epigenomics

Summary

Summary: The systematic study of the global gene expression changes due to EPIGENETIC PROCESSES and not due to DNA base sequence changes.

Top Publications

  1. Vidaki A, Ballard D, Aliferi A, Miller T, Barron L, Syndercombe Court D. DNA methylation-based forensic age prediction using artificial neural networks and next generation sequencing. Forensic Sci Int Genet. 2017;28:225-236 pubmed publisher
    ..5years), it is expected that future optimization of our strategy to account for technical variation as well as increasing the sample size will improve both the prediction accuracy and reproducibility. ..
  2. Schlosberg C, Vanderkraats N, Edwards J. Modeling complex patterns of differential DNA methylation that associate with gene expression changes. Nucleic Acids Res. 2017;45:5100-5111 pubmed publisher
    ..Using 17 whole-genome bisulfite sequencing and RNA-seq datasets from different tissues from the Roadmap Epigenomics Project, ME-Class significantly outperforms standard methods using methylation to predict differential gene ..
  3. Ascensión A, Arrospide Elgarresta M, Izeta A, Arauzo Bravo M. NaviSE: superenhancer navigator integrating epigenomics signal algebra. BMC Bioinformatics. 2017;18:296 pubmed publisher
    ..NaviSE, a user-friendly streamlined tool which performs a fully-automated parallel processing of genome-wide epigenomics data from sequencing files into a final report, built with a comprehensive set of annotated files that are ..
  4. Reid M, Dai Z, Locasale J. The impact of cellular metabolism on chromatin dynamics and epigenetics. Nat Cell Biol. 2017;19:1298-1306 pubmed publisher
  5. Cariaga Martinez A, Alelú Paz R. Rethinking the Epigenetic Framework to Unravel the Molecular Pathology of Schizophrenia. Int J Mol Sci. 2017;18: pubmed publisher
  6. Bucci M, Marques S, Oh D, Harris N. Toxic Stress in Children and Adolescents. Adv Pediatr. 2016;63:403-28 pubmed publisher
  7. Qu K, Zaba L, Satpathy A, Giresi P, Li R, Jin Y, et al. Chromatin Accessibility Landscape of Cutaneous T Cell Lymphoma and Dynamic Response to HDAC Inhibitors. Cancer Cell. 2017;32:27-41.e4 pubmed publisher
    ..These results provide a foundational framework to study personal regulomes in human cancer and epigenetic therapy. ..
  8. Hjelmeland L. Dark matters in AMD genetics: epigenetics and stochasticity. Invest Ophthalmol Vis Sci. 2011;52:1622-31 pubmed publisher
  9. Vaz M, Hwang S, Kagiampakis I, Phallen J, Patil A, O Hagan H, et al. Chronic Cigarette Smoke-Induced Epigenomic Changes Precede Sensitization of Bronchial Epithelial Cells to Single-Step Transformation by KRAS Mutations. Cancer Cell. 2017;32:360-376.e6 pubmed publisher
    ..Thus, epigenetic abnormalities may prime for changing oncogene senescence to addiction for a single key oncogene involved in lung cancer initiation. ..

More Information

Publications62

  1. Dennis J, Medina Rivera A, Truong V, Antounians L, Zwingerman N, Carrasco G, et al. Leveraging cell type specific regulatory regions to detect SNPs associated with tissue factor pathway inhibitor plasma levels. Genet Epidemiol. 2017;41:455-466 pubmed publisher
    ..Although this study did not result in new loci for TFPI, our work lays out a strategy to utilize epigenomic data in prioritization schemes for future GWAS studies. ..
  2. Tasaki S, Suzuki K, Nishikawa A, Kassai Y, Takiguchi M, Kurisu R, et al. Multiomic disease signatures converge to cytotoxic CD8 T cells in primary Sjögren's syndrome. Ann Rheum Dis. 2017;76:1458-1466 pubmed publisher
    ..These integrative relations across multiple layers will facilitate our understanding of SS at the system level. ..
