CVG Journal Club

Presentations 2015-2016

May 26, 2016 Presenter: Peter Schweitzer (Genomics Core Facility)
Understanding factors involved in Illumina sequencing: the unvarnished truth of Illumina sequencing technologies and platforms.
Apr 28, 2016 Presenter: Ezen Choo
“Ancient transposable elements transformed the uterine regulatory landscape and transcriptome during the evolution of mammalian pregnancy”Lynch, VJ et al., Cell Reports 10(4): 551-561 (2015) link
"Transposable elements and their KRAP-ZFP controllers regulate gene expression in adult tissues." Ecco, G et al. Developmental Cell 36(6): 611-623 (2016) link
Mar 24, 2016 Presenter: Anne McGavigan
“Genome-wide footprinting: ready for prime time?” Sung, MH et al., Nature 13: 222-228 (2016) link
“DNAse footprint signatures are dictated by factor dynamics and DNA sequence” Sung, MH et al., Nature 56(2): 275-285 (2014) link
Feb 25, 2016 Presenter: Joel Brown
“Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder.” Chen, Q et al., Science 351(6271):397-400 (2016) link
Jan 28, 2016 Presenters: John Lis and Jay Mahat
“Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers.” Core, LJ et al., Nat Genetics 46(12):1311-20 (2014) link
“Precise maps of RNA polymerase reveal how promoters direct initiation and pausing.” Kwak, H et al., Science 339(6122):950-3 (2013) link
Nov 19, 2015 Presenter: Nithya Kartha
Konermann, Silvana, et al. "Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex." Nature 517:583-88 (2014). link
Hilton, et al. "Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers." Nat Biotechnology 33:510-517 (2015) link
Oct 29, 2015 Presenter: David Taylor
Lupiáñez DG et al. "Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions." Cell. 2015 May 21;161(5):1012-25. link
Sep 17, 2015 Presenter: Adam Bisogni
Buenrostro, Jason D., et al. "Single-cell chromatin accessibility reveals principles of regulatory variation." Nature 523.7561 (2015): 486-490. link

Presentations 2014-2015

May 28, 2015 Presenter: Leonardo Campagna
Poelstra, Jelmer W., et al. "The genomic landscape underlying phenotypic integrity in the face of gene flow in crows." Science 344.6190 (2014): 1410-1414. link
Apr 30, 2015 Presenter: Lan Tu
Divergent reprogramming routes lead to alternative stem-cell states. Tonge PD, et. al. Nature 2014 Dec 11;516(7530):192-7 link
Mar 26, 2015 Presenter: Nithya Kartha
Variation in cancer risk among tissues can be explained by the number of stem cell divisions. Cristian Tomasetti and Bert Vogelstein. Science 2 January 2015: Vol. 347 no. 6217 pp. 78-81 link
Feb 26, 2015 Presenter: Dongsung Kim
Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components. C Alabert et al., Nature Cell Biology 16, 281-291 (2014) link
Jan 29, 2015 Presenter: Nick Fletcher
Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears. S Liu, Cell v157, May 2014 link
Nov 20, 2014 Presenter: Joel Brown
Cell fate inclination within 2-cell and 4-cell mouse embryos revealed by single-cell RNA sequencing. Biase et al. Genome Research Aug 2014 link
Oct 30, 2014 Presenter: Kate Alexander
Long non-coding RNAs as a source of new peptides. Ruiz-Orera J, et. al. eLife Sept 2014 link
Sept 25, 2014 Presenter: Chelsea Gregg
The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. P Grote Dev Cell Jan 28, 2013 24(2):206-214 link

Presentations 2013-2014

May 29, 2014 Presenter: Jishnu Das
A general framework for estimating the relative pathogenicity of human genetic variants. M Kircher, Nature Genetics 46, 310-315 (2014) link
Apr 24, 2014 Presenter: Sachi Horibata
Citrullination regulates pluripotency and histone H1 binding to chromatin. MA Christophorou, Nature 507, 104-108 (March 2014) link
Mar 27, 2014 Presenter: Ezra Lencer
Conservation and Divergence of Regulatory Strategies at Hox Loci and the Origin of Tetrapod Digits. JM Woltering, D Noordermeer, M Leleu, D Duboule. PLOS Jan 21, 2014. link
Feb 27, 2014 Presenter: Kaixiong Ye
Heteroplasmy of Mouse mtDNA Is Genetically Unstable and Results in Altered Behavior and Cognition. MS Sharpley et al. Cell Oct 2012; 151(2):333-43 link
Jan 30, 2014 Presenter: Iris Jonkers
The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome. Jesse M. Engreitz, et al. Science Aug 2013 link
Nov 21, 2013 Presenter: Botao Liu
Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition. Lee, et al. Nature 2013. link
Oct 31, 2013 Presenter: Jenny Feng
Optical control of mammalian endogenous transcription and epigenetic states, Konermann et. al. Nature 2013 link
Sep 26, 2013 Presenter: David Taylor
Multiple epigenetic mechanisms and the piRNA pathway enforce LINE1 silencing during adult spermatogenesis. Di Giacomo, et al. Mol Cell. 2013 link

