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Tytuł :
Long reads capture simultaneous enhancer-promoter methylation status for cell-type deconvolution.
Autorzy :
Margalit S; Department of Physical Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel.; Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel.
Abramson Y; Department of Physical Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel.; Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel.
Sharim H; Department of Physical Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel.; Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel.
Manber Z; Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel.; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel.
Bhattacharya S; Center for Genetic Medicine Research, Children's National Hospital, Washington, DC 20010, USA.
Chen YW; Center for Genetic Medicine Research, Children's National Hospital, Washington, DC 20010, USA.; Department of Genomics and Precision Medicine, George Washington University, Washington, DC 20052, USA.
Vilain E; Center for Genetic Medicine Research, Children's National Hospital, Washington, DC 20010, USA.; Department of Genomics and Precision Medicine, George Washington University, Washington, DC 20052, USA.
Barseghyan H; Center for Genetic Medicine Research, Children's National Hospital, Washington, DC 20010, USA.; Department of Genomics and Precision Medicine, George Washington University, Washington, DC 20052, USA.
Elkon R; Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel.; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel.
Sharan R; Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel.; School of Computer Science, Tel-Aviv University, Tel-Aviv 6997801, Israel.
Ebenstein Y; Department of Physical Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel.; Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel.
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Źródło :
Bioinformatics (Oxford, England) [Bioinformatics] 2021 Jul 12; Vol. 37 (Suppl_1), pp. i327-i333.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
DNA Methylation*
Genome-Wide Association Study*
Promoter Regions, Genetic*
Regulatory Sequences, Nucleic Acid*
Cell Line ; Enhancer Elements, Genetic ; Genomics ; Humans
Czasopismo naukowe
Tytuł :
PlantDeepSEA, a deep learning-based web service to predict the regulatory effects of genomic variants in plants.
Autorzy :
Zhao H; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
Tu Z; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
Liu Y; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
Zong Z; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
Li J; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
Liu H; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
Xiong F; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
Zhan J; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.
Hu X; Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China.
Xie W; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.; Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China.
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Źródło :
Nucleic acids research [Nucleic Acids Res] 2021 Jul 02; Vol. 49 (W1), pp. W523-W529.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Genetic Variation*
Genome, Plant*
Regulatory Sequences, Nucleic Acid*
Software*
Chromatin ; Deep Learning ; Genes, Plant ; Genomics ; Internet ; Oryza/genetics ; Plants/genetics ; Polymorphism, Genetic ; Quantitative Trait Loci ; Zea mays/genetics
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 :
Genetic and epigenetic features of promoters with ubiquitous chromatin accessibility support ubiquitous transcription of cell-essential genes.
Autorzy :
Fan K; Program in Bioinformatics and Integrative Biology, UMass Medical School, Worcester, MA, USA.
Moore JE; Program in Bioinformatics and Integrative Biology, UMass Medical School, Worcester, MA, USA.
Zhang XO; Program in Bioinformatics and Integrative Biology, UMass Medical School, Worcester, MA, USA.
Weng Z; Program in Bioinformatics and Integrative Biology, UMass Medical School, Worcester, MA, USA.
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Źródło :
Nucleic acids research [Nucleic Acids Res] 2021 Jun 04; Vol. 49 (10), pp. 5705-5725.
Typ publikacji :
Journal Article; Research Support, N.I.H., Extramural
MeSH Terms :
Epigenesis, Genetic*
Regulatory Sequences, Nucleic Acid*
Chromatin/*metabolism
Gene Expression Regulation/*genetics
Transcription Factors/*metabolism
Transcriptome/*genetics
Amino Acid Motifs ; Animals ; Base Composition ; Chromatin/genetics ; DNA Methylation ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Databases, Genetic ; Epigenomics ; Gene Ontology ; Genes, Essential ; Genome Components ; Genome, Human ; Humans ; Mice ; Neoplasm Proteins/genetics ; Neoplasm Proteins/metabolism ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; Organ Specificity/genetics ; Promoter Regions, Genetic ; Repressor Proteins/genetics ; Repressor Proteins/metabolism ; TATA Box ; Transcription Factors/genetics
Czasopismo naukowe
Tytuł :
Current Practice in Bicistronic IRES Reporter Use: A Systematic Review.
