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Results: 1288
Somatic mutant clones colonize the human esophagus with age.
Iñigo Martincorena, Joanna C Fowler, Agnieszka Wabik, Andrew RJ Lawson, Federico Abascal, Michael WJ Hall, Alex Cagan, Kasumi Murai, Krishnaa Mahbubani, Michael R Stratton, Rebecca C Fitzgerald, Penny A Handford, Peter J Campbell, Kourosh Saeb-Parsy, Philip H Jones
Dec 06, 2018
Genome-wide Estrogen Receptor-α activation is sustained, not cyclical.
Estrogen Receptor-alpha (ER) drives 75% of breast cancers. Stimulation of the ER by estra-2-diol forms a transcriptionally-active chromatin-bound complex. Previous studies reported that ER binding follows a cyclical pattern....
Estrogen estrogen receptor MCF7 Breast Cancer Chromosomes Computational Biology endocrine Gene Expression human Systems Biology Base Sequence Binding Sites Estradiol Estrogen Receptor alpha Female Gene Expression Regulation Neoplastic Genome Human Genome-Wide Association Study Humans MCF-7 Cells Neoplasm Proteins Promoter Regions Genetic Protein Binding Receptors CXCR Signal Transduction Sorting Nexins Trefoil Factor-1
Lipid-induced epigenomic changes in human macrophages identify a coronary artery disease-associated variant that regulates PPAP2B Expression through Altered C/EBP-beta binding.
Michael E Reschen, Kyle J Gaulton, Da Lin, Elizabeth J Soilleux, Andrew J Morris, Susan S Smyth, Christopher A O'Callaghan
Dec 17, 2018
Genome-wide association studies (GWAS) have identified over 40 loci that affect risk of coronary artery disease (CAD) and the causal mechanisms at the majority of loci are unknown. Recent studies have suggested that many causal...
Early loss of Crebbp confers malignant stem cell properties on lymphoid progenitors.
Sarah J Horton, George Giotopoulos, Haiyang Yun, Shabana Vohra, Olivia Sheppard, Rachael Bashford-Rogers, Mamunur Rashid, Alexandra Clipson, Wai-In Chan, Daniel Sasca, Loukia Yiangou, Hikari Osaki, Faisal Basheer, Paolo Gallipoli, Natalie Burrows, Ayşegül Erdem, Anastasiya Sybirna, Sarah Foerster, Wanfeng Zhao, Tonci Sustic, Anna Petrunkina Harrison, Elisa Laurenti, Jessica Okosun, Daniel Hodson, Penny Wright, Ken G Smith, Patrick Maxwell, Jude Fitzgibbon, Ming Q Du, David J Adams, Brian JP Huntly
Apr 06, 2018
Loss-of-function mutations of cyclic-AMP response element binding protein, binding protein (CREBBP) are prevalent in lymphoid malignancies. However, the tumour suppressor functions of CREBBP remain unclear. We demonstrate that...
Acetylation Animals CREB-Binding Protein Cell Proliferation Cell Self Renewal Cell Transformation Neoplastic Cells Cultured DNA Damage Epigenesis Genetic Gene Expression Regulation Neoplastic Genetic Predisposition to Disease Histones Lymphangiogenesis Lymphoid Progenitor Cells Lymphoma lymphopoiesis Methylation Mice Mice Inbred C57BL Mice Knockout Mutation Neoplastic Stem Cells Phenotype Signal Transduction Time Factors Transcription Genetic Tumor Suppressor Protein p53
Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition.
Clara Lopes Novo, Biola-Maria Javierre, Jonathan Cairns, Anne Segonds-Pichon, Steven W Wingett, Paula Freire-Pritchett, Mayra Furlan-Magaril, Stefan Schoenfelder, Peter Fraser, Peter J Rugg-Gunn
May 10, 2018
chromatin looping DIFFERENTIATION epigenetics Gene regulation genome organization Pluripotency promoter capture Hi-C Animals Cell Differentiation Enhancer Elements Genetic Gene Regulatory Networks Germ Layers Mice Mouse embryonic stem cells Nanog Homeobox Protein Pluripotent Stem Cells Promoter Regions Genetic Protein Binding
CTCF maintains regulatory homeostasis of cancer pathways.
