Aberrant JAK-STAT signaling-mediated chromatin remodeling impairs the sensitivity of NK/T-cell lymphoma to chidamide by Jinghong Chen, Zhixiang Zuo, Yan Gao, Xiaosai Yao, Peiyong Guan, Yali Wang, Zhimei Li, Zhilong Liu, Jing Han Hong, Peng Deng, Jason Yongsheng Chan, Daryl Ming Zhe Cheah, Jingquan Lim, Kelila Xin Ye Chai, Burton Kuan Hui Chia, Jane Wan Lu Pang, Joanna Koh, Dachuan Huang, Haixia He, Yichen Sun, Lizhen Liu, Shini Liu, Yuhua Huang, Xiaoxiao Wang, Hua You, Sahil Ajit Saraf, Nicholas Francis Grigoropoulos, Xiaoqiu Li, Jinxin Bei, Tiebang Kang, Soon Thye Lim, Bin Tean Teh, Huiqiang Huang, Choon Kiat Ong, Jing Tan

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Epigenetic Dysregulation and Its Correlation with the Steroidogenic Machinery Impacting Breast Pathogenesis: Data Mining and Molecular Insights into Therapeutics by Pulak R. Manna, Shengping Yang, P. Hemachandra Reddy

“…Along these lines, ingenuity pathway analysis (IPA) recognized a number of new targets and downstream effectors influencing BCs. Of note, genomic, epigenomic, transcriptional, and hormonal anomalies observed in human primary breast tumors were qualitatively similar in pertinent BC cell lines. …”
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Understanding 3D Genome Organization and Its Effect on Transcriptional Gene Regulation Under Environmental Stress in Plant: A Chromatin Perspective by Suresh Kumar, Simardeep Kaur, Karishma Seem, Santosh Kumar, Trilochan Mohapatra

“…While the A and B compartments are associated with active (euchromatic) and inactive (heterochromatic) chromatin, respectively, having well-defined genomic/epigenomic features, TADs are the structural units of chromatin. …”
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CRISPR/Cas: A powerful tool for gene function study and crop improvement by Dangquan Zhang, Zhiyong Zhang, Turgay Unver, Baohong Zhang

“…It can be used to target a sequence for gene knockin, knockout and replacement as well as monitoring and regulating gene expression at the genome and epigenome levels by binding a specific sequence. Agrobacterium-mediated method is still the major and efficient method for delivering CRISPR/Cas regents into targeted plant cells. …”
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Targeted expression profiling reveals distinct stages of early canine fibroblast reprogramming are regulated by 2-oxoglutarate hydroxylases by Ian C. Tobias, Mian-Mian C. Kao, Thomas Parmentier, Hailey Hunter, Jonathan LaMarre, Dean H. Betts

“…We ask how cFF reprogramming is influenced by small molecules affecting the epigenomic modification 5-hydroxymethylcytosine, specifically L-ascorbic acid and retinoic acid (AA/RA). …”
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Identification of Genetic and Epigenetic Variants Associated with Breast Cancer Prognosis by Integrative Bioinformatics Analysis by Arunima Shilpi, Yingtao Bi, Segun Jung, Samir K. Patra, Ramana V. Davuluri

“…Materialsand Methods We developed a novel method to identify prognostic gene signatures for breast cancer by integrating genomic and epigenomic data. This is based on the hypothesis that multiple sources of evidence pointing to the same gene or pathway are likely to lead to reduced false positives. …”
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Molecular signature of the imprintosome complex at the mating-type locus in fission yeast by Célia Raimondi, Bernd Jagla, Caroline Proux, Hervé Waxin, Serge Gangloff, Benoit Arcangioli

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The future role of personalized medicine in the treatment of glioblastoma multiforme by Jing Li, Chunhui Di, Austin K Mattox, et al

“…Over the past year, many investigations specifically focused simultaneously on strategies to target oncogenic pathways, angiogenesis, tumor immunology, epigenomic events, glioma stem cells (GSCs), and the highly migratory glioma cell population. …”
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Paternal obesity is associated with <it>IGF2 </it>hypomethylation in newborns: results from a Newborn Epigenetics Study (NEST) cohort by Soubry Adelheid, Schildkraut Joellen M, Murtha Amy, Wang Frances, Huang Zhiqing, Bernal Autumn, Kurtzberg Joanne, Jirtle Randy L, Murphy Susan K, Hoyo Cathrine

“…Our data suggest an increase in DNA methylation at the <it>IGF2 </it>and <it>H19 </it>DMRs among newborns from obese mothers, but a larger study is warranted to further explore the potential effects of maternal obesity or lifestyle on the offspring's epigenome.</p> <p>Conclusions</p> <p>While our small sample size is limited, our data indicate a preconceptional impact of paternal obesity on the reprogramming of imprint marks during spermatogenesis. …”
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Identification of Potential Biomarkers of Chronic Kidney Disease in Individuals with Diabetes: Protocol for a Cross-sectional Observational Study by Lecamwasam, Ashani R, Mohebbi, Mohammadreza, Ekinci, Elif I, Dwyer, Karen M, Saffery, Richard

“…ConclusionsRecent advances have improved our understanding of the epigenome, metabolomics, and the influence of the gut microbiome on the incidence of diseases such as cancers, particularly those related to environmental exposures. …”
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Master regulator analysis of paragangliomas carrying SDHx, VHL, or MAML3 genetic alterations by John A. Smestad, L. James Maher

