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Epigenetics News

February 2016

Histone modifications predispose genome regions to breakage and translocation.
In this paper, genome-wide histone modification datasets from a panel of cancer cell lines were used to identify the epigenetic identity of DNA breakage events. The authors were able to associate the presence of active chromatin marks such as H3K4 methylation with regions prone to DNA breakages and translocations. Additionally, by artificially tethering a SET2 methyltransferase-LacI fusion to a lacOp array, they were able to identify the presence of active marks on the lacOp array and an increase in double-stranded breaks (DSB) of DNA at these sites.
Burman et al. Genes & Development. 2015 Jul 1;29(13):1393-402. doi: 10.1101/gad.262170.115. Epub 2015 Jun 23
Abstract.

Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples.
Current DNAse I-seq protocols are limited by their requirement for large numbers of cells. The authors of this paper have established a new protocol applicable to single cell and FFPE tissue samples. This very sensitive technique is called scDNAse-seq and it relies on the presence of a carrier Circular DNA during the sequencing process. Using this method, the authors were able to predict enhancers that regulate cell-specific gene expression and correlate with active histone modification marks. Furthermore, using FFPE samples from patients with thyroid cancers the authors were able to detect DNAse-hypersensitivity sites (DHSs) related to cancer progression.
Zhao K. et al. Nature. 2015 Dec 3;528(7580):142-6. doi: 10.1038/nature15740.
Abstract.

A Multiplexed System for Quantitative Comparisons of Chromatin Landscapes
The authors of this study have developed a multiplexing system for ChIP-Seq that allows for the use of fewer cells. In the resulting protocol, Mint ChIP, indexed samples are pooled and then split for parallel ChIP assays. Using this advanced technology, the authors were able to quantitatively profile multiple epigenetic marks across a series of different cell types and conditions.
Bernstein, BE. et al. Mol. Cell. 2016 Jan 7;61(1):170-80. doi: 10.1016/j.molcel.2015.11.003. Epub 2015 Dec 10.
Abstract.
 

January 2016

Obesity and Bariatric surgery drive Epigenetic Variation of Spermatozoa in Humans
Obesity is a heritable disorder and children of obese fathers have an increased risk of manifesting disease. Environmental factors could alter the epigenetic status of obese fathers but thus far the molecular mechanism of heritability remains poorly understood. Donkin et al show for the first time that spermatozoa in obese men present a series of epigenetic changes. Notably, the expression profile of the scnRNAs that target the genes responsible for behaviour and food intake shows dramatic changes. Additionally, obese men present a distinct methylation pattern of genes controlling brain development and function. Bariatric surgery could alter the DNA methylation landscape of spermatozoa, especially in master genes associated with obesity and nutritional behaviour, thereby determining the epigenetic status of offspring.
Donklin et al. Cell Metab. 2015 Dec 6; pii: S1550-4131(15)00571-9. doi: 10.1016/j.cmet.2015.11.004. [Epub ahead of print]
Short Article.
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Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors
A very interesting study highlighting the importance of chromatin regulation in adult visual cortical plasticity. Lennartsson et al utilized HDAc inhibitor (VPA) in order to induce epigenetic alterations in the chromatin of brain cells in the mature visual cortex. After exposure to HDAC inhibitor, remodelling of chromatin leads to the increased accessibility of transcription factors in regulatory regions of brain specific genes and nucleosome eviction in SINEs.
Lennartsson et al. Epigenetics Chromatin. 2015 Dec 14; 8:55. doi: 10.1186/s13072-015-0043-3. eCollection 2015
Full Article.
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Hypomethylation of smoking-related genes is associated with future lung cancer in four prospective cohorts
This is the first study to evaluate the importance of genomic alterations to the disease aetiology of lung cancer patients by performing a genome-wide methylation analysis in peripheral blood. Although previous studies have shown an association of tobacco exposure and methylation of CPG islands at specific sites, it is not known whether the methylation status of these sites is related to lung cancer. In this study, DNA was extracted from pre-diagnostic blood of 132 pairs of lung cancer cases along with controls from different cohorts and DNA methylation status was determined. The results indicate that exposure to a toxic agent such a smoke results in hypo-methylation of smoking related genes and this status remains stable over series of mitotic divisions in blood cells.
Fasanelli F. et al. Nat. Communications. 2015 Dec 15. doi: 10.1038/ncomms10192
Full Article.
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December 2015

