Applying ChIP and ChIA-PET to identify p300, CTCF and Lamin B binding sites in stem cells

• Main Author: Sheng, Jianpeng
• Other Authors: Wei, Chialin
• Format: Final Year Project
• Language: English
• Published: 2009
• Subjects: DRNTU::Science::Biological sciences::Molecular biology
• Online Access: http://hdl.handle.net/10356/18920
• Institution: Nanyang Technological University

Embryonic stem cells (ESCs) have the ability of self-renewal and differentiating into many different cell types, which makes it good choice as the cell source for stem cell therapy. And to exploit the potential of ESCs, two key pathways should be elucidated: the self-renewal process which will amplify the cells to an enough number and the differentiation process which can provide specific cell type for a cell therapy. Both of the two pathways are maintained through the interactions between chromatins and transcription regulatory networks. The group I joined investigated such interactions by chromatin immunuoprecipiation coupled with ultra-high throughput sequencing platform (ChIP-Seq) and chromatin interaction analysis by pair end tag (ChIA-PET) technologies. First, the target sequences of ESCs and neuronal progenitor cells (NPCs) of the whole genome for three different factors, p300, CTCF and Lamin B, were detected by ChIP-Seq analysis. Second, based on the binding sites information obtained, higher order chromatin structures in ESCs and NPCs involved in chromatin interactions were detected by ChIA-PET, which are mainly targeted for p300 and CTCF. The goals are to map target genes, to detect the whole genome long range chromatin interactions, their dynamic changes during differentiation and determine their associations with gene expression.