We have been interested in the protein CTCF, which we first identified some years ago as having properties of an insulator, blocking interaction between enhancers and promoters when placed between them. We demonstrated that this activity plays an important role in regulating parent of origin allele-specific gene expression at the Igf2/H19 imprinted locus. Work in recent years has shown that a principal mode of action of CTCF is to stabilize interactions between CTCF binding sites on DNA, leading to formation of loop domains. Depending on the geometry of the interactions such loops can either exclude an enhancer leading to insulation, or bring enhancer and promoter closer together, leading to activation. Work in other laboratories has shown that the cohesin complex is associated with CTCF at many of its binding sites, and is essential for stabilizing long range contacts and for insulator activity involving those sites. We have recently shown that the only cohesin subunit that makes direct contact with CTCF is SA2, which is external to the cohesin ring. We have also explored the role of various biochemical modifications in CTCF function. We have recently extended our studies of CTCF function by identifying an interaction between CTCF and the DEAD box helicase, p68. We found that a non-coding RNA, SRA, which forms a complex with p68, is essential for this interaction. We are now investigating the nature of the p68-SRA interaction, and the role of the RNA in insulator activity of CTCF. A genome-wide survey of p68 and SRA binding sites is being carried out. We have also identified other proteins that interact with SRA and may be important for early development and for chromatin structure determination.

Project Start
Project End
Budget Start
Budget End
Support Year
7
Fiscal Year
2013
Total Cost
$528,213
Indirect Cost
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State
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Ghirlando, Rodolfo; Felsenfeld, Gary (2016) CTCF: making the right connections. Genes Dev 30:881-91
Xiao, Tiaojiang; Wongtrakoongate, Patompon; Trainor, Cecelia et al. (2015) CTCF Recruits Centromeric Protein CENP-E to the Pericentromeric/Centromeric Regions of Chromosomes through Unusual CTCF-Binding Sites. Cell Rep 12:1704-14
Wongtrakoongate, Patompon; Riddick, Gregory; Fucharoen, Suthat et al. (2015) Association of the Long Non-coding RNA Steroid Receptor RNA Activator (SRA) with TrxG and PRC2 Complexes. PLoS Genet 11:e1005615
Sutiwisesak, Rujapope; Kitiyanant, Narisorn; Kotchabhakdi, Naiphinich et al. (2014) Induced pluripotency enables differentiation of human nullipotent embryonal carcinoma cells N2102Ep. Biochim Biophys Acta 1843:2611-2619
Felsenfeld, Gary (2014) A brief history of epigenetics. Cold Spring Harb Perspect Biol 6:
Ghirlando, Rodolfo; Felsenfeld, Gary (2013) Chromatin structure outside and inside the nucleus. Biopolymers 99:225-32
Felsenfeld, Gary; Dekker, Job (2012) Genome architecture and expression. Curr Opin Genet Dev 22:59-61
Ghirlando, Rodolfo; Giles, Keith; Gowher, Humaira et al. (2012) Chromatin domains, insulators, and the regulation of gene expression. Biochim Biophys Acta 1819:644-51
Xiao, Tiaojiang; Wallace, Julie; Felsenfeld, Gary (2011) Specific sites in the C terminus of CTCF interact with the SA2 subunit of the cohesin complex and are required for cohesin-dependent insulation activity. Mol Cell Biol 31:2174-83
Yao, Hongjie; Brick, Kevin; Evrard, Yvonne et al. (2010) Mediation of CTCF transcriptional insulation by DEAD-box RNA-binding protein p68 and steroid receptor RNA activator SRA. Genes Dev 24:2543-55

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