Autophagy mediates degradation of nuclear lamina
Researchers from the Berger lab report on the role of autophagy in tumor suppression and degradation of the nuclear lamina. The interaction of autophagic protein LC3 with lamin B1 mediates lamin B1 degradation only upon ongogenic insults, such as those by activated RAS. This study elucidates a new role of autophagy in protecting cells from tumorigenesis.
Dou Z. et al. Nature. 2015 Nov 5;527(7576):105-9. doi: 10.1038/nature15548. Epub 2015 Oct 28.
Abstract.
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Continuous Histone Replacement by Hira Is Essential for Normal Transcriptional Regulation and De Novo DNA Methylation during Mouse Oogenesis.
In recent years, several studies have uncovered roles for new proteins in the maintenance of chromatin assembly and stability. Histone proteins and histone variants are central players in these pathways. In the current study Nashun and colleagues describe the role of the histone chaperone Hira in chromatin accessibility, transcription, and DNA methylation during mouse oogenesis.
Nashun B. et al. Mol. Cell.2015 Nov 4. pii: S1097-2765(15)00777-7. doi: 10.1016/j.molcel.2015.10.010. [Epub ahead of print]
Abstract.
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Protein-RNA networks revealed through covalent RNA marks
In the current study, the authors have developed a novel method to identify RNA-protein interactions in vivo without the need for crosslinking. This method uses an RNA-binding protein of interest fused to an enzyme that adds uridines to the end of RNA. Once covalently marked with uridines, RNA targets are identified by high-throughput sequencing. Using this methodology, the authors were able to identify hundreds of new & likely regulated targets of Puf3p RNA-binding protein.
Lapointe CP. et al. Nat. Methods.2015 Nov 2. doi: 10.1038/nmeth.3651. [Epub ahead of print]
Abstract.
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November 2015

A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulation
The authors of this study performed an adapted UV-CLIP protocol, at single nucleotide resolution, on human CD8+ T cells & mouse brains to locate m6 A residues on mammalian mRNA molecules. Results strongly suggest that m6A deposition is triggered, not by proximity to a stop codon, but by entry into the last exon of an mRNA.
Ke et al. (2015) Genes & Development. doi:10.1101/gad.269415.115
Abstract.
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Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state
Two limitations of chromatin mapping technologies are that they rely on large amounts of input material and that they average mixed cell populations. Although technologies for single-cell transcriptome studies are rapidly evolving, chromatin-based experiments in single cells have remained elusive thus far. The authors of this study developed an innovative microfluidics technology including single cell isolation and chromatin immunoprecipitation in order to map differences in epigenetic identity in cell subpopulations.
Rotem A, (2015) Nat. Biotechnol. doi: 10.1038/nbt.3383
Abstract.
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Tracing Dynamic Changes of DNA Methylation at Single-Cell Resolution
In this study, the Jaenisch lab describes a new reporter of genomic methylation (RGM) based on a methylation-sensitive promoter fused to a fluorescent protein. RGM reports on the methylation status of the regulatory elements adjacent to it and can be used to study methylation in single, living cells to visualize heterogeneity within wildtype or cancer specimens. Since the fluorescent proteins used in the study (GFP and tdTomato) have a long half-life, this technique may be further optimized using destabilized fluorescent proteins.
Stelzer et al (2015) Cell. doi: 10.1016/j.cell.2015.08.046
Abstract.
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October 2015

DNA-Demethylating Agents Target Colorectal Cancer Cells by Inducing Viral Mimicry by Endogenous Transcripts
DNA demethylating agents have shown clinical antitumor efficacy however the underlying mechanism of their function remains unknown. In the latest issue of Cell, David Roulois and collaborators uncover the role of the DNA methylation inhibitor 5-AZA-CdR in targeting colorectal cancer initiating cells (CICs).
Roulois et al. (2015) Cell. doi.org/10.1016/j.cell.2015.07.056
Abstract.
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Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells
Mammalian interphase chromosomes interact with lamina through well-defined lamin associated domains (LADs). Conformation data from genome-wide chromosome experiments have identified roughly 1000-1400 discrete LADs scattered across all chromosomes. Most of the genes in these LADs are expressed at very low levels and marked with repressive marks. In this study, researchers from Bas van Steensel’s lab have developed a new, high-resolution technology to conduct single cell Dam-ID experiments. Their 395 single cell maps provide insight into how 3D genomic conformation and gene localization varies from cell to cell.
Kind et al. (2015) Cell. doi.org/10.1016/j.cell.2015.08.040
Abstract.
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PARP1- and CTCF-Mediated Interactions between Active and Repressed Chromatin at the Lamina Promote Oscillating Transcription
The circadian clock is an important paradigm of adaptive transcriptional regulation in the cell. Periodic oscillations of gene products controlling cell signalling and metabolism contribute to timing-dependent combinatorial patterns in the proteome. In the current study, authors suggest that PARP1 and CTCF regulate interaction between active and inactive nuclear compartments to connect oscillating 3D chromatin conformations with the metabolic states of the cell.
Zhao et al (2015) Cell. doi.org/10.1016/j.molcel.2015.07.019
Abstract.
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September 2015

