Computer and Statistical Analysis of Transcription Factor Binding and Chromatin Modifications by ChlP-seq Data in Embryonic Stem Cell
Advances in high throughput sequencing technology have enabled the identification of transcription factor (TF) binding sites in genome scale. TF binding is important for medical applications and stem cell studies. Somatic cells can be reprogrammed to a pluripotent state by the combined introduction of factors such as Oct4, Sox2, c-Myc, Klf4. These reprogrammed cells share many characteristics with embryonic stem cells (ESCs) and are known as induced pluripotent stem cells (iPSCs). The signaling requirements for maintenance of human and murine embryonic stem cells (ESCs) differ considerably. Genome wide ChlP-seq TF binding maps in mouse stem cells include Oct4, Sox2, Nanog, Tbx3, Smad2 as well as group of other factors. ChlP-seq allows study of new candidate transcription factors for reprogramming. It was shown that Nr5a2 could replace Oct4 for reprogramming. Epigenetic modifications play important role in regulation of gene expression adding additional complexity to transcription network functioning. We have studied associations between different histone modification using published data together with RNA Pol II sites. We found strong associations between activation marks and TF binding sites and present it qualitatively. To meet issues of statistical analysis of genome ChIP-sequencing maps we developed computer program to filter out noise signals and find significant association between binding site affinity and number of sequence reads. The data provide new insights into the function of chromatin organization and regulation in stem cells.
Yuriy Orlov Nina Orlova Mikael Huss Konstantin Gunbin Nikolay Podkolodnyy Huck-Hui Ng Han Xu Dmitri Afonnikov Bing Lim Jian-Chien Heng Ping Yuan Ming Chen Junli Yan Neil Clarke
Genome Institute of Singapore, Singapore 138672, Singapore Institute of Cytology and Genetics SB RA Siberian University of Consumer Cooperatives, Novosibirsk, Russia Genome Institute of Singapore, Singapore 138672, Singapore Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Novosibirsk State University, Novosib Genome Institute of Singapore, Singapore 138672, Singapore Novosibirsk State University, Novosibirsk Zhejiang University, Hangzhou, China
国际会议
杭州
英文
80-92
2012-04-02（万方平台首次上网日期，不代表论文的发表时间）