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Tytuł:
Structures of +1 nucleosome-bound PIC-Mediator complex.
Autorzy:
Chen X; Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.
Wang X; Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.
Liu W; Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.
Ren Y; Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.
Qu X; Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.
Li J; Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.
Yin X; Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.
Xu Y; Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.; The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China.; Human Phenome Institute, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China.
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Źródło:
Science (New York, N.Y.) [Science] 2022 Oct 07; Vol. 378 (6615), pp. 62-68. Date of Electronic Publication: 2022 Oct 06.
Typ publikacji:
Journal Article
MeSH Terms:
Mediator Complex*/chemistry
Nucleosomes*/chemistry
Transcription Initiation, Genetic*
Chromatin/chemistry ; Humans ; RNA Polymerase II/chemistry ; Transcription Initiation Site
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Structural visualization of transcription initiation in action.
Autorzy:
Chen X; Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.; The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China.
Liu W; Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.
Wang Q; Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.
Wang X; Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.
Ren Y; Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.
Qu X; Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.
Li W; Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.
Xu Y; Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.; The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China.
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Źródło:
Science (New York, N.Y.) [Science] 2023 Dec 22; Vol. 382 (6677), pp. eadi5120. Date of Electronic Publication: 2023 Dec 22.
Typ publikacji:
Journal Article
MeSH Terms:
RNA*/biosynthesis
Transcription Factors, General*/metabolism
Transcription Initiation, Genetic*
DNA-Directed RNA Polymerases/chemistry ; RNA Polymerase II/chemistry ; Humans ; Animals ; Sus scrofa ; Cryoelectron Microscopy ; Motion Pictures
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Differences in transcription initiation directionality underlie distinctions between plants and animals in chromatin modification patterns at genes and cis-regulatory elements.
Autorzy:
Silver BD; Department of Biology, Emory University, Atlanta, GA 30322, USA.; Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, GA 30322, USA.
Willett CG; Department of Biology, Emory University, Atlanta, GA 30322, USA.; Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, GA 30322, USA.
Maher KA; Department of Biology, Emory University, Atlanta, GA 30322, USA.; Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University, Atlanta, GA 30322, USA.; Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
Wang D; Department of Biology, Emory University, Atlanta, GA 30322, USA.; School of Medicine, Emory University, Atlanta, GA 30322, USA.
Deal RB; Department of Biology, Emory University, Atlanta, GA 30322, USA.
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Źródło:
G3 (Bethesda, Md.) [G3 (Bethesda)] 2024 Mar 06; Vol. 14 (3).
Typ publikacji:
Journal Article
MeSH Terms:
Chromatin*/genetics
Arabidopsis*/genetics
Arabidopsis*/metabolism
Animals ; RNA Polymerase II/genetics ; RNA Polymerase II/metabolism ; Transcription, Genetic ; Drosophila melanogaster/genetics ; Drosophila melanogaster/metabolism ; Transcription Initiation Site ; Plants/genetics
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Genome-wide RNA pol II initiation and pausing in neural progenitors of the rat.
Autorzy:
Scheidegger A; Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA.; Present address: Omega Therapeutics, Cambridge, MA, 02139, USA.
Dunn CJ; Molecular and Cell Biology Department, School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA.
Samarakkody A; Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA.; Present address: Department of Pediatric Hematology-Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA.
Koney NK; Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA.
Perley D; Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA.
Saha RN; Molecular and Cell Biology Department, School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA.
Nechaev S; Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA. .
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Źródło:
BMC genomics [BMC Genomics] 2019 Jun 11; Vol. 20 (1), pp. 477. Date of Electronic Publication: 2019 Jun 11.
Typ publikacji:
Journal Article
MeSH Terms:
Genomics*
Transcription Initiation, Genetic*
Neural Stem Cells/*metabolism
RNA Polymerase II/*metabolism
Animals ; Female ; Pregnancy ; RNA, Antisense/genetics ; Rats ; Rats, Sprague-Dawley ; Sequence Analysis, RNA ; Transcription Initiation Site
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Physical Peculiarity of Two Sites in Human Promoters: Universality and Diverse Usage in Gene Function.
Autorzy:
Uemura K; Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
Ohyama T; Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.; Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
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Źródło:
International journal of molecular sciences [Int J Mol Sci] 2024 Jan 25; Vol. 25 (3). Date of Electronic Publication: 2024 Jan 25.
