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Wyszukujesz frazę ""Transcription Initiation Site"" wg kryterium: Temat


Tytuł :
Transcription imparts architecture, function and logic to enhancer units.
Autorzy :
Tippens ND; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA.; Department of Computational Biology, Cornell University, Ithaca, NY, USA.; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.; Tri-Institutional Training Program in Computational Biology and Medicine, Cornell University, Ithaca, NY, USA.
Liang J; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA.
Leung AK; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA.; Department of Computational Biology, Cornell University, Ithaca, NY, USA.
Wierbowski SD; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA.; Department of Computational Biology, Cornell University, Ithaca, NY, USA.
Ozer A; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
Booth JG; Department of Statistics and Data Science, Cornell University, Ithaca, NY, USA.
Lis JT; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA. .; Tri-Institutional Training Program in Computational Biology and Medicine, Cornell University, Ithaca, NY, USA. .
Yu H; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA. .; Department of Computational Biology, Cornell University, Ithaca, NY, USA. .; Tri-Institutional Training Program in Computational Biology and Medicine, Cornell University, Ithaca, NY, USA. .
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Źródło :
Nature genetics [Nat Genet] 2020 Oct; Vol. 52 (10), pp. 1067-1075. Date of Electronic Publication: 2020 Sep 21.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
MeSH Terms :
Transcription Initiation Site*
Transcription, Genetic*
Enhancer Elements, Genetic/*genetics
Histone Code/*genetics
Cell Line ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Humans ; Promoter Regions, Genetic/genetics ; Protein Processing, Post-Translational/genetics ; Transcription Initiation, Genetic
Czasopismo naukowe
Tytuł :
Alteration of genome folding via contact domain boundary insertion.
Autorzy :
Zhang D; Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, USA. .; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .
Huang P; Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Sharma M; Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Keller CA; Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA, USA.
Giardine B; Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA, USA.
Zhang H; Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Gilgenast TG; Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.
Phillips-Cremins JE; Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.; Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
Hardison RC; Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA, USA.
Blobel GA; Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, USA. .; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .
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Źródło :
Nature genetics [Nat Genet] 2020 Oct; Vol. 52 (10), pp. 1076-1087. Date of Electronic Publication: 2020 Aug 31.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
MeSH Terms :
Transcription Initiation Site*
CCCTC-Binding Factor/*genetics
Chromatin/*genetics
Chromosomes/*genetics
Animals ; Base Sequence/genetics ; Binding Sites/genetics ; DNA-Binding Proteins/genetics ; Genome/genetics ; Genome, Human/genetics ; Humans ; Protein Binding/genetics ; Protein Domains/genetics
Czasopismo naukowe
Tytuł :
Unfolding SARS-CoV-2 viral genome to understand its gene expression regulation.
Autorzy :
Dinka H; Department of Applied Biology, School of Applied Natural Science, Adama Science and Technology University, P.O.Box 1888, Adama, Ethiopia. Electronic address: .
Milkesa A; Department of Applied Biology, School of Applied Natural Science, Adama Science and Technology University, P.O.Box 1888, Adama, Ethiopia.
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Źródło :
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases [Infect Genet Evol] 2020 Oct; Vol. 84, pp. 104386. Date of Electronic Publication: 2020 May 29.
Typ publikacji :
Journal Article
MeSH Terms :
Gene Expression Regulation, Viral*
Genome, Viral*
Transcription Initiation Site*
Betacoronavirus/*genetics
Transcription Factors/*genetics
Viral Proteins/*genetics
Amino Acid Sequence ; Betacoronavirus/metabolism ; Binding Sites ; COVID-19 ; Computational Biology/methods ; Coronavirus Infections/virology ; CpG Islands ; Humans ; Nucleotide Motifs ; Open Reading Frames ; Pandemics ; Pneumonia, Viral/virology ; Promoter Regions, Genetic ; Protein Binding ; SARS-CoV-2 ; Transcription Factors/metabolism ; Viral Proteins/metabolism
Czasopismo naukowe
Tytuł :
Embryonic tissue differentiation is characterized by transitions in cell cycle dynamic-associated core promoter regulation.
Autorzy :
Wragg JW; Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
Roos L; Institute of Clinical Sciences and MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, W12 0NN, UK.
Vucenovic D; Institute of Clinical Sciences and MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, W12 0NN, UK.
Cvetesic N; Institute of Clinical Sciences and MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, W12 0NN, UK.
Lenhard B; Institute of Clinical Sciences and MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, W12 0NN, UK.