Autorzy :
van den Akker GGH; Department of Orthopedic Surgery, Maastricht University, Medical Center+, 6229 ER Maastricht, The Netherlands.
Zacchini F; Department of Experimental, Diagnostic and Specialty Medicine, Bologna University, I-40138 Bologna, Italy.; Centro di Ricerca Biomedica Applicata-CRBA, Bologna University, Policlinico di Sant'Orsola, I-40138 Bologna, Italy.
Housmans BAC; Department of Orthopedic Surgery, Maastricht University, Medical Center+, 6229 ER Maastricht, The Netherlands.
van der Vloet L; Department of Orthopedic Surgery, Maastricht University, Medical Center+, 6229 ER Maastricht, The Netherlands.
Caron MMJ; Department of Orthopedic Surgery, Maastricht University, Medical Center+, 6229 ER Maastricht, The Netherlands.
Montanaro L; Department of Experimental, Diagnostic and Specialty Medicine, Bologna University, I-40138 Bologna, Italy.; Centro di Ricerca Biomedica Applicata-CRBA, Bologna University, Policlinico di Sant'Orsola, I-40138 Bologna, Italy.; Programma Dipartimentale in Medicina di Laboratorio, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Via Albertoni 15, I-40138 Bologna, Italy.
Welting TJM; Department of Orthopedic Surgery, Maastricht University, Medical Center+, 6229 ER Maastricht, The Netherlands.
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Źródło :
International journal of molecular sciences [Int J Mol Sci] 2021 May 14; Vol. 22 (10). Date of Electronic Publication: 2021 May 14.
Typ publikacji :
Journal Article; Systematic Review
MeSH Terms :
Genes, Reporter*
Internal Ribosome Entry Sites*
Protein Biosynthesis*
Regulatory Sequences, Nucleic Acid*
Ribosomes/*metabolism
Animals ; Humans ; Ribosomes/genetics
Czasopismo naukowe
Tytuł :
G-quadruplex motifs are functionally conserved in cis-regulatory regions of pathogenic bacteria: An in-silico evaluation.
Autorzy :
Dey U; Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, 784028, Assam, India.
Sarkar S; Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, 784028, Assam, India.
Teronpi V; Department of Zoology, Pandit Deendayal Upadhyaya Adarsha Mahavidyalaya, Behali, Biswanath, 784184, Assam, India.
Yella VR; Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Guntur, 522502, Andhra Pradesh, India. Electronic address: .
Kumar A; Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, 784028, Assam, India. Electronic address: .
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Źródło :
Biochimie [Biochimie] 2021 May; Vol. 184, pp. 40-51. Date of Electronic Publication: 2021 Feb 04.
Typ publikacji :
Evaluation Study; Journal Article
MeSH Terms :
Computer Simulation*
G-Quadruplexes*
Genome, Bacterial*
Regulatory Sequences, Nucleic Acid*
Bacteria/*genetics
Bacteria/pathogenicity
Czasopismo naukowe
Tytuł :
A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome.
Autorzy :
Zhao Y; Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.
Hou Y; Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.
Xu Y; Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.
Luan Y; Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.
Zhou H; Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.
Qi X; Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.
Hu M; Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.
Wang D; Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.
Wang Z; Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.
Fu Y; Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.
Li J; Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.
Zhang S; Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.
Chen J; Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.
Han J; CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.; International Livestock Research Institute (ILRI), Nairobi, Kenya.
Li X; Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China. .; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China. .
Zhao S; Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China. .; The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China. .
