Discovery of Genetic Variation on Chromosome 5q22 Associated with Mortality in Heart Failure by Wang, Xinchen, Kellis, Manolis, Boyer, Laurie Ann

“…We provide evidence from reporter gene assays, computational predictions and epigenomic marks that this polymorphism increases activity of an enhancer region active in multiple human tissues. …”
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Low-input chromatin profiling in Arabidopsis endosperm using CUT&RUN by Zheng, Xiao-yu, Gehring, Mary

“…The versatility and simplicity of CUT&RUN make it a viable alternative to ChIP, which requires greater amounts of starting material, and will enable further study of tissue- or cell-type-specific epigenomes in Arabidopsis and other plant species.…”
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An immune-cell signature of bacterial sepsis by Reyes, Miguel, Filbin, Michael R., Bhattacharyya, Roby P., Billman, Kianna, Eisenhaure, Thomas, Hung, Deborah T., Levy, Bruce D., Baron, Rebecca M., Blainey, Paul C, Goldberg, Marcia B., Hacohen, Nir

“…We identified a panel of surface markers for isolation and quantification of the monocyte state and characterized its epigenomic and functional phenotypes, and propose a model for its induction from human bone marrow. …”
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Systems Biology Approaches for Elucidating Early ALS Disease Processes by Li, Jonathan

“…Next, I investigated the genetics of ALS using genomic, transcriptomic, and epigenomic data collected across 181 iPSC-derived motor neurons from ALS patients and controls. …”
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Succinate dehydrogenase inhibition leads to epithelial-mesenchymal transition and reprogrammed carbon metabolism by Aspuria, Paul-Joseph P., Lunt, Sophia Yunkyungkwon, Väremo, Leif, Vergnes, Laurent, Gozo, Maricel, Beach, Jessica A, Salumbides, Brenda, Reue, Karen, Wiedemeyer, W. R., Nielsen, Jens Kromann, Karlan, Beth Y., Orsulic, Sandra

“…We confirmed that Sdhb knockdown leads to a hypermethylated epigenome that is sufficient to promote EMT. Metabolically, the loss of Sdhb resulted in reprogrammed carbon source utilization and mitochondrial dysfunction. …”
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Sharing Information to Reconstruct Patient-Specific Pathways in Heterogeneous Diseases by Gitty, Anthony, Braunstein, Alfredo, Pagnani, Andrea, Baldassi, Carlo, Borgs, Christian, Chayes, Jennifer, Zecchina, Riccardo, Fraenkel, Ernest, Gitter, Anthony

“…Advances in experimental techniques resulted in abundant genomic, transcriptomic, epigenomic, and proteomic data that have the potential to reveal critical drivers of human diseases. …”
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Soy-derived phytochemical genistein modifies chromatome topology to restrict cancer cell proliferation by Dutta, Bamaprasad, Park, Jung Eun, Qing, Ivan Toh Yi, Kon, Oi Lian, Sze, Siu Kwan

“…These data indicate that soy derivative genistein exerts complex estrogen receptor-independent effects on the epigenome likely to influence tumorigenesis by restricting cell growth.…”
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Similarity network fusion for the integration of multi-omics and microbiomes in respiratory disease by Narayana, Jayanth Kumar, Mac Aogáin, Micheál, Nur A'tikah Mohamed Ali, Tsaneva-Atanasova, Krasimira, Chotirmall, Sanjay Haresh

“…Advances in platform technologies facilitate the design of largescale “multi-omic” studies that encompass genomic, transcriptomic, proteomic, epigenomic, metabolomic and microbiomic components, each representing different views of a single biological specimen [1]. …”
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Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing by Schuster, Stephan C., Beck, Stephan, Kim, Changhoon, Chambers, John Campbell, Loh, Marie, Zhou, Li, Ng, Hong Kiat, Drautz-Moses, Daniela I.

“…Whole genome bisulfite sequencing (WGBS), with its ability to interrogate methylation status at single CpG site resolution epigenome-wide, is a powerful technique for use in molecular experiments. …”
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The bovine alveolar macrophage DNA methylome is resilient to infection with Mycobacterium bovis by O'Doherty, A, Rue-Albrecht, K, Magee, D, Ahting, S, Irwin, R, Hall, T, Browne, J, Nalpas, N, Walsh, C, Gordon, S, Wojewodzic, M, MacHugh, D

“…Perturbation of the bovine alveolar macrophage (bAM) transcriptome, due to Mycobacterium bovis (M. bovis) infection, has been well documented; however, the impact of this intracellular pathogen on the bAM epigenome has not been determined. Here, whole genome bisulfite sequencing (WGBS) was used to assess the effect of M. bovis infection on the bAM DNA methylome. …”

The chromatin landscape of high-grade serous ovarian cancer metastasis identifies regulatory drivers in post-chemotherapy residual tumour cells by Croft, W, Pounds, R, Jeevan, D, Singh, K, Balega, J, Sundar, S, Williams, A, Ganesan, R, Kehoe, S, Ott, S, Zuo, J, Yap, J, Moss, P