Müller F; Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
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Źródło :
Nucleic acids research [Nucleic Acids Res] 2020 Sep 04; Vol. 48 (15), pp. 8374-8392.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Transcription Initiation Site*
Transcription, Genetic*
Gene Regulatory Networks/*genetics
Promoter Regions, Genetic/*genetics
Animals ; Binding Sites/genetics ; Cell Cycle/genetics ; Cell Differentiation/genetics ; Cell Proliferation/genetics ; Embryonic Development/genetics ; Humans ; Morphogenesis/genetics ; Sp1 Transcription Factor/genetics ; TATA Box/genetics ; Zebrafish/genetics
Czasopismo naukowe
Tytuł :
The RNA exosome shapes the expression of key protein-coding genes.
Autorzy :
Wu M; The Bioinformatics Centre, Department of Biology and Biotech and Research Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark.
Karadoulama E; The Bioinformatics Centre, Department of Biology and Biotech and Research Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark.; Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark.
Lloret-Llinares M; Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark.; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Rouviere JO; Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark.
Vaagensø CS; The Bioinformatics Centre, Department of Biology and Biotech and Research Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark.
Moravec M; Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark.
Li B; SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna 171 65, Sweden.
Wang J; SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna 171 65, Sweden.
Wu G; Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark.
Gockert M; Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark.
Pelechano V; SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna 171 65, Sweden.
Jensen TH; Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, Aarhus 8000, Denmark.
Sandelin A; The Bioinformatics Centre, Department of Biology and Biotech and Research Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark.
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Źródło :
Nucleic acids research [Nucleic Acids Res] 2020 Sep 04; Vol. 48 (15), pp. 8509-8528.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Transcription Initiation Site*
Exosomes/*genetics
Genome, Human/*genetics
Open Reading Frames/*genetics
RNA/*genetics
Gene Expression Regulation/genetics ; HeLa Cells ; Humans ; Molecular Sequence Annotation ; RNA Stability/genetics ; RNA, Messenger/genetics ; RNA, Untranslated/genetics
Czasopismo naukowe
Tytuł :
The transcription factor GLI1 cooperates with the chromatin remodeler SMARCA2 to regulate chromatin accessibility at distal DNA regulatory elements.
Autorzy :
Safgren SL; Schulze Center for Novel Therapeutics, Division of Oncology Research, Schulze Center for Novel Therapeutics, Rochester, Minnesota, USA.
Olson RLO; Schulze Center for Novel Therapeutics, Division of Oncology Research, Schulze Center for Novel Therapeutics, Rochester, Minnesota, USA.
Vrabel AM; Schulze Center for Novel Therapeutics, Division of Oncology Research, Schulze Center for Novel Therapeutics, Rochester, Minnesota, USA.
Almada LL; Schulze Center for Novel Therapeutics, Division of Oncology Research, Schulze Center for Novel Therapeutics, Rochester, Minnesota, USA.
Marks DL; Schulze Center for Novel Therapeutics, Division of Oncology Research, Schulze Center for Novel Therapeutics, Rochester, Minnesota, USA.
Hernandez-Alvarado N; Schulze Center for Novel Therapeutics, Division of Oncology Research, Schulze Center for Novel Therapeutics, Rochester, Minnesota, USA.
Gaspar-Maia A; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA.
Fernandez-Zapico ME; Schulze Center for Novel Therapeutics, Division of Oncology Research, Schulze Center for Novel Therapeutics, Rochester, Minnesota, USA .
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Źródło :
The Journal of biological chemistry [J Biol Chem] 2020 Jun 26; Vol. 295 (26), pp. 8725-8735. Date of Electronic Publication: 2020 May 06.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural
MeSH Terms :
Regulatory Elements, Transcriptional*
Transcription Initiation Site*
Chromatin/*genetics
Transcription Factors/*metabolism
Zinc Finger Protein GLI1/*metabolism
Cell Line, Tumor ; Chromatin/metabolism ; Chromatin Assembly and Disassembly ; DNA/genetics ; DNA/metabolism ; HEK293 Cells ; Humans ; Protein Domains ; Protein Interaction Maps ; Transcription Factors/chemistry ; Transcriptional Activation ; Zinc Finger Protein GLI1/chemistry
Czasopismo naukowe
Tytuł :
Characterization of the ZFX family of transcription factors that bind downstream of the start site of CpG island promoters.