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Źródło :
Nature communications [Nat Commun] 2021 Apr 13; Vol. 12 (1), pp. 2217. Date of Electronic Publication: 2021 Apr 13.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Epigenomics*
Regulatory Sequences, Nucleic Acid*
Swine/*genetics
Animals ; Chromatin Immunoprecipitation Sequencing ; Epigenesis, Genetic ; Gene Expression ; Genome ; Genome, Human ; HEK293 Cells ; Humans ; Mice ; RNA-Seq ; Receptors, G-Protein-Coupled/metabolism ; Transcriptome
Czasopismo naukowe
Tytuł :
Characterizing Transcriptional Regulatory Sequences in Coronaviruses and Their Role in Recombination.
Autorzy :
Yang Y; National Library of Medicine, National Institutes of Health, Bethesda, MD.
Yan W; National Library of Medicine, National Institutes of Health, Bethesda, MD.
Hall AB; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD.; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD.
Jiang X; National Library of Medicine, National Institutes of Health, Bethesda, MD.
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Źródło :
Molecular biology and evolution [Mol Biol Evol] 2021 Apr 13; Vol. 38 (4), pp. 1241-1248.
Typ publikacji :
Journal Article; Research Support, N.I.H., Intramural; Research Support, Non-U.S. Gov't
MeSH Terms :
Genome, Viral*
Recombination, Genetic*
Regulatory Sequences, Nucleic Acid*
Coronavirus/*genetics
RNA, Viral/*genetics
SARS-CoV-2/*genetics
Models, Genetic ; Nucleic Acid Conformation ; Phylogeny ; RNA, Messenger/genetics ; RNA-Seq ; Transcription, Genetic
Czasopismo naukowe
Tytuł :
Dissecting cis-regulatory control of quantitative trait variation in a plant stem cell circuit.
Autorzy :
Wang X; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Aguirre L; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.; School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Rodríguez-Leal D; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.; Inari Agriculture, Cambridge, MA, USA.
Hendelman A; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Benoit M; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
Lippman ZB; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. .; School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. .; Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. .
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Źródło :
Nature plants [Nat Plants] 2021 Apr; Vol. 7 (4), pp. 419-427. Date of Electronic Publication: 2021 Apr 12.
Typ publikacji :
Journal Article
MeSH Terms :
Phenotype*
Quantitative Trait Loci*
Regulatory Sequences, Nucleic Acid*
Lycopersicon esculentum/*genetics
Plant Cells/*physiology
Promoter Regions, Genetic/*genetics
Stem Cells/*physiology
Alleles ; Domestication
Czasopismo naukowe
Tytuł :
Characterization of Regulatory Elements of L11 and L1 Operons in Thermophilic Bacteria and Archaea.
Autorzy :
Mikhaylina AO; Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia. .
Nikonova EY; Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
Kostareva OS; Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
Piendl W; Division of Medical Biochemistry, Biocenter, Medical University of Innsbruck, Innsbruck, 6020, Austria. .
Erlacher M; Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, Innsbruck, 6020, Austria. .
Tishchenko SV; Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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Źródło :
Biochemistry. Biokhimiia [Biochemistry (Mosc)] 2021 Apr; Vol. 86 (4), pp. 397-408.
Typ publikacji :
Journal Article
MeSH Terms :
Regulatory Sequences, Nucleic Acid*
Haloarcula marismortui/*genetics
Operon/*genetics
Ribosomal Proteins/*genetics
Thermotoga maritima/*genetics
Thermus thermophilus/*genetics
Gene Expression Regulation, Archaeal ; Gene Expression Regulation, Bacterial ; Haloarcula marismortui/metabolism ; Hot Temperature ; Thermotoga maritima/metabolism ; Thermus thermophilus/metabolism
Czasopismo naukowe
Tytuł :
Defining the functionally sufficient regulatory region and liver-specific roles of the erythropoietin gene by transgene complementation.
Autorzy :
Yamazaki S; Division of Oxygen Biology, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan; Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan.
Hirano I; Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan.
Kato K; Division of Oxygen Biology, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan.
Yamamoto M; Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan.
Suzuki N; Division of Oxygen Biology, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan. Electronic address: .
