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Series GSE28286

Query DataSets for GSE28286

Status

Public on Apr 04, 2011

Title

Genome-wide analysis of transcription factor E2F1 mutant proteins reveals that N- and C-terminal protein interaction domains do not participate in targeting E2F1 to the human genome.

Project

ENCODE

Organism

Homo sapiens

Experiment type

Genome binding/occupancy profiling by high throughput sequencing

Summary

Previous studies of E2F family members have suggested that protein-protein interactions may be the mechanism by which E2Fs are recruited to specific genomic regions. We have addressed this hypothesis on a genome-wide scale using ChIP-seq analysis of MCF7 cell lines that express tagged wildtype and mutant E2F1 proteins. First, we performed ChIP-seq for tagged wt E2F1. Then, we analyzed E2F1 proteins that lacked the N terminal SP1 and cyclin A binding domains, the C terminal transactivation and pocket protein binding domains, and the internal marked box domain. Surprisingly, we found that the ChIP-seq patterns of the mutant proteins were identical to that of wt E2F1. However, mutation of the DNA binding domain abrogated all E2F1 binding to the genome. These results suggested that the interaction between the E2F1 DNA binding domain and a consensus motif may be the primary determinant of E2F1 recruitment. To address this possibility, we analyzed the in vivo binding sites for the in vitro-derived consensus E2F1 motif (TTTSSCGC) and also performed de novo motif analysis. We found that only 12% of the ChIP-seq peaks contained the TTTSSCGC motif. De novo motif analysis indicated that most of the in vivo sites lacked the 5â half of the in vitro derived consensus, having instead the in vivo consensus of CGCGC. In summary, our findings do not provide support for the model that protein-protein interactions are involved in recruiting E2F1 to the genome, but rather suggest that recognition of a motif found at most human promoters is the critical determinant.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf

Overall design

9 total ChIP-seq datasets; four different HA-ER-E2F1 mutants, and one HA ER E2F1 wild type dataset done in duplicate, from 5 different stable cell lines derived from MCF7 cells; Three Input replicates from 2 different stable cell lines derived from MCF7 cells; HA ER E2F1 wild type duplicate dataset from MCF7 stable cells; 1 HA ER E2F1 DBDmut replicate from MCF7 stable cells cells, 1 HA ER E2F1ÎC replicate from MCF7 stable cells cells, 1 HA ER E2F1ÎN/C replicate from MCF7 stable cells cells, 1 HA ER E2F1ÎMB replicate from MCF7 stable cells cells, 1 HA ER E2F1ÎMB replicate from MCF7 stable cells cells, 3 Input replicates from MCF7 stable cells cells.

Web link

http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/geo/info/ENCODE.html

Contributor(s)

Cao AR, Farnham PJ

Citation(s)

21310950

BioProject

PRJNA63447

Submission date

Mar 31, 2011

Last update date

May 15, 2019

Contact name

Philip Cayting

E-mail(s)

pcayting@stanford.edu

Organization name

Stanford University

Department

Genetics

Lab

Snyder

Street address

1501 S California Ave

City

Palo Alto

State/province

ZIP/Postal code

94304

Country

USA

Platforms (1)

GPL9052

Illumina Genome Analyzer (Homo sapiens)

Samples (9)

More...

GSM699984	HA ER E2F1 wild type_MCF7 stables_ChIP-seq_rep1
GSM699985	HA ER E2F1 wild type_MCF7 stables_ChIP-seq_rep2
GSM699986	HA ER E2F1 DNA Binding Domain mutant_MCF7 stables_ChIP-seq_rep1

Relations

SRA

SRP006205

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE28286_RAW.tar	1.9 Gb	(http)(custom)	TAR (of BAM)
SRA Run Selector
Processed data provided as supplementary file
Raw data are available in SRA