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Results: 68
Tensorial blind source separation for improved analysis of multi-omic data.
There is an increased need for integrative analyses of multi-omic data. We present and benchmark a novel tensorial independent component analysis (tICA) algorithm against current state-of-the-art methods. We find that tICA...
Cancer dimensional reduction Epigenome-wide association study Independent Component Analysis Multi-omic Tensor mQTL Algorithms DNA Copy Number Variations DNA Methylation Epigenesis Genetic Epigenomics Gene Expression Regulation Neoplastic Genetic Markers Genome-Wide Association Study Humans Neoplasms Quantitative Trait Loci
Alterations in sperm long RNA contribute to the epigenetic inheritance of the effects of postnatal trauma.
K Gapp, G van Steenwyk, PL Germain, W Matsushima, KLM Rudolph, F Manuella, M Roszkowski, G Vernaz, T Ghosh, P Pelczar, IM Mansuy, EA Miska
Nov 18, 2018
Psychiatric diseases have a strong heritable component known to not be restricted to DNA sequence-based genetic inheritance alone but to also involve epigenetic factors in germ cells. Initial evidence suggested that sperm RNA is...
Integrative epigenomics, transcriptomics and proteomics of patient chondrocytes reveal genes and pathways involved in osteoarthritis.
Julia Steinberg, Graham RS Ritchie, Theodoros I Roumeliotis, Raveen L Jayasuriya, Matthew J Clark, Roger A Brooks, Abbie LA Binch, Karan M Shah, Rachael Coyle, Mercedes Pardo, Christine L Le Maitre, Yolande FM Ramos, Rob GHH Nelissen, Ingrid Meulenbelt, Andrew W McCaskie, Jyoti S Choudhary, J Mark Wilkinson, Eleftheria Zeggini
Dec 05, 2017
Aquaporin 1 Arthroplasty Replacement Hip Arthroplasty Replacement Knee Case-Control Studies Chondrocytes Chromatography Liquid Collagen Type I Collagen Type I alpha 1 Chain DNA Methylation Disease Progression Epigenesis Genetic Epigenomics Gene Expression Profiling Gene Regulatory Networks Humans Lectins C-Type Male Mass Spectrometry Osteoarthritis Hip Osteoarthritis Knee Proteomics Sequence Analysis RNA
Single-cell epigenomics
Emerging single-cell epigenomic methods are being developed with the exciting potential to transform our knowledge of gene regulation. Here we review available techniques and future possibilities, arguing that the full potential...
A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry.
Samuel Wein, Byron Andrews, Timo Sachsenberg, Helena Santos-Rosa, Oliver Kohlbacher, Tony Kouzarides, Benjamin A Garcia, Hendrik Weisser
Apr 14, 2020
The field of epitranscriptomics continues to reveal how post-transcriptional modification of RNA affects a wide variety of biological phenomena. A pivotal challenge in this area is the identification of modified RNA residues...
Genetic background drives transcriptional variation in human induced pluripotent stem cells.
Foad Rouhani, Natsuhiko Kumasaka, Miguel Cardoso de Brito, Allan Bradley, Ludovic Vallier, Daniel Gaffney
Oct 14, 2020
Human iPS cells have been generated using a diverse range of tissues from a variety of donors using different reprogramming vectors. However, these cell lines are heterogeneous, which presents a limitation for their use in...
Maternally inherited piRNAs direct transient heterochromatin formation at active transposons during early Drosophila embryogenesis.
Martin H Fabry, Federica A Falconio, Fadwa Joud, Emily K Lythgoe, Benjamin Czech, Gregory J Hannon
Jul 13, 2021
The PIWI-interacting RNA (piRNA) pathway controls transposon expression in animal germ cells, thereby ensuring genome stability over generations. In Drosophila, piRNAs are intergenerationally inherited through the maternal...
D. melanogaster Drosophila Chromatin Chromosomes developmental biology embryogenesis epigenetics Gene Expression piRNA pathway transposable elements Animals Chromatin DNA Transposable Elements developmental biology Drosophila Drosophila Proteins Drosophila melanogaster Embryonic Development Epigenomics Female Gene Expression Germ Cells Heterochromatin Histones Male Maternal Inheritance RNA Small Interfering
Ageing affects DNA methylation drift and transcriptional cell-to-cell variability in mouse muscle stem cells.