Sarah J Aitken, Ximena Ibarra-Soria, Elissavet Kentepozidou, Paul Flicek, Christine Feig, John C Marioni, Duncan T Odom
Sep 20, 2018
CTCF Cancer Chromatin architecture chromatin state Hemizygosity Transcription Animals Breast Neoplasms CCCTC-Binding Factor Cell Line Chromatin DNA Neoplasm Enhancer Elements Genetic Female FIBROBLASTS Gene Expression Regulation Neoplastic Genome Hemizygote Homeostasis Humans Liver Neoplasms Experimental Mice Mice Inbred C57BL Mice Transgenic Protein Binding Signal Transduction Uterine Neoplasms
Transcriptional regulation of mammalian autophagy at a glance.
Macroautophagy, hereafter referred to as autophagy, is a catabolic process that results in the lysosomal degradation of cytoplasmic contents ranging from abnormal proteins to damaged cell organelles. It is activated under...
Genetic Sharing with Cardiovascular Disease Risk Factors and Diabetes Reveals Novel Bone Mineral Density Loci.
Sjur Reppe, Yunpeng Wang, Wesley K Thompson, Linda K McEvoy, Andrew J Schork, Verena Zuber, Marissa LeBlanc, Francesco Bettella, Ian G Mills, Rahul S Desikan, Srdjan Djurovic, Kaare M Gautvik, Anders M Dale, Ole A Andreassen, GEFOS Consortium
Mar 11, 2019
Bone Mineral Density (BMD) is a highly heritable trait, but genome-wide association studies have identified few genetic risk factors. Epidemiological studies suggest associations between BMD and several traits and diseases, but...
CyanoGate
Ravendran Vasudevan, Grant AR Gale, Alejandra A Schiavon, Anton Puzorjov, John Malin, Michael D Gillespie, Konstantinos Vavitsas, Valentin Zulkower, Baojun Wang, Christopher J Howe, David J Lea-Smith, Alistair J McCormick
Mar 14, 2019
Recent advances in synthetic biology research have been underpinned by an exponential increase in available genomic information and a proliferation of advanced DNA assembly tools. The adoption of plasmid vector assembly...
Fine-mapping inflammatory bowel disease loci to single-variant resolution.
Hailiang Huang, Ming Fang, Luke Jostins, Maša Umićević Mirkov, Gabrielle Boucher, Carl A Anderson, Vibeke Andersen, Isabelle Cleynen, Adrian Cortes, François Crins, Mauro D'Amato, Valérie Deffontaine, Julia Dmitrieva, Elisa Docampo, Mahmoud Elansary, Kyle Kai-How Farh, Andre Franke, Ann-Stephan Gori, Philippe Goyette, Jonas Halfvarson, Talin Haritunians, Jo Knight, Ian C Lawrance, Charlie W Lees, Edouard Louis, Rob Mariman, Theo Meuwissen, Myriam Mni, Yukihide Momozawa, Miles Parkes, Sarah L Spain, Emilie Théâtre, Gosia Trynka, Jack Satsangi, Suzanne van Sommeren, Severine Vermeire, Ramnik J Xavier, International Inflammatory Bowel Disease Genetics Consortium, Rinse K Weersma, Richard H Duerr, Christopher G Mathew, John D Rioux, Dermot PB McGovern, Judy H Cho, Michel Georges, Mark J Daly, Jeffrey C Barrett
Mar 19, 2019
Inflammatory bowel diseases are chronic gastrointestinal inflammatory disorders that affect millions of people worldwide. Genome-wide association studies have identified 200 inflammatory bowel disease-associated loci, but few...
Adolescent Adult Aged Aged 80 and over Binding Sites Chromatin Colitis Ulcerative Crohn Disease Epigenesis Genetic Female Genetic Predisposition to Disease genetic variation Genome-Wide Association Study Genotype Humans Inflammatory Bowel Diseases Linkage Disequilibrium Male Middle Aged Quantitative Trait Loci Smad3 Protein Transcription Factors Young Adult
Protein aggregation of the p63 transcription factor underlies severe skin fragility in AEC syndrome.
