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Series GSE77543 Query DataSets for GSE77543
Status Public on Jan 01, 2024
Title Dynamics of NRSF/REST motif evolution favor the canonical NRSE/RE1 form
Organisms Canis lupus familiaris; Equus caballus; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The transcription factor NRSF/REST represses many vertebrate neuronal genes in non-neuronal cells by binding to 3 distinct motif classes, which are the canonical 21bp NRSEs, longer non-canonical sites and solo half-sites. We used ChIP-seq in four mammalian species to determine the evolution of the NRSF binding repertoire. We show that while some NRSEs are deeply conserved, genes with several NRSEs show evidence of compensatory site turnover, suggesting that the association of the transcription factor to its target gene is more important than the specific binding site. We also found that many newborn sites in human are associated with primate specific indels and transposable elements. Our analysis of sites with conserved ChIP-binding in all 4 species demonstrates that both the non-canonical and solo half-sites convert preferentially to canonical motifs. These findings support a model of dynamic conversion between different motif types that account for the preferential accumulation of the canonical NRSE during evolution.
Overall design Performed NRSF/REST ChIP-seq on mouse macrophages, dog myelomonocytic leukemia cells and horse skin fibroblasts. Each group with two IP replicates and one DNA input.
Contributor(s) Jiang S, El-Ali N, Ramirez R, Mortazavi A
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Submission date Feb 03, 2016
Last update date Jan 01, 2024
Contact name Shan Jiang
Lab Mortazavi Lab
Street address 2300E Biological Sciences III
ZIP/Postal code 92697
Country USA
Platforms (3)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL21400 Illumina NextSeq 500 (Canis lupus familiaris)
GPL21401 Illumina NextSeq 500 (Equus caballus)
Samples (9)
GSM2054207 NRSF/REST_ChIPseq_Mm_R1
GSM2054208 NRSF/REST_ChIPseq_Mm_R2
GSM2054209 NRSF/REST_ChIPseq_Mm_Input
BioProject PRJNA310756
SRA SRP069246

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SOFT formatted family file(s) SOFTHelp
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Supplementary file Size Download File type/resource
GSE77543_NRSF.peaks.Cf.txt.gz 18.9 Kb (ftp)(http) TXT
GSE77543_NRSF.peaks.Eq.txt.gz 18.2 Kb (ftp)(http) TXT
GSE77543_NRSF.peaks.Hg.txt.gz 43.0 Kb (ftp)(http) TXT
GSE77543_NRSF.peaks.Mm.txt.gz 19.9 Kb (ftp)(http) TXT
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