Autorzy :
Ni W; Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
Perez AA; Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
Schreiner S; Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
Nicolet CM; Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
Farnham PJ; Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
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Źródło :
Nucleic acids research [Nucleic Acids Res] 2020 Jun 19; Vol. 48 (11), pp. 5986-6000.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
MeSH Terms :
Promoter Regions, Genetic*
Transcription Initiation Site*
CpG Islands/*genetics
DNA-Binding Proteins/*metabolism
Kruppel-Like Transcription Factors/*metabolism
Alleles ; Base Pairing ; Base Sequence ; DNA-Binding Proteins/genetics ; Female ; Gene Deletion ; HEK293 Cells ; Humans ; Kruppel-Like Transcription Factors/genetics ; Male ; Transcriptome ; Zinc Fingers
Czasopismo naukowe
Tytuł :
HIV-1 spliced RNAs display transcription start site bias.
Autorzy :
Esquiaqui JM; Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109-5620, USA.
Kharytonchyk S; Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109-5620, USA.
Drucker D; Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109-5620, USA.
Telesnitsky A; Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109-5620, USA.
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Źródło :
RNA (New York, N.Y.) [RNA] 2020 Jun; Vol. 26 (6), pp. 708-714. Date of Electronic Publication: 2020 Mar 23.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural
MeSH Terms :
RNA Splicing*
Transcription Initiation Site*
HIV-1/*genetics
RNA, Viral/*chemistry
5' Untranslated Regions ; HEK293 Cells ; HIV-1/metabolism ; Humans ; Nucleic Acid Conformation ; RNA, Viral/metabolism
Czasopismo naukowe
Tytuł :
DNA:RNA hybrid G-quadruplex formation upstream of transcription start site.
Autorzy :
Zhang JY; State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, P. R. China.; CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Multidisciplinary Research Division, Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing, 100049, P. R. China.
Xia Y; State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, P. R. China.
Hao YH; State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, P. R. China.
Tan Z; State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, P. R. China. .; Center for Healthy Aging, Changzhi Medical College, Changzhi, 046000, Shanxi, P. R. China. .
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Źródło :
Scientific reports [Sci Rep] 2020 May 04; Vol. 10 (1), pp. 7429. Date of Electronic Publication: 2020 May 04.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
G-Quadruplexes*
Transcription Initiation Site*
Guanine/*chemistry
Base Sequence ; Computational Biology ; DNA/genetics ; DNA-Directed RNA Polymerases/genetics ; Humans ; Nucleic Acid Conformation ; Oligonucleotides/genetics ; RNA/genetics ; Transcription, Genetic
Czasopismo naukowe
Tytuł :
Combining signal and sequence to detect RNA polymerase initiation in ATAC-seq data.
Autorzy :
Tripodi IJ; Computer Science, University of Colorado, Boulder, Colorado, United States of America.; BioFrontiers Institute, University of Colorado, Boulder, Colorado, United States of America.
Chowdhury M; Computer Science, University of Colorado, Boulder, Colorado, United States of America.
Gruca M; BioFrontiers Institute, University of Colorado, Boulder, Colorado, United States of America.
Dowell RD; Computer Science, University of Colorado, Boulder, Colorado, United States of America.; BioFrontiers Institute, University of Colorado, Boulder, Colorado, United States of America.; Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America.
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Źródło :
PloS one [PLoS One] 2020 Apr 30; Vol. 15 (4), pp. e0232332. Date of Electronic Publication: 2020 Apr 30 (Print Publication: 2020).
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms :
Transcription Initiation Site*
DNA-Directed RNA Polymerases/*metabolism
Sequence Analysis, DNA/*methods
A549 Cells ; HCT116 Cells ; Humans ; MCF-7 Cells ; Neural Networks, Computer ; Nucleotide Motifs ; Protein Binding ; Transcription Factors/metabolism
Czasopismo naukowe
Tytuł :
Structural basis for transcriptional start site control of HIV-1 RNA fate.
Autorzy :
Brown JD; Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Kharytonchyk S; Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109-5620, USA.
Chaudry I; Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Iyer AS; Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Carter H; Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Becker G; Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Desai Y; Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Glang L; Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Choi SH; Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Singh K; Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Lopresti MW; Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Orellana M; Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Rodriguez T; Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Oboh U; Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Hijji J; Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Ghinger FG; Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Stewart K; Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Francis D; Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Edwards B; Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Chen P; Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
Case DA; Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854-8087, USA.
Telesnitsky A; Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109-5620, USA. .
Summers MF; Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA. .