  3. Xi Z, Yunusova Y, van Blitterswijk M, Dib S, Ghani M, Moreno D, et al. Identical twins with the C9orf72 repeat expansion are discordant for ALS. Neurology. 2014;83:1476-8 pubmed publisher
  4. Ballestar E, Li T. New insights into the epigenetics of inflammatory rheumatic diseases. Nat Rev Rheumatol. 2017;13:593-605 pubmed publisher
  5. Feinberg A, Fallin M. Epigenetics at the Crossroads of Genes and the Environment. JAMA. 2015;314:1129-30 pubmed publisher
  6. Sethi I, Gluck C, Zhou H, Buck M, Sinha S. Evolutionary re-wiring of p63 and the epigenomic regulatory landscape in keratinocytes and its potential implications on species-specific gene expression and phenotypes. Nucleic Acids Res. 2017;45:8208-8224 pubmed publisher
  7. Bhat M, Kapila R. Dietary metabolites derived from gut microbiota: critical modulators of epigenetic changes in mammals. Nutr Rev. 2017;75:374-389 pubmed publisher
    ..The present review provides insights into the current understanding of the microbiota and its association with mammalian epigenomics as well as the interaction of pathogens and probiotics with host epigenetic machinery.
  8. Bell J, Spector T. DNA methylation studies using twins: what are they telling us?. Genome Biol. 2012;13:172 pubmed publisher
    ..Larger sample sizes, replication, genetic-epigenetic analyses and longitudinal assays are now needed to establish the role of epigenetic variants in disease. ..
  9. Barker S, Tsai L. MethyLock: DNA Demethylation Is the Epigenetic Key to Axon Regeneration. Neuron. 2017;94:221-223 pubmed publisher
    ..In this issue of Neuron, Weng et al. (2017) reveal a role for active DNA demethylation in allowing axon regeneration to occur in the mature nervous system following axonal injury. ..
  10. Lowe R. Heroes of peer review: Robert Lowe. Genome Biol. 2017;18:72 pubmed publisher
    ..In the second of our series of articles celebrating peer reviewers, we talk to Robert Lowe, who is a Lecturer in computational biology at Queen Mary University of London, UK, and a valued reviewer for Genome Biology. ..
  11. Li J, Ching T, Huang S, Garmire L. Using epigenomics data to predict gene expression in lung cancer. BMC Bioinformatics. 2015;16 Suppl 5:S10 pubmed publisher
    ..By considering a comprehensive list of epigenomic and genomic features, we have constructed an accurate model to predict transcriptomic differential expression, exemplified in lung cancer. ..
  12. Seuter S, Neme A, Carlberg C. Epigenomic PU.1-VDR crosstalk modulates vitamin D signaling. Biochim Biophys Acta Gene Regul Mech. 2017;1860:405-415 pubmed publisher
    ..In conclusion, PU.1 is an important modulator of VDR signaling in monocytes, including but also exceeding its role as a pioneer factor, but we found no evidence for a direct interaction of both proteins. ..
  13. Mahasneh A, Al Shaheri F, Jamal E. Molecular biomarkers for an early diagnosis, effective treatment and prognosis of colorectal cancer: Current updates. Exp Mol Pathol. 2017;102:475-483 pubmed publisher
    ..In this review, we will outline the most currently available and developing tumor tools, and blood molecular biomarkers. Also, we will illustrate their diagnostic, therapeutic and prognostic applications. ..
  14. Yoshihara M, Sato T, Saito D, Ohara O, Kuramoto T, Suyama M. A deletion in the intergenic region upstream of Ednrb causes head spot in the rat strain KFRS4/Kyo. BMC Genet. 2017;18:29 pubmed publisher
  15. Cole J, Robertson N, Rather M, Thomson J, McBryan T, Sproul D, et al. Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions. Genome Biol. 2017;18:58 pubmed publisher
    ..This study is a foundation to understand the epigenetic contribution to healthy aging and longevity and the molecular basis of the DNA methylation clock. ..
