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Open Access Research article

Nuclear Factor I genomic binding associates with chromatin boundaries

Milos Pjanic1*, Christoph D Schmid25, Armelle Gaussin16, Giovanna Ambrosini2, Jozef Adamcik37, Petar Pjanic4, Genta Plasari18, Jan Kerschgens1, Giovani Dietler3, Philipp Bucher2 and Nicolas Mermod1

Author Affiliations

1 Institute of Biotechnology and Center for Biotecghnology UNIL-EPFL, University of Lausanne, Lausanne, 1015, Switzerland

2 Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland

3 Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland

4 Peripheral Systems Laboratory, Ecole polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland

5 Present address: Swiss Tropical and Public Health Institute and University of Basel, Basel, Switzerland

6 Present address: Selexis SA, Geneva, Switzerland

7 Present address: ETH Zurich, Department of Health Science and Technology, Zurich, Switzerland

8 Present address: Regenlab SA, Mont-sur-Lausanne, Switzerland

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BMC Genomics 2013, 14:99  doi:10.1186/1471-2164-14-99

Published: 12 February 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.

Results

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.

Conclusions

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.

Keywords:
Chromatin immunoprecipitation; Chromatin domain boundaries; Histone modifications