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Wyszukujesz frazę ""Chromatin"" wg kryterium: Temat


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Tytuł :
CHIPIN: ChIP-seq inter-sample normalization based on signal invariance across transcriptionally constant genes.
Autorzy :
Polit L; Institut Cochin, Inserm U1016, CNRS UMR 8104, Paris Descartes University UMR-S1016, 75014, Paris, France.
Kerdivel G; Institut Cochin, Inserm U1016, CNRS UMR 8104, Paris Descartes University UMR-S1016, 75014, Paris, France.
Gregoricchio S; INSERM UMR1170, Equipe Labellisée Ligue Nationale Contre Le Cancer, Gustave Roussy, Paris-Saclay University, 94800, Villejuif, France.
Esposito M; INSERM UMR1170, Equipe Labellisée Ligue Nationale Contre Le Cancer, Gustave Roussy, Paris-Saclay University, 94800, Villejuif, France.
Guillouf C; INSERM UMR1170, Equipe Labellisée Ligue Nationale Contre Le Cancer, Gustave Roussy, Paris-Saclay University, 94800, Villejuif, France.
Boeva V; Institut Cochin, Inserm U1016, CNRS UMR 8104, Paris Descartes University UMR-S1016, 75014, Paris, France. .; Department of Computer Science, Institute for Machine Learning, ETH Zurich, 8092, Zurich, Switzerland. .; Swiss Institute for Bioinformatics (SIB), Zürich, Switzerland. .
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Źródło :
BMC bioinformatics [BMC Bioinformatics] 2021 Aug 17; Vol. 22 (1), pp. 407. Date of Electronic Publication: 2021 Aug 17.
Typ publikacji :
Journal Article
MeSH Terms :
Chromatin*
Chromatin Immunoprecipitation Sequencing*
Chromatin Immunoprecipitation ; Protein Binding ; Sequence Analysis, DNA
Czasopismo naukowe
Tytuł :
BANP opens chromatin and activates CpG-island-regulated genes.
Autorzy :
Grand RS; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
Burger L; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.; Swiss Institute of Bioinformatics, Basel, Switzerland.
Gräwe C; Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands.
Michael AK; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
Isbel L; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
Hess D; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
Hoerner L; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
Iesmantavicius V; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
Durdu S; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
Pregnolato M; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.; Faculty of Science, University of Basel, Basel, Switzerland.
Krebs AR; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.; Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
Smallwood SA; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
Thomä N; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
Vermeulen M; Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands.
Schübeler D; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. .; Faculty of Science, University of Basel, Basel, Switzerland. .
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Źródło :
Nature [Nature] 2021 Aug; Vol. 596 (7870), pp. 133-137. Date of Electronic Publication: 2021 Jul 07.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Chromatin Assembly and Disassembly*/genetics
Cell Cycle Proteins/*metabolism
Chromatin/*genetics
Chromatin/*metabolism
CpG Islands/*genetics
DNA-Binding Proteins/*metabolism
Nuclear Proteins/*metabolism
Animals ; Base Sequence ; Cell Line, Tumor ; Chromatin/chemistry ; DNA Methylation ; Gene Expression Regulation ; Genes, Essential ; Humans ; Mice ; Single Molecule Imaging
Czasopismo naukowe
Tytuł :
Structure and Function of Chromatin Remodelers.
Autorzy :
Reyes AA; Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208-3500, USA; Interdisciplinary Biological Sciences Program, Northwestern University, 2205 Tech Drive, Evanston, IL 60208-3500, USA. Electronic address: .
Marcum RD; Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208-3500, USA. Electronic address: .
He Y; Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208-3500, USA; Interdisciplinary Biological Sciences Program, Northwestern University, 2205 Tech Drive, Evanston, IL 60208-3500, USA; Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, 676 N. St. Clair, Chicago, IL 60611, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA. Electronic address: .
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Źródło :
Journal of molecular biology [J Mol Biol] 2021 Jul 09; Vol. 433 (14), pp. 166929. Date of Electronic Publication: 2021 Mar 10.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Review
MeSH Terms :
Chromatin Assembly and Disassembly*
Chromatin/*genetics
Chromatin/chemistry ; Chromatin/metabolism ; Gene Expression Regulation ; Humans ; Nucleosomes/metabolism ; Structure-Activity Relationship ; Yeasts
Czasopismo naukowe
Tytuł :
Transcriptional Profiling of Cardiac Cells Links Age-Dependent Changes in Acetyl-CoA Signaling to Chromatin Modifications.
