ENDOCRINE-RELATED CANCER, ISSN 1351-0088, 11/2019, Volume 26, Issue 11, pp. R611 - R626
The 3D organization of the genome within the cell nucleus has come into sharp focus over the last decade. This has largely arisen because of the application of...
REGULATORY INTERACTIONS | enhancer | DNA METHYLATION | ovarian cancer | SEA-URCHIN EGGS | breast cancer | CTCF | prostate cancer | cohesin | HUMAN GENOME | CHROMATIN DOMAINS | ONCOLOGY | ENDOCRINOLOGY & METABOLISM | GENE-EXPRESSION | BINDING SITES | topologically associated domain | DEVELOPMENTAL ENHANCERS | CTCF OCCUPANCY | DRIVING-FORCE
REGULATORY INTERACTIONS | enhancer | DNA METHYLATION | ovarian cancer | SEA-URCHIN EGGS | breast cancer | CTCF | prostate cancer | cohesin | HUMAN GENOME | CHROMATIN DOMAINS | ONCOLOGY | ENDOCRINOLOGY & METABOLISM | GENE-EXPRESSION | BINDING SITES | topologically associated domain | DEVELOPMENTAL ENHANCERS | CTCF OCCUPANCY | DRIVING-FORCE
Journal Article
Biogerontology, ISSN 1389-5729, 12/2019, Volume 20, Issue 6, pp. 857 - 869
Three-dimensional chromatin architecture and gene–gene interactions impact gene expression. We assembled this information, in silico, for the human renin gene...
Life Sciences | Gene–gene interaction | Diseases of aging | Geriatrics/Gerontology | Genomics | Topologically associated domains | Aging | Longevity | Developmental Biology | Renin-angiotensin system | Gene expression | Cell Biology | CELL IDENTITY | MOUSE | ANGIOTENSIN-ALDOSTERONE SYSTEM | GERIATRICS & GERONTOLOGY | PRESSURE | ELEMENTS | SUPER-ENHANCERS | GENOME-WIDE | Gene-gene interaction | PROMOTER | EXPRESSION | Medical research | Medical colleges | Anopheles | Chromatin | Genes | Angiotensin | Medicine, Experimental | Genetic research | Cell differentiation | Genomes | RNA polymerase | DNA-directed RNA polymerase | Chromosome 1 | Enhancers | Hypotheses | Renin | Archipelagoes | Angiotensin II | Cardiovascular diseases | Binding sites | Immune system
Life Sciences | Gene–gene interaction | Diseases of aging | Geriatrics/Gerontology | Genomics | Topologically associated domains | Aging | Longevity | Developmental Biology | Renin-angiotensin system | Gene expression | Cell Biology | CELL IDENTITY | MOUSE | ANGIOTENSIN-ALDOSTERONE SYSTEM | GERIATRICS & GERONTOLOGY | PRESSURE | ELEMENTS | SUPER-ENHANCERS | GENOME-WIDE | Gene-gene interaction | PROMOTER | EXPRESSION | Medical research | Medical colleges | Anopheles | Chromatin | Genes | Angiotensin | Medicine, Experimental | Genetic research | Cell differentiation | Genomes | RNA polymerase | DNA-directed RNA polymerase | Chromosome 1 | Enhancers | Hypotheses | Renin | Archipelagoes | Angiotensin II | Cardiovascular diseases | Binding sites | Immune system
Journal Article
BMC Bioinformatics, ISSN 1471-2105, 11/2017, Volume 18, Issue 1, pp. 480 - 14
Background: With the development of chromosomal conformation capturing techniques, particularly, the Hi-C technique, the study of the spatial conformation of a...
Topologically associated domain (TAD) | Genome structure | Hi-C | Chromosome conformation capturing | CTCF | Clustering | Chromosome organization | BIOCHEMICAL RESEARCH METHODS | GENE-REGULATION | ORGANIZATION | ELEMENTS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Promoter Regions, Genetic | Genomics | CCCTC-Binding Factor - metabolism | Sequence Analysis, DNA | Unsupervised Machine Learning | Animals | Chromatin Immunoprecipitation | Enhancer Elements, Genetic | Chromosomes - metabolism | Histone Code | Chromosomes - chemistry | Mice | Binding Sites | Cluster Analysis
Topologically associated domain (TAD) | Genome structure | Hi-C | Chromosome conformation capturing | CTCF | Clustering | Chromosome organization | BIOCHEMICAL RESEARCH METHODS | GENE-REGULATION | ORGANIZATION | ELEMENTS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Promoter Regions, Genetic | Genomics | CCCTC-Binding Factor - metabolism | Sequence Analysis, DNA | Unsupervised Machine Learning | Animals | Chromatin Immunoprecipitation | Enhancer Elements, Genetic | Chromosomes - metabolism | Histone Code | Chromosomes - chemistry | Mice | Binding Sites | Cluster Analysis
Journal Article
Genes, Chromosomes and Cancer, ISSN 1045-2257, 01/2020, Volume 59, Issue 1, pp. 13 - 22
Genetic interaction has been recognized to be an important cause of the missing heritability. The topologically associating domain (TAD) is a self‐interacting...
