Journal ArticleDOI
The complex language of chromatin regulation during transcription
TLDR
This work has shown that transcription occurs against a backdrop of mixtures of complex modifications, which probably have several roles, and suggests that a more likely model is of a sophisticated, nuanced chromatin 'language' in which different combinations of basic building blocks yield dynamic functional outcomes.Abstract:
An important development in understanding the influence of chromatin on gene regulation has been the finding that DNA methylation and histone post-translational modifications lead to the recruitment of protein complexes that regulate transcription. Early interpretations of this phenomenon involved gene regulation reflecting predictive activating or repressing types of modification. However, further exploration reveals that transcription occurs against a backdrop of mixtures of complex modifications, which probably have several roles. Although such modifications were initially thought to be a simple code, a more likely model is of a sophisticated, nuanced chromatin 'language' in which different combinations of basic building blocks yield dynamic functional outcomes.read more
Citations
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Journal ArticleDOI
Combinatorial patterns of histone acetylations and methylations in the human genome
Zhibin Wang,Chongzhi Zang,Jeffrey A. Rosenfeld,Jeffrey A. Rosenfeld,Dustin E. Schones,Artem Barski,Suresh Cuddapah,Kairong Cui,Tae-Young Roh,Weiqun Peng,Michael Q. Zhang,Keji Zhao +11 more
TL;DR: The data suggest that a large number of histone modifications may act cooperatively to prepare chromatin for transcriptional activation and be associated with promoters and enhancers.
Journal ArticleDOI
ChIP-Seq: advantages and challenges of a maturing technology
TL;DR: The benefits and challenges in harnessing ChIP–seq are described with an emphasis on issues related to experimental design and data analysis, and effective computational analysis will be crucial for uncovering biological mechanisms.
Journal ArticleDOI
Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions
Lars Guelen,Ludo Pagie,Emilie Brasset,Wouter Meuleman,Wouter Meuleman,Marius B. Faza,Wendy Talhout,Bert H.J. Eussen,Annelies de Klein,Lodewyk F. A. Wessels,Lodewyk F. A. Wessels,Wouter de Laat,Bas van Steensel +12 more
TL;DR: A high-resolution map of the interaction sites of the entire genome with NL components in human fibroblasts is constructed and demonstrates that the human genome is divided into large, discrete domains that are units of chromosome organization within the nucleus.
Journal ArticleDOI
IDH mutation impairs histone demethylation and results in a block to cell differentiation
Chao Lu,Patrick S. Ward,Patrick S. Ward,Gurpreet S. Kapoor,Dan Rohle,Dan Rohle,Sevin Turcan,Omar Abdel-Wahab,Christopher R. Edwards,Raya Khanin,Maria E. Figueroa,Ari Melnick,Kathryn E. Wellen,Donald M. O'Rourke,Shelley L. Berger,Timothy A. Chan,Ross L. Levine,Ingo K. Mellinghoff,Ingo K. Mellinghoff,Craig B. Thompson +19 more
TL;DR: It is reported that 2HG-producing IDH mutants can prevent the histone demethylation that is required for lineage-specific progenitor cells to differentiate into terminally differentiated cells, and that inhibition of histone methylation can be sufficient to block the differentiation of non-transformed cells.
Journal ArticleDOI
EMT, the cytoskeleton, and cancer cell invasion
TL;DR: This review has summarized recent novel insights into the molecular processes and players underlying EMT on one side and the formation of invasive membrane protrusions on the other side.
References
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Journal ArticleDOI
DNA methylation patterns and epigenetic memory
TL;DR: The heritability of methylation states and the secondary nature of the decision to invite or exclude methylation support the idea that DNA methylation is adapted for a specific cellular memory function in development.
Journal ArticleDOI
A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells
Bradley E. Bernstein,Tarjei S. Mikkelsen,Tarjei S. Mikkelsen,Xiaohui Xie,Michael Kamal,Dana J. Huebert,James Cuff,Ben Fry,Alexander Meissner,Marius Wernig,Kathrin Plath,Rudolf Jaenisch,Alexandre Wagschal,Robert Feil,Stuart L. Schreiber,Stuart L. Schreiber,Eric S. Lander,Eric S. Lander +17 more
TL;DR: It is proposed that bivalent domains silence developmental genes in ES cells while keeping them poised for activation, highlighting the importance of DNA sequence in defining the initial epigenetic landscape and suggesting a novel chromatin-based mechanism for maintaining pluripotency.
PatentDOI
Histone demethylation mediated by the nuclear amine oxidase homolog lsd1
Yang Shi,Yujiang Shi +1 more
TL;DR: In this paper, the authors identify a histone demethylase conserved from S. pombe to human and reveal dynamic regulation of histone methylation by both histonemethylases and demethylases.
Journal ArticleDOI
Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins.
TL;DR: It is shown that mammalian methyltransferases that selectively methylate histone H3 on lysine 9 (Suv39h HMTases) generate a binding site for HP1 proteins—a family of heterochromatic adaptor molecules implicated in both gene silencing and supra-nucleosomal chromatin structure.
Journal ArticleDOI
Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain.
Andrew J. Bannister,Philip Zegerman,Janet F. Partridge,Eric A. Miska,Jean O. Thomas,Robin C. Allshire,Tony Kouzarides +6 more
TL;DR: A stepwise model for the formation of a transcriptionally silent heterochromatin is provided: SUV39H1 places a ‘methyl marker’ on histone H3, which is then recognized by HP1 through its chromo domain, which may also explain the stable inheritance of theheterochromatic state.