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  1. Research: Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis
    • Maxim Pimkin,
    • Andrew V. Kossenkov,
    • Tejaswini Mishra,
    • Christapher S. Morrissey,
    • Weisheng Wu,
    • Cheryl A. Keller,
    • Gerd A. Blobel,
    • Dongwon Lee,
    • Michael A. Beer,
    • Ross C. Hardison,
    • and Mitchell J. Weiss
    Genome Res. December 2014 24: 1932-1944; Published in Advance October 15, 2014, doi:10.1101/gr.164178.113
    ...megakaryopoiesis as a transcriptional repressor at loci defined by a specific DNA signature. Our findings reveal important new insights into how ERY and MEG lineages arise from a common bipotential progenitor via overlapping and divergent functions of shared hematopoietic transcription factors. Footnotes...
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  2. Research: A heterozygous IDH1R132H/WT mutation induces genome-wide alterations in DNA methylation
    • Christopher G. Duncan,
    • Benjamin G. Barwick,
    • Genglin Jin,
    • Carlo Rago,
    • Priya Kapoor-Vazirani,
    • Doris R. Powell,
    • Jen-Tsan Chi,
    • Darell D. Bigner,
    • Paula M. Vertino,
    • and Hai Yan
    Genome Res. December 2012 22: 2339-2355; Published in Advance August 16, 2012, doi:10.1101/gr.132738.111
    ...A heterozygous IDH1 R132H/WT mutation induces genome-wide alterations in DNA methylation Christopher G. Duncan 1 , 6 , Benjamin G. Barwick 2 , 6 , Genglin Jin 1 , Carlo Rago 3 , Priya Kapoor-Vazirani 4 , Doris R. Powell 4...
  3. LETTER: A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3′ end RNA polyadenylation
    • Zheng Lian,
    • Alexander Karpikov,
    • Jin Lian,
    • Milind C. Mahajan,
    • Stephen Hartman,
    • Mark Gerstein,
    • Michael Snyder,
    • and Sherman M. Weissman
    Genome Res. August 2008 18: 1224-1237; Published in Advance May 16, 2008, doi:10.1101/gr.075804.107
    ...of the polymerase and perhaps dephosphorylation prior to release. Lysine 36 trimethylation occurs across transcribed genes, sometimes alternating with stretches of DNA in which lysine 36 dimethylation is more prominent. Lysine 36 methylation decreases at or near the site of polyadenylation, sometimes disappearing...
  4. Research: De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements
    • Felix Schlesinger,
    • Andrew D. Smith,
    • Thomas R. Gingeras,
    • Gregory J. Hannon,
    • and Emily Hodges
    Genome Res. October 2013 23: 1601-1614; Published in Advance June 28, 2013, doi:10.1101/gr.157271.113
    ...constraint on the methylation state. Together, these data show that intergenic loci, specifically putative enhancers, with methylation states that dynamically change during differentiation are also the most likely to vary both between individuals and between species. Discussion Patterns of DNA methylation...
  5. Research: Mouse endogenous retroviruses can trigger premature transcriptional termination at a distance
    • Jingfeng Li,
    • Keiko Akagi,
    • Yongjun Hu,
    • Anna L. Trivett,
    • Christopher J.W. Hlynialuk,
    • Deborah A. Swing,
    • Natalia Volfovsky,
    • Tamara C. Morgan,
    • Yelena Golubeva,
    • Robert M. Stephens,
    • David E. Smith,
    • and David E. Symer
    Genome Res. May 2012 22: 870-884; Published in Advance February 23, 2012, doi:10.1101/gr.130740.111
    ...) There are no other polymorphic genomic Figure 7. Differential methylation at ERVSlc15a2 reflects its parent of origin. DNAmethylation at left (L) 59 and right (R) 39 LTRs of ERVSlc15a2was assessed using bisulfite sequencing of genomic DNA purified from brains of indicated mouse lineages. (Top, schematic) In amplicon...
  6. Letter: Epigenetics of human T cells during the G0→G1 transition
    • Alexander E. Smith,
    • Constantinos Chronis,
    • Manolis Christodoulakis,
    • Stephen J. Orr,
    • Nicholas C. Lea,
    • Natalie A. Twine,
    • Akshay Bhinge,
    • Ghulam J. Mufti,
    • and N. Shaun B. Thomas
    Genome Res. August 2009 19: 1325-1337; Published in Advance June 22, 2009, doi:10.1101/gr.085530.108
    .... At the DNA level, cytosine methylation (meC) is enriched for nucleosomes that remain at the TSS, whereas in general there is a dearth of meC at TSSs. Furthermore, a drop in meC also marks 3′ transcription termination, and a peak of meC occurs at stop codons. This mimics the 3′ nucleosomal distribution...
  7. LETTER: A novel mode of enhancer evolution: The Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity
    • Aileen M. Smith,
    • Maria-Jose Sanchez,
    • George A. Follows,
    • Sarah Kinston,
    • Ian J. Donaldson,
    • Anthony R. Green,
    • and Berthold Göttgens
    Genome Res. September 2008 18: 1422-1432; Published in Advance August 7, 2008, doi:10.1101/gr.077008.108
    ...they function as information-processing units by integrating the inputs of their respective upstream regulators into tightly controlled spatiotemporal expression patterns. Repetitive DNA, largely derived from transposable elements, is known to make up ∼50% of the human ( Lander et al. 2001 ) and has...
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  8. Perspective: What does our genome encode?
    • John A. Stamatoyannopoulos
    Genome Res. September 2012 22: 1602-1611; doi:10.1101/gr.146506.112
    ...community, deserving of the same level of scrutiny applied to other genic or regulatory features. Leaving the flat behind Gene regulation is fundamentally a three-dimensional (3D) process involving dynamic interactions between genomic DNA and the nuclear protein machinery. And yet, common conceptions...
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  9. Research: A unique H3K4me2 profile marks tissue-specific gene regulation
    • Aleksandra Pekowska,
    • Touati Benoukraf,
    • Pierre Ferrier,
    • and Salvatore Spicuglia
    Genome Res. November 2010 20: 1493-1502; Published in Advance September 14, 2010, doi:10.1101/gr.109389.110
    ...surrounded by genomic DNA (Kornberg and Lorch 1999). The flexible amino termini of nucleosomal histones harbor multiple residues that can be subjected to different types of reversible post-translational modifications, including acetylation and methylation (Bernstein et al. 2007; Li et al. 2007; Mellor et al...
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