Irene Hernando-Herraez, Brendan Evano, Thomas Stubbs, Pierre-Henri Commere, Marc Jan Bonder, Stephen Clark, Simon Andrews, Shahragim Tajbakhsh, Wolf Reik
Nov 26, 2019
The International Human Epigenome Consortium
The International Human Epigenome Consortium (IHEC) coordinates the generation of a catalog of high-resolution reference epigenomes of major primary human cell types. The studies now presented (see the Cell Press IHEC web portal...
DNA methylation landscapes of 1538 breast cancers reveal a replication-linked clock, epigenomic instability and cis-regulation.
Rajbir Nath Batra, Aviezer Lifshitz, Ana Tufegdzic Vidakovic, Suet-Feung Chin, Ankita Sati-Batra, Stephen-John Sammut, Elena Provenzano, H Raza Ali, Ali Dariush, Alejandra Bruna, Leigh Murphy, Arnie Purushotham, Ian Ellis, Andrew Green, Francine E Garrett-Bakelman, Chris Mason, Ari Melnick, Samuel AJR Aparicio, Oscar M Rueda, Amos Tanay, Carlos Caldas
Nov 05, 2021
DNA methylation is aberrant in cancer, but the dynamics, regulatory role and clinical implications of such epigenetic changes are still poorly understood. Here, reduced representation bisulfite sequencing (RRBS) profiles of 1538...
DNA methylation epigenetically silences crossover hot spots and controls chromosomal domains of meiotic recombination in Arabidopsis.
Nataliya E Yelina, Christophe Lambing, Thomas J Hardcastle, Xiaohui Zhao, Bruno Santos, Ian R Henderson
Nov 13, 2015
Towards annotating the plant epigenome
Based on 98 public and internal small RNA high throughput sequencing libraries, we mapped small RNAs to the genome of the model organism Arabidopsis thaliana and defined loci based on their expression using an empirical Bayesian...
Obituary
Anne Ferguson-Smith and Marisa Bartolomei look back at the life and science of Denise Barlow, a pioneer in genomic imprinting and epigenetics.
Extensive co-operation between the Epstein-Barr virus EBNA3 proteins in the manipulation of host gene expression and epigenetic chromatin modification.
Robert E White, Ian J Groves, Ernest Turro, Jade Yee, Elisabeth Kremmer, Martin J Allday
Feb 01, 2021
Epstein-Barr virus (EBV) is able to drive the transformation of B-cells, resulting in the generation of lymphoblastoid cell lines (LCLs) in vitro. EBV nuclear proteins EBNA3A and EBNA3C are necessary for efficient...
Antigens Viral Cell Line Tumor Chromatin Cluster Analysis Epigenomics Epstein-Barr Virus Nuclear Antigens Gene Expression Profiling Gene Knockout Techniques HEK293 Cells Herpesvirus 4 Human Host-Pathogen Interactions Humans Oligonucleotide Array Sequence Analysis Reverse Transcriptase Polymerase Chain Reaction
The Absence of C-5 DNA Methylation in Leishmania donovani Allows DNA Enrichment from Complex Samples
Bart Cuypers, Franck Dumetz, Pieter Meysman, Kris Laukens, Géraldine De Muylder, Jean-Claude Dujardin, Malgorzata Anna Domagalska
Aug 19, 2020
Cytosine C5 methylation is an important epigenetic control mechanism in a wide array of eukaryotic organisms and generally carried out by proteins of the C-5 DNA methyltransferase family (DNMTs). In several protozoans, the...
Personalized and graph genomes reveal missing signal in epigenomic data
Abstract: Background: Epigenomic studies that use next generation sequencing experiments typically rely on the alignment of reads to a reference sequence. However, because of genetic diversity and the diploid nature of the human...
Single-cell Atlas of common variable immunodeficiency shows germinal center-associated epigenetic dysregulation in B-cell responses.
Javier Rodríguez-Ubreva, Anna Arutyunyan, Marc Jan Bonder, Lucía Del Pino-Molina, Stephen J Clark, Carlos de la Calle-Fabregat, Luz Garcia-Alonso, Louis-François Handfield, Laura Ciudad, Eduardo Andrés-León, Felix Krueger, Francesc Català-Moll, Virginia C Rodríguez-Cortez, Krzysztof Polanski, Lira Mamanova, Stijn van Dongen, Vladimir Yu Kiselev, María T Martínez-Saavedra, Holger Heyn, Javier Martín, Klaus Warnatz, Eduardo López-Granados, Carlos Rodríguez-Gallego, Oliver Stegle, Gavin Kelsey, Roser Vento-Tormo, Esteban Ballestar
May 02, 2022
Deciphering the genomic, epigenomic, and transcriptomic landscapes of pre-invasive lung cancer lesions.
