Journal ArticleDOI
Transcription factories: genetic programming in three dimensions.
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TLDR
These studies apply innovative technical approaches to gain insights into the molecular constituents, dynamical behaviour and organizational regulators of transcription factories, providing exciting insightsinto the spatial dimension of transcriptional control.About:
This article is published in Current Opinion in Genetics & Development.The article was published on 2012-04-01. It has received 132 citations till now. The article focuses on the topics: Transcription factories.read more
Citations
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Lamina-Associated Domains: Links with Chromosome Architecture, Heterochromatin, and Gene Repression
TL;DR: The properties of LADs, the molecular mechanisms that determine their association with the nuclear lamina, their dynamic links with other nuclear compartments, and their proposed roles in gene regulation are discussed.
Journal ArticleDOI
iRegulon: from a gene list to a gene regulatory network using large motif and track collections.
Rekin's Janky,Annelien Verfaillie,Hana Imrichova,Bram Van de Sande,Laura Standaert,Valerie Christiaens,Gert Hulselmans,Koen Herten,Marina Naval Sanchez,Delphine Potier,Dmitry Svetlichnyy,Zeynep Kalender Atak,Mark Fiers,Jean-Christophe Marine,Stein Aerts +14 more
TL;DR: Over-activate p53 in breast cancer cells, followed by RNA-seq and ChIP-seq, and could identify an extensive up-regulated network controlled directly by p53 and a repressive network with no indication of direct p53 regulation but rather an indirect effect via E2F and NFY are mapped.
Journal ArticleDOI
The 3D Genome in Transcriptional Regulation and Pluripotency
TL;DR: The relationship between genome organization and lineage-specific transcriptional regulation is discussed in this paper, where the authors argue that the two are inextricably linked and that the relationship can be seen as a direct consequence of 3D genome organization.
Journal ArticleDOI
Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate
Yin C. Lin,Christopher Benner,Christopher Benner,Robert Månsson,Sven Heinz,Kazuko Miyazaki,Masaki Miyazaki,Vivek Chandra,Claudia Bossen,Christopher K. Glass,Cornelis Murre +10 more
TL;DR: A spectrum of genes that switched nuclear location during early B cell development was identified and these genes switched compartments to establish new intra- and interdomain interactions associated with a B lineage–specific transcription signature.
Journal ArticleDOI
Transcription factories: genome organization and gene regulation.
Argyris Papantonis,Peter R. Cook +1 more
TL;DR: It is argued that transcription 'factories' are central organizers of the human genome during interphase, and that proximity to an appropriate factory determines the activity of a gene.
References
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Journal ArticleDOI
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
TL;DR: Hi-C is described, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing and demonstrates the power of Hi-C to map the dynamic conformations of entire genomes.
Journal ArticleDOI
Capturing Chromosome Conformation
TL;DR: Using the yeast Saccharomyces cerevisiae, this work could confirm known qualitative features of chromosome organization within the nucleus and dynamic changes in that organization during meiosis and found that chromatin is highly flexible throughout.
Journal ArticleDOI
An oestrogen-receptor-α-bound human chromatin interactome
Melissa J. Fullwood,Mei Hui Liu,You Fu Pan,Jun Liu,Han Xu,Yusoff Bin Mohamed,Yuriy L. Orlov,Stoyan Velkov,Andrea Ho,Poh Huay Mei,Elaine G.Y. Chew,Phillips Yao Hui Huang,Willem Welboren,Yuyuan Han,Hong Sain Ooi,Pramila N. Ariyaratne,Vinsensius B. Vega,Yanquan Luo,Peck Yean Tan,Pei Ye Choy,K. D. Senali Abayratna Wansa,Bing Zhao,Kar Sian Lim,Shi Chi Leow,Jit Sin Yow,Roy Joseph,Haixia Li,Kartiki V. Desai,Jane S. Thomsen,Yew Kok Lee,R. Krishna Murthy Karuturi,Thoreau Herve,Guillaume Bourque,Hendrik G. Stunnenberg,Xiaoan Ruan,Valere Cacheux-Rataboul,Wing-Kin Sung,Wing-Kin Sung,Edison T. Liu,Chia-Lin Wei,Edwin Cheung,Edwin Cheung,Edwin Cheung,Yijun Ruan,Yijun Ruan +44 more
TL;DR: It is proposed that chromatin interactions constitute a primary mechanism for regulating transcription in mammalian genomes and is described as a new strategy, chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) for the de novo detection of global Chromatin interactions.
Journal ArticleDOI
Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C)
Marieke Simonis,Petra Klous,Erik Splinter,Yuri M. Moshkin,Rob Willemsen,Elzo de Wit,Bas van Steensel,Wouter de Laat +7 more
TL;DR: It is demonstrated here that active and inactive genes are engaged in many long-range intrachromosomal interactions and can also form interchromosomal contacts and establish 4C technology as a powerful tool to study nuclear architecture.
Journal ArticleDOI
The multifunctional nucleolus
TL;DR: Although the nucleolus is primarily associated with ribosome biogenesis, several lines of evidence now show that it has additional functions, such as regulation of mitosis, cell-cycle progression and proliferation, many forms of stress response and biogenesis of multiple ribonucleoprotein particles.
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