Junk DNA is NOT Junk After All

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Tony Rook
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Junk DNA is NOT Junk After All

The June 2007 Issue (Vol. 17 Issue 16) of Genome Research
reports on the Encyclopedia of DNA Elements Project, or Encode.

An overriding theme of these 28 studies is that the DNA in between genes play a substantially increased role in human disease.

Here is a listing of this issue's TOC. Full text versions of all articles can be accessed at the Genome Research, an open-access journal.

Genome Research TOC
June 2007 Issue (Vol. 17 Issue 16)

COMMENTARY:
George M. Weinstock . ENCODE: More genomic empowerment. Genome Res. 2007 17: 667-668.

PERSPECTIVE:

Mark B. Gerstein, Can Bruce, Joel S. Rozowsky, Deyou Zheng, Jiang Du, Jan O. Korbel, Olof Emanuelsson, Zhengdong D. Zhang, Sherman Weissman, and Michael Snyder. What is a gene, post-ENCODE? History and updated definition . Genome Res. 2007 17: 669-681.

Thomas R. Gingeras . Origin of phenotypes: Genes and transcripts. Genome Res. 2007 17: 682-690.

ARTICLES:

Christoph M. Koch, Robert M. Andrews, Paul Flicek, Shane C. Dillon, Ulas Karaz, Gayle K. Clelland, Sarah Wilcox, David M. Beare, Joanna C. Fowler, Phillippe Couttet, Keith D. James, Gregory C. Lefebvre, Alexander W. Bruce, Oliver M. Dovey, Peter D. Ellis, Pawandeep Dhami, Cordelia F. Langford, Zhiping Weng, Ewan Birney, Nigel P. Carter, David Vetrie, and Ian Dunham. The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Res. 2007 17: 691-707.

Alvaro Rada-Iglesias, Stefan Enroth, Adam Ameur, Christoph M. Koch, Gayle K. Clelland, Patricia Respuela-Alonso, Sarah Wilcox, Oliver M. Dovey, Peter D. Ellis, Cordelia F. Langford, Ian Dunham, Jan Komorowski, and Claes Wadelius. Butyrate mediates decrease of histone acetylation centered on transcription start sites and down-regulation of associated genes. Genome Res. 2007 17: 708-719.

Nathan D. Trinklein, Ulas Karaz, Jiaqian Wu, Anason Halees, Shelley Force Aldred, Patrick J. Collins, Deyou Zheng, Zhengdong D. Zhang, Mark B. Gerstein, Michael Snyder, Richard M. Myers, and Zhiping Weng. Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome. Genome Res. 2007 17: 720-731.

Joel S. Rozowsky, Daniel Newburger, Fred Sayward, Jiaqian Wu, Greg Jordan, Jan O. Korbel, Ugrappa Nagalakshmi, Jin Yang, Deyou Zheng, Roderic Guigó, Thomas R. Gingeras, Sherman Weissman, Perry Miller, Michael Snyder, and Mark B. Gerstein. The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci. Genome Res. 2007 17: 732-745.

France Denoeud, Philipp Kapranov, Catherine Ucla, Adam Frankish, Robert Castelo, Jorg Drenkow, Julien Lagarde, Tyler Alioto, Caroline Manzano, Jacqueline Chrast, Sujit Dike, Carine Wyss, Charlotte N. Henrichsen, Nancy Holroyd, Mark C. Dickson, Ruth Taylor, Zahra Hance, Sylvain Foissac, Richard M. Myers, Jane Rogers, Tim Hubbard, Jennifer Harrow, Roderic Guigó, Thomas R. Gingeras, Stylianos E. Antonarakis, and Alexandre Reymond. Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions
Genome Res. 2007 17: 746-759

Elliott H. Margulies, Gregory M. Cooper, George Asimenos, Daryl J. Thomas, Colin N. Dewey, Adam Siepel, Ewan Birney, Damian Keefe, Ariel S. Schwartz, Minmei Hou, James Taylor, Sergey Nikolaev, Juan I. Montoya-Burgos, Ari Lytynoja, Simon Whelan, Fabio Pardi, Tim Massingham, James B. Brown, Peter Bickel, Ian Holmes, James C. Mullikin, Abel Ureta-Vidal, Benedict Paten, Eric A. Stone, Kate R. Rosenbloom, W. James Kent, Gerard G. Bouffard, Xiaobin Guan, Nancy F. Hansen, Jacquelyn R. Idol, Valerie V.B. Maduro, Baishali Maskeri, Jennifer C. McDowell, Morgan Park, Pamela J. Thomas, Alice C. Young, Robert W. Blakesley, Donna M. Muzny, Erica Sodergren, David A. Wheeler, Kim C. Worley, Huaiyang Jiang, George M. Weinstock, Richard A. Gibbs, Tina Graves, Robert Fulton, Elaine R. Mardis, Richard K. Wilson, Michele Clamp, James Cuff, Sante Gnerre, David B. Jaffe, Jean L. Chang, Kerstin Lindblad-Toh, Eric S. Lander, Angie Hinrichs, Heather Trumbower, Hiram Clawson, Ann Zweig, Robert M. Kuhn, Galt Barber, Rachel Harte, Donna Karolchik, Matthew A. Field, Richard A. Moore, Carrie A. Matthewson, Jacqueline E. Schein, Marco A. Marra, Stylianos E. Antonarakis, Serafim Batzoglou, Nick Goldman, Ross Hardison, David Haussler, Webb Miller, Lior Pachter, Eric D. Green, and Arend Sidow. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res. 2007 17: 760-774.

