The Landscape of Histone Modifications in Epigenomics Since 2020

References

• Tarashi S , BadiSA , MoshiriAet al. The inter-talk between Mycobacterium tuberculosis and the epigenetic mechanisms. Epigenomics12(5), 455–469 (2020).
   PubMed Web of Science ®Google Scholar
• Strelnikov VV , ZaletaevDV. Evolution of cancer DNA methylotyping. Epigenomics11(8), 857–859 (2019).
   PubMed Web of Science ®Google Scholar
• Tost J , HermanJG. Welcome to Epigenomics. Epigenomics1(1), 1–3 (2009).
   PubMed Web of Science ®Google Scholar
• Cherkasova V . DNA mismatch repair in mammals. In: Genome Stability: From Virus to Human Application.Academic Press, London, UK, 323–347 (2021).
   Google Scholar
• Al Emran A , MarzeseDM , MenonDRet al. Commonly integrated epigenetic modifications of differentially expressed genes lead to adaptive resistance in cancer. Epigenomics11(7), 723–737 (2019).
   Web of Science ®Google Scholar
• Fu E , ShenJ , DongZet al. Histone demethylase Kdm2a regulates germ cell genes and endogenous retroviruses in embryonic stem cells. Epigenomics11(7), 751–766 (2019).
   PubMed Web of Science ®Google Scholar
• Hillyar CRT , KanabarSS , RallisKS , VargheseJS. Complex cross-talk between EZH2 and miRNAs confers hallmark characteristics and shapes the tumor microenvironment. Epigenomics14(11), 699–709 (2022).
   PubMed Web of Science ®Google Scholar
• Kundu S , DasR , LaskarS , ChoudhuryY , GhoshSK. Principles of bi-sulfite conversion of DNA and methylation-specific PCR (MSP) in biological research. In: Epigenetics Methods.Academic Press, London, UK, 17–36 (2020).
   Google Scholar
• Li H , WangX , ZhaoHet al. Low folate concentration impacts mismatch repair deficiency in neural tube defects. Epigenomics12(1), 5–18 (2020).
   PubMed Web of Science ®Google Scholar
• Calcagno DQ , WisnieskiF , DaSilva Mota ERet al. Role of histone acetylation in gastric cancer: implications of dietetic compounds and clinical perspectives. Epigenomics11(3), 349–362 (2019).
   PubMed Web of Science ®Google Scholar
• Sousa LO , SobralLM , de AlmeidaLO , GarciaCB , GreeneLJ , LeopoldinoAM. SET protein modulates H4 histone methylation status and regulates miR-137 level in oral squamous cell carcinoma. Epigenomics12(6), 475–485 (2020).
   PubMed Web of Science ®Google Scholar
• Almeida LO , NetoMPC , SousaLO , TannousMA , CurtiC , LeopoldinoAM. SET oncoprotein accumulation regulates transcription through DNA demethylation and histone hypoacetylation. Oncotarget8(16), 26802–26818 (2017).
   PubMedGoogle Scholar
• Ghazi T , NagiahS , DhaniS , ChuturgoonAA. Fusaric acid-induced epigenetic modulation of hepatic H3K9me3 triggers apoptosis in vitro and in vivo. Epigenomics12(11), 955–972 (2020).
   PubMed Web of Science ®Google Scholar
• Melton D . “Stemness”: definitions, criteria, and standards. In: Essentials of Stem Cell Biology (Third Edition).Academic Press, London, UK, 7–17 (2014).
   Google Scholar
• Granit RZ , SlyperM , Ben-PorathI. Axes of differentiation in breast cancer: untangling stemness, lineage identity, and the epithelial to mesenchymal transition. Wiley Interdiscip. Rev. Syst. Biol. Med.6(1), 93–106 (2014).
   PubMed Web of Science ®Google Scholar
• Giorgio E DI , CutanoV , MinisiniM , TolottoV , DallaE , BrancoliniC. A regulative epigenetic circuit supervised by HDAC7 represses IGFBP6 and IGFBP7 expression to sustain mammary stemness. Epigenomics13(9), 683–698 (2021).
   PubMedGoogle Scholar
• Nikulin SV , RaigorodskayaMP , PoloznikovAAet al. In vitro model for studying of the role of IGFBP6 gene in breast cancer metastasizing. Bull. Exp. Biol. Med.164(5), 688–692 (2018).
   PubMed Web of Science ®Google Scholar
• Godina C , KhazaeiS , TryggvadottirHet al. Prognostic impact of tumor-specific insulin-like growth factor binding protein 7 (IGFBP7) levels in breast cancer: a prospective cohort study. Carcinogenesis42(11), 1314–1325 (2021).
   PubMed Web of Science ®Google Scholar
• Prado-Garcia H , Romero-GarciaS. The role of exhaustion in tumor-induced T-cell dysfunction in cancer. In: Cancer Immunology: A Translational Medicine Context (Second Edition).Springer International Publishing, Switzerland, 117–132 (2020).