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Źródło :
Life sciences [Life Sci] 2021 Mar 15; Vol. 269, pp. 119075. Date of Electronic Publication: 2021 Jan 16.
Typ publikacji :
Journal Article
MeSH Terms :
Erythropoiesis*
Regulatory Sequences, Nucleic Acid*
Anemia/*prevention & control
Erythropoietin/*metabolism
Liver/*metabolism
Transgenes/*physiology
Anemia/genetics ; Anemia/pathology ; Animals ; Erythropoietin/genetics ; Mice ; Mice, Knockout ; Mice, Transgenic
Czasopismo naukowe
Tytuł :
Genomic Space of MGMT in Human Glioma Revisited: Novel Motifs, Regulatory RNAs, NRF1, 2, and CTCF Involvement in Gene Expression.
Autorzy :
Ibrahim Al-Obaide MA; Department of Pharmaceutical Sciences, Jerry H. Hodge School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX 79106, USA.
Arutla V; Department of Pharmaceutical Sciences, Jerry H. Hodge School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX 79106, USA.
Bacolod MD; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA.
Wang W; Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX 77204, USA.
Zhang R; Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX 77204, USA.
Srivenugopal KS; Department of Pharmaceutical Sciences, Jerry H. Hodge School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX 79106, USA.
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Źródło :
International journal of molecular sciences [Int J Mol Sci] 2021 Mar 02; Vol. 22 (5). Date of Electronic Publication: 2021 Mar 02.
Typ publikacji :
Journal Article
MeSH Terms :
Epigenesis, Genetic*
Gene Expression Regulation, Neoplastic*
Regulatory Sequences, Nucleic Acid*
Biomarkers, Tumor/*metabolism
DNA Modification Methylases/*metabolism
DNA Repair Enzymes/*metabolism
Glioma/*metabolism
Tumor Suppressor Proteins/*metabolism
Biomarkers, Tumor/genetics ; Brain Neoplasms/genetics ; Brain Neoplasms/metabolism ; Brain Neoplasms/pathology ; CCCTC-Binding Factor/genetics ; CCCTC-Binding Factor/metabolism ; DNA Methylation ; DNA Modification Methylases/genetics ; DNA Repair Enzymes/genetics ; Genomics ; Glioma/genetics ; Glioma/pathology ; Humans ; NF-E2-Related Factor 2/genetics ; NF-E2-Related Factor 2/metabolism ; Nuclear Respiratory Factor 1/genetics ; Nuclear Respiratory Factor 1/metabolism ; Promoter Regions, Genetic ; RNA, Small Interfering/genetics ; RNA, Untranslated/genetics ; Tumor Suppressor Proteins/genetics
Czasopismo naukowe
Tytuł :
Trans-ancestral dissection of urate- and gout-associated major loci SLC2A9 and ABCG2 reveals primate-specific regulatory effects.
Autorzy :
Takei R; Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand.; Department of Biochemistry, University of Otago, Dunedin, New Zealand.
Cadzow M; Department of Biochemistry, University of Otago, Dunedin, New Zealand.
Markie D; Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand.
Bixley M; Department of Biochemistry, University of Otago, Dunedin, New Zealand.
Phipps-Green A; Department of Biochemistry, University of Otago, Dunedin, New Zealand.
Major TJ; Department of Biochemistry, University of Otago, Dunedin, New Zealand.
Li C; Shandong Gout Clinical Medical Center, Qingdao, 266003, China.; Shandong Provincial Key Laboratory of Metabolic Disease, The Affiliated Hospital of Qingdao University, Qingdao, 266003, China.
Choi HK; Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
Li Z; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China.; Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China.
Hu H; Department of Occupational and Environmental Health and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, 430030, Hubei, China.
Guo H; Center for Biostatistics, School of Health Sciences, The University of Manchester, Manchester, UK.
He M; Department of Occupational and Environmental Health and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, 430030, Hubei, China.