LETTERS:

David C. King, James Taylor, Ying Zhang, Yong Cheng, Heather A. Lawson, Joel Martin, ENCODE groups for Transcriptional Regulation and Multispecies Sequence Analysis, Francesca Chiaromonte, Webb Miller, and Ross C. Hardison . Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data
Genome Res. 2007 17: 775-786

Zhengdong D. Zhang, Alberto Paccanaro, Yutao Fu, Sherman Weissman, Zhiping Weng, Joseph Chang, Michael Snyder, and Mark B. Gerstein. Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions. Genome Res. 2007 17: 787-797

Hualin Xi, Yong Yu, Yutao Fu, Jonathan Foley, Anason Halees, and Zhiping Weng. Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1. Genome Res. 2007 17: 798-806.

Victor X. Jin, Henriette OGeen, Sushma Iyengar, Roland Green, and Peggy J. Farnham. Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches. Genome Res. 2007 17: 807-817.

Jane M. Lin, Patrick J. Collins, Nathan D. Trinklein, Yutao Fu, Hualin Xi, Richard M. Myers, and Zhiping Weng. Transcription factor binding and modified histones in human bidirectional promoters. Genome Res. 2007 17: 818-827.

Yijun Ruan, Hong Sain Ooi, Siew Woh Choo, Kuo Ping Chiu, Xiao Dong Zhao, K.G. Srinivasan, Fei Yao, Chiou Yu Choo, Jun Liu, Pramila Ariyaratne, Wilson G.W. Bin, Vladimir A. Kuznetsov, Atif Shahab, Wing-Kin Sung, Guillaume Bourque, Nallasivam Palanisamy, and Chia-Lin Wei. Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs). Genome Res. 2007 17: 828-838.

Deyou Zheng, Adam Frankish, Robert Baertsch, Philipp Kapranov, Alexandre Reymond, Siew Woh Choo, Yontao Lu, France Denoeud, Stylianos E. Antonarakis, Michael Snyder, Yijun Ruan, Chia-Lin Wei, Thomas R. Gingeras, Roderic Guigó, Jennifer Harrow, and Mark B. Gerstein. Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution. Genome Res. 2007 17: 839-851.

Stefan Washietl, Jakob S. Pedersen, Jan O. Korbel, Claudia Stocsits, Andreas R. Gruber, Jrg Hackermüller, Jana Hertel, Manja Lindemeyer, Kristin Reiche, Andrea Tanzer, Catherine Ucla, Carine Wyss, Stylianos E. Antonarakis, France Denoeud, Julien Lagarde, Jorg Drenkow, Philipp Kapranov, Thomas R. Gingeras, Roderic Guigó, Michael Snyder, Mark B. Gerstein, Alexandre Reymond, Ivo L. Hofacker, and Peter F. Stadler. Structured RNAs in the ENCODE selected regions of the human genome. Genome Res. 2007 17: 852-864.

Neerja Karnani, Christopher Taylor, Ankit Malhotra, and Anindya Dutta. Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas. Genome Res. 2007 17: 865-876.

METHODS:

Paul G. Giresi, Jonghwan Kim, Ryan M. McDaniell, Vishwanath R. Iyer, and Jason D. Lieb. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res. 2007 17: 877-885. Published in Advance December 19, 2006, 10.1101/gr.5533506

Olof Emanuelsson, Ugrappa Nagalakshmi, Deyou Zheng, Joel S. Rozowsky, Alexander E. Urban, Jiang Du, Zheng Lian, Viktor Stolc, Sherman Weissman, Michael Snyder, and Mark B. Gerstein. Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome
Genome Res. 2007 17: 886-897. Published in Advance November 21, 2006, 10.1101/gr.5014606

Ghia M. Euskirchen, Joel S. Rozowsky, Chia-Lin Wei, Wah Heng Lee, Zhengdong D. Zhang, Stephen Hartman, Olof Emanuelsson, Viktor Stolc, Sherman Weissman, Mark B. Gerstein, Yijun Ruan, and Michael Snyder. Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies. Genome Res. 2007 17: 898-909.

Akshay A. Bhinge, Jonghwan Kim, Ghia M. Euskirchen, Michael Snyder, and Vishwanath R. Iye. Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE). Genome Res. 2007 17: 910-916.

Robert E. Thurman, Nathan Day, William S. Noble, and John A. Stamatoyannopoulos. Identification of higher-order functional domains in the human ENCODE regions. Genome Res. 2007 17: 917-927

Jonathan H. Dennis, Hua-Ying Fan, Sheila M. Reynolds, Guocheng Yuan, James C. Meldrim, Daniel J. Richter, Daniel G. Peterson, Oliver J. Rando, William S. Noble, and Robert E. Kingston. Independent and complementary methods for large-scale structural analysis of mammalian chromatin. Genome Res. 2007 17: 928-939.

Jason A. Greenbaum, Stephen C.J. Parker, and Thomas D. Tullius. Detection of DNA structural motifs in functional genomic elements. Genome Res. 2007 17: 940-946.

RESOURCES:

Jason A. Greenbaum, Bo Pang, and Thomas D. Tullius. Construction of a genome-scale structural map at single-nucleotide resolution. Genome Res. 2007 17: 947-953.

Laura L. Elnitski, Prachi Shah, R. Travis Moreland, Lowell Umayam, Tyra G. Wolfsberg, and Andreas D. Baxevanis. The ENCODEdb portal: Simplified access to ENCODE Consortium data. Genome Res. 2007 17: 954-959.

Daniel Blankenberg, James Taylor, Ian Schenck, Jianbin He, Yi Zhang, Matthew Ghent, Narayanan Veeraraghavan, Istvan Albert, Webb Miller, Kateryna D. Makova, Ross C. Hardison, and Anton Nekrutenko. A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly. Genome Res. 2007 17: 960-964.