   Google Scholar
• Nair VS , SalehR , ToorSMet al. Epigenetic regulation of immune checkpoints and T cell exhaustion markers in tumor-infiltrating T cells of colorectal cancer patients. Epigenomics12(21), 1871–1882 (2020).
   PubMed Web of Science ®Google Scholar
• Oryani MA , TavasoliA , GhalavandMAet al. Epigenetics and its therapeutic potential in colorectal cancer. Epigenomics14(11), 683–697 (2022).
   PubMed Web of Science ®Google Scholar
• Goel A . The era of biomarkers and precision medicine in colorectal cancer: an interview with Ajay Goel. Epigenomics14(6), 345–349 (2022).
   PubMed Web of Science ®Google Scholar
• Jirtle RL . The science of hope: an interview with Randy Jirtle. Epigenomics14(6), 299–302 (2022).
   PubMed Web of Science ®Google Scholar
• Zhu J , SuM , GuYet al. Development of a method for identifying and functionally analyzing allele-specific DNA methylation based on BS-seq data. Epigenomics11(15), 1679–1692 (2019).
   PubMed Web of Science ®Google Scholar
• Thamban T , SowpatiDiT , PaiVet al. The putative Neuronatin imprint control region is an enhancer that also regulates the Blcap gene. Epigenomics11(3), 251–266 (2019).
   PubMed Web of Science ®Google Scholar
• Hanna CW , KelseyG. Features and mechanisms of canonical and noncanonical genomic imprinting. Genes Dev.38(11–12), 821–834 (2021).
   Google Scholar
• Chen Z , YinQ , InoueA , ZhangC , ZhangY. Allelic H3K27me3 to allelic DNA methylation switch maintains noncanonical imprinting in extraembryonic cells. Sci. Adv.5(12), eaay7246 (2019).
   PubMed Web of Science ®Google Scholar
• Zeng T-B , PierceN , LiaoJ , SzabóPE. H3K9 methyltransferase EHMT2/G9a controls ERVK-driven noncanonical imprinted genes. Epigenomics13(16), 1301–1316 (2021).
   Web of Science ®Google Scholar
• Tao H , SongZY , DingXS , YangJJ , ShiKH , LiJ. Epigenetic signatures in cardiac fibrosis, special emphasis on DNA methylation and histone modification. Heart Fail. Rev.23(5), 789–799 (2018).
   PubMed Web of Science ®Google Scholar
• Schuetze KB , McKinseyTA. Suppression of pathological cardiac fibrosis by histone deacetylase inhibitors. Prog. Pediatr. Cardiol.37(1–2), 37–1 (2014).
   Google Scholar
• Aguiar CM , GawdatK , LegereSet al. Fibrosis independent atrial fibrillation in older patients is driven by substrate leukocyte infiltration: diagnostic and prognostic implications to patients undergoing cardiac surgery. J. Transl. Med.17(1), 413 (2019).
   PubMed Web of Science ®Google Scholar
• Chandra S , EhrlichKC , LaceyM , BaribaultC , EhrlichM. Epigenetics and expression of key genes associated with cardiac fibrosis: NLRP3, MMP2, MMP9, CCN2/CTGF and AGT. Epigenomics13(3), 219–234 (2021).
   PubMedGoogle Scholar
• Morley JE , FarrSA. Alzheimer mythology: a time to think out of the box. J. Am. Med. Dir. Assoc.17(9), 769–774 (2016).
   PubMed Web of Science ®Google Scholar
• Li Y , HuangH , ZhuM , BaiH , HuangX. Roles of the MYST family in the pathogenesis of Alzheimer’s disease via histone or non-histone acetylation. Aging Dis.12(1), 132–142 (2021).
   PubMed Web of Science ®Google Scholar
• Santana DA , BedratA , PugaRDet al. The role of H3K9 acetylation and gene expression in different brain regions of Alzheimer’s disease patients. Epigenomics14(11), 651–670 (2022).
   PubMed Web of Science ®Google Scholar
• Medhasi S , ChantratitaN. Human leukocyte antigen (HLA) system: genetics and association with bacterial and viral infections. J. Immunol. Res.2022, 9710376 (2022).
   PubMed Web of Science ®Google Scholar
• Mészárosová M , MészárosG , MoravcíkováN , KasardaR. Linkage disequilibrium, genomic inbreeding and effective populations size to unravel population history. Acta Fytotech. Zootech.24(2), 161–166 (2021).
   Google Scholar
• Tutino VM , KuoCC , AvasthiNet al. Chromatin architecture around stroke haplotypes provides evidence that genetic risk is conferred through vascular cells. Epigenomics14(5), 243–259 (2022).
   PubMed Web of Science ®Google Scholar
• Wang X , NieY , NingSet al. Rs17042171 at chromosome 4q25 is associated with atrial fibrillation in the Chinese Han population from the central plains. J. Cent. South Univ.43(6), 594–603 (2018).