Typ publikacji:
Journal Article
MeSH Terms:
DNA*
Humans ; Promoter Regions, Genetic ; TATA Box/genetics ; Transcription Initiation Site
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation.
Autorzy:
Nikumbh S; Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London, United Kingdom.; Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom.
Lenhard B; Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London, United Kingdom.; Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom.
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Źródło:
PLoS computational biology [PLoS Comput Biol] 2023 Nov 20; Vol. 19 (11), pp. e1011491. Date of Electronic Publication: 2023 Nov 20 (Print Publication: 2023).
Typ publikacji:
Journal Article
MeSH Terms:
Algorithms*
Software*
Promoter Regions, Genetic/genetics ; Transcription Initiation Site ; Nucleosomes
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Ribosomal DNA promoter recognition is determined in vivo by cooperation between UBTF1 and SL1 and is compromised in the UBTF-E210K neuroregression syndrome.
Autorzy:
Tremblay MG; Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Québec, Canada.
Sibai DS; Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Québec, Canada.; Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Québec, Canada.
Valère M; Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Québec, Canada.; Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Québec, Canada.
Mars JC; Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Québec, Canada.; Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Québec, Canada.
Lessard F; Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Québec, Canada.
Hori RT; Departments of Microbiology, Immunology and Biochemistry.
Khan MM; Departments of Neurology and Anatomy & Neurobiology, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America.
Stefanovsky VY; Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Québec, Canada.
LeDoux MS; Department of Psychology, University of Memphis, Memphis TN and Veracity Neuroscience LLC, Memphis, Tennessee, United States of America.
Moss T; Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Québec, Canada.; Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Québec, Canada.
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Źródło:
PLoS genetics [PLoS Genet] 2022 Feb 09; Vol. 18 (2), pp. e1009644. Date of Electronic Publication: 2022 Feb 09 (Print Publication: 2022).
Typ publikacji:
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
MeSH Terms:
Pol1 Transcription Initiation Complex Proteins*/genetics
Pol1 Transcription Initiation Complex Proteins*/metabolism
RNA Polymerase I*/genetics
Animals ; Child ; DNA, Ribosomal/genetics ; DNA, Ribosomal/metabolism ; Humans ; Mice ; Nucleosomes ; Promoter Regions, Genetic ; RNA, Ribosomal/genetics ; Transcription, Genetic
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Non-canonical transcriptional start sites in E. coli O157:H7 EDL933 are regulated and appear in surprisingly high numbers.
Autorzy:
Zehentner B; Chair for Microbial Ecology, TUM School of Life Sciences, Department of Molecular Life Sciences, Technical University of Munich, Freising, Germany.
Scherer S; Chair for Microbial Ecology, TUM School of Life Sciences, Department of Molecular Life Sciences, Technical University of Munich, Freising, Germany.; ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany.
Neuhaus K; ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany. .; Core Facility Microbiome, ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany. .
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Źródło:
BMC microbiology [BMC Microbiol] 2023 Aug 31; Vol. 23 (1), pp. 243. Date of Electronic Publication: 2023 Aug 31.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Escherichia coli O157*/genetics
Enterohemorrhagic Escherichia coli*
Transcription Initiation Site ; Cell Cycle ; Culture Media
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Genome-Wide Prediction of Transcription Start Sites in Conifers.
Autorzy:
Bondar EI; Laboratory of Forest Genomics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036 Krasnoyarsk, Russia.; Laboratory of Genomic Research and Biotechnology, Federal Research Center 'Krasnoyarsk Science Center' Siberian Branch, Russian Academy of Sciences, 660036 Krasnoyarsk, Russia.
Troukhan ME; Persephone Software LLC, Agoura Hills, CA 91301, USA.
Krutovsky KV; Laboratory of Forest Genomics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660036 Krasnoyarsk, Russia.; Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, 37077 Göttingen, Germany.; Center for Integrated Breeding Research, Georg-August University of Göttingen, 37075 Göttingen, Germany.; Laboratory of Population Genetics, N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia.; Scientific and Methodological Center, G. F. Morozov Voronezh State University of Forestry and Technologies, 394087 Voronezh, Russia.; Department of Genomics and Bioinformatics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660074 Krasnoyarsk, Russia.
