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Series GSE109690 Query DataSets for GSE109690
Status Public on Apr 16, 2018
Title A Nucleosome Destabilizing Factor that Facilitates Transcription in Chromatin
Organisms Homo sapiens; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Our understanding of transcription by RNA polymerase II (Pol II) is limited by our knowledge of the factors that mediate this critically important process. Here we describe the identification of NDF, a nucleosome destabilizing factor that facilitates Pol II transcription in chromatin. NDF has a PWWP motif, interacts with nucleosomes near the dyad, destabilizes nucleosomes in an ATP-independent manner, and facilitates transcription by Pol II through nucleosomes in a purified and defined transcription system as well as in cell nuclei. Upon transcriptional induction, NDF is recruited to the transcribed regions of thousands of genes and co-localizes with a subset of H3K36me3-enriched regions. Notably, the recruitment of NDF to gene bodies is accompanied by an increase in the transcript levels of many of the NDF-enriched genes. In addition, the global loss of NDF results in a decrease in the RNA levels of many genes. In humans, NDF is present at high levels in all tested tissue types, is essential in stem cells, and is frequently overexpressed in breast cancer. These findings indicate that NDF is a nucleosome destabilizing factor that is recruited to gene bodies during transcriptional activation and facilitates Pol II transcription through nucleosomes.
Overall design ChIP-seq analysis of NDF and H3K36me3 in HeLa S3 (WT) and NDF CRISPR-knockout (KO) cells; ChIP-seq of NDF and H3K36me3 in mouse primary bone marrow-derived macrophages (BMDM) treated with Kdo2-Lipid A (KLA) for 0 h or 6 h; RNA-seq of HeLa WT and KO cells; RNA-seq of mouse BMDMs treated with KLA for 0h or 6 h; GRO-seq analysis of WT and NDF KO cells.

Please note that the 'diffNDF7regions_F8_6hKLA_vs_notx.*' files (available on Series records) are generated from both BMDM_ChIP_NDF7_0hKLA and BMDM_ChIP_NDF7_6hKLA samples.
Contributor(s) Ishii H, Hoeksema MA, Fei J, Glass CK, Ren B, Kadonaga JT
Citation(s) 29759984
NIH grant(s)
Grant ID Grant title Affiliation Name
R35 GM118060 Mechanisms of Eukaryotic Gene Regulation THE REGENTS OF THE UNIV. OF CALIF., UNIV. OF CALIF., SAN DIEGO James T. Kadonaga
R01 DK091183 Transcriptional co-regulators and macrophage gene expression THE REGENTS OF THE UNIV. OF CALIF., UNIV. OF CALIF., SAN DIEGO Christopher K Glass
R01 GM074207 Analysis of Centrosome Dynamics Ludwig Institute for Cancer Research Ltd KAREN OEGEMA
Submission date Jan 26, 2018
Last update date Mar 21, 2019
Contact name Jia Fei
Phone 8484456896
Organization name Rutgers University - New Brunswick
Department Molecular Biology and Biochemistry
Street address 604 Allison Road
City Piscataway
State/province New Jersey
ZIP/Postal code 08854
Country USA
Platforms (2)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (28)
GSM2948520 BMDM_ChIP_H3K36me3_0hKLA
GSM2948521 BMDM_ChIP_H3K36me3_6hKLA
GSM2948522 BMDM_ChIP_input_0hKLA
BioProject PRJNA431727
SRA SRP131467

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE109690_RAW.tar 5.0 Gb (http)(custom) TAR (of BIGWIG, BW, TXT)
GSE109690_diffNDF7regions_F8_6hKLA_vs_notx.bed.gz 6.4 Kb (ftp)(http) BED
GSE109690_diffNDF7regions_F8_6hKLA_vs_notx.txt.gz 8.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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