ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data
TLDR
ReplicationDomain is a novel and powerful tool to facilitate the comparative visualization of replication timing in various cell types as well as other genome-wide chromatin features and is considerably faster and more convenient than existing browsers when viewing multi-megabase segments of chromosomes.Abstract:
Eukaryotic DNA replication is regulated at the level of large chromosomal domains (0.5–5 megabases in mammals) within which replicons are activated relatively synchronously. These domains replicate in a specific temporal order during S-phase and our genome-wide analyses of replication timing have demonstrated that this temporal order of domain replication is a stable property of specific cell types. We have developed ReplicationDomain http://www.replicationdomain.org
as a web-based database for analysis of genome-wide replication timing maps (replication profiles) from various cell lines and species. This database also provides comparative information of transcriptional expression and is configured to display any genome-wide property (for instance, ChIP-Chip or ChIP-Seq data) via an interactive web interface. Our published microarray data sets are publicly available. Users may graphically display these data sets for a selected genomic region and download the data displayed as text files, or alternatively, download complete genome-wide data sets. Furthermore, we have implemented a user registration system that allows registered users to upload their own data sets. Upon uploading, registered users may choose to: (1) view their data sets privately without sharing; (2) share with other registered users; or (3) make their published or "in press" data sets publicly available, which can fulfill journal and funding agencies' requirements for data sharing. ReplicationDomain is a novel and powerful tool to facilitate the comparative visualization of replication timing in various cell types as well as other genome-wide chromatin features and is considerably faster and more convenient than existing browsers when viewing multi-megabase segments of chromosomes. Furthermore, the data upload function with the option of private viewing or sharing of data sets between registered users should be a valuable resource for the scientific community.read more
Citations
More filters
Journal ArticleDOI
Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types
Tyrone Ryba,Ichiro Hiratani,Junjie Lu,Mari Itoh,Michael Kulik,Jinfeng Zhang,Thomas C. Schulz,Allan J. Robins,Stephen Dalton,David M. Gilbert +9 more
TL;DR: The results reveal evolutionarily conserved aspects of developmentally regulated replication programs in mammals, demonstrate the power of replication profiling to distinguish closely related cell types, and strongly support the hypothesis that replication timing domains are spatially compartmentalized structural and functional units of three-dimensional chromosomal architecture.
Journal ArticleDOI
Collisions between Replication and Transcription Complexes Cause Common Fragile Site Instability at the Longest Human Genes
TL;DR: The results show that, on the longest human genes, collisions of the transcription machinery with a replication fork are inevitable, creating R-loops and consequent CFS formation, and functional replication machinery needs to be involved in the resolution of conflicts between transcription and replication machineries to ensure genomic stability.
Journal Article
Genome-wide DNA replication profile for Drosophila melanogaster: a link between transcription and replication timing: a link between transcription and replication timing
TL;DR: A strategy to measure the timing of DNA replication for thousands of genes in a single DNA array hybridization experiment generated a genome-wide map of replication timing for Drosophila melanogaster and found a strong correlation between DNA replication early in S phase and transcriptional activity.
Journal ArticleDOI
Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis
Ichiro Hiratani,Tyrone Ryba,Mari Itoh,Joy Rathjen,Michael Kulik,Bernadett Papp,Eden Fussner,David P. Bazett-Jones,Kathrin Plath,Stephen Dalton,Peter D. Rathjen,David M. Gilbert +11 more
TL;DR: A model in which a distinct set of replication domains undergoes a form of "autosomal Lyonization" in the epiblast that is difficult to reprogram and coincides with an epigenetic commitment to differentiation prior to germ layer specification is supported.
Journal ArticleDOI
Independence of Repressive Histone Marks and Chromatin Compaction during Senescent Heterochromatic Layer Formation
Tamir Chandra,Kristina Kirschner,Jean Yves Thuret,Benjamin D. Pope,Tyrone Ryba,Scott Newman,Kashif Ahmed,Shamith A. Samarajiwa,Rafik Salama,Thomas L. Carroll,Rory Stark,Rekin's Janky,Masako Narita,Lixiang Xue,Agustin Chicas,Sabrina Nũnez,Ralf Janknecht,Yoko Hayashi-Takanaka,Michael D. Wilson,Aileen Marshall,Duncan T. Odom,M. Madan Babu,David P. Bazett-Jones,Simon Tavaré,Paul A.W. Edwards,Scott W. Lowe,Scott W. Lowe,Hiroshi Kimura,David M. Gilbert,Masashi Narita +29 more
TL;DR: The experiments reveal that high-order heterochromatin formation and epigenetic remodeling of the genome can be discrete events.
