MLL3 regulates the CDKN2A tumor suppressor locus in liver cancer by Changyu Zhu, Yadira M Soto-Feliciano, John P Morris, Chun-Hao Huang, Richard P Koche, Yu-jui Ho, Ana Banito, Chun-Wei Chen, Aditya Shroff, Sha Tian, Geulah Livshits, Chi-Chao Chen, Myles Fennell, Scott A Armstrong, C David Allis, Darjus F Tschaharganeh, Scott W Lowe

“…Here, we combined genetic, epigenomic, and animal modeling approaches to demonstrate that one of the mechanisms by which MLL3 links chromatin remodeling to tumor suppression is by co-activating the Cdkn2a tumor suppressor locus. …”
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Targeting Class I Histone Deacetylases in Human Uterine Leiomyosarcoma by Qiwei Yang, Ali Falahati, Azad Khosh, Hanaa Mohammed, Wenjun Kang, Ana Corachán, Maria Victoria Bariani, Thomas G. Boyer, Ayman Al-Hendy

“…Moreover, multiple epigenetic analyses suggested that Tucidinostat may alter the transcriptome via reprogramming the oncogenic epigenome and inducing the changes in microRNA-target interaction in uLMS cells. …”
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CBX2 shapes chromatin accessibility promoting AML via p38 MAPK signaling pathway by Nunzio Del Gaudio, Antonella Di Costanzo, Ning Qing Liu, Lidio Conte, Carmela Dell’Aversana, Guglielmo Bove, Rosaria Benedetti, Liliana Montella, Fortunato Ciardiello, Vincenzo Carafa, Concetta Ambrosino, Valeria Tucci, Mariarosaria Conte, Joost H. A. Martens, Hendrik G. Stunnenberg, Angela Nebbioso, Lucia Altucci

“…Abstract Background The dynamic epigenome and proteins specialized in the interpretation of epigenetic marks critically contribute to leukemic pathogenesis but also offer alternative therapeutic avenues. …”
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Newcastle 1000 (NEW1000) Study: an Australian population-based prospective pregnancy cohort study design and protocol by Simon Keely, John Attia, Andrew Boyle, Sarah R Valkenborghs, Roger Smith, Clare Collins, Penny Reeves, John Wiggers, Joerg Mattes, Andrew Searles, Frances Kay-Lambkin, Linda Campbell, Vanessa E Murphy, Peter Gibson, Craig Gedye, Tegan Grace, Rodney Scott, Kirsty Pringle, Maralyn Foureur, Craig E Pennell, Vanessa McDonald, Joshua Fisher, Carol Wang, Jonathan J Hirst, Craig Pennell, Mike Calford, Vanessa Murphy, Tracey Dudding-Bythe, Nick Talley, Emily Hoedt, Jay Horvat, Mitch Duncan, Sarah Valkenborghs, Emily Freeman

“…Biological samples will be used for biomarker discovery and sequencing of the genome, transcriptome, epigenome, microbiome and metabolome.Ethics and dissemination Ethics approval was obtained from Hunter New England Local Health District Ethics Committee (2020/ETH02881). …”
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DNA methylation signatures in cord blood associated with birthweight are enriched for dmCpGs previously associated with maternal hypertension or pre-eclampsia, smoking and folic ac... by E Antoun, P Titcombe, K Dalrymple, NT Kitaba, SJ Barton, Ac Flynn, R Murray, ES Garratt, PT Seed, SL White, Cyrus Cooper, H M Inskip, M Hanson, L Poston, KM Godfrey, KA Lillycrop, UPBEAT Consortium/EpiGen Consortium

“…Adjusting for gestational age and other covariates, an epigenome-wide association study identified 2911 (FDR≤0.05) and 236 (Bonferroni corrected p ≤ 6.45×10−8) differentially methylated CpGs (dmCpGs), and 1230 differentially methylated regions (DMRs) (Stouffer ≤0.05) associated with birthweight. …”
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Integrative analysis reveals distinct subtypes with therapeutic implications in KRAS-mutant lung adenocarcinomaResearch in context by Ke Liu, Jintao Guo, Kuai Liu, Peiyang Fan, Yuanyuan Zeng, Chaoqun Xu, Jiaxin Zhong, Qiyuan Li, Ying Zhou