Claudia Russo, Christian Osterburg, Anna Sirico, Dario Antonini, Raffaele Ambrosio, Julia Maren Würz, Jörg Rinnenthal, Marco Ferniani, Sebastian Kehrloesser, Birgit Schäfer, Peter Güntert, Satrajit Sinha, Volker Dötsch, Caterina Missero
Aug 31, 2018
AEC syndrome mouse model p63 protein aggregation Skin Animals Cleft Lip Cleft Palate Ectoderm Eye Abnormalities Frameshift Mutation HEK293 Cells Heterozygote Humans Mice Mutation Mutation Missense Phosphoproteins Protein Binding Protein Denaturation Skin Trans-Activators Transcription Factors Transcription Genetic Tumor Suppressor Proteins
Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis.
Lovorka Stojic, Aaron TL Lun, Jasmin Mangei, Patrice Mascalchi, Valentina Quarantotti, Alexis R Barr, Chris Bakal, John C Marioni, Fanni Gergely, Duncan T Odom
Sep 05, 2018
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...
Genome-wide association study implicates immune dysfunction in the development of Hodgkin lymphoma.
Amit Sud, Hauke Thomsen, Giulia Orlando, Asta Försti, Philip J Law, Peter Broderick, Rosie Cooke, Fadi Hariri, Tomi Pastinen, Douglas F Easton, Paul DP Pharoah, Alison M Dunning, Julian Peto, Federico Canzian, Rosalind Eeles, Zsofia Kote-Jarai, Kenneth Muir, Nora Pashayan, Daniele Campa, Per Hoffmann, Markus M Nöthen, Karl-Heinz Jöckel, Elke Pogge von Strandmann, Anthony J Swerdlow, Andreas Engert, Nick Orr, Kari Hemminki, Richard S Houlston
Nov 21, 2018
PomBase 2018
Antonia Lock, Kim Rutherford, Midori A Harris, Jacqueline Hayles, Stephen G Oliver, Jürg Bähler, Valerie Wood
Nov 21, 2018
PomBase (www.pombase.org), the model organism database for the fission yeast Schizosaccharomyces pombe, has undergone a complete redevelopment, resulting in a more fully integrated, better-performing service. The new...
Genomic identification of cryptic susceptibility to penicillins and β-lactamase inhibitors in methicillin-resistant Staphylococcus aureus.
Ewan M Harrison, Xiaoliang Ba, Francesc Coll, Beth Blane, Olivier Restif, Henry Carvell, Claudio U Köser, Dorota Jamrozy, Sandra Reuter, Andrew Lovering, Nicholas Gleadall, Katherine L Bellis, Anne-Catrin Uhlemann, Franklin D Lowy, Ruth C Massey, Inês R Grilo, Rita Sobral, Jesper Larsen, Anders Rhod Larsen, Carina Vingsbo Lundberg, Julian Parkhill, Gavin K Paterson, Matthew TG Holden, Sharon J Peacock, Mark A Holmes
May 03, 2019
Amino Acid Substitution Animals Anti-Bacterial Agents Bacterial Proteins Clavulanic Acid Drug Therapy Combination Methicillin-Resistant Staphylococcus aureus Mice Microbial Sensitivity Tests Moths Mutation Penicillin-Binding Proteins Penicillins Promoter Regions Genetic Staphylococcal Infections beta-Lactam Resistance beta-Lactamase Inhibitors
Epigenetic activation of meiotic recombination near Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation.
Charles J Underwood, Kyuha Choi, Christophe Lambing, Xiaohui Zhao, Heïdi Serra, Filipe Borges, Joe Simorowski, Evan Ernst, Yannick Jacob, Ian R Henderson, Robert A Martienssen
Jun 04, 2018
Eukaryotic centromeres contain the kinetochore, which connects chromosomes to the spindle allowing segregation. During meiosis, centromeres are suppressed for inter-homolog crossover, as recombination in these regions can cause...
Genome-Wide Epigenetic and Transcriptomic Characterization of Human-Induced Pluripotent Stem Cell-Derived Intestinal Epithelial Organoids.