Presentations 2012-2013

May 30, 2013 Presenter: Ashley Palmer
Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. M Murtaza, et al. Nature May 2; 497(7447):108-12 link
Apr 25, 2013 Presenter: Aparna Mahadevan
Direct production of mouse disease models by embryo microinjection of TALENs and oligodeoxynucleotides. B Wefers, et. al. PNAS Vol 110, no. 10, March 5, 2013 link
Mar 28, 2013 Presenter: Adam Bisogni
CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification. T Hashimshony et al, Cell Reports, Vol 2, Issue 3, 30 August 2012 link
Feb 28, 2013 Presenter: Katherine Alexander
The Dynamics of Genome-wide DNA Methylation Reprogramming in Mouse Primordial Germ Cells S. Seisenberger, et al. Molecular Cell Vol 78, Issue 6, 28 December 2012 link
Jan 24, 2013 Presenter: Leo Arbiza
Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq. DA Cosmas et al, Science Jan 17 2013 link
Nov 29, 2012 Presenter: Pei Xin Lim
Exome Capture Reveals ZNF423 and CEP164 Mutations, Linking Renal Ciliopathies to DNA Damage Response Signaling, Moumita Chaki, et al. Cell August 2012, p533-548 link
Oct 25, 2012 Presenter: Ashley Palmer
Six2 and Wnt Regulate Self-Renewal and Commitment of Nephron Progenitors through Shared Regulatory Gene Networks. Park JS at al. (2012) Dev Cell. 23(3):637-51 link
Sept 27, 2012 Presenter: Erin Wissink
Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage, Wamstad JA,, Cell 13 Sept 2012. link

Presentations 2011-2012

May 31, 2012 Presenter: Ian Welsh
Montavon et al. A Regulatory Archipelago Controls Hox Genes Transcription in Digits. Cell (2011) vol. 147 (5) pp. 1132-1145. link
April 26, 2012 Presenter: Stephanie Hilz
Deng D, Yan C, Pan X, Mahfouz M, Wang J, Zhu JK, Shi Y, Yan N. Structural basis for sequence-specific recognition of DNA by TAL effectors. Science. 2012 Feb 10;335(6069):720-3. link
March 29, 2012 Presenter: Alex Wang
Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Rhee HS, Pugh BF. Cell 2001 Dec 9; 147(6) link
February 23, 2012 Presenter: Marla Lujan
Abdominal subcutaneous fat gene expression and circulating levels of leptin and adiponectin in polycystic ovary syndrome. Lecke SB, Mattei F, Morsch DM, Spritzer PM. Fertil Steril. 2011 May;95(6):2044-9. Epub 2011 Mar 21.
January 26, 2012 Generation of Chimeric Rhesus Monkeys. Tachibana et. al. Cell Jan 2012. link
November 17, 2011 Germline deletion of the miR-17-92 cluster causes skeletal and growth defects in humans. de Pontual L, et. al. Nat Genet. 2011 Sep 4;43(10):1026-30. doi: 10.1038/ng.915. link
October 27, 2011 Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis. Ichiro Hiratani, et. al. Genome Res. 2010. 20: 155-169 link
September 29, 2011 Integrated genomic analyses of ovarian carcinoma. Cancer Genome Atlas Research Network, Nature, 2011 Jun 29; 474(7353). link

Presentations 2010-2011

May 26, 2011 Global quantification of mammalian gene expression control. Nature Volume: 473, Pages:337Ð342 Date published: (19 May 2011) doi:10.1038/nature10098
April 28, 2011 Mutations in U4atac snRNA, a Component of the Minor Spliceosome, in the Developmental Disorder MOPD I; Huiling He et. al. Science 8 April 2011, Vol 332 no. 6026, p238-240
March 24, 2011 Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding, D Schmidt, et al., Science v.328 no.5981, 21 May 2010
February 24, 2011 Polycomb-Dependent Regulatory Contacts between Distant Hox Loci in Drosophila, Bantignies et al., Cell 144, 214-216, January 21, 2011
January 26, 2011 PiggyBac transposon mutagenesis: a tool for cancer gene discovery in mice. Rad R, et. al. Science. 2010 Nov 19;330(6007):1104-7. Epub 2010 Oct 14.
November 18, 2010 A Large Intergenic Noncoding RNA induced by p53 Mediates Global Gene Repression in the p53 Response. Huarte M, et. al., Cell. 6 Aug 2010, vol 142.
October 28, 2010 Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases. Hockemeyer D,, Nat Biotechnol. 2009 Sep.
September 30, 2010 Hum Mol Genet. 2010 Aug 18. [Epub ahead of print] Ancestral paternal genotype controls body weight and food intake for multiple generations. Yazbek SN, et al
August 26, 2010 Organizational Meeting. Open to anyone interested in attending or helping to organize the journal club meetings.