“…Interpretation: The heterogeneity of KRAS-mutant LUAD is associated with smoking-related genomic and epigenomic aberration along with other features such as immunogenicity, KRAS dependency and STK11/KEAP1 co-mutations. …”
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A genome-wide association study of quantitative computed tomographic emphysema in Korean populations by Sooim Sin, Hye-Mi Choi, Jiwon Lim, Jeeyoung Kim, So Hyeon Bak, Sun Shim Choi, Jinkyeong Park, Jin Hwa Lee, Yeon-Mok Oh, Mi Kyeong Lee, Brian D. Hobbs, Michael H. Cho, Edwin K. Silverman, Woo Jin Kim

“…We also compared our GWAS results with an epigenome-wide association study and previous differential gene expression analysis. …”
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Umbilical cord DNA methylation is associated with body mass index trajectories from birth to adolescenceResearch in context by Anat Yaskolka Meir, Wanyu Huang, Tingyi Cao, Xiumei Hong, Guoying Wang, Colleen Pearson, William G. Adams, Xiaobin Wang, Liming Liang

“…Methods: Using data from a US predominantly urban, low-income, multi-ethnic birth cohort (N = 831), we first applied non-parametric methods to identify body-mass-index percentile (BMIPCT) trajectories from birth to age 18 y (the outcome); then, conducted epigenome-wide association study (EWAS) of the outcome, interrogating over 700,000 CpG sites profiled by the Illumina Infinium MethylationEPIC BeadChip. …”
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Epigenetic silencing and tumor suppressor gene of HAND2 by targeting ERK signaling in colorectal cancer by Zixu Yuan, Xihu Yu, Wenle Chen, Daici Chen, Jian Cai, Yingming Jiang, Xiaoxia Liu, Zhijie Wu, Lei Wang, William M. Grady, Hui Wang

“…We conducted integrative analyses of epigenome-wide Human Methylation 450 K arrays and transcriptome to screen out candidate epigenetic driver genes with transcription silencing. …”
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Network reconstruction for trans acting genetic loci using multi-omics data and prior information by Johann S. Hawe, Ashis Saha, Melanie Waldenberger, Sonja Kunze, Simone Wahl, Martina Müller-Nurasyid, Holger Prokisch, Harald Grallert, Christian Herder, Annette Peters, Konstantin Strauch, Fabian J. Theis, Christian Gieger, John Chambers, Alexis Battle, Matthias Heinig

“…Abstract Background Molecular measurements of the genome, the transcriptome, and the epigenome, often termed multi-omics data, provide an in-depth view on biological systems and their integration is crucial for gaining insights in complex regulatory processes. …”
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Loss of carnitine palmitoyltransferase 1a reduces docosahexaenoic acid-containing phospholipids and drives sexually dimorphic liver disease in mice by Mikala M. Zelows, Corissa Cady, Nikitha Dharanipragada, Anna E. Mead, Zachary A. Kipp, Evelyn A. Bates, Venkateshwari Varadharajan, Rakhee Banerjee, Se-Hyung Park, Nathan R. Shelman, Harrison A. Clarke, Tara R. Hawkinson, Terrymar Medina, Ramon C. Sun, Todd A. Lydic, Terry D. Hinds, Jr., J. Mark Brown, Samir Softic, Gregory A. Graf, Robert N. Helsley

“…Background and aims: Genome and epigenome wide association studies identified variants in carnitine palmitoyltransferase 1a (CPT1a) that associate with lipid traits. …”
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SIRT1-dependent modulation of methylation and acetylation of histone H3 on lysine 9 (H3K9) in the zygotic pronuclei improves porcine embryo development by Katerina Adamkova, Young-Joo Yi, Jaroslav Petr, Tereza Zalmanova, Kristyna Hoskova, Pavla Jelinkova, Jiri Moravec, Milena Kralickova, Miriam Sutovsky, Peter Sutovsky, Jan Nevoral

“…Stimulation of SIRT1 activity coincided with fluorometric signal intensity of ooplasmic ubiquitin ligase MDM2, a known substrate of SIRT1 and known limiting factor of epigenome remodeling. Conclusions We conclude that SIRT1 modulates zygotic histone code, obviously through direct deacetylation and via non-histone targets resulting in increased H3K9me3. …”
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The performance of whole genome bisulfite sequencing on DNBSEQ-Tx platform examined by different library preparation strategies by Boyang Cao, Huijuan Luo, Tian Luo, Nannan Li, Kang Shao, Kui Wu, Sunil Kumar Sahu, Fuqiang Li, Cong Lin