  16. Wang X, Snieder H. Genome-wide association studies and beyond: what's next in blood pressure genetics?. Hypertension. 2010;56:1035-7 pubmed publisher
  17. O Geen H, Ren C, Nicolet C, Perez A, Halmai J, Le V, et al. dCas9-based epigenome editing suggests acquisition of histone methylation is not sufficient for target gene repression. Nucleic Acids Res. 2017;45:9901-9916 pubmed publisher
    ..The easily programmable dCas9 toolkit allowed precise control of epigenetic information and dissection of the relationship between the epigenome and gene regulation...
  18. Rager J, Auerbach S, Chappell G, Martin E, Thompson C, Fry R. Benchmark Dose Modeling Estimates of the Concentrations of Inorganic Arsenic That Induce Changes to the Neonatal Transcriptome, Proteome, and Epigenome in a Pregnancy Cohort. Chem Res Toxicol. 2017;30:1911-1920 pubmed publisher
    ..Together, findings present a variety of BMD measures to estimate doses at which prenatal iAs exposure influences neonatal outcome-relevant transcriptomic, proteomic, and epigenomic profiles. ..
  19. Hwang J, Aromolaran K, Zukin R. The emerging field of epigenetics in neurodegeneration and neuroprotection. Nat Rev Neurosci. 2017;18:347-361 pubmed publisher
    ..Although not somatically heritable, epigenetic modifications in neurons are dynamic and reversible, which makes them good targets for therapeutic intervention. ..
  20. Gurgul A, Opiela J, Pawlina K, Szmatoła T, Bochenek M, Bugno Poniewierska M. The effect of histone deacetylase inhibitor trichostatin A on porcine mesenchymal stem cell transcriptome. Biochimie. 2017;139:56-73 pubmed publisher
  21. Szabad J. [Pre-programmed genes]. Orv Hetil. 2017;158:1323-1330 pubmed publisher
    ..It summarizes how genetic crosses reveal the involvement of epigenesis, explains its meaning and impact on life of the organisms. An understanding of epigenesis provides guidance to improve our life. Orv Hetil. 2017; 158(34): 1323-1330. ..
  22. . 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. Cell. 2016;166:481-491 pubmed publisher
    ..thaliana natural variation through integration of genomes and epigenomes with molecular and non-molecular phenotypes. ..
  23. Roukos D. Next-generation sequencing and epigenome technologies: potential medical applications. Expert Rev Med Devices. 2010;7:723-6 pubmed publisher
  24. Kaiser J. The epigenetics heretic. Science. 2014;343:361-3 pubmed publisher
  25. Cole S, Fredrickson B. Errors in the Brown et al. critical reanalysis. Proc Natl Acad Sci U S A. 2014;111:E3581 pubmed publisher
  26. Zentner G, Henikoff S. Surveying the epigenomic landscape, one base at a time. Genome Biol. 2012;13:250 pubmed publisher
    b>Epigenomics, the determination of epigenetic landscapes on a genome-wide scale, has progressed at an astounding rate over the past decade...
  27. Goswami S, Sanyal S, Chakraborty P, Das C, Sarkar M. Interaction of a common painkiller piroxicam and copper-piroxicam with chromatin causes structural alterations accompanied by modulation at the epigenomic/genomic level. Biochim Biophys Acta Gen Subj. 2017;1861:2048-2059 pubmed publisher
    ..Our results provide the proof of concept that DNA binding ability of the copper complexes of a traditional NSAID, opens up the possibility of modulations at the epigenomic/genomic level. ..
  28. Long M, Smiraglia D, Campbell M. The Genomic Impact of DNA CpG Methylation on Gene Expression; Relationships in Prostate Cancer. Biomolecules. 2017;7: pubmed publisher
    ..This revealed that genes that control the synthesis of S-adenosyl-l-methionine (SAM) associate with altered expression of DNA methylation targets in a subset of aggressive tumors. ..