“…Disease recurrence following chemotherapy is a major clinical challenge in ovarian cancer (OC), but little is known regarding how the tumour epigenome regulates transcriptional programs underpinning chemoresistance. …”

The bovine alveolar macrophage DNA methylome is resilient to infection with Mycobacterium bovis by O'Doherty, AM, Rue-Albrecht, K, Magee, DA, Ahting, S, Irwin, RE, Hall, TJ, Browne, J, Nalpas, N, Walsh, C, Gordon, SV, Wojewodzic, MW, Machugh, DE

“…Perturbation of the bovine alveolar macrophage (bAM) transcriptome, due to Mycobacterium bovis (M. bovis) infection, has been well documented; however, the impact of this intracellular pathogen on the bAM epigenome has not been determined. Here, whole genome bisulfite sequencing (WGBS) was used to assess the effect of M. bovis infection on the bAM DNA methylome. …”

Genetic variants associated with mosaic Y chromosome loss highlight cell cycle genes and overlap with cancer susceptibility. by Wright, D, Day, F, Kerrison, N, Zink, F, Cardona, A, Sulem, P, Thompson, D, Sigurjonsdottir, S, Gudbjartsson, D, Helgason, A, Chapman, J, Jackson, S, Langenberg, C, Wareham, N, Scott, R, Thorsteindottir, U, Ong, K, Stefansson, K, Perry, J

“…Cumulatively, these loci also predicted X-chromosome loss in women (N=96,123, P=4x10-6). Additional epigenome-wide methylation analyses in whole blood highlighted 36 differentially methylated sites associated with mLOY. …”

Multigenerational exposure to silver ions and silver nanoparticles reveals heightened sensitivity and epigenetic memory in Caenorhabditis elegans. by Schultz, C, Wamucho, A, Tsyusko, O, Unrine, J, Crossley, A, Svendsen, C, Spurgeon, D

“…The mechanisms of transgenerational transfer of sensitivity are probably organized through the epigenome, and we encourage others to investigate such effects as a priority for mechanistic toxicology.…”

Deoxyribonucleic acid (DNA) methylation in children exposed to air pollution: a possible mechanism underlying respiratory health effects development by Suhaimi, Nur Faseeha, Jalaludin, Juliana, Abu Bakar @ Jamaludin, Suhaili

“…The review found that epigenetic changes have been linked with exposure to air pollutants during early life with evidence and reports of how they may deregulate the epigenome balance, thus inducing disease progression in the future. …”
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A transcription-centric model of SNP-age interaction. by Kun Wang, Mahashweta Basu, Justin Malin, Sridhar Hannenhalli

“…The detected SNPs are enriched for epigenomic marks indicative of regulatory activity, exhibit allele-specific chromatin accessibility, and spatial proximity to their putative gene targets. …”
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ClusTrack: feature extraction and similarity measures for clustering of genome-wide data sets. by Halfdan Rydbeck, Geir Kjetil Sandve, Egil Ferkingstad, Boris Simovski, Morten Rye, Eivind Hovig

“…While clustering is routinely applied to gene expression data, there is a lack of appropriate general methodology for clustering of sequence-level genomic and epigenomic data, e.g. ChIP-based data. We here introduce a general methodology for clustering data sets of coordinates relative to a genome assembly, i.e. genomic tracks. …”
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One step generation of customizable gRNA vectors for multiplex CRISPR approaches through string assembly gRNA cloning (STAgR). by Christopher T Breunig, Tamara Durovic, Andrea M Neuner, Valentin Baumann, Maximilian F Wiesbeck, Anna Köferle, Magdalena Götz, Jovica Ninkovic, Stefan H Stricker

“…Novel applications based on the bacterial CRISPR system make genetic, genomic, transcriptional and epigenomic engineering widely accessible for the first time. …”
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Chromatin Dynamics in Digestive System Cancer: Commander and Regulator by Zeru Li, Bangbo Zhao, Cheng Qin, Yuanyang Wang, Tianhao Li, Weibin Wang

“…Although a great number of studies are devoted to the molecular biological mechanism, early diagnostic markers, and application of new targeted drugs in digestive system tumors, the therapeutic effect is still not satisfactory. Epigenomic alterations including histone modification and chromatin remodeling are present in human cancers and are now known to cooperate with genetic changes to drive the cancer phenotype. …”
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GWAS and 3D chromatin mapping identifies multicancer risk genes associated with hormone-dependent cancers. by Isela Sarahi Rivera, Juliet D French, Mainá Bitar, Haran Sivakumaran, Sneha Nair, Susanne Kaufmann, Kristine M Hillman, Mahdi Moradi Marjaneh, Jonathan Beesley, Stacey L Edwards

“…Integrating GWAS data, epigenomic profiling and promoter capture HiC maps from diverse cell line models, we annotated 53 candidate risk genes at 22 multi-HDC risk regions. …”
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