“…However, the International Human Epigenome Consortium propose a full DNA methylome should have at least 30 fold redundant coverage of the reference genome from a single biological replicate. …”
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Epigenetic programming underpins B‐cell dysfunction in peanut and multi‐food allergy by Samira Imran, Melanie R Neeland, Jennifer Koplin, Shyamali Dharmage, Mimi LK Tang, Susan Sawyer, Thanh Dang, Vicki McWilliam, Rachel Peters, Kirsten P Perrett, Boris Novakovic, Richard Saffery

“…Conclusion Our data highlight epigenetic changes in B cells associated with peanut allergy, distinguishing features of the epigenome between single‐food‐ and multi‐food‐allergic individuals and revealing differential developmental pathways potentially underpinning these distinct phenotypes.…”
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Integrative analysis of methylomic and transcriptomic data in fetal sheep muscle tissues in response to maternal diet during pregnancy by Hadjer Namous, Francisco Peñagaricano, Marcello Del Corvo, Emanuele Capra, David L. Thomas, Alessandra Stella, John L. Williams, Paolo Ajmone Marsan, Hasan Khatib

“…Conclusions The findings of this study imply that maternal diet from mid- to late-gestation can shape the epigenome and the transcriptome of fetal tissues, and putatively affect phenotypes of the lambs.…”
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Anaplasma phagocytophilum Ankyrin A Protein (AnkA) Enters the Nucleus Using an Importin-β-, RanGTP-Dependent Mechanism by Yuri Kim, Yuri Kim, Jianyang Wang, Jianyang Wang, Emily G. Clemens, Dennis J. Grab, J. Stephen Dumler

“…Ankyrin A (AnkA), an effector protein with multiple ankyrin repeats (AR) is injected via type IV-secretion into the host neutrophil to gain access to the nucleus where it modifies the epigenome to promote microbial fitness and propagation. …”
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The dynamics of smoking-related disturbed methylation: a two time-point study of methylation change in smokers, non-smokers and former smokers by Rory Wilson, Simone Wahl, Liliane Pfeiffer, Cavin K. Ward-Caviness, Sonja Kunze, Anja Kretschmer, Eva Reischl, Annette Peters, Christian Gieger, Melanie Waldenberger

“…Abstract Background The evidence for epigenome-wide associations between smoking and DNA methylation continues to grow through cross-sectional studies. …”
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Reactive gliosis in traumatic brain injury: a comprehensive review by Zuzana Amlerova, Martina Chmelova, Martina Chmelova, Miroslava Anderova, Miroslava Anderova, Lydia Vargova, Lydia Vargova

“…Novel technologies including whole-genome transcriptomic and epigenomic analyses, and unbiased proteomics, show that both astrocytes and microglia represent groups of heterogenic cell subpopulations with different genomic and functional characteristics, that are responsible for their role in neurodegeneration, neuroprotection and regeneration. …”
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An integrated -omics analysis of the epigenetic landscape of gene expression in human blood cells by Elizabeth M. Kennedy, George N. Goehring, Michael H. Nichols, Chloe Robins, Divya Mehta, Torsten Klengel, Eleazar Eskin, Alicia K. Smith, Karen N. Conneely

“…Conclusions This work sheds new light on the interplay between epigenetic changes and gene expression, and provides useful data for mining biologically-relevant results from epigenome-wide association studies.…”
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Investigating the impact of oral health on pregnancy and offspring outcomes: protocol for the Lifetime Impact of ORal heAlth (LIORA) cohort study by Ting Zhang, Hua Zhang, Ping Ji, Chang Chen, Xin Jin, Richard Saffery, Yinyin Xia, Pamela Leong, Ting-li Han, Mei-Ling Zhao, Feng-Jing Zhang, Wen-Rong Jiang, Xin-Yang Yu, Peter Mei, Hong-Mei Zhang, Boris Novakovic, Murray Thompson, Richard D Cannon

“…Biological samples will undergo comprehensive metabolomic, microbiome and epigenome analyses. Associations between maternal oral health and general health, pregnancy outcomes, offspring oral health and offspring general health will be investigated and the underlying mechanisms explored.Ethics and dissemination This project has been approved by the Research Ethics Committee of the Affiliated Hospital of Stomatology of Chongqing Medical University (CQHS-REC-2021 LSNo.23). …”
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