Active promoters give rise to false positive 'Phantom Peaks' in ChIP-seq experiments
In this issue of Nucleic Acid Research, researchers in the Becker Lab identify a series of “phantom peaks” that commonly appear in ChIP-Seq experiments including modENCODE ChIP-Seq profiles. According to the authors, “phantom peaks” are false positive signals from ChIP-Seq, most likely caused by non-specific immunoprecipitation. The authors also suggest that these profiles, and other ChIP-Seq data featuring prominent Phantom Peaks, must be validated with chromatin from cells in which the protein of interest has been depleted.
Becker et al. (2015) Nucleic Acids Res. doi:10.1093/nar/gkv637
Abstract.
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MicroRNA-224 promotes tumor progression in nonsmall cell lung cancer
In this study, Ri Cui and his collaborators explore the functional link between miR-224 and tumor progression in nonsmall cell lung cancer (NSCLC). Despite recent advancements, the survival rate of lung cancer patients remains extremely poor and the molecular mechanism of NSCLC invasion remains poorly understood. The results of this study indicate that miR-224 promotes cellular migratory, invasive, and proliferative capacity and tumor growth both in vitro and in vivo. Additionally, the authors identify TNFα-induced protein 1 and SMAD4 as targets of miR-224 and suggest that targeting miR-224 might be a promising therapeutic strategy in the treatment of NSCLC.
Croce et al. (2015) PNAS. doi:10.1073/pnas.1502068112
Abstract.
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A CTCF Code for 3D Genome Architecture
The architectural protein CTCF, as part of the cohesion complex, plays an important role in higher order chromosomal organization by contributing to the formation of loops, especially between distal enhancers and target promoters. In this current paper, the authors emphasize the importance of the orientation of CTCF binding sites (CBS) in 3D genome architecture and propose a model for orientation-specific loop formation.
Corces, V. G., & M.H. Nichols (2015) Cell. doi:10.1016/j.cell.2015.07.053
Abstract.
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August 2015

Single-cell chromatin accessibility mapping by scATAC-seq
In this recent Nature paper, Will Greenleaf and his colleagues at Stanford detail the single-cell ATAC-seq (scATAC-seq) method, which they‘ve recently developed for mapping the accessible genome of individual cells. By integrating an assay for transposase-accessible chromatin using sequencing (ATAC-seq) with a programmable microfluidics platform, Greenleaf and his colleagues have been able to gather single-cell ATAC-seq (scATAC-seq) maps from hundreds of single cells and assemble an aggregate of these accessibility profiles. The results of which provide new insight into the cellular variation of the ‘regulome’.
Greenleaf et al. (2015) Nature. 10.1038/nature14590.
Abstract.
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Putting Non-coding RNA on Display with CRISPR
In this recent issue of Nature Methods, Shechner et al. reported the development of CRISPR Display (CRISP-Disp), which is a sophisticated, flexible, modular, and multiplexable platform for targeting different types of non-coding RNAs (ncRNAs) to genomic loci. CRISP-Disp will facilitate synthetic-biology applications and enable the elucidation of ncRNA functions.
Rinn et al. (2015) Nature Methods. 10.1038/nmeth.3433.
Abstract.
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5hmdC and 5fdC recycling as a new therapeutic target in cancer
In this recent paper, Kriaucionis et al. set out to understand what happens to 5-hydroxymethyldeoxycytidine (5hmdC) and 5-formyldeoxycytidine (5fdC) during nucleotide recycling. The results indicate that although such nucleotides are normally discarded, their recycling and incorporation into DNA in certain cancers constitutes a new therapeutically-exploitable avenue for cancer research.
Kriaucionis et al. (2015) Nature. doi: 10.1038/nature14948
Abstract.
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