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Źródło :
Science (New York, N.Y.) [Science] 2020 Apr 24; Vol. 368 (6489), pp. 413-417.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
MeSH Terms :
Base Pairing*
Gene Expression Regulation, Viral*
Transcription Initiation Site*
HIV-1/*genetics
RNA Caps/*genetics
RNA, Viral/*genetics
5' Untranslated Regions/genetics ; Base Composition ; Eukaryotic Initiation Factor-4E/metabolism ; Guanosine/chemistry ; Humans ; Nuclear Magnetic Resonance, Biomolecular ; Protein Biosynthesis ; RNA Caps/chemistry ; RNA, Messenger/genetics
Czasopismo naukowe
Tytuł :
Continuous transcription initiation guarantees robust repair of all transcribed genes and regulatory regions.
Autorzy :
Liakos A; Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', 34 Fleming st., 16672, Vari, Athens, Greece.; Department of Biology, School of Science, National & Kapodistrian University of Athens, Athens, Greece.
Konstantopoulos D; Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', 34 Fleming st., 16672, Vari, Athens, Greece.; Department of Biology, University of Crete, 70013, Herakleion, Greece.
Lavigne MD; Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', 34 Fleming st., 16672, Vari, Athens, Greece. .
Fousteri M; Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', 34 Fleming st., 16672, Vari, Athens, Greece. .
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Źródło :
Nature communications [Nat Commun] 2020 Feb 14; Vol. 11 (1), pp. 916. Date of Electronic Publication: 2020 Feb 14.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
DNA Repair*
Transcription Initiation Site*
Transcription, Genetic*
Chromatin/genetics ; Chromatin/metabolism ; DNA Damage ; Gene Expression Regulation ; Humans ; Promoter Regions, Genetic ; RNA/genetics ; RNA/metabolism ; RNA Polymerase II/genetics ; RNA Polymerase II/metabolism ; Regulatory Sequences, Nucleic Acid
Czasopismo naukowe
Tytuł :
Humanizing the yeast origin recognition complex.
Autorzy :
Lee CSK; School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong.
Cheung MF; Center for Epigenomics Research, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong.; Division of Life Science, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong.
Li J; Quantitative and Computational Biology, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, CA, 90089, USA.
Zhao Y; Division of Life Science, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong.; Institute for Advanced Study, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong.
Lam WH; School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong.
Ho V; Center for Epigenomics Research, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong.; Division of Life Science, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong.
Rohs R; Quantitative and Computational Biology, Departments of Biological Sciences, Chemistry, Physics & Astronomy, and Computer Science, University of Southern California, Los Angeles, CA, 90089, USA.
Zhai Y; School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong. .
Leung D; Center for Epigenomics Research, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong. .; Division of Life Science, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong. .
Tye BK; Division of Life Science, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong. .; Institute for Advanced Study, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong. .; Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, 14853, USA. .
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Źródło :
Nature communications [Nat Commun] 2021 Jan 04; Vol. 12 (1), pp. 33. Date of Electronic Publication: 2021 Jan 04.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
MeSH Terms :
Origin Recognition Complex/*metabolism
Saccharomyces cerevisiae/*metabolism
Amino Acid Sequence ; Base Sequence ; Binding Sites ; DNA, Fungal/metabolism ; G2 Phase/genetics ; Genome, Fungal ; Humans ; Models, Genetic ; Mutation/genetics ; Nucleosomes/metabolism ; Nucleotide Motifs/genetics ; Origin Recognition Complex/chemistry ; S Phase ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Stochastic Processes ; Transcription Initiation Site
Czasopismo naukowe
Tytuł :
Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing.
Autorzy :
Nepal C; Biotech Research and Innovation Centre, Department of Health and Medical Sciences, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen, Denmark. .
Hadzhiev Y; Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
Balwierz P; Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.; Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, W12 0NN, London, UK.; MRC Clinical Sciences Centre, Hammersmith Hospital Campus, W12 0NN, London, UK.
Tarifeño-Saldivia E; Laboratory for Molecular Biology and Genetic Engineering, GIGA-R, Université de Liège, Liège, Belgium.; Department of Biochemistry and Molecular Biology, Faculty of Biological Sciences, University of Concepcion, Concepción, Chile.
Cardenas R; Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
Wragg JW; Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
Suzuki AM; Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
Carninci P; Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.; Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
Peers B; Laboratory for Molecular Biology and Genetic Engineering, GIGA-R, Université de Liège, Liège, Belgium.
Lenhard B; Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, W12 0NN, London, UK.; MRC Clinical Sciences Centre, Hammersmith Hospital Campus, W12 0NN, London, UK.
