[ged] Journal Club June 14th 3PM

[Qingpeng]

I will talk about this paper about variation of TF binding  in the JC.
See you then.

http://www.ncbi.nlm.nih.gov/pubmed/20299548

Science. 2010 Apr 9;328(5975):232-5. Epub 2010 Mar 18.
Variation in transcription factor binding among humans.
Kasowski M, Grubert F, Heffelfinger C, Hariharan M, Asabere A, Waszak
SM, Habegger L, Rozowsky J, Shi M, Urban AE, Hong MY, Karczewski KJ,
Huber W, Weissman SM, Gerstein MB, Korbel JO, Snyder M.

Department of Molecular, Cellular, and Developmental Biology, Yale
University, New Haven, CT 06520, USA.
Abstract
Differences in gene expression may play a major role in speciation and
phenotypic diversity. We examined genome-wide differences in
transcription factor (TF) binding in several humans and a single
chimpanzee by using chromatin immunoprecipitation followed by
sequencing. The binding sites of RNA polymerase II (PolII) and a key
regulator of immune responses, nuclear factor kappaB (p65), were
mapped in 10 lymphoblastoid cell lines, and 25 and 7.5% of the
respective binding regions were found to differ between individuals.
Binding differences were frequently associated with single-nucleotide
polymorphisms and genomic structural variants, and these differences
were often correlated with differences in gene expression, suggesting
functional consequences of binding variation. Furthermore, comparing
PolII binding between humans and chimpanzee suggests extensive
divergence in TF binding. Our results indicate that many differences
in individuals and species occur at the level of TF binding, and they
provide insight into the genetic events responsible for these
differences.



Sincerely yours,

Qingpeng Zhang
Graduate Student
Department of Computer Science and Engineering
GED Lab in 316/318 Giltner
Michigan State University
East Lansing, MI 48824