Tatarinova TV; Department of Genomics and Bioinformatics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, 660074 Krasnoyarsk, Russia.; Department of Biology, University of La Verne, La Verne, CA 91750, USA.; Functional Genomics Group, N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia.; A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 127051 Moscow, Russia.
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Źródło:
International journal of molecular sciences [Int J Mol Sci] 2022 Feb 03; Vol. 23 (3). Date of Electronic Publication: 2022 Feb 03.
Typ publikacji:
Journal Article
MeSH Terms:
Genome, Plant*
Transcription Initiation Site*
Tracheophyta/*genetics
Base Composition/genetics ; Binding Sites ; DNA, Plant/genetics ; Exons/genetics ; Molecular Sequence Annotation ; Nucleotide Motifs/genetics ; Nucleotides/metabolism ; Open Reading Frames/genetics ; Promoter Regions, Genetic ; Transcription Factors/metabolism
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Integrative transcription start site analysis and physiological phenotyping reveal torpor-specific expression program in mouse skeletal muscle.
Autorzy:
Deviatiiarov R; Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Volkova str.18, Kazan, Tatarstan, 420012, Russian Federation.; Endocrinology Research Center, Dmitriya Ul'yanova str. 11, 115478, Moscow, Russian Federation.
Ishikawa K; Laboratory for Retinal Regeneration, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
Gazizova G; Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Volkova str.18, Kazan, Tatarstan, 420012, Russian Federation.
Abe T; Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
Kiyonari H; Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
Takahashi M; Laboratory for Retinal Regeneration, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
Gusev O; Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Volkova str.18, Kazan, Tatarstan, 420012, Russian Federation. .; Endocrinology Research Center, Dmitriya Ul'yanova str. 11, 115478, Moscow, Russian Federation. .; Department of Regulatory Transcriptomics for Medical Genetic Diagnostics, Graduate School of Medicine, Juntendo University, Tokyo, 113-8421, Japan. .; RIKEN Center for Integrative Medical Sciences, RIKEN, 351-0198, Yokohama, Japan. .
Sunagawa GA; Laboratory for Retinal Regeneration, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojimaminami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan. .
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Źródło:
Communications biology [Commun Biol] 2021 Nov 15; Vol. 4 (1), pp. 1290. Date of Electronic Publication: 2021 Nov 15.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Phenotype*
Transcription Initiation Site*
Gene Expression/*physiology
Muscle, Skeletal/*metabolism
Torpor/*genetics
Animals ; Female ; Male ; Mice ; Oxygen Consumption ; RNA/metabolism ; Torpor/physiology
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
TSSFinder-fast and accurate ab initio prediction of the core promoter in eukaryotic genomes.
Autorzy:
de Medeiros Oliveira M; Instituto Carlos Chagas, Fundação Oswaldo Cruz, Paraná, Brazil.
Bonadio I; Data Science, Elo7 Research Lab, São Paulo, Brazil.
Lie de Melo A; Biochemistry Department, Universidade de São Paulo, São Paulo, Brazil.
Mendes Souza G; Biochemistry Department, Universidade de São Paulo, São Paulo, Brazil.
Durham AM; Computer Science, Universidade de São Paulo, São Paulo, Brazil.
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Źródło:
Briefings in bioinformatics [Brief Bioinform] 2021 Nov 05; Vol. 22 (6).
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Genome*
Promoter Regions, Genetic*
Software*
Transcription Initiation Site*
Computational Biology/*methods
Eukaryota/*genetics
Genomics/*methods
Algorithms ; Databases, Genetic ; Reproducibility of Results ; Sequence Analysis, DNA ; Web Browser
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Precisely Monomeric Linear RNAs of Viroids Belonging to Pospiviroid and Hostuviroid Genera Are Infectious Regardless of Transcription Initiation Site and 5'-Terminal Structure.
Autorzy:
Hataya T; Pathogen-Plant Interactions, Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan.; Pathogen-Plant Interactions, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan.
Naoi T; Pathogen-Plant Interactions, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan.
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Źródło:
Cells [Cells] 2021 Nov 01; Vol. 10 (11). Date of Electronic Publication: 2021 Nov 01.
Typ publikacji:
Journal Article
MeSH Terms:
Transcription Initiation Site*
RNA, Viral/*genetics
Viroids/*genetics
Viroids/*pathogenicity
Base Sequence ; Cucumis sativus/virology ; DNA, Complementary/genetics ; Solanum lycopersicum/virology ; Plant Diseases/virology ; RNA Processing, Post-Transcriptional/genetics ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; RNA, Viral/isolation & purification ; Time Factors
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Transcription initiation of distant core promoters in a large-sized genome of an insect.
