Next generation sequencing journal club

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The next-gen journal club meets the third Thursday of every month and discusses articles of interest to those analysing next-generation sequencing data. Topics of interest will include RNA-Seq, Chip-SEQ, targeted re-sequencing and other applications of next-generation sequencing to biological problems.

Future meeting times and topics will be listed here before each meeting.

2010:

  • Jan 21 4-5PM Dr. Olivier Elemento will present Human DNA methylomes at base resolution show widespread epigenomic differences Lyster R et al Nature Nov 2009.
  • Feb 18 4-5PM. Steve Lianoglou will present Biased Chromatin Signatures around Polyadenylation Sites and Exons Spies N et al Mol. Cell 2009.
  • March 25 4-5PM. Chris Mason will present Understanding mechanisms underlying human gene expression variation with RNA sequencing Pickrell et al, Nature 2010 doi:10.1038/nature08872 and Sequencing technologies - the next generation, Metzker ML Nat Rev Genet. 2010 Jan;11(1):31-46.
  • April 8 4-5PM. Dr. Fabien Campagne. Discussion of estimates of transcript expression and statistical tests recently applied to RNA-Seq data to detect differential expression. We will specifically discuss Bullard et al. BMC Bioinformatics 2010.
  • May 20 4-5PM. Dr. Stuart Andrews. Discussion of Yoseph Barash et al. Deciphering the splicing code. Nature, 465:7294, May 6, 2010.
  • June 17 4-5 PM. Dr. Weigang Qiu. Discussion of A human gut microbial gene catalogue established by metagenomic sequencing. Junjie Qin et al. Nature 2010.
  • Sept 16 5-6PM. Ms. Naysha Chambwe will present Conserved role of intragenic DNA methylation in regulating alternative promoters Alika K. Maunakea et al. Nature 2010 doi:10.1038/nature09165
  • Oct 7 5-6PM Dr. Eugenia Giannopoulou will present Mediator and cohesin connect gene expression and chromatin architecture Hagey AL et al Nature 2010
  • Nov 18 5-6PM Dr. Chris Mason will present A map of human genome variation from population-scale sequencing. The 1000 Genomes Project Consortium, Nature 2010.
  • Dec 15 5-6PM Mark Carty will present A Three-Dimensional Model of the Yeast Genome (Erez Lieberman-Aiden et al. Nature. 2010 May 20; 465(7296): 363–367. doi:10.1038/nature08973) and Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome (Zhijun Duan et al. Science 9 October 2009: Vol. 326 no. 5950 pp. 289-293 DOI: 10.1126/science.1181369).

2011:

  • Jan 13 5-6PM Dr. Doron Betel will present Statistical Design and Analysis of RNA Sequencing Data Paul L. Auer and R. W. Doerge. Genetics 2010.
  • Feb 3 5-6PM. Dr. Fabien Campagne will present Dindel: Accurate indel calls from short-read data. CA Albers, G Lunter, Daniel G MacArthur, Gilean McVean, Willem H Ouwehand, Richard Durbin. Genome Research 2010
  • Feb 24 5-6PM. Dr. Altuna Akalin will present Widespread transcription at neuronal activity-regulated enhancers, Tae-Kyung Kim et al. Nature 2010.
  • April 14 5-6PM. Dr. Juan Rodriguez-Flores will present Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. [1] Yingrui Li et al. Nat Genet 2010.
  • June 2nd 2011 5-6PM. Dr. Chris Mason and Fabien Campagne will present A framework for variation discovery and genotyping using next-generation DNA sequencing data [2] De Presto et al. Nat Genet 2011.
  • Sept 22 2011. 5-6PM. Ms. Nyash Chambwe will present Full-length transcriptome assembly from RNA-Seq data without a reference genome. Grabherr MG et al. Nature Biotech. 2011.
  • Oct 27 2011. 5-6PM. Dr. Olivier Elemento. Tumour evolution inferred by single-cell sequencing. Navin, N et al. Nature 472, 90–94 2011.
  • Nov 17 2011. 5-6PM. Cancelled.
  • Dec 1 2011. 5-6PM. Stefanie Gerstberger. Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes Nicholas T. Ingolia, Liana F. Lareau, and Jonathan S. Weissman. Cell. 2011; 147 (4): 789-802
  • Dec 15 2011. 5-6PM. Dr. Juan Rodriguez-Flores. An integrated semiconductor device enabling non-optical genome sequencing. Jonathan M. Rothberg et al. Nature 2011. doi:10.1038/nature10242

2012:

  • Feb 8th 2012. 5-6PM. Nyasha Chambwe. DNA methylome analysis using short bisulfite sequencing data Felix Krueger et al. Nature Methods 9, 145–151 (2012) doi:10.1038/nmeth.1828

We resume the journal club with an ENCODE series, one journal club per week. We are looking for volunteers who are interested in presenting one of the papers.

The journal club does not follow a strict agenda for meeting dates. The best way to learn about the next discussion it join the mailing list. If you would like to subscribe to the mailing list, please email Fabien Campagne. If you attend the meetings, please volunteer to present papers you would like to discuss with the rest of the group.

Meetings will be in the ICB conference room. See directions to the ICB.

An expansive human regulatory lexicon encoded in transcription factor footprints.

Abstract Regulatory factor binding to genomic DNA protects the underlying sequence from cleavage by DNase I, leaving nucleotide-resolution footprints. Using genomic DNase I footprinting across 41 diverse cell and tissue types, we detected 45 million transcription factor occupancy events within regulatory regions, representing differential binding to 8.4 million distinct short sequence elements. Here we show that this small genomic sequence compartment, roughly twice the size of the exome, encodes an expansive repertoire of conserved recognition sequences for DNA-binding proteins that nearly doubles the size of the human cis–regulatory lexicon. We find that genetic variants affecting allelic chromatin states are concentrated in footprints, and that these elements are preferentially sheltered from DNA methylation. High-resolution DNase I cleavage patterns mirror nucleotide-level evolutionary conservation and track the crystallographic topography of protein–DNA interfaces, indicating that transcription factor structure has been evolutionarily imprinted on the human genome sequence. We identify a stereotyped 50-base-pair footprint that precisely defines the site of transcript origination within thousands of human promoters. Finally, we describe a large collection of novel regulatory factor recognition motifs that are highly conserved in both sequence and function, and exhibit cell-selective occupancy patterns that closely parallel major regulators of development, differentiation and pluripotency.

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