Shi Y; Shandong Gout Clinical Medical Center, Qingdao, 266003, China.; Shandong Provincial Key Laboratory of Metabolic Disease, The Affiliated Hospital of Qingdao University, Qingdao, 266003, China.; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China.; Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China.
Stamp LK; Department of Medicine, University of Otago, Christchurch, Christchurch, New Zealand.
Dalbeth N; Department of Medicine, University of Auckland, Auckland, New Zealand.
Merriman TR; Department of Biochemistry, University of Otago, Dunedin, New Zealand.
Wei WH; Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand. .
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Corporate Authors :
Eurogout Consortium
Źródło :
Journal of human genetics [J Hum Genet] 2021 Feb; Vol. 66 (2), pp. 161-169. Date of Electronic Publication: 2020 Aug 10.
Typ publikacji :
Journal Article
MeSH Terms :
Quantitative Trait Loci*
Quantitative Trait, Heritable*
Regulatory Sequences, Nucleic Acid*
ATP Binding Cassette Transporter, Subfamily G, Member 2/*genetics
Glucose Transport Proteins, Facilitative/*genetics
Gout/*genetics
Hyperuricemia/*genetics
Neoplasm Proteins/*genetics
Animals ; Evolution, Molecular ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Gout/pathology ; Humans ; Hyperuricemia/pathology ; Male ; Polymorphism, Single Nucleotide ; Primates ; Species Specificity ; Uric Acid/blood
Czasopismo naukowe
Tytuł :
JAZF1, A Novel p400/TIP60/NuA4 Complex Member, Regulates H2A.Z Acetylation at Regulatory Regions.
Autorzy :
Procida T; Institute for Genetics, Justus-Liebig University Giessen, 35392 Giessen, Germany.
Friedrich T; Institute for Genetics, Justus-Liebig University Giessen, 35392 Giessen, Germany.; Institute for Biochemistry, Justus-Liebig-University Giessen, 35392 Giessen, Germany.
Jack APM; Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany.
Peritore M; Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany.
Bönisch C; Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany.
Eberl HC; Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
Daus N; Institute for Genetics, Justus-Liebig University Giessen, 35392 Giessen, Germany.
Kletenkov K; Institute for Genetics, Justus-Liebig University Giessen, 35392 Giessen, Germany.
Nist A; Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps-University Marburg, 35043 Marburg, Germany.
Stiewe T; Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps-University Marburg, 35043 Marburg, Germany.
Borggrefe T; Institute for Biochemistry, Justus-Liebig-University Giessen, 35392 Giessen, Germany.
Mann M; Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
Bartkuhn M; Institute for Genetics, Justus-Liebig University Giessen, 35392 Giessen, Germany.; Biomedical Informatics and Systems Medicine, Justus-Liebig-University Giessen, 35392 Giessen, Germany.
Hake SB; Institute for Genetics, Justus-Liebig University Giessen, 35392 Giessen, Germany.; Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany.
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Źródło :
International journal of molecular sciences [Int J Mol Sci] 2021 Jan 12; Vol. 22 (2). Date of Electronic Publication: 2021 Jan 12.
Typ publikacji :
Journal Article
MeSH Terms :
Regulatory Sequences, Nucleic Acid*
Co-Repressor Proteins/*metabolism
DNA-Binding Proteins/*metabolism
Histones/*metabolism
Acetylation ; Cell Line ; Chromatin Assembly and Disassembly ; Computational Biology/methods ; DNA Helicases/metabolism ; Enhancer Elements, Genetic ; Gene Expression Regulation ; Genomics/methods ; Humans ; Introns ; Lysine Acetyltransferase 5/metabolism ; Molecular Chaperones/metabolism ; Multiprotein Complexes ; Protein Binding ; Ribosomes ; Transcription Factors/metabolism
Czasopismo naukowe
Tytuł :
LincSNP 3.0: an updated database for linking functional variants to human long non-coding RNAs, circular RNAs and their regulatory elements.