References
More filters
Journal ArticleDOI
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
Ewan Birney,John A. Stamatoyannopoulos,Anindya Dutta,Roderic Guigó,Thomas R. Gingeras,Elliott H. Margulies,Zhiping Weng,Michael Snyder,Emmanouil T. Dermitzakis,Robert E. Thurman,Michael S. Kuehn,Christopher M. Taylor,Shane Neph,Christoph M. Koch,Saurabh Asthana,Ankit Malhotra,Ivan Adzhubei,Jason A. Greenbaum,Robert M. Andrews,Paul Flicek,Patrick J. Boyle,Hua Cao,Nigel P. Carter,Gayle K. Clelland,Sean Davis,Nathan Day,Pawandeep Dhami,Shane C. Dillon,Michael O. Dorschner,Heike Fiegler,Paul G. Giresi,Jeff Goldy,Michael Hawrylycz,Andrew Haydock,Richard Humbert,Keith D. James,Brett E. Johnson,Ericka M. Johnson,Tristan Frum,Elizabeth Rosenzweig,Neerja Karnani,Kirsten Lee,Gregory Lefebvre,Patrick A. Navas,Fidencio Neri,Stephen C. J. Parker,Peter J. Sabo,Richard Sandstrom,Anthony Shafer,David Vetrie,Molly Weaver,Sarah Wilcox,Man Yu,Francis S. Collins,Job Dekker,Jason D. Lieb,Thomas D. Tullius,Gregory E. Crawford,Shamil R. Sunyaev,William Stafford Noble,Ian Dunham,Alexandre Reymond,Alexandre Reymond,Philipp Kapranov,Joel Rozowsky,Deyou Zheng,Robert Castelo,Adam Frankish,Jennifer Harrow,Srinka Ghosh,Albin Sandelin,Ivo L. Hofacker,Robert Baertsch,Damian Keefe,Sujit Dike,Jill Cheng,Heather A. Hirsch,Edward A. Sekinger,Julien Lagarde,Josep F. Abril,Josep F. Abril,Atif Shahab,Christoph Flamm,Christoph Flamm,Claudia Fried,Jörg Hackermüller,Jana Hertel,Manja Lindemeyer,Kristin Missal,Andrea Tanzer,Andrea Tanzer,Stefan Washietl,Jan O. Korbel,Olof Emanuelsson,Jakob Skou Pedersen,Nancy Holroyd,Ruth Taylor,David Swarbreck,Nicholas Matthews,Mark Dickson,Daryl J. Thomas,Matthew T. Weirauch,James G. R. Gilbert,Jorg Drenkow,Ian Bell,Xiaodong Zhao,Kandhadayar G. Srinivasan,Wing-Kin Sung,Hong Sain Ooi,Kuo Ping Chiu,Sylvain Foissac,Tyler Alioto,Michael R. Brent,Lior Pachter,Michael L. Tress,Alfonso Valencia,Siew Woh Choo,Chiou Yu Choo,Catherine Ucla,Caroline Manzano,Carine Wyss,Evelyn Cheung,Taane G. Clark,James B. Brown,Madhavan Ganesh,Sandeep Patel,Hari Tammana,Jacqueline Chrast,Charlotte N. Henrichsen,Chikatoshi Kai,Jun Kawai,Ugrappa Nagalakshmi,Jia Qian Wu,Zheng Lian,Jin Lian,Peter E. Newburger,Xueqing Zhang,Peter J. Bickel,John S. Mattick,Piero Carninci,Yoshihide Hayashizaki,Sherman M. Weissman,Tim Hubbard,Richard M. Myers,Jane Rogers,Peter F. Stadler,Peter F. Stadler,Peter F. Stadler,Todd M. Lowe,Chia-Lin Wei,Yijun Ruan,Kevin Struhl,Mark Gerstein,Stylianos E. Antonarakis,Yutao Fu,Eric D. Green,Ulas Karaoz,Adam Siepel,Adam Siepel,James Taylor,Laura A. Liefer,Kris A. Wetterstrand,Peter J. Good,Elise A. Feingold,Mark S. Guyer,Gregory M. Cooper,Gregory M. Cooper,George Asimenos,Colin N. Dewey,Minmei Hou,Sergey Nikolaev,Juan I. Montoya-Burgos,Ari Löytynoja,Simon Whelan,Fabio Pardi,Tim Massingham,Haiyan Huang,Nan Zhang,Nan Zhang,Ian Holmes,James C. Mullikin,Abel Ureta-Vidal,Benedict Paten,Michael Seringhaus,Deanna M. Church,Kate R. Rosenbloom,W. James Kent,Eric A. Stone,Serafim Batzoglou,Nick Goldman,Ross C. Hardison,David Haussler,Webb Miller,Arend Sidow,Nathan D. Trinklein,Zhengdong D. Zhang,Leah O. Barrera,Rhona K. Stuart,David C. King,Adam Ameur,Stefan Enroth,Mark Bieda,Jonghwan Kim,Akshay Bhinge,Nan Jiang,Jun Liu,Fei Yao,Vinsensius B. Vega,Charlie W.H. Lee,Patrick Ng,Annie Yang,Zarmik Moqtaderi,Zhou Zhu,Xiaoqin Xu,Sharon L. Squazzo,Matthew J. Oberley,David R. Inman,Michael A. Singer,Todd Richmond,Kyle J. Munn,Kyle J. Munn,Alvaro Rada-Iglesias,Ola Wallerman,Jan Komorowski,Joanna C. Fowler,Phillippe Couttet,Alexander W. Bruce,Oliver M. Dovey,Peter D. Ellis,Cordelia Langford,David A. Nix,Ghia Euskirchen,Stephen Hartman,Alexander E. Urban,Peter Kraus,Sara Van Calcar,Nate Heintzman,Tae Hoon Kim,Kun Wang,Chunxu Qu,Gary