Autorzy :
Kurian J; Center for Metabolic Disease Research (CMDR), LKSOM, Temple University, Philadelphia, PA 19140, USA.
Bohl V; Center for Metabolic Disease Research (CMDR), LKSOM, Temple University, Philadelphia, PA 19140, USA.
Behanan M; Center for Metabolic Disease Research (CMDR), LKSOM, Temple University, Philadelphia, PA 19140, USA.
Mohsin S; Cardiovascular Research Center (CVRC), LKSOM, Temple University, Philadelphia, PA 19140, USA.
Khan M; Center for Metabolic Disease Research (CMDR), LKSOM, Temple University, Philadelphia, PA 19140, USA.; Department of Physiology, LKSOM, Temple University, Philadelphia, PA 19140, USA.
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Źródło :
International journal of molecular sciences [Int J Mol Sci] 2021 Jun 29; Vol. 22 (13). Date of Electronic Publication: 2021 Jun 29.
Typ publikacji :
Journal Article
MeSH Terms :
Chromatin Assembly and Disassembly*
Gene Expression Profiling*
Gene Expression Regulation*
Signal Transduction*
Transcriptome*
Acetyl Coenzyme A/*metabolism
Myocytes, Cardiac/*metabolism
Chromatin/genetics ; Chromatin/metabolism ; Cluster Analysis ; Computational Biology/methods ; Gene Regulatory Networks ; Histones/metabolism ; Humans ; Protein Processing, Post-Translational ; Stem Cells/cytology ; Stem Cells/metabolism
Czasopismo naukowe
Tytuł :
Chromatin Immunoprecipitation and Sequencing (ChIP-seq) Optimized for Application in Caenorhabditis elegans.
Autorzy :
Sen I; Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Karolinska Institute, Huddinge, Sweden.; Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden.
Kavšek A; Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Karolinska Institute, Huddinge, Sweden.; Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden.
Riedel CG; Department of Medicine, Integrated Cardio Metabolic Centre (ICMC), Karolinska Institute, Huddinge, Sweden.; Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden.
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Źródło :
Current protocols [Curr Protoc] 2021 Jul; Vol. 1 (7), pp. e187.
Typ publikacji :
Journal Article
MeSH Terms :
Caenorhabditis elegans*/genetics
Chromatin Immunoprecipitation Sequencing*
Animals ; Chromatin Immunoprecipitation ; High-Throughput Nucleotide Sequencing ; Reproducibility of Results
Czasopismo naukowe
Tytuł :
The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription-replication conflicts.
Autorzy :
Bayona-Feliu A; Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain.; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain.
Barroso S; Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain.
Muñoz S; Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain.
Aguilera A; Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain. .; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain. .
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Źródło :
Nature genetics [Nat Genet] 2021 Jul; Vol. 53 (7), pp. 1050-1063. Date of Electronic Publication: 2021 May 13.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Chromatin Assembly and Disassembly*
DNA Replication*
R-Loop Structures*
Transcription, Genetic*
Chromosomal Proteins, Non-Histone/*metabolism
Transcription Factors/*metabolism
Adenosine Triphosphatases/metabolism ; Chromatin/genetics ; Chromatin/metabolism ; Fanconi Anemia Complementation Group D2 Protein/genetics ; Fanconi Anemia Complementation Group D2 Protein/metabolism ; Genetic Loci ; Genomic Instability ; Humans
Czasopismo naukowe
Tytuł :
Nucleosome-induced homology recognition in chromatin.
Autorzy :
Hedley JG; Department of Chemistry, Faculty of Natural Sciences, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, UK.
Teif VB; School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK.
Kornyshev AA; Department of Chemistry, Faculty of Natural Sciences, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, UK.
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Źródło :
Journal of the Royal Society, Interface [J R Soc Interface] 2021 Jun; Vol. 18 (179), pp. 20210147. Date of Electronic Publication: 2021 Jun 16.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Chromatin*
Nucleosomes*
Chromatin Assembly and Disassembly ; DNA ; Histones/metabolism
Czasopismo naukowe
Tytuł :
Stretch-Induced Tenomodulin Expression Promotes Tenocyte Migration via F-Actin and Chromatin Remodeling.
Autorzy :
Xu P; Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China.
Deng B; Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China.
Zhang B; Chongqing Engineering Research Center of Medical Electronics and Information Technology, College of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing 400065, China.