Presentations 2009-2010

May 24, 2010 Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome Gibson et al. ScienceExpress; May 20 2010 (link)
April 26, 2010 Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content. Hughes et al. 2010 Nature 463:536
March 22, 2010 Murgatroyd et al., Dynamic DNA methylation programs persistent adverse effects of early-life stress. Nature Neuroscience 12, 1559 - 1566 (2009).
February 22, 2010 Bannasch D, Safra N, Young A, Karmi N, Schaible RS, Ling GV. Mutations in the SLC2A9 gene cause hyperuricosuria and hyperuricemia in the dog. PLoS Genet. 2008 Nov;4(11):e1000246. Epub 2008 Nov 7. PubMed PMID: 18989453
January 25, 2010 Coat Variation in the Domestic Dog Is Governed by Variants in Three Genes; Science 326, 150 (2009); Edouard Cadieu, et al.
November 23, 2009 Aging and Environmental Exposures Alter Tissue-Specific DNA Methylation Dependent upon CpG Island Context, Christensen et al. Plos Genetics. August 2009
October 26, 2009 Real-Time DNA Sequencing from Single Polymerase Molecules, Science 2 January 2009: Vol. 323. no. 5910, pp. 133 - 138
September 28, 2009 Topic: Human Genome and Personal Genomics
September 2, 2009 Organizational Meeting

Presentations 2008-2009

May 28, 2009 George A. Garinis, Lieneke M. Uittenboogaard, Heike Stachelscheid, Maria Fousteri, Wilfred van Ijcken, Timo M. Breit, Harry van Steeg, Leon H. F. Mullenders, Gijsbertus T. J. van der Horst, Jens C. Brüning, Carien M. Niessen, Jan H. J. Hoeijmakers and Björn Schumacher. (2009). Persistent transcription-blocking DNA lesions trigger somatic growth attenuation associated with longevity. Nat. Cell Biol. 11:604-615.
April 30, 2009 Fischer J, Koch L, Emmerling C, Vierkotten J, Peters T, Brüning JC, Rüther U. Inactivation of the Fto gene protects from obesity. Nature. 2009 Apr 16;458(7240):894-8.
March 26, 2009 Pollard KS, Salama SR, Lambert N, Lambot MA, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, Kern AD, Dehay C, Igel H, Ares M Jr, Vanderhaeghen P, Haussler D. An RNA gene expressed during cortical development evolved rapidly in humans. Nature. 443, 167-172. (14 September 2006).
February 26, 2009 Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells; Bo Wen, Hao Wu, Yoichi Shinkai, Rafael A Irizarry & Andrew P Feinberg; Nature Genetics Vol 41, No 2, Feb 2009
January 29, 2009 Ondrej Mihola et al, A Mouse Speciation Gene Encodes a Meiotic Histone H3 Methyltransferase; Science 323, 373 (2009)
November 20, 2008 Guillaume Bourque et al, Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res. November 2008 18:1752-1762;
October 30, 2008 Regulation of Hepatic Lipogenesis by the Transcription Factor XBP1 Ann-Hwee Lee, Erez F. Scapa, David E. Cohen, Laurie H. Glimcher Science 13 June 2008: Vol. 320. no. 5882, pp. 1492 - 1496
September 18, 2008 Wang T, Zeng J, Lowe CB, Sellers RG, Salama SR, Yang M, Burgess SM, Brachmann RK, Haussler D. Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. Proc. Natl Acad. Sci. USA (2007) 104:18613–18618.