Judith Kraiczy, Alexander DB Ross, Jessica L Forbester, Gordon Dougan, Ludovic Vallier, Matthias Zilbauer
Jan 15, 2019
Widespread inter-individual gene expression variability in Arabidopsis thaliana.
A fundamental question in biology is how gene expression is regulated to give rise to a phenotype. However, transcriptional variability is rarely considered although it could influence the relationship between genotype and...
Arabidopsis thaliana RNA‐seq inter‐individual heterogeneity noise in gene expression transcriptional variability Arabidopsis Arabidopsis Proteins Chromatin Circadian Rhythm Epigenesis Genetic Gene Expression Regulation Plant LIGHT Photoperiod Seedlings Sequence Analysis RNA Software Transcription Factors Transcriptome
NF-κB-Dependent Lymphoid Enhancer Co-option Promotes Renal Carcinoma Metastasis.
Paulo Rodrigues, Saroor A Patel, Louise Harewood, Ioana Olan, Erika Vojtasova, Saiful E Syafruddin, M Nazhif Zaini, Emma K Richardson, Johanna Burge, Anne Y Warren, Grant D Stewart, Kourosh Saeb-Parsy, Shamith A Samarajiwa, Sakari Vanharanta
Jul 25, 2018
Metastases, the spread of cancer cells to distant organs, cause the majority of cancer-related deaths. Few metastasis-specific driver mutations have been identified, suggesting aberrant gene regulation as a source of metastatic...
Epstein-Barr virus nuclear antigen EBNA-LP is essential for transforming naïve B cells, and facilitates recruitment of transcription factors to the viral genome.
Agnieszka Szymula, Richard D Palermo, Amr Bayoumy, Ian J Groves, Mohammed Ba Abdullah, Beth Holder, Robert E White
Jul 31, 2018
The Epstein-Barr virus (EBV) nuclear antigen leader protein (EBNA-LP) is the first viral latency-associated protein produced after EBV infection of resting B cells. Its role in B cell transformation is poorly defined, but it has...
Adult B-Lymphocytes Cell Transformation Viral Cells Cultured Epstein-Barr Virus Infections Female Gene Expression Regulation Viral Genome Viral HEK293 Cells Herpesvirus 4 Human Humans Infant Newborn Leukemia B-Cell Pregnancy Promoter Regions Genetic Protein Binding Transcription Factors Viral Proteins
modMine
Sergio Contrino, Richard N Smith, Daniela Butano, Adrian Carr, Fengyuan Hu, Rachel Lyne, Kim Rutherford, Alex Kalderimis, Julie Sullivan, Seth Carbon, Ellen T Kephart, Paul Lloyd, EO Stinson, Nicole L Washington, Marc D Perry, Peter Ruzanov, Zheng Zha, Suzanna E Lewis, Lincoln D Stein, Gos Micklem
Aug 01, 2018
In an effort to comprehensively characterize the functional elements within the genomes of the important model organisms Drosophila melanogaster and Caenorhabditis elegans, the NHGRI model organism Encyclopaedia of DNA Elements...
The African Genome Variation Project shapes medical genetics in Africa.
Deepti Gurdasani, Tommy Carstensen, Fasil Tekola-Ayele, Luca Pagani, Ioanna Tachmazidou, Konstantinos Hatzikotoulas, Savita Karthikeyan, Louise Iles, Martin O Pollard, Ananyo Choudhury, Graham RS Ritchie, Yali Xue, Jennifer Asimit, Rebecca N Nsubuga, Elizabeth H Young, Cristina Pomilla, Katja Kivinen, Kirk Rockett, Anatoli Kamali, Ayo P Doumatey, Gershim Asiki, Janet Seeley, Fatoumatta Sisay-Joof, Muminatou Jallow, Stephen Tollman, Ephrem Mekonnen, Rosemary Ekong, Tamiru Oljira, Neil Bradman, Kalifa Bojang, Michele Ramsay, Adebowale Adeyemo, Endashaw Bekele, Ayesha Motala, Shane A Norris, Fraser Pirie, Pontiano Kaleebu, Dominic Kwiatkowski, Chris Tyler-Smith, Charles Rotimi, Eleftheria Zeggini, Manjinder S Sandhu
Aug 15, 2018
Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to...
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