Volume 21, Issue 2 | February 2011

Research
- - Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin
    Nicole C. Riddle
    Aki Minoda
    Peter V. Kharchenko
    Artyom A. Alekseyenko
    Yuri B. Schwartz
    Michael Y. Tolstorukov Andrey A. Gorchakov Jacob D. Jaffe Cameron Kennedy Daniela Linder-Basso Sally E. Peach Gregory Shanower Haiyan Zheng Mitzi I. Kuroda
    ...[+9 authors]...,
    Vincenzo Pirrotta
    Peter J. Park
    Sarah C.R. Elgin
    Gary H. Karpen
    First Published December 22, 2010
  - Chromatin signatures of the Drosophila replication program
    Matthew L. Eaton
    Joseph A. Prinz
    Heather K. MacAlpine
    George Tretyakov
    Peter V. Kharchenko
    First Published December 22, 2010
  - Developmental control of the DNA replication and transcription programs
    Jared Nordman
    Sharon Li
    Thomas Eng
    David MacAlpine
    Terry L. Orr-Weaver
    First Published December 22, 2010
  - Genome-wide analysis of promoter architecture in Drosophila melanogaster
    Roger A. Hoskins
    Jane M. Landolin
    James B. Brown
    Jeremy E. Sandler
    Hazuki Takahashi
    Timo Lassmann Charles Yu Benjamin W. Booth Dayu Zhang Kenneth H. Wan Li Yang Nathan Boley Justen Andrews Thomas C. Kaufman Brenton R. Graveley
    ...[+10 authors]...,
    Peter J. Bickel
    Piero Carninci
    Joseph W. Carlson
    Susan E. Celniker
    First Published December 22, 2010
  - Conservation of an RNA regulatory map between Drosophila and mammals
    Angela N. Brooks
    Li Yang
    Michael O. Duff
    Kasper D. Hansen
    Jung W. Park
    First Published October 4, 2010
  - Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence
    Eugene Berezikov
    Nicolas Robine
    Anastasia Samsonova
    Jakub O. Westholm
    Ammar Naqvi
    Jui-Hung Hung Katsutomo Okamura Qi Dai Diane Bortolamiol-Becet Raquel Martin Yongjun Zhao Phillip D. Zamore Gregory J. Hannon
    ...[+8 authors]...,
    Marco A. Marra
    Zhiping Weng
    Norbert Perrimon
    Eric C. Lai
    First Published December 22, 2010
  - Polycomb preferentially targets stalled promoters of coding and noncoding transcripts
    Daniel Enderle
    Christian Beisel
    Michael B. Stadler
    Moritz Gerstung
    Prashanth Athri
    First Published December 22, 2010
  - Broad chromosomal domains of histone modification patterns in C. elegans
    Tao Liu
    Andreas Rechtsteiner
    Thea A. Egelhofer
    Anne Vielle
    Isabel Latorre
    Ming-Sin Cheung Sevinc Ercan Kohta Ikegami Morten Jensen Paulina Kolasinska-Zwierz Heidi Rosenbaum Hyunjin Shin Scott Taing Teruaki Takasaki A. Leonardo Iniguez Arshad Desai Abby F. Dernburg Hiroshi Kimura
    ...[+13 authors]...,
    Jason D. Lieb
    Julie Ahringer
    Susan Strome
    X. Shirley Liu
    First Published December 22, 2010
  - High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans
    Sevinç Ercan
    Yaniv Lubling
    Eran Segal
    Jason D. Lieb
    First Published December 22, 2010
  - Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans
    Wei Niu
    Zhi John Lu
    Mei Zhong
    Mihail Sarov
    John I. Murray
    Cathleen M. Brdlik Judith Janette Chao Chen Pedro Alves Elicia Preston Cindie Slightham Lixia Jiang Anthony A. Hyman Stuart K. Kim
    ...[+9 authors]...,
    Robert H. Waterston
    Mark Gerstein
    Michael Snyder
    Valerie Reinke
    First Published December 22, 2010
  - A global analysis of C. elegans trans-splicing
    Mary Ann Allen
    LaDeana W. Hillier
    Robert H. Waterston
    Thomas Blumenthal
    First Published December 22, 2010
Methods
- - Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome
    Ayelet T. Lamm
    Michael R. Stadler
    Huibin Zhang
    Jonathan I. Gent
    Andrew Z. Fire
    First Published December 22, 2010
  - Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data
    Zhi John Lu
    Kevin Y. Yip
    Guilin Wang
    Chong Shou
    LaDeana W. Hillier
    Ekta Khurana Ashish Agarwal Raymond Auerbach Joel Rozowsky Chao Cheng Masaomi Kato David M. Miller Frank Slack
    ...[+8 authors]...,
    Michael Snyder
    Robert H. Waterston
    Valerie Reinke
    Mark B. Gerstein
    First Published December 22, 2010
  - Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans
    Wei-Jen Chung
    Phaedra Agius
    Jakub O. Westholm
    Michael Chen
    Katsutomo Okamura
    First Published December 22, 2010
Resources
- - The transcriptional diversity of 25 Drosophila cell lines
    Lucy Cherbas
    Aarron Willingham
    Dayu Zhang
    Li Yang
    Yi Zou
    Brian D. Eads Joseph W. Carlson Jane M. Landolin Philipp Kapranov Jacqueline Dumais Anastasia Samsonova Jeong-Hyeon Choi Johnny Roberts Carrie A. Davis Haixu Tang Marijke J. van Baren Srinka Ghosh Alexander Dobin Kim Bell Wei Lin Laura Langton Michael O. Duff Aaron E. Tenney Chris Zaleski Michael R. Brent Roger A. Hoskins Thomas C. Kaufman Justen Andrews Brenton R. Graveley
    ...[+24 authors]...,
    Norbert Perrimon
    Susan E. Celniker
    Thomas R. Gingeras
    Peter Cherbas
    First Published December 22, 2010
  - The Drosophila melanogaster transcriptome by paired-end RNA sequencing
    Bryce Daines
    Hui Wang
    Liguo Wang
    Yumei Li
    Yi Han
    David Emmert William Gelbart
    ...[+2 authors]...,
    Xia Wang
    Wei Li
    Richard Gibbs
    Rui Chen
    First Published December 22, 2010
  - A spatial and temporal map of C. elegans gene expression
    W. Clay Spencer
    Georg Zeller
    Joseph D. Watson
    Stefan R. Henz
    Kathie L. Watkins
    Rebecca D. McWhirter Sarah Petersen Vipin T. Sreedharan Christian Widmer Jeanyoung Jo Valerie Reinke Lisa Petrella Susan Strome Stephen E. Von Stetina
    ...[+9 authors]...,
    Menachem Katz
    Shai Shaham
    Gunnar Rätsch
    David M. Miller
    First Published December 22, 2010
  - Genome-wide analysis of alternative splicing in Caenorhabditis elegans
    Arun K. Ramani
    John A. Calarco
    Qun Pan
    Sepand Mavandadi
    Ying Wang
    Andrew C. Nelson Leo J. Lee
    ...[+2 authors]...,
    Quaid Morris
    Benjamin J. Blencowe
    Mei Zhen
    Andrew G. Fraser
    First Published December 22, 2010

Table of Contents

Volume 21, Issue 2 | February 2011

Research

Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin

Chromatin signatures of the Drosophila replication program

Developmental control of the DNA replication and transcription programs

Genome-wide analysis of promoter architecture in Drosophila melanogaster

Conservation of an RNA regulatory map between Drosophila and mammals

Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence

Polycomb preferentially targets stalled promoters of coding and noncoding transcripts

Broad chromosomal domains of histone modification patterns in C. elegans

High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans

Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans

A global analysis of C. elegans trans-splicing

Methods

Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome

Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data

Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans

Resources

The transcriptional diversity of 25 Drosophila cell lines

The Drosophila melanogaster transcriptome by paired-end RNA sequencing

A spatial and temporal map of C. elegans gene expression

Genome-wide analysis of alternative splicing in Caenorhabditis elegans

Table of Contents

Volume 21, Issue 2 | February 2011

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Research

Methods

Resources