Presentations 2007-2008

May 29, 2008 Sequential Expression of Pluripotency Markers during Direct Reprogramming ofMouse Somatic Cells; Brambrink Cell Stem Cell Volume 2, Issue 2, 7 February 2008, Pages 151-159
April 24, 2008 A Mouse Model of Mitochondrial Disease Reveals Germline Selection Against Severe mtDNA Mutations. Weiwei Fan, et. al. Science 15 February 2008: Vol. 319. no. 5865, pp. 958 - 962
March 27, 2008 The genomic landscapes of human breast and colorectal cancers. Wood LD, Science. 2007 Nov 16;318(5853):1108-13.
February 28, 2008 Genome-wide network of regulatory genes for construction of a chordate embryo. Shoguchi E, Hamaguchi M, Satoh N. Dev Biol. 2008 Jan 26
January 31, 2008 Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218.
November 29, 2007 Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions; France Denoeud, et. al.; Genome Research 2007 17:746-759
October 25, 2007 Heat Shock Factor 1 Is a Powerful Multifaceted Modifier of Carcinogenesis; Chengkai Dai, Luke Whitesell, Arlin B. Rogers and Susan Lindquist; Cell Volume 130, Issue 6, 21 September 2007, Pages 1005-1018
September 27, 2007 Bernstein BE, et al. A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells. (2006) Cell 125, 315-326.
August 30, 2007 Angiotensin II causes hypertension and cardiac hypertrophy through its receptors in the kidney.
PNAS | November 21, 2006 | vol. 103 | no. 47 | 17985-17990

Presentations 2006-2007

April 26, 2007 A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature 445, 881-885 (22 February 2007)
March 29, 2007 Genome-wide prediction of imprinted murine genes. Philippe P. Luedi,Alexander J. Hartemink, and Randy L. Jirtle. Genome Res. 15:875-884, 2005.
February 22, 2007 "Transcriptional profiling of aging in human muscle reveals a common aging signature" Jacob M. Zahn1, Rebecca Sonu1, Hannes Vogel, Emily Crane1, Krystyna Mazan-Mamczarz, Ralph Rabkin, Ronald W. Davis, Kevin G. Becker, Art B. Owen, Stuart K. Kim.
January 25, 2007 L.J. Niedernhofer et al., "A new progeroid syndrome reveals that genotoxic stress suppresses the somatotroph axis," Nature, 444:1038 - 43, 21/28 December 2006.
November 30, 2006 "Analysis of one million base pairs of Neanderthal DNA" Green et al, Nature 444, 330-336 (16 November 2006)
"Sequencing and Analysis of Neanderthal Genomic DNA" Noonan et al. Science 17 November 2006: Vol. 314. no. 5802, pp. 1113 - 1118
October 26, 2006 Sperm Chromatin Proteomics Identifies Evolutionarily Conserved Fertility Factors.
Diana S. Chu, Hongbin Liu, Paola Nix, Tammy F. Wu, Edward J. Ralston, John R. Yates III and Barbara J.Meyer.
Nature. 2006 Sep 7;443(7107):101-5
August 24, 2006 Interchromosomal Interactions and Olfactory Receptor Choice
Authors: Stravos Lomvardas, Gilad Barnea, David Pisapia, Monica Mendelsohn, Jennifer Kirkland, and Richard Axel.
Cell 126, 403-413 July 28, 2006
September 28, 2006 Evidence that DNA (Cytosine-5) Methyltransferase Regulates Synaptic Plasticity in the Himpocampus
JM Levenson, TL Roth, FD Lubin, CA Miller, I Huang, P Desal, LM Malone, and JD Sweatt
J. Biol. Chem., Vol. 281, Issue 23, 15763-15773, June 9, 2006

Presentations 2005-2006

May 25, 2006 The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells" Loh et al. Nature Genetics. 2006 Apr;38(4):431-40.
April 27, 2006 The microRNA miR-196 acts upstream of Hoxb8 and Shh in limb development; Eran Hornstein, Jennifer H. Mansfield, Soraya Yekta, Jimmy Kuang-Hsien Hu, Brian D. Harfe, Michael T. McManus, Scott Baskerville, David P. Bartel & Clifford J. Tabin
March 23, 2006 SNP technologies and human/dog/mouse HapMap issues and technology to use for LD mapping
February 23, 2006 Lamason et al. (2005). SLC24A5, a Putative Cation Exchanger, Affects Pigmentation in Zebrafish and Humans. Science. 310: 1782-1786
January 26, 2006 Mankad, et al. Natural gene therapy in monozygotic twins with Fanconi anemia.
December 1, 2005 Rens W., et al.Resolution and evolution of the duck-billed platypus karyotype with an X1Y1X2Y2X3Y3X4Y4X5Y5 male sex chromosome constitution. Proc Natl Acad Sci U S A. 2004 Nov 16;101(46):16257-61.
October 27, 2005 Fraga, M. F. et al. Epigenetic differences arise during the lifetime of monozygotic twins. Proc. Natl Acad. Sci. 102, 10604−10609 (2005)
September 29, 2005 First Meeting
Serum response factor regulates a muscle Specific microRNA that targets Hand2 during cardiogenesis. Zhao et al. Nature. 436:14July2005;214-220.