Nuclear Factor I genomic binding associates with chromatin boundaries.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:23402308", "kind": "science-record", "revision": 6, "content_hash": "sha256:a981746c6dfc9e87c52716c57340406d74f404b64325975667cdc68c3c433eb8", "created_at": "2026-11-01T15:40:02Z", "updated_at": "2026-11-01T21:19:40Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Nuclear Factor I genomic binding associates with chromatin boundaries.", "doi": "10.1186/1471-2164-14-99", "pmid": "23402308", "authors": ["Milos Pjanic", "Christoph D Schmid", "Armelle Gaussin", "Giovanna Ambrosini", "Jozef Adamcik", "Petar Pjanic", "Genta Plasari", "Jan Kerschgens", "Giovani Dietler", "Philipp Bucher", "Nicolas Mermod"], "journal": "BMC genomics", "year": 2013, "abstract": "BACKGROUND: The Nuclear Factor I (NFI) family of DNA binding proteins (also called CCAAT box transcription factors or CTF) is involved in both DNA replication and gene expression regulation. Using chromatin immuno-precipitation and high throughput sequencing (ChIP-Seq), we performed a genome-wide mapping of NFI DNA binding sites in primary mouse embryonic fibroblasts.\nRESULTS: We found that in vivo and in vitro NFI DNA binding specificities are indistinguishable, as in vivo ChIP-Seq NFI binding sites matched predictions based on previously established position weight matrix models of its in vitro binding specificity. Combining ChIP-Seq with mRNA profiling data, we found that NFI preferentially associates with highly expressed genes that it up-regulates, while binding sites were under-represented at expressed but unregulated genes. Genomic binding also correlated with markers of transcribed genes such as histone modifications H3K4me3 and H3K36me3, even outside of annotated transcribed loci, implying NFI in the control of the deposition of these modifications. Positional correlation between + and - strand ChIP-Seq tags revealed that, in contrast to other transcription factors, NFI associates with a nucleosomal length of cleavage-resistant DNA, suggesting an interaction with positioned nucleosomes. In addition, NFI binding prominently occurred at boundaries displaying discontinuities in histone modifications specific of expressed and silent chromatin, such as loci submitted to parental allele-specific imprinted expression.\nCONCLUSIONS: Our data thus suggest that NFI nucleosomal interaction may contribute to the partitioning of distinct chromatin domains and to epigenetic gene expression regulation.NFI ChIP-Seq and input control DNA data were deposited at Gene Expression Omnibus (GEO) repository under accession number GSE15844. Gene expression microarray data for mouse embryonic fibroblasts are on GEO accession number GSE15871.", "claims": [{"id": "claim-method", "statement": "NFI-bound genes showed a higher average transcription level than genes not associated to NFI (6.61 vs. 5.85, respectively, p=2.91E-31, two tailed t-test).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:23402308", "locator": "sections[12] \"NFIC as an activator of gene transcription\" paragraph 2", "quote": "NFI-bound genes showed a higher average transcription level than genes not associated to NFI (6.61 vs. 5.85, respectively, p=2.91E-31, two tailed t-test)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "NFI ChIP-Seq data from wild type and NFI-C knock-out mouse embryonic fibroblasts, as well as sequenced input control DNA, were deposited at Gene Expression Omnibus (GEO) repository under the accession number GSE15844. Gene expression microarray data for mouse embryonic fibroblasts were taken from GEO repository under the accession number GSE15871. ChIP-Seq data for histone modifications H3K4me3, H3K27me3, H3K36me3 in mouse embryonic fibroblasts were obtained from GEO repository under the accession number GSE12241.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:23402308", "locator": "sections[21] \"Datasets repository\" paragraph 2", "quote": "NFI ChIP-Seq data from wild type and NFI-C knock-out mouse embryonic fibroblasts, as well as sequenced input control DNA, were deposited at Gene Expression Omnibus (GEO) repository under the accession number GSE15844. Gene expression microarray data for mouse embryonic fibroblasts were taken from GEO repository under the accession number GSE15871. ChIP-Seq data for histone modifications H3K4me3, H3K27me3, H3K36me3 in mouse embryonic fibroblasts were obtained from GEO repository under the accession number GSE12241."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using ChIP-Seq and the ChIP-Peak statistical peak-finding method, the study found that in vivo and in vitro NFI DNA-binding specificities are indistinguishable; the ChIP-Seq and input-control data are available through GEO under accession GSE15844.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:23402308", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "We found that in vivo and in vitro NFI DNA binding specificities are indistinguishable, as in vivo ChIP-Seq NFI binding sites matched predictions based on previously established position weight matrix models of its in vitro binding specificity."}, {"asset": "source:pmid:23402308", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "NFI ChIP-Seq and input control DNA data were deposited at Gene Expression Omnibus (GEO) repository under accession number GSE15844."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using ChIP-Seq and the ChIP-Peak statistical peak-finding method, the study found that in vivo and in vitro NFI DNA-binding specificities are indistinguishable; the ChIP-Seq and input-control data are available through GEO under accession GSE15844.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:23402308"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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