lung cancer | tumor suppressor | interaction analyses | missing heritability | topologically associating domain | Adenocarcinoma | Squamous cell carcinoma | Nucleotide sequence | Lung cancer | Sex | Health risks | Sex differences | Single-nucleotide polymorphism | Lung carcinoma | Gene expression | Survival | Gene sequencing | Domains | Gender aspects | Genetic analysis | Tumor suppressor genes | Heritability | Deoxyribonucleic acid--DNA | Tumors
lung cancer | tumor suppressor | interaction analyses | missing heritability | topologically associating domain | Adenocarcinoma | Squamous cell carcinoma | Nucleotide sequence | Lung cancer | Sex | Health risks | Sex differences | Single-nucleotide polymorphism | Lung carcinoma | Gene expression | Survival | Gene sequencing | Domains | Gender aspects | Genetic analysis | Tumor suppressor genes | Heritability | Deoxyribonucleic acid--DNA | Tumors
Journal Article
EPIGENETICS & CHROMATIN, ISSN 1756-8935, 10/2018, Volume 11, Issue 1, pp. 62 - 18
BackgroundIn animals with XY sex chromosomes, X-linked genes from a single X chromosome in males are imbalanced relative to autosomal genes. To minimize the...
MSL complex | Dosage compensation | MOF | ACETYLATION | Lamina-associated domain | NUCLEAR LAMINA INTERACTIONS | Topologically associated domain | CAENORHABDITIS-ELEGANS | EVOLUTION | MODELS | GENETICS & HEREDITY | GENE-EXPRESSION | SITES | Drosophila melanogaster | MELANOGASTER | Drosophila | Chromatin Assembly and Disassembly | Male | Nuclear Proteins - metabolism | Transcription Factors - genetics | Drosophila Proteins - metabolism | Hemizygote | Transcription Factors - metabolism | Dosage Compensation, Genetic | Animals | Chromosomes, Insect - genetics | Female | Drosophila Proteins - genetics | Nuclear Proteins - genetics | X Chromosome - genetics | Genetic aspects | Research | Gene expression | X chromosome | Sex chromosomes | Chromatin | Genomics | Genomes | RNA polymerase | Males | Recruitment | Proteins | Acids | Insects | Derepression | Sexes | X Chromosomes | Bioinformatics | Chromosomes
MSL complex | Dosage compensation | MOF | ACETYLATION | Lamina-associated domain | NUCLEAR LAMINA INTERACTIONS | Topologically associated domain | CAENORHABDITIS-ELEGANS | EVOLUTION | MODELS | GENETICS & HEREDITY | GENE-EXPRESSION | SITES | Drosophila melanogaster | MELANOGASTER | Drosophila | Chromatin Assembly and Disassembly | Male | Nuclear Proteins - metabolism | Transcription Factors - genetics | Drosophila Proteins - metabolism | Hemizygote | Transcription Factors - metabolism | Dosage Compensation, Genetic | Animals | Chromosomes, Insect - genetics | Female | Drosophila Proteins - genetics | Nuclear Proteins - genetics | X Chromosome - genetics | Genetic aspects | Research | Gene expression | X chromosome | Sex chromosomes | Chromatin | Genomics | Genomes | RNA polymerase | Males | Recruitment | Proteins | Acids | Insects | Derepression | Sexes | X Chromosomes | Bioinformatics | Chromosomes
Journal Article
Russian Journal of Bioorganic Chemistry, ISSN 1068-1620, 03/2017, Volume 43, Issue 2, pp. 99 - 106
A number of recent experimental approaches demonstrated that a three-dimensional organization of the eukaryotic genome play an important role in the regulation...
