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Results: 83
Genomic footprints of activated telomere maintenance mechanisms in cancer.
Lina Sieverling, Chen Hong, Sandra D Koser, Philip Ginsbach, Kortine Kleinheinz, Barbara Hutter, Delia M Braun, Isidro Cortés-Ciriano, Ruibin Xi, Rolf Kabbe, Peter J Park, Roland Eils, Matthias Schlesner, PCAWG-Structural Variation Working Group, Benedikt Brors, Karsten Rippe, David TW Jones, Lars Feuerbach, PCAWG Consortium
Mar 05, 2021
Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ICGC/TCGA...
Origins of chromosomal rearrangement hotspots in the human genome
RNAcentral
AI Petrov, SJE Kay, I Kalvari, KL Howe, KA Gray, EA Bruford, PJ Kersey, G Cochrane, RD Finn, A Bateman, A Kozomara, S Griffiths-Jones, A Frankish, CW Zwieb, BY Lau, KP Williams, PP Chan, TM Lowe, JJ Cannone, RR Gutell, MA Machnicka, JM Bujnicki, M Yoshihama, N Kenmochi, B Chai, JR Cole, M Szymanski, WM Karlowski, V Wood, E Huala, TZ Berardini, Y Zhao, R Chen, W Zhu, MD Paraskevopoulou, IS Vlachos, AG Hatzigeorgiou, L Ma, Z Zhang, J Puetz, PF Stadler, D McDonald, S Basu, P Fey, SR Engel, JM Cherry, PJ Volders, P Mestdagh, J Wower, M Clark, XC Quek, ME Dinger
Jul 31, 2017
Complete vertebrate mitogenomes reveal widespread repeats and gene duplications.
Giulio Formenti, Arang Rhie, Jennifer Balacco, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, Samara Brown, Marco Rosario Capodiferro, Farooq O Al-Ajli, Roberto Ambrosini, Peter Houde, Sergey Koren, Karen Oliver, Michelle Smith, Jason Skelton, Emma Betteridge, Jale Dolucan, Craig Corton, Iliana Bista, James Torrance, Alan Tracey, Jonathan Wood, Marcela Uliano-Silva, Kerstin Howe, Shane McCarthy, Sylke Winkler, Woori Kwak, Jonas Korlach, Arkarachai Fungtammasan, Daniel Fordham, Vania Costa, Simon Mayes, Matteo Chiara, David S Horner, Eugene Myers, Richard Durbin, Alessandro Achilli, Edward L Braun, Adam M Phillippy, Erich D Jarvis, Vertebrate Genomes Project Consortium
Jun 18, 2021
BACKGROUND: Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. RESULTS: As part of...
Identification of regulatory variants associated with genetic susceptibility to meningococcal disease.
Lisa Borghini, Eileen Png, Alexander Binder, Victoria J Wright, Ellie Pinnock, Ronald de Groot, Jan Hazelzet, Marieke Emonts, Michiel Van der Flier, Luregn J Schlapbach, Suzanne Anderson, Fatou Secka, Antonio Salas, Colin Fink, Enitan D Carrol, Andrew J Pollard, Lachlan J Coin, Taco W Kuijpers, Federico Martinon-Torres, Werner Zenz, Michael Levin, Martin L Hibberd, Sonia Davila, EUCLIDS consortium
Nov 17, 2020
Non-coding genetic variants play an important role in driving susceptibility to complex diseases but their characterization remains challenging. Here, we employed a novel approach to interrogate the genetic risk of such...
Case-Control Studies Cohort Studies Genetic Association Studies Genetic Predisposition to Disease Genomics High-Throughput Nucleotide Sequencing Humans Hypopharyngeal Neoplasms Meningococcal Infections Neisseria meningitidis Phenotype Polymorphism Single Nucleotide Regulatory Sequences Nucleic Acid Tumor Cells Cultured
A mouse chromosome 4 balancer ENU-mutagenesis screen isolates eleven lethal lines.
Melissa K Boles, Bonney M Wilkinson, Andrea Maxwell, Lihua Lai, Alea A Mills, Ichiko Nishijima, Andrew P Salinger, Ivan Moskowitz, Karen K Hirschi, Bin Liu, Allan Bradley, Monica J Justice
Oct 14, 2020
BACKGROUND: ENU-mutagenesis is a powerful technique to identify genes regulating mammalian development. To functionally annotate the distal region of mouse chromosome 4, we performed an ENU-mutagenesis screen using a balancer...