Luo Q; Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China.
Song G; Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China.
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Źródło :
International journal of molecular sciences [Int J Mol Sci] 2021 May 06; Vol. 22 (9). Date of Electronic Publication: 2021 May 06.
Typ publikacji :
Journal Article
MeSH Terms :
Cell Movement*
Chromatin Assembly and Disassembly*
Stress, Mechanical*
Actins/*metabolism
Membrane Proteins/*metabolism
Tenocytes/*cytology
Tenocytes/*metabolism
Animals ; Cells, Cultured ; Chromatin/metabolism ; Membrane Proteins/genetics ; Rats, Sprague-Dawley ; Stress Fibers/metabolism ; Up-Regulation/genetics
Czasopismo naukowe
Tytuł :
Stromal induction of BRD4 phosphorylation Results in Chromatin Remodeling and BET inhibitor Resistance in Colorectal Cancer.
Autorzy :
Wang W; Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, China. .; Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, China. .; Cancer Precision Medicine, Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore, 138672, Singapore. .
Tang YA; Cancer Precision Medicine, Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore, 138672, Singapore.; Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, 70101, Taiwan.
Xiao Q; Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, China.; Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, China.
Lee WC; Cancer Precision Medicine, Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore, 138672, Singapore.
Cheng B; Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, China.; Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, China.
Niu Z; Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, China.; Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, China.
Oguz G; Cancer Precision Medicine, Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore, 138672, Singapore.
Feng M; Cancer Precision Medicine, Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore, 138672, Singapore.
Lee PL; Cancer Precision Medicine, Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore, 138672, Singapore.
Li B; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200240, China.
Yang ZH; Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, China.; Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, China.
Chen YF; Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, China.; Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, China.; Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China.
Lan P; Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, China.; Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, China.; Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China.
Wu XJ; Guangdong Provincial Key laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, China. .; Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510655, China. .; Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China. .
Yu Q; Cancer Precision Medicine, Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore, 138672, Singapore. .; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore. .; Cancer and Stem Cell Biology, DUKE-NUS Graduate Medical School of Singapore, Singapore, 169857, Singapore. .
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Źródło :
Nature communications [Nat Commun] 2021 Jul 21; Vol. 12 (1), pp. 4441. Date of Electronic Publication: 2021 Jul 21.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Chromatin Assembly and Disassembly*
Drug Resistance, Neoplasm*
Cell Cycle Proteins/*metabolism
Colorectal Neoplasms/*metabolism
Transcription Factors/*metabolism
Antineoplastic Agents/metabolism ; Antineoplastic Agents/pharmacology ; Cancer-Associated Fibroblasts/metabolism ; Cell Cycle Proteins/antagonists & inhibitors ; Chromatin/metabolism ; Colorectal Neoplasms/pathology ; Gene Expression Regulation, Neoplastic/drug effects ; Humans ; Interleukin-6/metabolism ; Interleukin-8/metabolism ; Janus Kinase 2/metabolism ; Phosphorylation ; Protein Domains ; STAT3 Transcription Factor/metabolism ; Signal Transduction ; Transcription Factors/antagonists & inhibitors ; Tumor Microenvironment ; Ubiquitin Thiolesterase/metabolism
Czasopismo naukowe
Tytuł :
UniBind: maps of high-confidence direct TF-DNA interactions across nine species.
Autorzy :
Puig RR; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0349, Oslo, Norway.
Boddie P; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0349, Oslo, Norway.
Khan A; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0349, Oslo, Norway.; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Castro-Mondragon JA; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0349, Oslo, Norway.
Mathelier A; Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0349, Oslo, Norway. .; Department of Medical Genetics, Oslo University Hospital, Oslo, 0424, Norway. .
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Źródło :
BMC genomics [BMC Genomics] 2021 Jun 26; Vol. 22 (1), pp. 482. Date of Electronic Publication: 2021 Jun 26.
Typ publikacji :
Journal Article
MeSH Terms :
Chromatin Immunoprecipitation Sequencing*
DNA*/metabolism
Binding Sites ; Chromatin Immunoprecipitation ; Computational Biology ; Protein Binding
Czasopismo naukowe
Tytuł :
Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas.
Autorzy :
Stępniak K; Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland.
Machnicka MA; Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland.
Mieczkowski J; Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland.; Medical University of Gdansk, International Research Agenda 3P Medicine Laboratory, Gdansk, Poland.
Macioszek A; Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland.
Wojtaś B; Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland.
