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Nuclear Factor I genomic binding associates with chromatin boundaries
Milos Pjanic1, Christoph D Schmid, Armelle Gaussin
1Institute of Biotechnology and Center for Biotecghnology UNIL-EPFL, University of Lausanne, 1015, Lausanne, Switzerland. pjanic.milos@gmail.com
BMC Genomics
|February 14, 2013
Summary
Nuclear Factor I (NFI) preferentially binds to highly expressed genes, potentially regulating chromatin domains and epigenetic gene expression. This interaction involves nucleosomes and influences histone modifications, impacting gene regulation.
Area of Science:
- Molecular Biology
- Epigenetics
- Genomics
Background:
- Nuclear Factor I (NFI) proteins regulate DNA replication and gene expression.
- NFI is also known as CCAAT box transcription factors (CTF).
Purpose of the Study:
- To map NFI DNA binding sites genome-wide in primary mouse embryonic fibroblasts using ChIP-Seq.
- To investigate the relationship between NFI binding, gene expression, and epigenetic modifications.
Main Methods:
- Chromatin immuno-precipitation and high-throughput sequencing (ChIP-Seq) for genome-wide NFI binding site mapping.
- Integration of ChIP-Seq data with mRNA profiling and histone modification data (H3K4me3, H3K36me3).
Main Results:
- In vivo and in vitro NFI DNA binding specificities were found to be indistinguishable.
- NFI preferentially associates with and up-regulates highly expressed genes.
- NFI binding correlated with histone modifications and occurred at boundaries of distinct chromatin domains, including imprinted loci.
- NFI associates with a nucleosomal length of DNA, suggesting interaction with positioned nucleosomes.
Conclusions:
- NFI's nucleosomal interaction may partition distinct chromatin domains.
- NFI plays a role in epigenetic gene expression regulation.
- Data deposited in GEO under accession numbers GSE15844 and GSE15871.
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