Autorzy:
Liu Q; Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.; Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China.; Department of Biology, University of Copenhagen, Copenhagen, Denmark.
Jiang F; Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China.
Zhang J; Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.
Li X; State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
Kang L; Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China. .; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China. .; State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China. .
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Źródło:
BMC biology [BMC Biol] 2021 Mar 30; Vol. 19 (1), pp. 62. Date of Electronic Publication: 2021 Mar 30.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Genome, Insect*
Promoter Regions, Genetic*
Transcription Initiation Site*
Transcription Initiation, Genetic*
Locusta migratoria/*genetics
Animals ; Genome Size
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation.
Autorzy:
Umarov R; Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.
Li Y; Department of Computer Science and Engineering (CSE), The Chinese University of Hong Kong (CUHK), Hong Kong, People's Republic of China.
Arakawa T; Laboratory for Applied Regulatory Genomics Network Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan.
Takizawa S; Laboratory for Applied Regulatory Genomics Network Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan.
Gao X; King Abdullah University of Science and Technology, Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, Thuwal, Saudi Arabia.
Arner E; Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.; Laboratory for Applied Regulatory Genomics Network Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan.
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Źródło:
PLoS computational biology [PLoS Comput Biol] 2021 Sep 07; Vol. 17 (9), pp. e1009376. Date of Electronic Publication: 2021 Sep 07 (Print Publication: 2021).
Typ publikacji:
Journal Article
MeSH Terms:
Deep Learning*
Models, Genetic*
Regulatory Sequences, Nucleic Acid*
Transcription Initiation, Genetic*
Computational Biology ; Enhancer Elements, Genetic ; Gene Expression Regulation ; Genes, Reporter ; Genome, Human ; Genome-Wide Association Study/statistics & numerical data ; Humans ; Molecular Sequence Annotation ; Mutation ; Promoter Regions, Genetic
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Explainability in transformer models for functional genomics.
Autorzy:
Clauwaert J; Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links 653, 9000 Gent, Belgium.
Menschaert G; Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links 653, 9000 Gent, Belgium.
Waegeman W; Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links 653, 9000 Gent, Belgium.
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Źródło:
Briefings in bioinformatics [Brief Bioinform] 2021 Sep 02; Vol. 22 (5).
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Deep Learning*
Genome, Bacterial*
Transcription Initiation Site*
Escherichia coli/*genetics
Genomics/*methods
Base Sequence ; Binding Sites ; DNA, Bacterial/genetics ; DNA, Bacterial/metabolism ; Escherichia coli/metabolism ; Promoter Regions, Genetic/genetics ; Transcription Factors/genetics ; Transcription Factors/metabolism
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Multi-landmark alignment of genomic signals reveals conserved expression patterns across transcription start sites.
Autorzy:
Vilar JMG; Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country (UPV/EHU), P.O. Box 644, 48080, Bilbao, Spain. .; IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Spain. .
Saiz L; Department of Biomedical Engineering, University of California, 451 E. Health Sciences Drive, Davis, CA, 95616, USA. .
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Źródło:
Scientific reports [Sci Rep] 2023 Jul 05; Vol. 13 (1), pp. 10835. Date of Electronic Publication: 2023 Jul 05.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Genomics*/methods
DNA*
Humans ; Transcription Initiation Site ; Promoter Regions, Genetic
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Global Analysis of Transcription Start Sites and Enhancers in Endometrial Stromal Cells and Differences Associated with Endometriosis.
Autorzy:
Marla S; The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
Mortlock S; The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
Yoon S; The Genome Innovation Hub, The University of Queensland, Brisbane, QLD 4072, Australia.
Crawford J; The Genome Innovation Hub, The University of Queensland, Brisbane, QLD 4072, Australia.
Andersen S; The Genome Innovation Hub, The University of Queensland, Brisbane, QLD 4072, Australia.
Mueller MD; Department of Gynecology and Gynecological Oncology, Inselspital, Bern University Hospital, University of Bern, 3010 Berne, Switzerland.
McKinnon B; The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.; Department of Gynecology and Gynecological Oncology, Inselspital, Bern University Hospital, University of Bern, 3010 Berne, Switzerland.