Vitor H Teixeira, Christodoulos P Pipinikas, Adam Pennycuick, Henry Lee-Six, Deepak Chandrasekharan, Jennifer Beane, Tiffany J Morris, Anna Karpathakis, Andrew Feber, Charles E Breeze, Paschalis Ntolios, Robert E Hynds, Mary Falzon, Arrigo Capitanio, Bernadette Carroll, Pascal F Durrenberger, Georgia Hardavella, James M Brown, Andy G Lynch, Henry Farmery, Dirk S Paul, Rachel C Chambers, Nicholas McGranahan, Neal Navani, Ricky M Thakrar, Charles Swanton, Stephan Beck, Phillip Jeremy George, Avrum Spira, Peter J Campbell, Christina Thirlwell, Sam M Janes
Oct 02, 2019
The molecular alterations that occur in cells before cancer is manifest are largely uncharted. Lung carcinoma in situ (CIS) lesions are the pre-invasive precursor to squamous cell carcinoma. Although microscopically identical...
Adult Aged Aged 80 and over Carcinogenesis Carcinoma in Situ Carcinoma Squamous Cell chromosomal instability Cohort Studies DNA Copy Number Variations DNA Methylation Disease Progression Epigenomics Female Gene Expression Profiling Gene Expression Regulation Neoplastic Genomics Humans Longitudinal Studies Lung Neoplasms Male Middle Aged Mutation
Identifying Human Naïve Pluripotent Stem Cells - Evaluating State-Specific Reporter Lines and Cell-Surface Markers.
Genetic and environmental causes of variation in epigenetic aging across the lifespan.
Shuai Li, Tuong L Nguyen, Ee Ming Wong, Pierre-Antoine Dugué, Gillian S Dite, Nicola J Armstrong, Jeffrey M Craig, Karen A Mather, Perminder S Sachdev, Richard Saffery, Joohon Sung, Qihua Tan, Anbupalam Thalamuthu, Roger L Milne, Graham G Giles, Melissa C Southey, John L Hopper
Oct 22, 2021
BACKGROUND: DNA methylation-based biological age (DNAm age) is an important biomarker for adult health. Studies in specific age ranges have found widely varying results about its genetic and environmental causes of variation....
aging Biological age DNA Methylation Epigenetic aging Epigenetic clock Twin study Adolescent Adult Aged Aged 80 and over aging Case-Control Studies Child Child Preschool DNA Methylation Epigenesis Genetic Epigenomics Female Gene-Environment Interaction genetic variation Genome-Wide Association Study Humans Infant Infant Newborn longevity Male Middle Aged Twins Dizygotic Twins Monozygotic Young Adult
Epigenetic and transcriptomic reprogramming in monocytes of severe COVID-19 patients reflects alterations in myeloid differentiation and the influence of inflammatory cytokines.
Gerard Godoy-Tena, Anis Barmada, Octavio Morante-Palacios, Carlos de la Calle-Fabregat, Ricardo Martins-Ferreira, Anna G Ferreté-Bonastre, Laura Ciudad, Adolfo Ruiz-Sanmartín, Mónica Martínez-Gallo, Ricard Ferrer, Juan Carlos Ruiz-Rodriguez, Javier Rodríguez-Ubreva, Roser Vento-Tormo, Esteban Ballestar
Nov 29, 2022
BACKGROUND: COVID-19 manifests with a wide spectrum of clinical phenotypes, ranging from asymptomatic and mild to severe and critical. Severe and critical COVID-19 patients are characterized by marked changes in the myeloid...
Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells
MS Vijayabaskar, Debbie K Goode, Nadine Obier, Monika Lichtinger, Amber ML Emmett, Fatin N Zainul Abidin, Nisar Shar, Rebecca Hannah, Salam A Assi, Michael Lie-A-Ling, Berthold Gottgens, Georges Lacaud, Valerie Kouskoff, Constanze Bonifer, David R Westhead
Aug 30, 2019
Animals Cell Differentiation Chromatin Databases Genetic Epigenesis Genetic Epigenomics Gene Expression Regulation Genome High-Throughput Screening Assays MACROPHAGES Mice Mouse embryonic stem cells Myocytes Cardiac Promoter Regions Genetic Regulatory Elements Transcriptional Regulatory Sequences Nucleic Acid Transcription Factors
Developmental programming
EF Sutton, LA Gilmore, DB Dunger, BT Heijmans, M-F Hivert, C Ling, JA Martinez, SE Ozanne, RA Simmons, M Szyf, RA Waterland, LM Redman, E Ravussin
May 15, 2019
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