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  1. Research

    The Arabidopsis SWI/SNF protein BAF60 mediates seedling growth control by modulating DNA accessibility

    Plant adaptive responses to changing environments involve complex molecular interplays between intrinsic and external signals. Whilst much is known on the signaling components mediating diurnal, light, and tem...

    Teddy Jégu, Alaguraj Veluchamy, Juan S. Ramirez-Prado, Charley Rizzi-Paillet, Magalie Perez, Anaïs Lhomme, David Latrasse, Emeline Coleno, Serge Vicaire, Stéphanie Legras, Bernard Jost, Martin Rougée, Fredy Barneche, Catherine Bergounioux, Martin Crespi, Magdy M. Mahfouz…

    Genome Biology 2017 18:114

    Published on: 15 June 2017

  2. Correspondence

    Correspondence on Lovell et al.: response to Bornelöv et al.

    While the analysis of Bornelöv et al. is informative, they provide evidence for the existence of only 3% of the reported avian missing genes set, and thus do not significantly challenge our main findings that ...

    Peter V. Lovell and Claudio V. Mello

    Genome Biology 2017 18:113

    Published on: 14 June 2017

  3. Research Highlight

    Epigenetic aging clocks in mice and men

    Epigenetic clocks provide powerful tools to evaluate nutritional, hormonal, and genetic effects on aging. What can we learn from differences between species in how these clocks tick?

    Wolfgang Wagner

    Genome Biology 2017 18:107

    Published on: 14 June 2017

  4. Correspondence

    Correspondence on Lovell et al.: identification of chicken genes previously assumed to be evolutionarily lost

    Through RNA-Seq analyses, we identified 137 genes that are missing in chicken, including the long-sought-after nephrin and tumor necrosis factor genes. These genes tended to cluster in GC-rich regions that hav...

    Susanne Bornelöv, Eyal Seroussi, Sara Yosefi, Ken Pendavis, Shane C. Burgess, Manfred Grabherr, Miriam Friedman-Einat and Leif Andersson

    Genome Biology 2017 18:112

    Published on: 14 June 2017

  5. Method

    CRISPR/Cas9-mediated genome editing induces exon skipping by alternative splicing or exon deletion

    CRISPR is widely used to disrupt gene function by inducing small insertions and deletions. Here, we show that some single-guide RNAs (sgRNAs) can induce exon skipping or large genomic deletions that delete exo...

    Haiwei Mou, Jordan L. Smith, Lingtao Peng, Hao Yin, Jill Moore, Xiao-Ou Zhang, Chun-Qing Song, Ankur Sheel, Qiongqiong Wu, Deniz M. Ozata, Yingxiang Li, Daniel G. Anderson, Charles P. Emerson, Erik J. Sontheimer, Melissa J. Moore, Zhiping Weng…

    Genome Biology 2017 18:108

    Published on: 14 June 2017

  6. Research

    “Like sugar in milk”: reconstructing the genetic history of the Parsi population

    The Parsis are one of the smallest religious communities in the world. To understand the population structure and demographic history of this group in detail, we analyzed Indian and Pakistani Parsi populations...

    Gyaneshwer Chaubey, Qasim Ayub, Niraj Rai, Satya Prakash, Veena Mushrif-Tripathy, Massimo Mezzavilla, Ajai Kumar Pathak, Rakesh Tamang, Sadaf Firasat, Maere Reidla, Monika Karmin, Deepa Selvi Rani, Alla G. Reddy, Jüri Parik, Ene Metspalu, Siiri Rootsi…

    Genome Biology 2017 18:110

    Published on: 14 June 2017

  7. Research

    Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification

    The functional divergence of duplicate genes (ohnologues) retained from whole genome duplication (WGD) is thought to promote evolutionary diversification. However, species radiation and phenotypic diversificat...

    Fiona M. Robertson, Manu Kumar Gundappa, Fabian Grammes, Torgeir R. Hvidsten, Anthony K. Redmond, Sigbjørn Lien, Samuel A. M. Martin, Peter W. H. Holland, Simen R. Sandve and Daniel J. Macqueen

    Genome Biology 2017 18:111

    Published on: 14 June 2017

  8. Research

    Regulatory landscape fusion in rhabdomyosarcoma through interactions between the PAX3 promoter and FOXO1 regulatory elements

    The organisation of vertebrate genomes into topologically associating domains (TADs) is believed to facilitate the regulation of the genes located within them. A remaining question is whether TAD organisation ...

    Cristina Vicente-García, Barbara Villarejo-Balcells, Ibai Irastorza-Azcárate, Silvia Naranjo, Rafael D. Acemel, Juan J. Tena, Peter W. J. Rigby, Damien P. Devos, Jose L. Gómez-Skarmeta and Jaime J. Carvajal

    Genome Biology 2017 18:106

    Published on: 14 June 2017

  9. Research

    Multiple gene movements into and out of haploid sex chromosomes

    Long-term evolution of sex chromosomes is a dynamic process shaped by gene gain and gene loss. Sex chromosome gene traffic has been studied in XY and ZW systems but no detailed analyses have been carried out f...