Andersen JB; Biotech Research and Innovation Centre, Department of Health and Medical Sciences, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen, Denmark.
Müller F; Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK. .
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Źródło :
Nature communications [Nat Commun] 2020 Jan 10; Vol. 11 (1), pp. 168. Date of Electronic Publication: 2020 Jan 10.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Gene Expression Regulation, Developmental*
Gene Regulatory Networks*
Transcription Initiation Site*
Transcription, Genetic*
Promoter Regions, Genetic/*genetics
Animals ; Base Sequence ; Drosophila/genetics ; Drosophila/growth & development ; Humans ; RNA/genetics ; RNA/physiology ; RNA, Small Nucleolar/genetics ; RNA, Small Nucleolar/metabolism ; RNA, Small Untranslated/genetics ; RNA, Small Untranslated/physiology ; RNA, Untranslated/genetics ; RNA, Untranslated/physiology ; Regulatory Elements, Transcriptional ; Zebrafish/genetics ; Zebrafish/growth & development ; Zygote
Czasopismo naukowe
Tytuł :
In silico analysis of the promoter region of olfactory receptors in cattle ( Bos indicus ) to understand its gene regulation.
Autorzy :
Samuel B; Department of Applied Biology, School of Applied Natural Sciences, Adama Science and Technology University, Adama, Ethiopia.; Department of Animal Science, Faculty of Agriculture, Salale University, Fitche, Ethiopia.
Dinka H; Department of Applied Biology, School of Applied Natural Sciences, Adama Science and Technology University, Adama, Ethiopia.
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Źródło :
Nucleosides, nucleotides & nucleic acids [Nucleosides Nucleotides Nucleic Acids] 2020; Vol. 39 (6), pp. 853-865. Date of Electronic Publication: 2020 Feb 06.
Typ publikacji :
Journal Article
MeSH Terms :
Computer Simulation*
Transcription Initiation Site*
Gene Expression Regulation/*genetics
Promoter Regions, Genetic/*genetics
Receptors, Odorant/*genetics
Animals ; Base Sequence ; Binding Sites ; Cattle ; CpG Islands/genetics ; Models, Genetic ; Nucleic Acid Conformation ; Nucleotide Motifs ; Protein Binding ; Receptors, Odorant/metabolism ; Regulatory Elements, Transcriptional ; Transcription Factors/metabolism
Czasopismo naukowe
Tytuł :
Changes in transcription start sites of Zap1-regulated genes during zinc deficiency: Implications for HNT1 gene regulation.
Autorzy :
Tatip S; Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand.; Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA.
Taggart J; Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA.
Wang Y; Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA.
MacDiarmid CW; Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA.
Eide DJ; Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA.
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Źródło :
Molecular microbiology [Mol Microbiol] 2020 Jan; Vol. 113 (1), pp. 285-296. Date of Electronic Publication: 2019 Nov 24.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural
MeSH Terms :
Transcription Initiation Site*
Hydrolases/*genetics
RNA, Fungal/*genetics
Saccharomyces cerevisiae/*genetics
Saccharomyces cerevisiae Proteins/*genetics
Transcription Factors/*genetics
Zinc/*deficiency
Gene Expression Regulation, Fungal ; Promoter Regions, Genetic
Czasopismo naukowe
Tytuł :
Determinants of correlated expression of transcription factors and their target genes.
Autorzy :
Zaborowski AB; Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
Walther D; Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
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Źródło :
Nucleic acids research [Nucleic Acids Res] 2020 Nov 18; Vol. 48 (20), pp. 11347-11369.
Typ publikacji :
Journal Article
MeSH Terms :
Arabidopsis/*genetics
Arabidopsis Proteins/*metabolism
Gene Expression Regulation, Plant/*genetics
MicroRNAs/*metabolism
RNA, Messenger/*metabolism
Transcription Factors/*metabolism
Arabidopsis/metabolism ; Arabidopsis Proteins/genetics ; Binding Sites/genetics ; DNA Polymerase II/genetics ; DNA Polymerase II/metabolism ; Databases, Genetic ; Gene Ontology ; Gene Regulatory Networks ; Genome ; Genome-Wide Association Study ; Genomics ; Machine Learning ; MicroRNAs/genetics ; Oligonucleotide Array Sequence Analysis ; Promoter Regions, Genetic ; Protein Binding ; Protein Interaction Maps/genetics ; Protein Processing, Post-Translational ; RNA Processing, Post-Transcriptional ; RNA, Messenger/genetics ; Transcription Factors/genetics ; Transcription Initiation Site
Czasopismo naukowe
Tytuł :
Alignment and quantification of ChIP-exo crosslinking patterns reveal the spatial organization of protein-DNA complexes.