Gielniewski B; Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland.
Poleszak K; Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland.
Perycz M; Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland.
Król SK; Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland.
Guzik R; Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland.
Dąbrowski MJ; Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland.
Dramiński M; Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland.
Jardanowska M; Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland.
Grabowicz I; Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland.
Dziedzic A; Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland.
Kranas H; Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland.; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
Sienkiewicz K; Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland.
Diamanti K; Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
Kotulska K; Departments of Neurology, Neurosurgery, Neuropathology, The Children's Memorial Health Institute, Warsaw, Poland.
Grajkowska W; Departments of Neurology, Neurosurgery, Neuropathology, The Children's Memorial Health Institute, Warsaw, Poland.
Roszkowski M; Departments of Neurology, Neurosurgery, Neuropathology, The Children's Memorial Health Institute, Warsaw, Poland.
Czernicki T; Department of Neurosurgery, Medical University of Warsaw, Warsaw, Poland.
Marchel A; Department of Neurosurgery, Medical University of Warsaw, Warsaw, Poland.
Komorowski J; Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
Kaminska B; Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland. .
Wilczyński B; Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland. .
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Źródło :
Nature communications [Nat Commun] 2021 Jun 15; Vol. 12 (1), pp. 3621. Date of Electronic Publication: 2021 Jun 15.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Chromatin*
Regulatory Sequences, Nucleic Acid*
Glioma/*genetics
Binding Sites ; Brain Neoplasms/genetics ; Chromatin Immunoprecipitation ; DNA/metabolism ; DNA Methylation ; DNA-Binding Proteins/metabolism ; Enhancer of Zeste Homolog 2 Protein ; Epigenesis, Genetic ; Epigenomics ; Forkhead Box Protein M1 ; Gene Expression ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Glioblastoma ; Histone Code ; Histones ; Humans ; Promoter Regions, Genetic ; Transcription Factors/metabolism
Czasopismo naukowe
Tytuł :
Increased peak detection accuracy in over-dispersed ChIP-seq data with supervised segmentation models.
Autorzy :
Liehrmann A; Institut des Sciences des Plantes de Paris-Saclay (IPS2), Université Paris-Saclay, Université Evry, CNRS, INRAE, 91405, Orsay, France. .; Laboratoire de Mathématiques et Modélisation d'Evry (LAMME), Université Paris-Saclay, Université Evry, CNRS, 91037, Evry, France. .
Rigaill G; Institut des Sciences des Plantes de Paris-Saclay (IPS2), Université Paris-Saclay, Université Evry, CNRS, INRAE, 91405, Orsay, France.; Laboratoire de Mathématiques et Modélisation d'Evry (LAMME), Université Paris-Saclay, Université Evry, CNRS, 91037, Evry, France.
Hocking TD; School of Informatics, Computing, and Cyber Systems (SICCS), Northern Arizona University, 86011, Flagstaff, AZ, USA.
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Źródło :
BMC bioinformatics [BMC Bioinformatics] 2021 Jun 14; Vol. 22 (1), pp. 323. Date of Electronic Publication: 2021 Jun 14.
Typ publikacji :
Journal Article
MeSH Terms :
Chromatin Immunoprecipitation Sequencing*
High-Throughput Nucleotide Sequencing*
Algorithms ; Chromatin Immunoprecipitation ; Sequence Analysis, DNA
Czasopismo naukowe
Tytuł :
Fast detection of differential chromatin domains with SCIDDO.
Autorzy :
Ebert P; Institute for Medical Biometry and Bioinformatics, Heinrich Heine University, 40225 Düsseldorf, Germany.; Max Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany.
Schulz MH; Max Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany.; Cluster of Excellence on Multimodal Computing and Interaction, Saarland Informatics Campus, 66123 Saarbrücken, Germany.; Institute for Cardiovascular Regeneration, Goethe University, 60590 Frankfurt am Main, Germany.; German Center for Cardiovascular Research (DZHK), Partner site Rhein-Main, 60590 Frankfurt am Main, Germany.
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Źródło :
Bioinformatics (Oxford, England) [Bioinformatics] 2021 Jun 09; Vol. 37 (9), pp. 1198-1205.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Chromatin*
Chromosomes*
Chromatin Immunoprecipitation ; Genome ; Histone Code
Czasopismo naukowe
Tytuł :
Impact of DNA methylation on 3D genome structure.