  29. Braun K, Dhana K, de Vries P, Voortman T, van Meurs J, Uitterlinden A, et al. Epigenome-wide association study (EWAS) on lipids: the Rotterdam Study. Clin Epigenetics. 2017;9:15 pubmed publisher
    ..These results provide insight in the mechanisms that are involved in lipid metabolism. ..
  30. Teschendorff A, Breeze C, Zheng S, Beck S. A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies. BMC Bioinformatics. 2017;18:105 pubmed publisher
    ..inference, which leverages cell-type specific DNAse Hypersensitive Site (DHS) information from the NIH Epigenomics Roadmap to construct an improved reference DNA methylation database...
  31. Kumar R, Deivendran S, Santhoshkumar T, Pillai M. Signaling coupled epigenomic regulation of gene expression. Oncogene. 2017;36:5917-5926 pubmed publisher
  32. Zhang J, Huang K. Pan-cancer analysis of frequent DNA co-methylation patterns reveals consistent epigenetic landscape changes in multiple cancers. BMC Genomics. 2017;18:1045 pubmed publisher
    ..We also found that genes commonly believed to be silenced via hypermethylation in cancers may still display highly variable methylation levels among cancer cells, and should be considered while using them as epigenetic biomarkers. ..
  33. Winnefeld M, Lyko F. The aging epigenome: DNA methylation from the cradle to the grave. Genome Biol. 2012;13:165 pubmed publisher
    ..Whole-genome methylation analysis of newborns and centenarians reveals widespread epigenetic alterations, and provides new insight into age-related methylation pattern changes. ..
  34. Barrett J. Programming the Future: Epigenetics in the Context of DOHaD. Environ Health Perspect. 2017;125:A72 pubmed publisher
  35. Ng B, White C, Klein H, Sieberts S, McCabe C, Patrick E, et al. An xQTL map integrates the genetic architecture of the human brain's transcriptome and epigenome. Nat Neurosci. 2017;20:1418-1426 pubmed publisher
  36. . Taking the next step: building an Arabidopsis information portal. Plant Cell. 2012;24:2248-56 pubmed
    ..We now invite broader participation in the AIP development process so that the resource can be implemented in a timely manner. ..
  37. Siu C, Wiseman S, Gakkhar S, Heravi Moussavi A, Bilenky M, Carles A, et al. Characterization of the human thyroid epigenome. J Endocrinol. 2017;235:153-165 pubmed publisher
  38. Park S, Kang K, Giannopoulou E, Qiao Y, Kang K, Kim G, et al. Type I interferons and the cytokine TNF cooperatively reprogram the macrophage epigenome to promote inflammatory activation. Nat Immunol. 2017;18:1104-1116 pubmed publisher
    ..Our comprehensive epigenomics approach to the analysis of human macrophages showed that the proinflammatory cytokines TNF and type I ..
  39. Valavanis I, Sifakis E, Georgiadis P, Kyrtopoulos S, Chatziioannou A. A composite framework for the statistical analysis of epidemiological DNA methylation data with the Infinium Human Methylation 450K BeadChip. IEEE J Biomed Health Inform. 2014;18:817-23 pubmed publisher
    ..Overall, in comparison to traditional approaches, the superior performance of the proposed framework in terms of technical bias correction, along with its generic character, support its suitability for various microarray technologies. ..
  40. Huang A, Wu H, Iriyama T, Zhang Y, Sun K, Song A, et al. Elevated Adenosine Induces Placental DNA Hypomethylation Independent of A2B Receptor Signaling in Preeclampsia. Hypertension. 2017;70:209-218 pubmed publisher
    ..Altogether, both mouse and human studies reveal novel mechanisms underlying placental DNA hypomethylation and potential therapeutic approaches for preeclampsia. ..