insulators | computer simulation | active genes | chromatin | topologically-associated domain | FUNCTIONAL DIVERSITY | DROSOPHILA GENOME | BIOCHEMISTRY & MOLECULAR BIOLOGY | TRANSCRIPTION | ENHANCER | CHEMISTRY, ORGANIC | GENE-REGULATION | PRINCIPLES | MAMMALIAN GENOMES | CHROMOSOME | 4Q35 LOCUS | REGULATORY LANDSCAPE | Anopheles | Chromatin | Genes | Genomics
insulators | computer simulation | active genes | chromatin | topologically-associated domain | FUNCTIONAL DIVERSITY | DROSOPHILA GENOME | BIOCHEMISTRY & MOLECULAR BIOLOGY | TRANSCRIPTION | ENHANCER | CHEMISTRY, ORGANIC | GENE-REGULATION | PRINCIPLES | MAMMALIAN GENOMES | CHROMOSOME | 4Q35 LOCUS | REGULATORY LANDSCAPE | Anopheles | Chromatin | Genes | Genomics
Journal Article
Epigenetics and Chromatin, 10/2018, Volume 11, Issue 1
Journal Article
Current Bioinformatics, ISSN 1574-8936, 2018, Volume 13, Issue 4, pp. 420 - 425
Background: Recent studies suggest that the one-dimensional genomic feature, isochore, underlie the three-dimensional chromatin architecture. It has also been...
Topologically associated domain | Isochore | Chromatin | Drosophila melanogaster | GC profile | BLOODED VERTEBRATES | MOUSE | BIOCHEMICAL RESEARCH METHODS | isochore | MATHEMATICAL & COMPUTATIONAL BIOLOGY | GENE-EXPRESSION | topologically associated domain | CHROMOSOME CONFORMATION | CAPTURE | INTERPHASE NUCLEI | Statistical analysis | Architecture | Computer simulation | Drosophila | Isochores | Segments | Genomes | Statistical methods | Density | Insects | Dimensional analysis | X Chromosomes | Chromosomes
Topologically associated domain | Isochore | Chromatin | Drosophila melanogaster | GC profile | BLOODED VERTEBRATES | MOUSE | BIOCHEMICAL RESEARCH METHODS | isochore | MATHEMATICAL & COMPUTATIONAL BIOLOGY | GENE-EXPRESSION | topologically associated domain | CHROMOSOME CONFORMATION | CAPTURE | INTERPHASE NUCLEI | Statistical analysis | Architecture | Computer simulation | Drosophila | Isochores | Segments | Genomes | Statistical methods | Density | Insects | Dimensional analysis | X Chromosomes | Chromosomes
Journal Article
BMC biology, ISSN 1741-7007, 08/2018, Volume 16, Issue 1, pp. 87 - 12
Background: The human genome is highly organized in the three-dimensional nucleus. Chromosomes fold locally into topologically associating domains (TADs)...
Genome rearrangements | Topologically associating domains | Hi-C | Structural variants | Gene regulation | Selection | TAD | Evolution | Chromatin interactions | 3D genome architecture | NEIGHBORHOODS | DROSOPHILA GENOME | FRAGILITY | CHROMOSOMES | REARRANGEMENTS | PRINCIPLES | CHROMATIN ARCHITECTURE | ORGANIZATION | 3D GENOME | BIOLOGY | EXPRESSION | Evolutionary biology | Genetic research | Models | Research | Gene expression | Properties | Chromosomes | Breakpoints | Chromatin | Genetic disorders | Genomics | Genes | Biological evolution | Genomes | Regulatory sequences | Boundaries | Data bases | Gene sequencing | Domains | Vertebrates | Enhancers | Insects | Gene loci
Genome rearrangements | Topologically associating domains | Hi-C | Structural variants | Gene regulation | Selection | TAD | Evolution | Chromatin interactions | 3D genome architecture | NEIGHBORHOODS | DROSOPHILA GENOME | FRAGILITY | CHROMOSOMES | REARRANGEMENTS | PRINCIPLES | CHROMATIN ARCHITECTURE | ORGANIZATION | 3D GENOME | BIOLOGY | EXPRESSION | Evolutionary biology | Genetic research | Models | Research | Gene expression | Properties | Chromosomes | Breakpoints | Chromatin | Genetic disorders | Genomics | Genes | Biological evolution | Genomes | Regulatory sequences | Boundaries | Data bases | Gene sequencing | Domains | Vertebrates | Enhancers | Insects | Gene loci
Journal Article
BioEssays, ISSN 0265-9247, 12/2019, Volume 41, Issue 12, pp. 1900106 - n/a
Recent investigations have revealed 1) that the isochores of the human genome group into two super‐families characterized by two different long‐range 3D...
isochores | chromatin folding principles | lamina‐associated domains | topologically associating domains
isochores | chromatin folding principles | lamina‐associated domains | topologically associating domains
Journal Article
BioEssays : news and reviews in molecular, cellular and developmental biology, ISSN 0265-9247, 07/2019, Volume 41, Issue 9, p. e1900048
The organization of the genome into topologically associated domains (TADs) appears to be a fundamental process occurring across a wide range of eukaryote...
