Research 1725 Genetic and environmental exposures constrain epigenetic drift over the human...

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Research 1725 Genetic and environmental exposures constrain epigenetic drift over the human...
Volume 24 Issue 11 November 2014
Research
Genetic and environmental exposures constrain epigenetic drift over the human life course
1725
Sonia Shah, Allan F. McRae, Riccardo E. Marioni, Sarah E. Harris, Jude Gibson, Anjali K. Henders,
Paul Redmond, Simon R. Cox, Alison Pattie, Janie Corley, Lee Murphy, Nicholas G. Martin,
Grant W. Montgomery, John M. Starr, Naomi R. Wray, Ian J. Deary, and Peter M. Visscher
Estimating genotype error rates from high-coverage next-generation sequence data
1734
Jeffrey D. Wall, Ling Fung Tang, Brandon Zerbe, Mark N. Kvale, Pui-Yan Kwok,
Catherine Schaefer, and Neil Risch
Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation
patterns and human origins of replication
1740
€ ksenin,
Eve Shinbrot, Erin E. Henninger, Nils Weinhold, Kyle R. Covington, A. Yasemin Go
Nikolaus Schultz, Hsu Chao, HarshaVardhan Doddapaneni, Donna M. Muzny, Richard A. Gibbs,
Chris Sander, Zachary F. Pursell, and David A. Wheeler
Heterogeneous polymerase fidelity and mismatch repair bias genome variation
and composition
1751
Scott A. Lujan, Anders R. Clausen, Alan B. Clark, Heather K. MacAlpine, David M. MacAlpine,
Ewa P. Malc, Piotr A. Mieczkowski, Adam B. Burkholder, David C. Fargo, Dmitry A. Gordenin,
and Thomas A. Kunkel
RNA-seq of 272 gliomas revealed a novel, recurrent PTPRZ1-MET fusion transcript
in secondary glioblastomas
1765
Zhao-Shi Bao, Hui-Min Chen, Ming-Yu Yang, Chuan-Bao Zhang, Kai Yu, Wan-Lu Ye,
Bo-Qiang Hu, Wei Yan, Wei Zhang, Johnny Akers, Valya Ramakrishnan, Jie Li, Bob Carter,
Yan-Wei Liu, Hui-Min Hu, Zheng Wang, Ming-Yang Li, Kun Yao, Xiao-Guang Qiu,
Chun-Sheng Kang, Yong-Ping You, Xiao-Long Fan, Wei Sonya Song, Rui-Qiang Li,
Xiao-Dong Su, Clark C. Chen, and Tao Jiang
Widespread intron retention in mammals functionally tunes transcriptomes
1774
Ulrich Braunschweig, Nuno L. Barbosa-Morais, Qun Pan, Emil N. Nachman, Babak Alipanahi,
Thomas Gonatopoulos-Pournatzis, Brendan Frey, Manuel Irimia, and Benjamin J. Blencowe
Cell fate inclination within 2-cell and 4-cell mouse embryos revealed by single-cell RNA
sequencing
1787
Fernando H. Biase, Xiaoyi Cao, and Sheng Zhong
High-resolution mapping of transcriptional dynamics across tissue development reveals
a stable mRNA–tRNA interface
1797 OA
Bianca M. Schmitt, Konrad L.M. Rudolph, Panagiota Karagianni, Nuno A. Fonseca,
Robert J. White, Iannis Talianidis, Duncan T. Odom, John C. Marioni, and Claudia Kutter
H3S28 phosphorylation is a hallmark of the transcriptional response to cellular stress
Anna Sawicka, Dominik Hartl, Malgorzata Goiser, Oliver Pusch, Roman R. Stocsits, Ido M. Tamir,
Karl Mechtler, and Christian Seiser
(continued)
1808 OA
Environmentally responsive genome-wide accumulation of de novo Arabidopsis thaliana
mutations and epimutations
1821 OA
Caifu Jiang, Aziz Mithani, Eric J. Belfield, Richard Mott, Laurence D. Hurst,
and Nicholas P. Harberd
Preservation of genetic and regulatory robustness in ancient gene duplicates
of Saccharomyces cerevisiae
1830
Orla M. Keane, Christina Toft, Lorenzo Carretero-Paulet, Gary W. Jones, and Mario A. Fares
Methods
Application of histone modification-specific interaction domains as an alternative
to antibodies
1842
Goran Kungulovski, Ina Kycia, Raluca Tamas, Renata Z. Jurkowska, Srikanth Kudithipudi,
Chisato Henry, Richard Reinhardt, Paul Labhart, and Albert Jeltsch
Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C
1854
Nicola H. Dryden, Laura R. Broome, Frank Dudbridge, Nichola Johnson, Nick Orr,
Stefan Schoenfelder, Takashi Nagano, Simon Andrews, Steven Wingett, Iwanka Kozarewa,
Ioannis Assiotis, Kerry Fenwick, Sarah L. Maguire, James Campbell, Rachael Natrajan,
Maryou Lambros, Eleni Perrakis, Alan Ashworth, Peter Fraser, and Olivia Fletcher
Linking signaling pathways to transcriptional programs in breast cancer
1869 OA
Hatice U. Osmanbeyoglu, Raphael Pelossof, Jacqueline F. Bromberg, and Christina S. Leslie
TITAN: inference of copy number architectures in clonal cell populations from tumor
whole-genome sequence data
1881 OA
Gavin Ha, Andrew Roth, Jaswinder Khattra, Julie Ho, Damian Yap, Leah M. Prentice,
Nataliya Melnyk, Andrew McPherson, Ali Bashashati, Emma Laks, Justina Biele, Jiarui Ding,
Alan Le, Jamie Rosner, Karey Shumansky, Marco A. Marra, C. Blake Gilks, David G. Huntsman,
Jessica N. McAlpine, Samuel Aparicio, and Sohrab P. Shah
Resource
The landscape of human STR variation
1894OA
Thomas Willems, Melissa Gymrek, Gareth Highnam, The 1000 Genomes Project Consortium,
David Mittelman, and Yaniv Erlich
OA
Open Access paper
Cover Like the opposite but interconvertible halves of Yin and Yang, the first two cells
of a mouse embryo may have a tendency to choose different cell fates. In this issue, it
is determined via single-cell RNA sequencing that cells in the same embryo express
different genes. This suggests that mammalian embryonic cells exhibit reproducible
molecular differences at much earlier developmental stages than previously thought. In
the illustration, pink-colored cells represent the lineage primarily contributing to the
inner cell mass and eventual offspring (the ‘‘Yang’’ half of the central embryo),
whereas teal-colored cells (the ‘‘Yin’’ half) are inclined to become trophoblasts, the
progenitor to the majority of extraembryonic tissues. Artwork Ó Victor O. Leshyk,
2014, www.victorleshyk.com.