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Genome-wide mapping of transcription factor Oct4, Sox2 and Nanog
binding-sites in mouse embryonic stem cells
Genome Institute of SingaporeDepartment of Biological SciencesNational University of Singapore
ChIP-PET technology to map ES cell specific transcription factors
Yijun Ruan / Chia-Lin Wei (Cloning & Sequencing, Genome Institute of Singapore)
ChIP-PETcapturesOct4binding profile
Determination of cutoff for ChIP-PET data
cutoff
Oct4 Sox2 Nanog
No. of binding sites ~1000 ~1000 ~3000
Based on 4 PET overlap as a cutoff.
Distribution of Oct4 binding sites
Binding site in gene desert
Sox2
Distribution of Nanog binding sites
Oct4Oct4Sox2Sox2
de novo prediction of motifs
Oct4Sox2
The code for targeting Oct4 to the genome
Oct4Oct4Sox2Sox2
Oct4Sox2
1000 Sox2 binding sites1000 Sox2 binding sites
Sox2 binding sites contain a prominent Sox2-Oct4 motifSox2 binding sites contain a prominent Sox2-Oct4 motif
de novode novopredictionpredictionof motifof motif
Question 1: What are the motifs bound by these TFs?Question 1: What are the motifs bound by these TFs?
Oct4 Sox2 Nanog
Oct4 Oct4Sox2 Sox2
?
Oct4 and Sox2 are primarily recruited to the genomeOct4 and Sox2 are primarily recruited to the genomethrough the joint sox2 oct4 motifsthrough the joint sox2 oct4 motifs
de novo prediction of motifs using the ChIP-PET data
What are the motifs bound by Nanog?What are the motifs bound by Nanog?
What are the motifs bound by Nanog?What are the motifs bound by Nanog?
Refined using ChIP-PET dataRefined using ChIP-PET data
Sequences found in EMSA validated probesSequences found in EMSA validated probes
Oct4 positively regulates the expression of novel target genes
Oct4 negatively regulates the expression of Cdx2(trophectoderm transcription factor)
Nanog
Sox2
microRNAs targeted by Nanog
“Core” Target Genes of Oct4, Sox2 and Nanog in mouse ES cells
Nanog
Sox2
Oct4
Configuration of transcription factors interaction with upstream regulatory regionConfiguration of transcription factors interaction with upstream regulatory region
Co-occupancy of sites by OCt4/Sox2/nanog
Whole genome mapsFor Oct4 and Nanog
Oct4 Nanog Sox2
Mouse vs Human comparison of Oct4, Nanog and Sox2 TFBS
Comparison between mouse and human Sox2 binding sitesSox2
SummarySummary
Oct4 and Sox2 make use of oct-sox joint motifs for binding Oct4 and Sox2 make use of oct-sox joint motifs for binding (increased specificities?)(increased specificities?)
Nanog’s motif is abundant in the genomeNanog’s motif is abundant in the genome
Co-targeting of genes by the 3 transcription factorsCo-targeting of genes by the 3 transcription factors Coordinated regulationCoordinated regulation
The 3 transcription factors can regulate positively andThe 3 transcription factors can regulate positively andnegatively regulate transcriptionnegatively regulate transcription
The target genes fall into diverse functional categoriesThe target genes fall into diverse functional categories DNA response pathwayDNA response pathway Cellular proliferationCellular proliferation Inhibitors of lineage specific genesInhibitors of lineage specific genes
Acknowledgement:
Huck Hui NgQiang WuJoon-Lin ChewYuin-Han LohXi ChenWeiwei Zhang
Cloning & Sequencing GroupYijun RuanChia-Lin Wei
Stem Cell Biology GroupBing LimPaul RobsonLarry Stanton
InformaticsVegaKen SungGuillaume BourqueVladLeonard
Funding:
Biomedical Research CouncilA*STARNational University of SingaporeSingapore Millennium Foundation
Comparison between mouse and human Oct4 binding sitesOct4