BEGIN:VCALENDAR
VERSION:2.0
PRODID:-//Memento EPFL//
BEGIN:VEVENT
SUMMARY:BioE COLLOQUIA SERIES:  Towards Predicting Gene Expression from DN
 A Sequence
DTSTART:20191202T121500
DTSTAMP:20260508T120417Z
UID:00a9d0b077ad13a47c8c081bf656a6becb38f6ee3e38d0957c495032
CATEGORIES:Conferences - Seminars
DESCRIPTION:Prof. Jussi Taipale\, University of Cambridge (UK)\nWEEKLY BIO
 ENGINEERING COLLOQUIA SERIES\n(sandwiches served)\n\nAbstract: \nUnderstan
 ding the information encoded in the human genome requires two genetic code
 s\, the first code specifies how mRNA sequence is converted to protein seq
 uence\, and the second code determines where and when the mRNAs are expres
 sed. Although the proteins that read the second\, regulatory code – tran
 scription factors (TFs) – have been largely identified\, the code is poo
 rly understood as it is not known which sequences TFs can bind in the geno
 me. To understand the regulatory code\, we have analyzed the sequence-spec
 ific binding of TFs to unmodified and epigenetically modified DNA in the p
 resence and absence of nucleosomes\, using multiple different methods. Our
  findings indicate that DNA commonly mediates interactions between TFs\, a
 nd that dimer formation results in changes in the binding preferences of T
 Fs. We also found that CpG methylation has both negative and positive effe
 cts on TF binding. The effect of nucleosome is largely negative\, but seve
 ral different TFs from diverse structural families can access nucleosomal 
 DNA using five distinct binding modes. Despite the extensive knowledge of 
 TF binding preferences\, reading the regulatory code still remains a chall
 enge. To address this\, we have taken a multiomic approach to identify the
  sources of this problem by performing several experiments that bridge the
  gap between in vivo analyses such as massively parallel reporter assays a
 nd in vitro studies such as HT-SELEX. A binding model that is required to 
 understand binding of TFs to the genome\, which incorporates information a
 bout cellular TF DNA binding and transcriptional activity\, protein-protei
 n interactions induced by DNA\, and inheritance of epigenetic states acros
 s cell division will be discussed.\n\nBio:\nJussi Taipale obtained his Ph.
 D. at the University of Helsinki (Finland) in 1996. His scientific career 
 continued with postdoctoral work at the University of Helsinki and Johns H
 opkins University (Baltimore\, MD\, USA)\, and group leader positions at t
 he Karolinska Institute (Stockholm\, Sweden) and the University of Cambrid
 ge (UK).\nSince 2017 he is Herchel Smith Professor of Biochemistry at the 
 University of Cambridge (UK).\n\nZoom link for attending remotely:  https
 ://epfl.zoom.us/j/855402627
LOCATION:SV 1717 https://plan.epfl.ch/?room==SV%201717
STATUS:CONFIRMED
END:VEVENT
END:VCALENDAR