In situ functional dissection of RNA cis-regulatory elements by multiplex CRISPR-Cas9 genome engineering.
Qianxin Wu, Quentin RV Ferry, Toni A Baeumler, Yale S Michaels, Dimitrios M Vitsios, Omer Habib, Roland Arnold, Xiaowei Jiang, Stefano Maio, Bruno R Steinkraus, Marta Tapia, Paolo Piazza, Ni Xu, Georg A Holländer, Thomas A Milne, Jin-Soo Kim, Anton J Enright, Andrew R Bassett, Tudor A Fulga
May 01, 2018
RNA regulatory elements (RREs) are an important yet relatively under-explored facet of gene regulation. Deciphering the prevalence and functional impact of this post-transcriptional control layer requires technologies for...
Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions.
Kyuha Choi, Xiaohui Zhao, Andrew J Tock, Christophe Lambing, Charles J Underwood, Thomas J Hardcastle, Heïdi Serra, Juhyun Kim, Hyun Seob Cho, Jaeil Kim, Piotr A Ziolkowski, Nataliya E Yelina, Ildoo Hwang, Robert A Martienssen, Ian R Henderson
Jun 04, 2018
Meiotic recombination initiates from DNA double-strand breaks (DSBs) generated by SPO11 topoisomerase-like complexes. Meiotic DSB frequency varies extensively along eukaryotic chromosomes, with hotspots controlled by chromatin...
Estimating telomere length from whole genome sequence data.
Zhihao Ding, Massimo Mangino, Abraham Aviv, Tim Spector, Richard Durbin, UK10K consortium
Jun 25, 2018
Telomeres play a key role in replicative ageing and undergo age-dependent attrition in vivo. Here, we report a novel method, TelSeq, to measure average telomere length from whole genome or exome shotgun sequence data. In 260...
miRBase
Sam Griffiths-Jones, Russell J Grocock, Stijn van Dongen, Alex Bateman, Anton J Enright
Nov 16, 2017
The miRBase database aims to provide integrated interfaces to comprehensive microRNA sequence data, annotation and predicted gene targets. miRBase takes over functionality from the microRNA Registry and fulfils three main roles...
Effects of BRCA2 cis-regulation in normal breast and cancer risk amongst BRCA2 mutation carriers.
Ana-Teresa Maia, Antonis C Antoniou, Martin O'Reilly, Shamith Samarajiwa, Mark Dunning, Christiana Kartsonaki, Suet-Feung Chin, Christina N Curtis, Lesley McGuffog, Susan M Domchek, EMBRACE, Douglas F Easton, Susan Peock, Debra Frost, D Gareth Evans, Ros Eeles, Louise Izatt, Julian Adlard, Diana Eccles, GEMO Study Collaborators, Olga M Sinilnikova, Sylvie Mazoyer, Dominique Stoppa-Lyonnet, Marion Gauthier-Villars, Laurence Faivre, Laurence Venat-Bouvet, Capucine Delnatte, Heli Nevanlinna, Fergus J Couch, Andrew K Godwin, Maria Adelaide Caligo, SWE-BRCA, Rosa B Barkardottir, kConFab Investigators, Xiaoqing Chen, Jonathan Beesley, Sue Healey, Carlos Caldas, Georgia Chenevix-Trench, Bruce AJ Ponder
May 17, 2012
HOT1 is a mammalian direct telomere repeat-binding protein contributing to telomerase recruitment.
Dennis Kappei, Falk Butter, Christian Benda, Marion Scheibe, Irena Draškovič, Michelle Stevense, Clara Lopes Novo, Claire Basquin, Masatake Araki, Kimi Araki, Dragomir Blazhev Krastev, Ralf Kittler, Rolf Jessberger, J Arturo Londoño-Vallejo, Matthias Mann, Frank Buchholz
Jun 28, 2019
Telomeres are repetitive DNA structures that, together with the shelterin and the CST complex, protect the ends of chromosomes. Telomere shortening is mitigated in stem and cancer cells through the de novo addition of telomeric...
