Correlated alterations in genome organization, histone methylation, and DNA–lamin A/C interactions in Hutchinson-Gilford progeria syndrome
Rachel Patton McCord,Ashley E. Nazario-Toole,Haoyue Zhang,Peter S. Chines,Ye Zhan,Michael R. Erdos,Francis S. Collins,Job Dekker,Kan Cao +8 more
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TLDR
The results support a model that the accumulation of progerin in the nuclear lamina leads to altered H3K27me3 marks in heterochromatin, possibly through the down-regulation of EZH2, and disrupts heterochromeatin-lamina interactions, and trigger the global loss of spatial chromatin compartmentalization in late passage HGPS fibroblasts.Citations
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Epigenetic modulators, modifiers and mediators in cancer aetiology and progression
TL;DR: This work suggests a framework for cancer epigenetics involving three types of genes: 'epigenetic mediators', corresponding to the tumour progenitor genes suggested earlier; 'Epigenetic modifiers' of the mediators, which are frequently mutated in cancer; and 'epigetic modulators' upstream of the modifiers, which is responsive to changes in the cellular environment and often linked to the nuclear architecture.
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Epigenetic Mechanisms of Longevity and Aging.
TL;DR: This review provides a comprehensive overview of epigenetic studies from invertebrate organisms, vertebrate models, tissues, and in vitro systems and establishes links between common operative aging pathways and hallmark chromatin signatures that can be used to identify "druggable" targets to counter human aging and age-related disease.
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Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition
Ilya M. Flyamer,Johanna Gassler,Maxim Imakaev,Hugo B. Brandão,Sergey V. Ulianov,Nezar Abdennur,Sergey V. Razin,Sergey V. Razin,Leonid A. Mirny,Leonid A. Mirny,Kikuë Tachibana-Konwalski +10 more
TL;DR: In this paper, a single-nucleus Hi-C (high-resolution chromosome conformation capture) protocol was developed to study three-dimensional chromatin organization in rare cell types.
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Lamin B1 depletion in senescent cells triggers large-scale changes in gene expression and the chromatin landscape
Parisha P. Shah,Greg Donahue,Gabriel L. Otte,Brian C. Capell,David M. Nelson,Kajia Cao,Varun Aggarwala,Hazel A Cruickshanks,Taranjit Singh Rai,Tony McBryan,Brian D. Gregory,Peter D. Adams,Shelley L. Berger +12 more
TL;DR: Comparing genome-wide Lys4 trimethylation on histone H3 and H3K27me3 distributions between proliferating and senescent human cells found dramatic differences in senescence, suggesting that pre-malignant senescent chromatin changes foreshadow epigenetic cancer changes.
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Telomeres and telomerase: three decades of progress.
Jerry W. Shay,Woodring E. Wright +1 more
TL;DR: This Timeline article highlights the key advances that have expanded the views on the mechanistic underpinnings of telomeres and telomerase and their roles in ageing and disease.
References
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Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang,Tao Liu,Clifford A. Meyer,Jérôme Eeckhoute,David S. Johnson,Bradley E. Bernstein,Bradley E. Bernstein,Chad Nusbaum,Richard M. Myers,Myles Brown,Wei Li,X. Shirley Liu +11 more
TL;DR: This work presents Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer, and uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions.
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
Genome-Wide Mapping of in Vivo Protein-DNA Interactions
David S. Johnson,Ali Mortazavi,Ali Mortazavi,Richard M. Myers,Richard M. Myers,Barbara J. Wold,Barbara J. Wold +6 more
TL;DR: A large-scale chromatin immunoprecipitation assay based on direct ultrahigh-throughput DNA sequencing was developed, which was then used to map in vivo binding of the neuron-restrictive silencer factor (NRSF; also known as REST) to 1946 locations in the human genome.
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CpG Islands and the Regulation of Transcription
Aimee M. Deaton,Adrian Bird +1 more
TL;DR: Vertebrate CpG islands are generically equipped to influence local chromatin structure and simplify regulation of gene activity.
Journal ArticleDOI
Recurrent de novo point mutations in lamin A cause Hutchinson-Gilford progeria syndrome
Maria Eriksson,W. Ted Brown,Leslie B. Gordon,Leslie B. Gordon,Michael W. Glynn,Joel Singer,Laura J. Scott,Michael R. Erdos,Christiane M. Robbins,Tracy Moses,Peter Berglund,Amalia Dutra,Evgenia Pak,Sandra G. Durkin,Antonei B. Csoka,Michael Boehnke,Thomas W. Glover,Francis S. Collins +17 more
TL;DR: Evidence of mutations in lamin A (LMNA) as the cause of Hutchinson–Gilford progeria syndrome is presented, and the discovery of the molecular basis of this disease may shed light on the general phenomenon of human ageing.
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Recurrent de novo point mutations in lamin A cause Hutchinson-Gilford progeria syndrome
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