Autorzy :
Gao Y; College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Li X; College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Shang S; College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Guo S; College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Wang P; College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Sun D; College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Gan J; College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Sun J; College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Zhang Y; College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Wang J; College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Wang X; College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Li X; College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Zhang Y; College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
Ning S; College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
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Źródło :
Nucleic acids research [Nucleic Acids Res] 2021 Jan 08; Vol. 49 (D1), pp. D1244-D1250.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Databases, Nucleic Acid*
Genome, Human*
Regulatory Sequences, Nucleic Acid*
Disease/*genetics
RNA, Circular/*genetics
RNA, Long Noncoding/*genetics
Binding Sites ; Chromatin/chemistry ; Chromatin/metabolism ; Deoxyribonuclease I/genetics ; Deoxyribonuclease I/metabolism ; Disease/classification ; Humans ; Internet ; Linkage Disequilibrium ; Molecular Sequence Annotation ; Polymorphism, Single Nucleotide ; Protein Binding ; RNA, Circular/classification ; RNA, Circular/metabolism ; RNA, Long Noncoding/classification ; RNA, Long Noncoding/metabolism ; Software ; Transcription Factors/genetics ; Transcription Factors/metabolism
Czasopismo naukowe
Tytuł :
Identification and Downstream Analyses of Domains Amplified in Plant Genomes: The Case of StAR-Related Lipid Transfer (START) Domains in Rice.
Autorzy :
Mahtha SK; National Institute of Plant Genome Research (NIPGR), New Delhi, India.
Purama RK; National Institute of Plant Genome Research (NIPGR), New Delhi, India.
Kumari R; National Institute of Plant Genome Research (NIPGR), New Delhi, India.
Yadav G; National Institute of Plant Genome Research (NIPGR), New Delhi, India. .; Department of Plant Sciences, University of Cambridge, Cambridge, UK. .
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Źródło :
Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2021; Vol. 2238, pp. 325-338.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Genome, Plant*
Regulatory Sequences, Nucleic Acid*
Chromosomes, Plant/*genetics
Oryza/*metabolism
Phosphoproteins/*metabolism
Plant Proteins/*metabolism
Proteome/*analysis
Gene Amplification ; Gene Expression Regulation, Plant ; Oryza/genetics ; Oryza/growth & development ; Phosphoproteins/genetics ; Phylogeny ; Plant Proteins/genetics ; Protein Domains
Czasopismo naukowe
Tytuł :
Analysis of Regulatory DNA Sequences by Dual-Luciferase Reporter Assays in Ewing Sarcoma.
Autorzy :
Hölting TLB; Max-Eder Research Group for Pediatric Sarcoma Biology, Faculty of Medicine, Institute of Pathology, LMU Munich, Munich, Germany. .
Knott MML; Max-Eder Research Group for Pediatric Sarcoma Biology, Faculty of Medicine, Institute of Pathology, LMU Munich, Munich, Germany.; Faculty of Medicine, Institute of Pathology, LMU Munich, Munich, Germany.
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Źródło :
Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2021; Vol. 2226, pp. 139-149.
Typ publikacji :
Journal Article
MeSH Terms :
Biological Assay*/methods
Gene Expression Regulation, Neoplastic*
Genes, Reporter*
Regulatory Sequences, Nucleic Acid*
Bone Neoplasms/*genetics
Sarcoma, Ewing/*genetics
Cloning, Molecular ; Enhancer Elements, Genetic ; Gene Order ; Humans ; Oncogene Proteins, Fusion/genetics ; Plasmids/genetics ; Promoter Regions, Genetic
Czasopismo naukowe
Tytuł :
Reverse Chromatin Immunoprecipitation (R-ChIP) enables investigation of the upstream regulators of plant genes.
Autorzy :
Wen X; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.; Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, 838008, China.
Wang J; State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China.
Zhang D; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.; Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, 838008, China.
Ding Y; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.; Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, 838008, China.; University of Chinese Academy of Sciences, Beijing, 100049, China.