C. Hon,Rosa Luna,Christopher K. Glass,M. Geoff Rosenfeld,Shelley Force Aldred,Sara J. Cooper,Anason S. Halees,Jane M. Lin,Hennady P. Shulha,Xiaoling Zhang,Mousheng Xu,Jaafar N. Haidar,Yong Yu,Vishwanath R. Iyer,Roland Green,Claes Wadelius,Peggy J. Farnham,Bing Ren,Rachel A. Harte,Angie S. Hinrichs,Heather Trumbower,Hiram Clawson,Jennifer Hillman-Jackson,Ann S. Zweig,Kayla E. Smith,Archana Thakkapallayil,Galt P. Barber,Robert M. Kuhn,Donna Karolchik,Lluís Armengol,Christine P. Bird,Paul I.W. de Bakker,Andrew D. Kern,Nuria Lopez-Bigas,Joel D. Martin,Barbara E. Stranger,Abigail Woodroffe,Eugene Davydov,Antigone S. Dimas,Eduardo Eyras,Ingileif B. Hallgrímsdóttir,Julian L. Huppert,Michael C. Zody,Gonçalo R. Abecasis,Xavier Estivill,Gerard G. Bouffard,Xiaobin Guan,Nancy F. Hansen,Jacquelyn R. Idol,Valerie 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 S. 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,Eric S. Lander,Maxim Koriabine,Mikhail Nefedov,Kazutoyo Osoegawa,Yuko Yoshinaga,Baoli Zhu,Pieter J. de Jong +320 more
TL;DR: Functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project are reported, providing convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts.
Journal ArticleDOI
The in vitro development of blastocyst-derived embryonic stem cell lines: formation of visceral yolk sac, blood islands and myocardium
TL;DR: The in vitro developmental potential of mouse blastocyst-derived embryonic stem cell lines and the consistency with which the cells express this potential are presented as aspects which open up new approaches to the investigation of embryogenesis.
Journal ArticleDOI
Treatment of Sickle Cell Anemia Mouse Model with iPS Cells Generated from Autologous Skin
Jacob H. Hanna,Marius Wernig,Marius Wernig,Styliani Markoulaki,Styliani Markoulaki,Chiao-Wang Sun,Chiao-Wang Sun,Alexander Meissner,Alexander Meissner,John P. Cassady,John P. Cassady,Caroline Beard,Caroline Beard,Tobias Brambrink,Tobias Brambrink,Li-Chen Wu,Li-Chen Wu,Tim M. Townes,Tim M. Townes,Rudolf Jaenisch,Rudolf Jaenisch +20 more
TL;DR: It is shown that mice can be rescued after transplantation with hematopoietic progenitors obtained in vitro from autologous iPS cells, providing proof of principle for using transcription factor–induced reprogramming combined with gene and cell therapy for disease treatment in mice.
Journal ArticleDOI
Conversion of embryonic stem cells into neuroectodermal precursors in adherent monoculture.
TL;DR: It is reported that neither multicellular aggregation nor coculture is necessary for ES cells to commit efficiently to a neural fate and this system provides a platform for defining the molecular machinery of neural commitment and optimizing the efficiency of neuronal and glial cell production from pluripotent mammalian stem cells.
Journal ArticleDOI
Global Reorganization of Replication Domains During Embryonic Stem Cell Differentiation
Ichiro Hiratani,Tyrone Ryba,Mari Itoh,Tomoki Yokochi,M. Schwaiger,Chia-Wei Chang,Yung Lyou,Tim M. Townes,Dirk Schübeler,David M. Gilbert +9 more
TL;DR: It is concluded that replication profiles are cell-type specific, and changes in these profiles reveal chromosome segments that undergo large changes in organization during differentiation, a novel characteristic of the pluripotent state.
Related Papers (5)
Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Erez Lieberman Aiden,Nynke L. van Berkum,Louise Williams,Maxim Imakaev,Tobias Ragoczy,Tobias Ragoczy,Agnes Telling,Agnes Telling,Ido Amit,Bryan R. Lajoie,Peter J. Sabo,Michael O. Dorschner,Richard Sandstrom,Bradley E. Bernstein,Bradley E. Bernstein,Michaël Bender,Mark Groudine,Mark Groudine,Andreas Gnirke,John A. Stamatoyannopoulos,Leonid A. Mirny,Eric S. Lander,Eric S. Lander,Job Dekker +23 more