Sequence determinants of human gene regulatory elements.
Biswajyoti Sahu, Tuomo Hartonen, Päivi Pihlajamaa, Bei Wei, Kashyap Dave, Fangjie Zhu, Eevi Kaasinen, Katja Lidschreiber, Michael Lidschreiber, Carsten O Daub, Patrick Cramer, Teemu Kivioja, Jussi Taipale
Mar 15, 2022
Complex Coding and Regulatory Polymorphisms in a Restriction Factor Determine the Susceptibility of Drosophila to Viral Infection.
It is common to find that major-effect genes are an important cause of variation in susceptibility to infection. Here we have characterized natural variation in a gene called pastrel that explains over half of the genetic...
DCV Drosophila Genetics of immunity natural variation pastrel viral infection Animals Disease Resistance Drosophila Proteins Drosophila melanogaster Genetic Heterogeneity Genomic Structural Variation Insect Viruses Mutation Open Reading Frames Polymorphism Single Nucleotide Regulatory Sequences Nucleic Acid
microRNA-122 as a regulator of mitochondrial metabolic gene network in hepatocellular carcinoma.
Julja Burchard, Chunsheng Zhang, Angela M Liu, Ronnie TP Poon, Nikki PY Lee, Kwong-Fai Wong, Pak C Sham, Brian Y Lam, Mark D Ferguson, George Tokiwa, Ryan Smith, Brendan Leeson, Rebecca Beard, John R Lamb, Lee Lim, Mao Mao, Hongyue Dai, John M Luk
Aug 08, 2017
Tumorigenesis involves multistep genetic alterations. To elucidate the microRNA (miRNA)-gene interaction network in carcinogenesis, we examined their genome-wide expression profiles in 96 pairs of tumor/non-tumor tissues from...
Animals Carcinoma Hepatocellular Cell Line Tumor Down-Regulation Energy Metabolism Gene Expression Profiling Gene Expression Regulation Neoplastic Gene Regulatory Networks Genes Mitochondrial Humans Liver Liver Neoplasms Mice Mice Inbred C57BL MicroRNAs Mitochondria RNA Messenger Reproducibility of Results Sequence Homology Nucleic Acid Signal Transduction Survival Analysis Up-Regulation
Novel cis-regulatory modules control expression of the Hairy and Enhancer of Split-1 (HES1) transcription factor in myoblasts
The expression profile of a gene is controlled by DNA sequences called cis-regulatory modules (CRMs). CRMs can function over large genomic distances and can be located many kilobases away from their target promoters. hes1 is...
Animals Basic Helix-Loop-Helix Transcription Factors Cell Line Computational Biology Conserved Sequence Enhancer Elements Genetic Gene Expression Regulation Homeodomain Proteins Immunoglobulin J Recombination Signal Sequence-Binding Protein Mice Myoblasts Nucleotide Motifs Promoter Regions Genetic Receptors Notch Regulatory Sequences Nucleic Acid Signal Transduction Transcription Initiation Site /dk/atira/pure/sustainabledevelopmentgoals/good_health_and_well_being name=SDG 3 - Good Health and Well-being
Cohesin-dependent regulation of gene expression during differentiation is lost in cohesin-mutated myeloid malignancies.
Daniel Sasca, Haiyang Yun, George Giotopoulos, Jakub Szybinski, Theo Evan, Nicola K Wilson, Moritz Gerstung, Paolo Gallipoli, Anthony R Green, Robert Hills, Nigel Russell, Cameron S Osborne, Elli Papaemmanuil, Berthold Göttgens, Peter Campbell, Brian JP Huntly
Oct 03, 2019
Cohesin complex disruption alters gene expression, and cohesin mutations are common in myeloid neoplasia, suggesting a critical role in hematopoiesis. Here, we explore cohesin dynamics and regulation of hematopoietic stem cell...
Biomarkers Tumor Cell Cycle Proteins Cell Line Tumor Chromosomal Proteins Non-Histone Female Gene Dosage Gene Expression Regulation Leukemic Hematopoietic Stem Cells Histones Humans Male Mutation Myeloproliferative Disorders Neoplasm Grading Protein Binding Proto-Oncogene Proteins c-ets Regulatory Sequences Nucleic Acid Repressor Proteins
The regulation and functions of DNA and RNA G-quadruplexes.