Autorzy :
Yamada N; Center for Eukaryotic Gene Regulation, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
Rossi MJ; Center for Eukaryotic Gene Regulation, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
Farrell N; Center for Eukaryotic Gene Regulation, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
Pugh BF; Center for Eukaryotic Gene Regulation, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
Mahony S; Center for Eukaryotic Gene Regulation, Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
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Źródło :
Nucleic acids research [Nucleic Acids Res] 2020 Nov 18; Vol. 48 (20), pp. 11215-11226.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms :
Chromatin Immunoprecipitation/*methods
DNA-Binding Proteins/*metabolism
Exonucleases/*chemistry
RNA, Transfer/*genetics
Ribosomal Proteins/*genetics
Sequence Alignment/*methods
Transcription Factors/*metabolism
Algorithms ; Animals ; Binding Sites ; Computer Simulation ; DNA-Binding Proteins/chemistry ; Databases, Genetic ; Drosophila/chemistry ; Drosophila/genetics ; Drosophila/metabolism ; Promoter Regions, Genetic ; Protein Binding ; RNA Polymerase II/chemistry ; RNA Polymerase II/genetics ; RNA Polymerase II/metabolism ; RNA Polymerase III/chemistry ; RNA Polymerase III/genetics ; RNA Polymerase III/metabolism ; RNA, Transfer/chemistry ; RNA, Transfer/metabolism ; Ribosomal Proteins/chemistry ; Ribosomal Proteins/metabolism ; Saccharomyces cerevisiae/chemistry ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Sequence Analysis, DNA/methods ; Transcription Factor TFIIIB/chemistry ; Transcription Factor TFIIIB/genetics ; Transcription Factor TFIIIB/metabolism ; Transcription Factors/chemistry ; Transcription Factors/genetics ; Transcription Factors, TFIII/chemistry ; Transcription Factors, TFIII/genetics ; Transcription Factors, TFIII/metabolism ; Transcription Initiation Site
Czasopismo naukowe
Tytuł :
Chromatin accessibility landscapes of skin cells in systemic sclerosis nominate dendritic cells in disease pathogenesis.
Autorzy :
Liu Q; Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China.
Zaba LC; Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.; Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Satpathy AT; Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
Longmire M; Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.; Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Zhang W; Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China.
Li K; Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China.
Granja J; Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.; Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Guo C; Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China.
Lin J; Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China.
Li R; Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.; Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Tolentino K; Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.; Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Kania G; Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland.
Distler O; Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland.
Fiorentino D; Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Chung L; Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA.; Division of Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.
Qu K; Department of Oncology, The First Affiliated Hospital of USTC, Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230021, China. .; CAS Center for Excellence in Molecular Cell Sciences, University of Science and Technology of China, Hefei, 230027, China. .; School of Data Sciences, University of Science and Technology of China, Hefei, 230027, China. .
Chang HY; Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA. .; Department of Dermatology, Stanford University School of Medicine, Stanford, CA, 94305, USA. .
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Źródło :
Nature communications [Nat Commun] 2020 Nov 17; Vol. 11 (1), pp. 5843. Date of Electronic Publication: 2020 Nov 17.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
MeSH Terms :
Chromatin/*metabolism
Langerhans Cells/*pathology
Scleroderma, Systemic/*pathology
Skin/*pathology
Case-Control Studies ; Cell Communication ; Chromatin/genetics ; Epigenome ; Fibrosis ; Genetic Predisposition to Disease ; Humans ; Polymorphism, Single Nucleotide ; Regulatory Sequences, Nucleic Acid ; Skin/cytology ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Transcription Initiation Site
Czasopismo naukowe
Tytuł :
Coexistence of two quadruplex-duplex hybrids in the PIM1 gene.
Autorzy :
Tan DJY; School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
Winnerdy FR; School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
Lim KW; School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
Phan AT; School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.; NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore.
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Źródło :
Nucleic acids research [Nucleic Acids Res] 2020 Nov 04; Vol. 48 (19), pp. 11162-11171.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
G-Quadruplexes*
DNA/*chemistry
Proto-Oncogene Proteins c-pim-1/*genetics
Humans ; Transcription Initiation Site ; Triple Negative Breast Neoplasms/genetics
Czasopismo naukowe

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