    Agnieszka P. Lipinska, Nicholas R. T. Toda, Svenja Heesch, Akira F. Peters, J. Mark Cock and Susana M. Coelho

    Genome Biology 2017 18:104

    Published on: 8 June 2017

  10. Research

    Epigenomic and functional analyses reveal roles of epialleles in the loss of photoperiod sensitivity during domestication of allotetraploid cottons

    Polyploidy is a pervasive evolutionary feature of all flowering plants and some animals, leading to genetic and epigenetic changes that affect gene expression and morphology. DNA methylation changes can produc...

    Qingxin Song, Tianzhen Zhang, David M. Stelly and Z. Jeffrey Chen

    Genome Biology 2017 18:99

    Published on: 31 May 2017

  11. Research

    The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci

    The chromodomain helicase DNA-binding family of ATP-dependent chromatin remodeling factors play essential roles during eukaryote growth and development. They are recruited by specific transcription factors and...

    Rong Yang, Zhimin Zheng, Qing Chen, Lan Yang, Huan Huang, Daisuke Miki, Wenwu Wu, Liang Zeng, Jun Liu, Jin-Xing Zhou, Joe Ogas, Jian-Kang Zhu, Xin-Jian He and Heng Zhang

    Genome Biology 2017 18:103

    Published on: 31 May 2017

  12. Software

    Millstone: software for multiplex microbial genome analysis and engineering

    Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. We describe Millstone, a...

    Daniel B. Goodman, Gleb Kuznetsov, Marc J. Lajoie, Brian W. Ahern, Michael G. Napolitano, Kevin Y. Chen, Changping Chen and George M. Church

    Genome Biology 2017 18:101

    Published on: 25 May 2017

  13. Method

    Optimizing complex phenotypes through model-guided multiplex genome engineering

    We present a method for identifying genomic modifications that optimize a complex phenotype through multiplex genome engineering and predictive modeling. We apply our method to identify six single nucleotide m...

    Gleb Kuznetsov, Daniel B. Goodman, Gabriel T. Filsinger, Matthieu Landon, Nadin Rohland, John Aach, Marc J. Lajoie and George M. Church

    Genome Biology 2017 18:100

    Published on: 25 May 2017

  14. Research

    N-BLR, a primate-specific non-coding transcript leads to colorectal cancer invasion and migration

    Non-coding RNAs have been drawing increasing attention in recent years as functional data suggest that they play important roles in key cellular processes. N-BLR is a primate-specific long non-coding RNA that ...

    Isidore Rigoutsos, Sang Kil Lee, Su Youn Nam, Simone Anfossi, Barbara Pasculli, Martin Pichler, Yi Jing, Cristian Rodriguez-Aguayo, Aristeidis G. Telonis, Simona Rossi, Cristina Ivan, Tina Catela Ivkovic, Linda Fabris, Peter M. Clark, Hui Ling, Masayoshi Shimizu…

    Genome Biology 2017 18:98

    Published on: 24 May 2017

  15. Research Highlight

    Going beyond genetics to discover cancer targets

    Two recent studies demonstrate the power of integrating tumor genotype information with epigenetic and proteomic studies to discover potential therapeutic targets in breast cancer.

    Gabriel J. Sandoval and William C. Hahn

    Genome Biology 2017 18:95

    Published on: 22 May 2017

  16. Research

    A comparative evaluation of genome assembly reconciliation tools

    The majority of eukaryotic genomes are unfinished due to the algorithmic challenges of assembling them. A variety of assembly and scaffolding tools are available, but it is not always obvious which tool or par...

    Hind Alhakami, Hamid Mirebrahim and Stefano Lonardi

    Genome Biology 2017 18:93

    Published on: 18 May 2017

  17. Research

    The histone H3 variant H3.3 regulates gene body DNA methylation in Arabidopsis thaliana

    Gene bodies of vertebrates and flowering plants are occupied by the histone variant H3.3 and DNA methylation. The origin and significance of these profiles remain largely unknown. DNA methylation and H3.3 enri...

    Heike Wollmann, Hume Stroud, Ramesh Yelagandula, Yoshiaki Tarutani, Danhua Jiang, Li Jing, Bhagyshree Jamge, Hidenori Takeuchi, Sarah Holec, Xin Nie, Tetsuji Kakutani, Steven E. Jacobsen and Frédéric Berger

    Genome Biology 2017 18:94

    Published on: 18 May 2017

  18. Research

    Easi-CRISPR: a robust method for one-step generation of mice carrying conditional and insertion alleles using long ssDNA donors and CRISPR ribonucleoproteins

    Conditional knockout mice and transgenic mice expressing recombinases, reporters, and inducible transcriptional activators are key for many genetic studies and comprise over 90% of mouse models created. Condit...

    Rolen M. Quadros, Hiromi Miura, Donald W. Harms, Hisako Akatsuka, Takehito Sato, Tomomi Aida, Ronald Redder, Guy P. Richardson, Yutaka Inagaki, Daisuke Sakai, Shannon M. Buckley, Parthasarathy Seshacharyulu, Surinder K. Batra, Mark A. Behlke, Sarah A. Zeiner, Ashley M. Jacobi…

    Genome Biology 2017 18:92

    Published on: 17 May 2017

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