Dhaval Varshney, Jochen Spiegel, Katherine Zyner, David Tannahill, Shankar Balasubramanian
Mar 13, 2020
LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions.
Maša Roller, Ericca Stamper, Diego Villar, Osagie Izuogu, Fergal Martin, Aisling M Redmond, Raghavendra Ramachanderan, Louise Harewood, Duncan T Odom, Paul Flicek
Feb 18, 2021
Enhancers Gene regulation LINE L1 LINE L2 Long Interspersed Nuclear Elements (LINEs) Mammals Promoters regulatory evolution transposable elements Animals Chromosome Mapping Conserved Sequence Enhancer Elements Genetic evolution Molecular Gene Expression Regulation Humans Long Interspersed Nucleotide Elements Mammals Organ Specificity Promoter Regions Genetic Regulatory Sequences Nucleic Acid Retroelements
Novel cis-regulatory modules control expression of the Hairy and Enhancer of Split-1 (HES1) transcription factor in myoblasts
The expression profile of a gene is controlled by DNA sequences called cis-regulatory modules (CRMs). CRMs can function over large genomic distances and can be located many kilobases away from their target promoters. hes1 is...
Animals Basic Helix-Loop-Helix Transcription Factors Cell Line Computational Biology Conserved Sequence Enhancer Elements Genetic Gene Expression Regulation Homeodomain Proteins Immunoglobulin J Recombination Signal Sequence-Binding Protein Mice Myoblasts Nucleotide Motifs Promoter Regions Genetic Receptors Notch Regulatory Sequences Nucleic Acid Signal Transduction Transcription Initiation Site /dk/atira/pure/sustainabledevelopmentgoals/good_health_and_well_being name=SDG 3 - Good Health and Well-being
Identification, variation and transcription of pneumococcal repeat sequences.
BACKGROUND: Small interspersed repeats are commonly found in many bacterial chromosomes. Two families of repeats (BOX and RUP) have previously been identified in the genome of Streptococcus pneumoniae, a nasopharyngeal commensal...
The landscape of DNA repeat elements in human heart failure.
Syed Haider, Lina Cordeddu, Emma Robinson, Mehregan Movassagh, Lee Siggens, Ana Vujic, Mun-Kit Choy, Martin Goddard, Pietro Lio, Roger Foo
Sep 18, 2020
BACKGROUND: The epigenomes of healthy and diseased human hearts were recently examined by genome-wide DNA methylation profiling. Repetitive elements, heavily methylated in post-natal tissue, have variable methylation profiles in...
SWI/SNF chromatin remodeling controls Notch-responsive enhancer accessibility.
Notch signaling plays a key role in many cell fate decisions during development by directing different gene expression programs via the transcription factor CSL, known as Su(H) in Drosophila Which target genes are responsive to...
Drosophila Notch SWI/SNF histone H3.3 nucleosome turnover Acetylation Animals Chromatin Chromatin Assembly and Disassembly Chromosomal Proteins Non-Histone Drosophila Drosophila Proteins Gene Expression Regulation Histones Nucleosomes Receptors Notch Regulatory Sequences Nucleic Acid Transcription Factors Transcription Genetic
Nuclear RNA sequencing of the mouse erythroid cell transcriptome.
Jennifer A Mitchell, Ieuan Clay, David Umlauf, Chih-Yu Chen, Catherine A Moir, Christopher H Eskiw, Stefan Schoenfelder, Lyubomira Chakalova, Takashi Nagano, Peter Fraser
Jul 15, 2019
In addition to protein coding genes a substantial proportion of mammalian genomes are transcribed. However, most transcriptome studies investigate steady-state mRNA levels, ignoring a considerable fraction of the transcribed...
Animals Chromatin Immunoprecipitation Erythroid Cells Gene Expression Regulation Gene Library High-Throughput Nucleotide Sequencing Mice Protein Binding RNA Polymerase II RNA Long Noncoding RNA Nuclear Regulatory Sequences Nucleic Acid Reproducibility of Results Sequence Analysis RNA Transcription Genetic Transcriptome
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