Autorzy :
Buitrago D; Institute for Research in Biomedicine (IRB Barcelona) - The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.; Joint IRB-BSC Program in Computational Biology, Barcelona, Spain.; Departamento de Física y Matemáticas, Universidad Autónoma de Manizales, Manizales, Colombia.
Labrador M; Institute for Research in Biomedicine (IRB Barcelona) - The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.; Joint IRB-BSC Program in Computational Biology, Barcelona, Spain.
Arcon JP; Institute for Research in Biomedicine (IRB Barcelona) - The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.; Joint IRB-BSC Program in Computational Biology, Barcelona, Spain.
Lema R; Institute for Research in Biomedicine (IRB Barcelona) - The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.; Joint IRB-BSC Program in Computational Biology, Barcelona, Spain.
Flores O; Institute for Research in Biomedicine (IRB Barcelona) - The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.; Joint IRB-BSC Program in Computational Biology, Barcelona, Spain.
Esteve-Codina A; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
Blanc J; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
Villegas N; Institute for Research in Biomedicine (IRB Barcelona) - The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.; Joint IRB-BSC Program in Computational Biology, Barcelona, Spain.
Bellido D; Centres Cientifics i Tecnologics, Universitat de Barcelona, Barcelona, Spain.
Gut M; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
Dans PD; Institute for Research in Biomedicine (IRB Barcelona) - The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.; Joint IRB-BSC Program in Computational Biology, Barcelona, Spain.; Department of Biological Sciences, CENUR North Coast. University of the Republic, Salto, Uruguay.
Heath SC; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
Gut IG; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
Brun Heath I; Institute for Research in Biomedicine (IRB Barcelona) - The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .; Joint IRB-BSC Program in Computational Biology, Barcelona, Spain. .
Orozco M; Institute for Research in Biomedicine (IRB Barcelona) - The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .; Joint IRB-BSC Program in Computational Biology, Barcelona, Spain. .; Departament de Bioquímica i Biomedicina, Universitat de Barcelona, Barcelona, Spain. .
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Źródło :
Nature communications [Nat Commun] 2021 May 28; Vol. 12 (1), pp. 3243. Date of Electronic Publication: 2021 May 28.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Chromatin Assembly and Disassembly*
DNA Methylation*
Epigenesis, Genetic*
Nucleosomes/*metabolism
Saccharomyces cerevisiae/*genetics
5' Untranslated Regions/genetics ; Centromere/metabolism ; Chromatin/metabolism ; DNA (Cytosine-5-)-Methyltransferase 1/genetics ; DNA (Cytosine-5-)-Methyltransferase 1/metabolism ; DNA (Cytosine-5-)-Methyltransferases/genetics ; DNA (Cytosine-5-)-Methyltransferases/metabolism ; Genome, Fungal ; Histones/genetics ; Histones/metabolism ; Intravital Microscopy ; Mutagenesis, Site-Directed ; Mutation ; Nucleosomes/genetics ; RNA-Seq ; Recombinant Proteins/genetics ; Recombinant Proteins/isolation & purification ; Recombinant Proteins/metabolism ; Repressor Proteins/genetics ; Repressor Proteins/isolation & purification ; Repressor Proteins/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/isolation & purification ; Saccharomyces cerevisiae Proteins/metabolism ; Whole Genome Sequencing
Czasopismo naukowe
Tytuł :
NoPeak: k-mer-based motif discovery in ChIP-Seq data without peak calling.
Autorzy :
Menzel M; MNI, Technische Hochschule Mittelhessen, University of Applied Sciences, Giessen 35390, Germany.
Hurka S; Institute for Insect Biotechnology, Justus Liebig University, Giessen 35392, Germany.
Glasenhardt S; MNI, Technische Hochschule Mittelhessen, University of Applied Sciences, Giessen 35390, Germany.
Gogol-Döring A; MNI, Technische Hochschule Mittelhessen, University of Applied Sciences, Giessen 35390, Germany.
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Źródło :
Bioinformatics (Oxford, England) [Bioinformatics] 2021 May 05; Vol. 37 (5), pp. 596-602.
Typ publikacji :
Journal Article
MeSH Terms :
Chromatin Immunoprecipitation Sequencing*
High-Throughput Nucleotide Sequencing*
Binding Sites ; Chromatin Immunoprecipitation ; Sequence Analysis, DNA
Czasopismo naukowe
Tytuł :
Spatial Organization of Chromatin: Transcriptional Control of Adaptive Immune Cell Development.