   Google Scholar
• Brown EM , BarrattBJ. The HapMap–a haplotype map of the human genome. In: Bioinformatics for Geneticists: A Bioinformatics Primer for the Analysis of Genetic Data (Second Edition).Academic Press, London, UK, 33–58 (2007).
   Google Scholar
• Ehrlich M . Risks and rewards of big-data in epigenomics research: an interview with Melanie Ehrlich. Epigenomics14(6), 351–358 (2022).
   PubMed Web of Science ®Google Scholar
• Ugrinova I , PashevaE,Donev R.HMGB1 protein: a therapeutic target inside and outside the cell. In: Advances in Protein Chemistry and Structural Biology.( Ed.). Academic Press, London UK, 37–76 (2017).
   Google Scholar
• Yasom S , WatcharanurakP , BhummaphanNet al. The roles of HMGB1-produced DNA gaps in DNA protection and aging biomarker reversal. FASEB BioAdvances4(6), 408–434 (2022).
   PubMedGoogle Scholar
• Nakanishi K . Anatomy of four human Argonaute proteins. Nucleic Acids Res.50(12), 6618–6638 (2022).
   PubMed Web of Science ®Google Scholar
• Watcharanurak P , MutiranguraA. Human RNA-directed DNA methylation methylates high-mobility group box 1 protein-produced DNA gaps. Epigenomics14(12), 741–756 (2022).
   PubMed Web of Science ®Google Scholar
• Abdelgalil AA , AlkahtaniHM , Al-JenoobiFI. Sorafenib. In: Profiles of Drug Substances, Excipients and Related Methodology.Academic Press, London, UK, 239–266 (2019).
   Google Scholar
• Du W , ChenW , ShuZet al. Identification of prognostic biomarkers of hepatocellular carcinoma via long noncoding RNA expression and copy number alterations. Epigenomics12(15), 1303–1315 (2020).
   PubMed Web of Science ®Google Scholar
• Ming XL , FengYL , HeDDet al. Role of BCYRN1 in hepatocellular carcinoma pathogenesis by lncRNA-miRNA-mRNA network analysis and its diagnostic and prognostic value. Epigenomics11(10), 1209–1231 (2019).
   PubMed Web of Science ®Google Scholar
• Llovet JM , RicciS , MazzaferroVet al. Sorafenib in advanced hepatocellular carcinoma. N. Engl. J. Med.359(4), 378–390 (2008).
   PubMed Web of Science ®Google Scholar
• Kang N , EcclestonM , ClermontPLet al. EZH2 inhibition: a promising strategy to prevent cancer immune editing. Epigenomics12(16), 1457–1476 (2020).
   PubMed Web of Science ®Google Scholar
• Li XJ , LiQL , JuLGet al. Deficiency of histone methyltransferase SET domain-containing 2 in liver leads to abnormal lipid metabolism and HCC. Hepatology73(5), 1797–1815 (2021).
   PubMed Web of Science ®Google Scholar
• Salani F , LataraniM , Casadei-GardiniAet al. Predictive significance of circulating histones in hepatocellular carcinoma patients treated with sorafenib. Epigenomics14(9), 507–517 (2022).
   PubMed Web of Science ®Google Scholar
• Zhu Z , HanZ , HalabelianLet al. Identification of lysine isobutyrylation as a new histone modification mark. Nucleic Acids Res.49(1), 177–189 (2021).
   PubMed Web of Science ®Google Scholar
• Goyal M , HeinbergA , MitesserV , Kandelis-ShalevS , SinghBK , DzikowskiR. Phosphorylation of the canonical histone H2A marks foci of damaged DNA in malaria parasites. mSphere6(1), e01131–20 (2021).
   PubMed Web of Science ®Google Scholar
• Frasca F , MatteucciM , LeoneM , MorelliMJ , MasseroliM. Accurate and highly interpretable prediction of gene expression from histone modifications. BMC Bioinformatics23(1), 151 (2022).
   PubMed Web of Science ®Google Scholar
• Sekhon A , SinghR , QiY. DeepDiff: DEEP-learning for predicting DIFFerential gene expression from histone modifications. Bioinformatics34(17), i891–i900 (2018).
   PubMed Web of Science ®Google Scholar
• Li B , WangZ , XiongS , ZhangY. Densely convolutional neural network for transcription factor binding sites prediction using DNA sequence and histone modification. Presented at: 2022 IEEE 5th International Conference on Artificial Intelligence and Big Data.Chengdu, China (May 27–30, 2022).
   Google Scholar
• Noberini R , SavoiaEO , BrandiniSet al. Spatial epi-proteomics enabled by histone post-translational modification analysis from low-abundance clinical samples. Clin. Epigenetics13(1), 145 (2021).
   PubMed Web of Science ®Google Scholar