Nguyen Q; The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
Montgomery GW; The Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.; The Genome Innovation Hub, The University of Queensland, Brisbane, QLD 4072, Australia.
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Źródło:
Cells [Cells] 2023 Jun 28; Vol. 12 (13). Date of Electronic Publication: 2023 Jun 28.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Genome-Wide Association Study*
Endometriosis*/genetics
Humans ; Female ; Transcription Initiation Site ; Promoter Regions, Genetic/genetics ; Gene Expression Regulation
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
The MMP-2 histone H3 N-terminal tail protease is selectively targeted to the transcription start sites of active genes.
Autorzy:
Weekley BH; Department of Biochemistry and Molecular Medicine, University of Southern California Keck School of Medicine, 1450 Biggy Street, HNRT 6506, Los Angeles, CA, 90033, USA.
Rice JC; Department of Biochemistry and Molecular Medicine, University of Southern California Keck School of Medicine, 1450 Biggy Street, HNRT 6506, Los Angeles, CA, 90033, USA. .
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Źródło:
Epigenetics & chromatin [Epigenetics Chromatin] 2023 May 10; Vol. 16 (1), pp. 16. Date of Electronic Publication: 2023 May 10.
Typ publikacji:
Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
MeSH Terms:
Peptide Hydrolases*
Matrix Metalloproteinase 2*/genetics
Humans ; Histones ; Transcription Initiation Site ; Chromatin
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Evolution of tissue and developmental specificity of transcription start sites in Bos taurus indicus.
Autorzy:
Forutan M; Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia. .
Ross E; Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia.
Chamberlain AJ; Agriculture Victoria, Centre for AgriBiosciences, Bundoora, VIC, Australia.
Nguyen L; Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia.
Mason B; Agriculture Victoria, Centre for AgriBiosciences, Bundoora, VIC, Australia.
Moore S; Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia.
Garner JB; Agriculture Victoria, Animal Production Sciences, Ellinbank Dairy Centre, Ellinbank, VIC, Australia.
Xiang R; Faculty of Veterinary & Agricultural Science, The University of Melbourne, Parkville, VIC, Australia.
Hayes BJ; Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia.
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Źródło:
Communications biology [Commun Biol] 2021 Jul 01; Vol. 4 (1), pp. 829. Date of Electronic Publication: 2021 Jul 01.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Polymorphism, Single Nucleotide*
Transcription Initiation Site*
Cattle/*genetics
Genetic Variation/*genetics
Transcription, Genetic/*genetics
Animals ; Cattle/classification ; Evolution, Molecular ; Gene Expression ; Gene Frequency ; Genetic Speciation ; Heat-Shock Proteins/genetics ; Liver/metabolism ; Muscles/metabolism ; Organ Specificity/genetics ; Species Specificity ; Spleen/metabolism
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Structures of the human Mediator and Mediator-bound preinitiation complex.
Autorzy:
Chen X; Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.
Yin X; Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.
Li J; Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.
Wu Z; Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.
Qi Y; Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.
Wang X; Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.
Liu W; Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.
Xu Y; Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China. .; International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China.; Human Phenome Institute, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China.
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Źródło:
Science (New York, N.Y.) [Science] 2021 Jun 04; Vol. 372 (6546). Date of Electronic Publication: 2021 May 06.
Typ publikacji:
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:
Transcription Initiation, Genetic*
Mediator Complex/*chemistry
RNA Polymerase II/*chemistry
Transcription Factor TFIID/*chemistry
Cryoelectron Microscopy ; Cyclin-Dependent Kinases/chemistry ; Cyclin-Dependent Kinases/metabolism ; DNA Helicases/chemistry ; DNA-Binding Proteins/chemistry ; Humans ; Mediator Complex/metabolism ; Mediator Complex Subunit 1/chemistry ; Models, Molecular ; Phosphorylation ; Promoter Regions, Genetic ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Domains ; Protein Folding ; Protein Structure, Quaternary ; Protein Subunits/chemistry ; RNA Polymerase II/metabolism ; Transcription Factor TFIID/metabolism ; Transcription Factor TFIIH/chemistry ; Transcription Factor TFIIH/metabolism ; Cyclin-Dependent Kinase-Activating Kinase
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknieSzczegóły
Wyświetlanie 1-20 z 3047

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