  41. Kaushik P, Anderson J. Obesity: epigenetic aspects. Biomol Concepts. 2016;7:145-55 pubmed publisher
    ..Fortunately, epigenetic phenomena are dynamic and rather quickly reversible with intensive lifestyle changes. This is a very promising and sustainable resolution to the obesity pandemic. ..
  42. Flax J, Soloway P. Methylation on the mind. Nat Neurosci. 2011;14:1494-6 pubmed publisher
  43. van der Poll T, van de Veerdonk F, Scicluna B, Netea M. The immunopathology of sepsis and potential therapeutic targets. Nat Rev Immunol. 2017;17:407-420 pubmed publisher
    ..Pivotal for the clinical development of new sepsis therapies is the selection of patients on the basis of biomarkers and/or functional defects that provide specific insights into the expression or activity of the therapeutic target. ..
  44. Gassler J, Brandão H, Imakaev M, Flyamer I, Ladstätter S, Bickmore W, et al. A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture. EMBO J. 2017;36:3600-3618 pubmed publisher
    ..Our simulations and experimental data provide evidence that cohesin-dependent loop extrusion organizes mammalian genomes over multiple scales from the one-cell embryo onward. ..
  45. Davies J. Pax2: A "Keep to the Path" Sign on Waddington's Epigenetic Landscape. Dev Cell. 2017;41:331-332 pubmed publisher
    ..2017) show that targeted Pax2 deletion converts nephrogenic cells to the stromogenic path, suggesting that Pax2 normally represses an otherwise inevitable transition between sister lineages. ..
  46. Wojtasik W, Kulma A, Boba A, Szopa J. Oligonucleotide treatment causes flax ?-glucanase up-regulation via changes in gene-body methylation. BMC Plant Biol. 2014;14:261 pubmed publisher
  47. Richmond R, Joubert B. Contrasting the effects of intra-uterine smoking and one-carbon micronutrient exposures on offspring DNA methylation. Epigenomics. 2017;9:351-367 pubmed publisher
  48. Cui X, Meng J, Rao M, Chen Y, Huang Y. HEPeak: an HMM-based exome peak-finding package for RNA epigenome sequencing data. BMC Genomics. 2015;16 Suppl 4:S2 pubmed publisher
    ..RNA Immunoprecipatation combined with RNA sequencing (MeRIP-seq) is revolutionizing the de novo study of RNA epigenomics at a higher resolution...
  49. Saito Y, Kunitomi A, Seki T, Tohyama S, Kusumoto D, Takei M, et al. Epigenetic barrier against the propagation of fluctuating gene expression in embryonic stem cells. FEBS Lett. 2017;591:2879-2889 pubmed publisher
    ..We suggest that an epigenetic barrier is key to preventing the propagation of fluctuating pluripotency gene expression in ES cells. ..
  50. Falahi F, van Kruchten M, Martinet N, Hospers G, Rots M. Current and upcoming approaches to exploit the reversibility of epigenetic mutations in breast cancer. Breast Cancer Res. 2014;16:412 pubmed publisher
    ..Finally, we describe epigenetic editing as a promising new approach for possible applications towards more targeted breast cancer treatment. ..
  51. Saleem M, Mendoza Parra M, Cholley P, Blum M, Gronemeyer H. Epimetheus - a multi-profile normalizer for epigenomic sequencing data. BMC Bioinformatics. 2017;18:259 pubmed publisher
    ..Epimetheus has been successfully used to normalize epigenomics data in previous studies on X inactivation in breast cancer and in integrative studies of neuronal cell fate ..
  52. Rahmani E, Shenhav L, Schweiger R, Yousefi P, Huen K, Eskenazi B, et al. Genome-wide methylation data mirror ancestry information. Epigenetics Chromatin. 2017;10:1 pubmed publisher
    ..Implementation of EPISTRUCTURE is available in GLINT, our recently released toolset for DNA methylation analysis at: http://glint-epigenetics.readthedocs.io. ..
  53. Chi K. The RNA code comes into focus. Nature. 2017;542:503-506 pubmed publisher