“…Although hypotheses propose that succinate accumulation after SDH loss poisons dioxygenases and activates pseudohypoxia and epigenomic hypermethylation, it remains unclear whether these mechanisms account for oncogenic transcriptional patterns. …”
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The NASA Twins Study: The Effect of One Year in Space on Long-Chain Fatty Acid Desaturases and Elongases by Michael A. Schmidt, Cem Meydan, Caleb M. Schmidt, Ebrahim Afshinnekoo, Christopher E. Mason

“…Longitudinal assessments included the genome, epige­nome, transcriptome, proteome, metabolome, microbiome, and immunome during the mission, as well as 6 months before and after. …”
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The developmental miR-17–92 cluster and the Sfmbt2 miRNA cluster cannot rescue the abnormal embryonic development generated using obstructive epididymal environment-producing sperm... by Xunwei Wu, Xiaomei He, Qian Liu, Honggang Li

“…It implies that epididymis is important in early embryonic development and may play a potential role in sperm epigenome.…”
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Association of Forced Vital Capacity with the Developmental Gene NCOR2. by Cosetta Minelli, Charlotte H Dean, Matthew Hind, Alexessander Couto Alves, André F S Amaral, Valerie Siroux, Ville Huikari, María Soler Artigas, David M Evans, Daan W Loth, Yohan Bossé, Dirkje S Postma, Don Sin, John Thompson, Florence Demenais, John Henderson, SpiroMeta consortium, CHARGE consortium, Emmanuelle Bouzigon, Deborah Jarvis, Marjo-Riitta Järvelin, Peter Burney

“…For SNPs with evidence of replication, effects on the expression levels of nearby genes in lung tissue were tested in 1,111 lung samples (Lung eQTL consortium), with further functional investigation performed using public epigenomic profiling data (ENCODE). RESULTS:NCOR2-rs12708369 showed strong replication in children (p = 0.0002), with replication unavailable in adults due to low imputation quality. …”
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Development and validation of prognostic markers in sarcomas base on a multi-omics analysis by Yongchun Song, Kui Yang, Tuanhe Sun, Ruixiang Tang

“…Conclusion The current comprehensive analysis of genomic and epigenomic regulation provides new insights into multilayered pathobiology of sarcomas. …”
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Cross-tissue patterns of DNA hypomethylation reveal genetically distinct histories of cell development by Timothy J. Scott, Tyler J. Hansen, Evonne McArthur, Emily Hodges

“…Ultimately, these data provide novel insights into how DNA hypo-methylation provides genetically distinct historical records of a cell’s journey through development, highlighting HMRs as functionally distinct from other epigenomic annotations.…”
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CCNB1 and AURKA are critical genes for prostate cancer progression and castration-resistant prostate cancer resistant to vinblastine by Xi Chen, Junjie Ma, Xin’an Wang, Tong Zi, Duocheng Qian, Chao Li, Chengdang Xu

“…Genetic alterations have been speculated to play a critical role in CRPC resistance to vinblastine; however, its mechanism remains unclear.MethodsVarious databases, such as Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA) and Chinese Prostate Cancer Genome and Epigenome Atlas (CPGEA), were used to collect the RNA-sequence data of PCa and CRPC patients and vinblastine-resistant PCa cells. …”
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DNA methylation biomarker selected by an ensemble machine learning approach predicts mortality risk in an HIV-positive veteran population by Chang Shu, Amy C. Justice, Xinyu Zhang, Vincent C. Marconi, Dana B. Hancock, Eric O. Johnson, Ke Xu

“…Abbreviations: AUC: Area Under Curve; CI: Confidence interval; DMR: differentially methylated region; DNA: Deoxyribonucleic acid; DNAm: DNA methylation; DAVID: Database for Annotation, Visualization, and Integrated Discovery; EWA: epigenome-wide association; FDR: False discovery rate; FWER: Family-wise error rate; GLMNET: elastic-net-regularized generalized linear models; GO: Gene ontology; HIV: Human immunodeficiency virus; HM450K: Human Methylation 450 K BeadChip; k-NN: k-nearest neighbours; NK: Natural killer; PC: Principal component; PLWH: people living with HIV; QC: Quality control; SVM: Support Vector Machines; VACS: Veterans Ageing Cohort Study; XGBoost: Extreme Gradient Boosting Tree…”
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The MMP-2 histone H3 N-terminal tail protease is selectively targeted to the transcription start sites of active genes by Benjamin H. Weekley, Judd C. Rice

“…Abstract Background Proteolysis of the histone H3 N-terminal tail (H3NT) is an evolutionarily conserved epigenomic feature of nearly all eukaryotes, generating a cleaved H3 product that is retained in ~ 5–10% of the genome. …”
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Systematic and benchmarking studies of pipelines for mammal WGBS data in the novel NGS platform by Qun-ting Lin, Wei Yang, Xin Zhang, Qi-gang Li, Yong-feng Liu, Qin Yan, Lei Sun

“…It is a powerful technique for epigenome in various cell types, and tissues. As a recently established next-generation sequencing (NGS) platform, GenoLab M is a promising alternative platform. …”
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