Ji X; College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China.
Tan Z; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.; Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, 838008, China.; University of Chinese Academy of Sciences, Beijing, 100049, China.
Wang Y; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China. .; Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan, 838008, China. .; State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China. .
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Źródło :
Communications biology [Commun Biol] 2020 Dec 14; Vol. 3 (1), pp. 770. Date of Electronic Publication: 2020 Dec 14.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Gene Expression Regulation, Plant*
Genes, Plant*
Regulatory Sequences, Nucleic Acid*
Chromatin Immunoprecipitation/*methods
DNA-Binding Proteins/*metabolism
Arabidopsis/genetics ; Arabidopsis/metabolism ; Arabidopsis Proteins/genetics ; Binding Sites ; Catalase/genetics ; Chromatin/genetics ; Chromatin/metabolism ; Promoter Regions, Genetic ; Protein Binding ; Temperature
Czasopismo naukowe
Tytuł :
Genetic Diversity of the Noncoding Control Region of the Novel Human Polyomaviruses.
Autorzy :
Moens U; Department of Medical Biology, Faculty of Health Sciences, University of Tromsø-The Arctic University of Norway, 9037 Tromsø, Norway.
Prezioso C; Department of Public Health and Infectious Diseases, 'Sapienza' University of Rome, 00185 Rome, Italy.; IRCSS San Raffaele Pisana, Microbiology of Chronic Neuro-degenerative Pathologies, 00160 Rome, Italy.
Pietropaolo V; Department of Public Health and Infectious Diseases, 'Sapienza' University of Rome, 00185 Rome, Italy.
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Źródło :
Viruses [Viruses] 2020 Dec 07; Vol. 12 (12). Date of Electronic Publication: 2020 Dec 07.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't; Review
MeSH Terms :
Genetic Variation*
Genome, Viral*
Regulatory Sequences, Nucleic Acid*
Untranslated Regions*
Polyomavirus/*genetics
Polyomavirus Infections/*virology
Alleles ; Gene Expression Regulation, Viral ; Genes, Viral ; Genomics/methods ; Genotype ; Humans ; Mutation
Czasopismo naukowe
Tytuł :
Inhibition of the alternative lengthening of telomeres pathway by subtelomeric sequences in Saccharomyces cerevisiae.
Autorzy :
Grandin N; GReD Institute, CNRS UMR6293, INSERM U1103, Faculty of Medicine, University Clermont-Auvergne, 28 place Henri Dunant, BP 38, 63001 Clermont-Ferrand Cedex, France.
Gallego ME; GReD Institute, CNRS UMR6293, INSERM U1103, Faculty of Medicine, University Clermont-Auvergne, 28 place Henri Dunant, BP 38, 63001 Clermont-Ferrand Cedex, France.
White CI; GReD Institute, CNRS UMR6293, INSERM U1103, Faculty of Medicine, University Clermont-Auvergne, 28 place Henri Dunant, BP 38, 63001 Clermont-Ferrand Cedex, France.
Charbonneau M; GReD Institute, CNRS UMR6293, INSERM U1103, Faculty of Medicine, University Clermont-Auvergne, 28 place Henri Dunant, BP 38, 63001 Clermont-Ferrand Cedex, France. Electronic address: .
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Źródło :
DNA repair [DNA Repair (Amst)] 2020 Dec; Vol. 96, pp. 102996. Date of Electronic Publication: 2020 Oct 19.
Typ publikacji :
Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms :
Cellular Senescence*
Recombination, Genetic*
Regulatory Sequences, Nucleic Acid*
Telomere Homeostasis*
Saccharomyces cerevisiae/*genetics
Rad51 Recombinase/metabolism ; Rad52 DNA Repair and Recombination Protein/metabolism ; Saccharomyces cerevisiae/physiology ; Saccharomyces cerevisiae Proteins/metabolism ; Telomerase ; Telomere/metabolism
Czasopismo naukowe

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