secretion of LM while FN declines during the wounding process might signal to epithelial cells the proper time to stop migrating by inducing the degradation of key transcription factors through the proteasome, such as Sp1, thereby shutting down expression of a large number of genes required for cell proliferation and adhesion. Another function LM might play, besides restricting cell migration, would be to stimulate the differentiation of the basal epithelial cells into suprabasal cells as they migrate toward the apical surface of the cornea through their vertical stratification.⁹⁴ Recently, polycarbonic membranes coated with various ECM components were implanted on the wounded corneas of adult cats and were assessed for rapidity and for completeness and persistence of epithelial overgrowth.⁹⁵ It turned out that FN, though efficient for wound closing, could not support persistent epithelial overgrowth, whereas LM, collagen type IV, and collagen type I were all effective in yielding multiple-layered epithelia. These results further support a role for FN in the migration of basal epithelial cells early in wound healing so that the wounded area becomes rapidly covered with epithelial cells, whereas LM, CI, and CIV would act at a later stage to favor differentiation and vertical stratification of the basal cells to reconstitute an intact corneal epithelium.

In summary, each component from the ECM appears to trigger specific transcriptional regulatory signals when taken individually. Some, such as FN and collagen type IV, mediate positive, cell density-specific influences on gene expression (reviewed in Ref. ⁷² ), whereas others, such as LM, suppress gene transcription. Investigating how they influence gene expression when used in combination should be particularly valuable to the understanding of tissue wound healing.

	Acknowledgements

 
The authors thank Claudia Fugère and Lucie Germain (Laboratoire d’Organogénèse Expérimentale [LOEX], Hôpital du Saint-Sacrement, CHA and Department of Surgery and Ophthalmology, Laval University, Québec, QC, Canada) for providing primary cultures of HSKs, HCECs, and HSFs. They also thank Vito Quaranta (Department of Cell Biology, The Scripps Research Institute, La Jolla, CA) for providing the complete 6 cDNA, and Jean-Franois Beaulieu (Centre Hospitalier de l’Université de Sherbrooke [CHUS], Sherbrooke, QC, Canada) for providing the Caco2/15 cells.

	Footnotes

 
Supported by the Canadian Institutes for Health Research (CIHR; Grant 37946) and the Vision Network of the Fonds de la Recherche en Santé du Québec (FRSQ). MG and FV hold Doctoral Research Awards from the FRSQ and the CIHR, respectively. SLG is a research scholar from the FRSQ.

Submitted for publication January 5, 2007; revised March 29, 2007; accepted June 12, 2007.

Disclosure: M. Gaudreault, None; F. Vigneault, None; S. Leclerc, None; S.L. Guérin, None

The publication costs of this article were defrayed in part by page charge payment. This article must therefore be marked "advertisement" in accordance with 18 U.S.C. 1734 solely to indicate this fact.

Corresponding author: Sylvain L. Guérin, Oncology and Molecular Endocrinology Research Center, Centre Hospitalier Universitaire de Québec and Laval University, 2705 Laurier Boulevard, Québec, G1V 4G2, Canada; sylvain.guerin{at}crchul.ulaval.ca.

	References

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