Volume 23, Issue 10 | October 2013

Research
- - Sumoylation at chromatin governs coordinated repression of a transcriptional program essential for cell growth and proliferation
    Hélène Neyret-Kahn
    Moussa Benhamed
    Tao Ye
    Stéphanie Le Gras
    Jack-Christophe Cossec
    Pierre Lapaquette Oliver Bischof Maia Ouspenskaia
    ...[+3 authors]...,
    Mary Dasso
    Jacob Seeler
    Irwin Davidson
    Anne Dejean
    First Published July 26, 2013
  - Lamin A/C-promoter interactions specify chromatin state–dependent transcription outcomes
    Eivind Lund
    Anja R. Oldenburg
    Erwan Delbarre
    Christel T. Freberg
    Isabelle Duband-Goulet
    First Published July 16, 2013
  - GC skew at the 5′ and 3′ ends of human genes links R-loop formation to epigenetic regulation and transcription termination
    Paul A. Ginno
    Yoong Wearn Lim
    Paul L. Lott
    Ian Korf
    Frédéric Chédin
    First Published July 18, 2013
  - De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements
    Felix Schlesinger
    Andrew D. Smith
    Thomas R. Gingeras
    Gregory J. Hannon
    Emily Hodges
    First Published June 28, 2013
  - Frac-seq reveals isoform-specific recruitment to polyribosomes
    Timothy Sterne-Weiler
    Rocio Teresa Martinez-Nunez
    Jonathan M. Howard
    Ivan Cvitovik
    Sol Katzman
    First Published June 19, 2013
  - Genome-wide and parental allele-specific analysis of CTCF and cohesin DNA binding in mouse brain reveals a tissue-specific binding pattern and an association with imprinted differentially methylated regions
    Adam R. Prickett
    Nikolaos Barkas
    Ruth B. McCole
    Siobhan Hughes
    Samuele M. Amante
    First Published June 26, 2013
  - Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay
    Jessica A. Hurt
    Alex D. Robertson
    Christopher B. Burge
    First Published June 13, 2013
  - The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA
    Michael Regulski
    Zhenyuan Lu
    Jude Kendall
    Mark T.A. Donoghue
    Jon Reinders
    Victor Llaca Stephane Deschamps Andrew Smith Dan Levy W. Richard McCombie Scott Tingey
    ...[+6 authors]...,
    Antoni Rafalski
    James Hicks
    Doreen Ware
    Robert A. Martienssen
    First Published June 5, 2013
  - Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population
    Robert J. Schmitz
    Yupeng He
    Oswaldo Valdés-López
    Saad M. Khan
    Trupti Joshi
    Mark A. Urich Joseph R. Nery
    ...[+2 authors]...,
    Brian Diers
    Dong Xu
    Gary Stacey
    Joseph R. Ecker
    First Published June 5, 2013
  - Multiple RNA recognition patterns during microRNA biogenesis in plants
    Nicolás G. Bologna
    Arnaldo L. Schapire
    Jixian Zhai
    Uciel Chorostecki
    Jerome Boisbouvier
    First Published August 29, 2013
  - DNA damage induces targeted, genome-wide variation of poly(A) sites in budding yeast
    Joel H. Graber
    Fathima I. Nazeer
    Pei-chun Yeh
    Jason N. Kuehner
    Sneha Borikar
    First Published June 20, 2013
  - Meta-analyses of studies of the human microbiota
    Catherine A. Lozupone
    Jesse Stombaugh
    Antonio Gonzalez
    Gail Ackermann
    Doug Wendel
    First Published July 16, 2013
  - Sympatric chimpanzees and gorillas harbor convergent gut microbial communities
    Andrew H. Moeller
    Martine Peeters
    Jean-Basco Ndjango
    Yingying Li
    Beatrice H. Hahn
    First Published June 26, 2013
Methods
- - Pathoscope: Species identification and strain attribution with unassembled sequencing data
    Owen E. Francis
    Matthew Bendall
    Solaiappan Manimaran
    Changjin Hong
    Nathan L. Clement
    Eduardo Castro-Nallar Quinn Snell
    ...[+2 authors]...,
    G. Bruce Schaalje
    Mark J. Clement
    Keith A. Crandall
    W. Evan Johnson
    First Published July 10, 2013
  - Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data
    Song Li
    Louisa M. Liberman
    Neelanjan Mukherjee
    Philip N. Benfey
    Uwe Ohler
    First Published July 1, 2013
Resources
- - Coelacanth genomes reveal signatures for evolutionary transition from water to land
    Masato Nikaido
    Hideki Noguchi
    Hidenori Nishihara
    Atsushi Toyoda
    Yutaka Suzuki
    Rei Kajitani Hikoyu Suzuki Miki Okuno Mitsuto Aibara Benjamin P. Ngatunga Semvua I. Mzighani Hassan W.J. Kalombo Kawilarang W.A. Masengi Josef Tuda Sadao Nogami Ryuichiro Maeda Masamitsu Iwata Yoshitaka Abe Koji Fujimura Masataka Okabe Takanori Amano Akiteru Maeno Toshihiko Shiroishi Takehiko Itoh
    ...[+19 authors]...,
    Sumio Sugano
    Yuji Kohara
    Asao Fujiyama
    Norihiro Okada
    First Published July 22, 2013
  - The million mutation project: A new approach to genetics in Caenorhabditis elegans
    Owen Thompson
    Mark Edgley
    Pnina Strasbourger
    Stephane Flibotte
    Brent Ewing
    Ryan Adair Vinci Au Iasha Chaudhry Lisa Fernando Harald Hutter Armelle Kieffer Joanne Lau Norris Lee Angela Miller Greta Raymant Bin Shen Jay Shendure Jon Taylor
    ...[+13 authors]...,
    Emily H. Turner
    LaDeana W. Hillier
    Donald G. Moerman
    Robert H. Waterston
    First Published June 25, 2013

Table of Contents

Volume 23, Issue 10 | October 2013

Research

Sumoylation at chromatin governs coordinated repression of a transcriptional program essential for cell growth and proliferation

Lamin A/C-promoter interactions specify chromatin state–dependent transcription outcomes

GC skew at the 5′ and 3′ ends of human genes links R-loop formation to epigenetic regulation and transcription termination

De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements

Frac-seq reveals isoform-specific recruitment to polyribosomes

Genome-wide and parental allele-specific analysis of CTCF and cohesin DNA binding in mouse brain reveals a tissue-specific binding pattern and an association with imprinted differentially methylated regions

Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay

The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA

Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population

Multiple RNA recognition patterns during microRNA biogenesis in plants

DNA damage induces targeted, genome-wide variation of poly(A) sites in budding yeast

Meta-analyses of studies of the human microbiota

Sympatric chimpanzees and gorillas harbor convergent gut microbial communities

Methods

Pathoscope: Species identification and strain attribution with unassembled sequencing data

Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data

Resources

Coelacanth genomes reveal signatures for evolutionary transition from water to land

The million mutation project: A new approach to genetics in Caenorhabditis elegans

Table of Contents

Volume 23, Issue 10 | October 2013

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Research

Methods

Resources