Autorzy :
Pongubala JMR; Department of Animal Biology, University of Hyderabad, Hyderabad, India.
Murre C; Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States.
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Źródło :
Frontiers in immunology [Front Immunol] 2021 Mar 29; Vol. 12, pp. 633825. Date of Electronic Publication: 2021 Mar 29 (Print Publication: 2021).
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Review
MeSH Terms :
Adaptive Immunity*/genetics
Chromatin Assembly and Disassembly*
Transcription, Genetic*
B-Lymphocytes/*metabolism
Chromatin/*metabolism
T-Lymphocytes/*metabolism
Animals ; B-Lymphocytes/immunology ; Chromatin/genetics ; Chromatin/immunology ; Humans ; Nucleic Acid Conformation ; Protein Conformation ; T-Lymphocytes/immunology
Czasopismo naukowe
Tytuł :
The emerging role of chromatin remodelers in neurodevelopmental disorders: a developmental perspective.
Autorzy :
Mossink B; Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.; Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands.
Negwer M; Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.; Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands.
Schubert D; Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands.
Nadif Kasri N; Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands. .; Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands. .
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Źródło :
Cellular and molecular life sciences : CMLS [Cell Mol Life Sci] 2021 Mar; Vol. 78 (6), pp. 2517-2563. Date of Electronic Publication: 2020 Dec 02.
Typ publikacji :
Journal Article; Review
MeSH Terms :
Chromatin Assembly and Disassembly*
Chromatin/*metabolism
Neurodevelopmental Disorders/*pathology
Animals ; Chromatin/chemistry ; DNA Helicases/genetics ; DNA Helicases/metabolism ; Epigenesis, Genetic ; Histones/genetics ; Histones/metabolism ; Humans ; Neurodevelopmental Disorders/metabolism ; Neurons/metabolism ; Protein Processing, Post-Translational/genetics
Czasopismo naukowe
Tytuł :
SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data.
Autorzy :
Yu M; State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.; Ludwig Institute for Cancer Research, La Jolla, CA, USA.
Abnousi A; Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.
Zhang Y; Ludwig Institute for Cancer Research, La Jolla, CA, USA.
Li G; Ludwig Institute for Cancer Research, La Jolla, CA, USA.
Lee L; Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.
Chen Z; State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.
Fang R; Ludwig Institute for Cancer Research, La Jolla, CA, USA.; Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
Lagler TM; Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA.
Yang Y; Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, USA.; McAllister Heart Institute, University of North Carolina, Chapel Hill, NC, USA.
Wen J; Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.
Sun Q; Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA.
Li Y; Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA.; Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.; Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA.
Ren B; Ludwig Institute for Cancer Research, La Jolla, CA, USA. .; Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA. .
Hu M; Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA. .
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Źródło :
Nature methods [Nat Methods] 2021 Sep; Vol. 18 (9), pp. 1056-1059. Date of Electronic Publication: 2021 Aug 26.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural
MeSH Terms :
Chromatin/*chemistry
Computational Biology/*methods
Single-Cell Analysis/*methods
Algorithms ; Animals ; Chromatin/genetics ; Chromatin Immunoprecipitation Sequencing ; Data Visualization ; Databases, Factual ; Gene Expression ; Humans ; Mental Disorders/genetics ; Mice ; Mouse Embryonic Stem Cells/cytology ; Mouse Embryonic Stem Cells/physiology ; Polymorphism, Single Nucleotide ; Prefrontal Cortex/cytology ; Reproducibility of Results ; Sequence Analysis, DNA/methods
Czasopismo naukowe
Tytuł :
CTCF and transcription influence chromatin structure re-configuration after mitosis.
Autorzy :
Zhang H; Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China. .; Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. .
Lam J; Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Zhang D; Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Lan Y; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Vermunt MW; Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Keller CA; Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
Giardine B; Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
Hardison RC; Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
Blobel GA; Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA. .; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .
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Źródło :
Nature communications [Nat Commun] 2021 Aug 27; Vol. 12 (1), pp. 5157. Date of Electronic Publication: 2021 Aug 27.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural
MeSH Terms :
Mitosis*
Transcription, Genetic*
CCCTC-Binding Factor/*metabolism
Chromatin/*metabolism
Animals ; CCCTC-Binding Factor/genetics ; Cell Division ; Cell Line ; Chromatin/genetics ; Chromatin Assembly and Disassembly ; Enhancer Elements, Genetic ; Mice ; Promoter Regions, Genetic
Czasopismo naukowe

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