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Series GSE15844 Query DataSets for GSE15844
Status Public on Apr 24, 2010
Title Genome-wide mapping of Nuclear Factor I binding sites using ChIP-Seq in WT and NFI-C knock-out MEFs
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The Nuclear Factor I (NFI) family of DNA binding proteins (also called CAAT box transcription factors or CTF) is involved both in replication of adenoviral DNA and in regulation of gene expression. Using chromatin immuno-precipitation and high throughput sequencing (method termed ChIP-Seq) we performed genome-wide mapping of Nuclear Factor I DNA binding sites in mouse embryonic fibroblasts. We found that in vivo and in vitro NFI binding specificities are identical, since previously established position weight matrix was found to accurately predict binding sites for NFI group of proteins. Positional correlation between + and - strand ChIP-Seq tags revealed that NFI is a nucleosome-binding protein, unlike some other transcription factors. We further found that NFI binding correlates with the specific histone modification H3K4me3, the marker of transcribed promoters. Combining ChIP-Seq with the microarray expression data, we found that NFI associates with promoters with higher transcription level. We estimate that transcribed promoters may be more accessible to transcription factor binding than their nearby regions since NFI preferentially bind their DNA target sites located around transcription start sites. Knocking-out one of the NFI proteins (NFI-C), reduced the occupancy of predicted sites, however at the same time indicating that cells could compensate the missing protein with the other members of the family.

Keywords: ChIP-Seq (chromatin immunoprecipitation and high throughput sequencing)
Overall design ChIP-Seq (chromatin immunoprecipitation and high throughput sequencing) using antibody against NFI family of transcription factors in two cell types (wild type and NFI-C knock-out mouse embryonic fibroblasts MEFs)
Contributor(s) Pjanic M, Schmid C, Ambrosini G, Bucher P, Mermod N
Citation(s) 21473784, 23402308
Submission date Apr 27, 2009
Last update date May 15, 2019
Contact name Milos Pjanic
Phone +41 21 693 61 48
Fax +41 21 693 76 10
Organization name Faculty of Biology and Medicine, University of Lausanne
Department Institute of Biotechnology
Lab Laboratory of Molecular Biotechnology
Street address EPFL CH B1 426 Station 6
City Lausanne
State/province VD
ZIP/Postal code 1015
Country Switzerland
Platforms (1)
GPL9185 Illumina Genome Analyzer (Mus musculus)
Samples (3)
GSM398010 NFI ChIP-Seq in wild-type MEF
GSM398011 NFI ChIP-Seq in NFI-C knock-out MEF
GSM398012 INPUT DNA in wild-type MEF
SRA SRP002010
BioProject PRJNA116819

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE15844_RAW.tar 1.0 Gb (http)(custom) TAR (of BED, SGA, TXT, WIG)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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