COMPLEX | loop domains | PROTEIN | Drosophila | BIOCHEMISTRY & MOLECULAR BIOLOGY | CTCF | chromatin | GENOME | PRINCIPLES | CCCTC-binding factor (CTCF) | ORGANIZATION | cohesin | BIOLOGY | insulators | BINDING-SITES | topologically associated domains
COMPLEX | loop domains | PROTEIN | Drosophila | BIOCHEMISTRY & MOLECULAR BIOLOGY | CTCF | chromatin | GENOME | PRINCIPLES | CCCTC-binding factor (CTCF) | ORGANIZATION | cohesin | BIOLOGY | insulators | BINDING-SITES | topologically associated domains
Journal Article
BioEssays, ISSN 0265-9247, 09/2019, Volume 41, Issue 9, p. n/a
The organization of the genome into topologically associated domains (TADs) appears to be a fundamental process occurring across a wide range of eukaryote...
CCCTC‐binding factor (CTCF) | cohesin | loop domains | Drosophila | insulators | chromatin | topologically associated domains | Domains | Chromatin | Architecture | Insects | Gene regulation | Extrusion | Genomes | Cohesin | Mammals | Gene expression
CCCTC‐binding factor (CTCF) | cohesin | loop domains | Drosophila | insulators | chromatin | topologically associated domains | Domains | Chromatin | Architecture | Insects | Gene regulation | Extrusion | Genomes | Cohesin | Mammals | Gene expression
Journal Article
Nature Genetics, ISSN 1061-4036, 01/2017, Volume 49, Issue 1, pp. 36 - 45
textabstractDespite the clinical significance of balanced chromosomal abnormalities (BCAs), their characterization has largely been restricted to cytogenetic...
INTELLECTUAL DISABILITY | CHROMOSOME REARRANGEMENTS | DE-NOVO MUTATIONS | SEVERE MENTAL-RETARDATION | GENETICS & HEREDITY | MICRODELETION SYNDROME | DEVELOPMENTAL DELAY | OF-FUNCTION MUTATIONS | SPECTRUM | EPILEPSY | STRUCTURAL VARIATION | Genetic Predisposition to Disease | Genome-Wide Association Study | Congenital Abnormalities - genetics | Gene Rearrangement | Genetic Markers - genetics | Humans | Chromosome Aberrations | Female | Male | Cytogenetics | Nucleotide sequencing | Analysis | Genomics | DNA sequencing | Studies | Medical research | Genetic counseling | Congenital diseases | Intellectual disabilities | Genomes | Mutation | Grants | Localization | structural variation | MEF2C | translocation | inversion | Hi-C | chromothripsis | topologically associated domain (TAD) | congenital anomaly | intellectual disability | autism | balanced chromosomal abnormality
INTELLECTUAL DISABILITY | CHROMOSOME REARRANGEMENTS | DE-NOVO MUTATIONS | SEVERE MENTAL-RETARDATION | GENETICS & HEREDITY | MICRODELETION SYNDROME | DEVELOPMENTAL DELAY | OF-FUNCTION MUTATIONS | SPECTRUM | EPILEPSY | STRUCTURAL VARIATION | Genetic Predisposition to Disease | Genome-Wide Association Study | Congenital Abnormalities - genetics | Gene Rearrangement | Genetic Markers - genetics | Humans | Chromosome Aberrations | Female | Male | Cytogenetics | Nucleotide sequencing | Analysis | Genomics | DNA sequencing | Studies | Medical research | Genetic counseling | Congenital diseases | Intellectual disabilities | Genomes | Mutation | Grants | Localization | structural variation | MEF2C | translocation | inversion | Hi-C | chromothripsis | topologically associated domain (TAD) | congenital anomaly | intellectual disability | autism | balanced chromosomal abnormality
Journal Article
FEBS Letters, ISSN 0014-5793, 10/2015, Volume 589, Issue 20, pp. 2944 - 2957
Recent analysis of genome-wide epigenetic modification data, mean replication timing (MRT) profiles and chromosome conformation data in mammals have provided...
Chromatin states | Equilibrium and fractal globule models | Replication timing domains | Chromatin conformation | Lamina-associated domains | Topologically associated domains | CTR | heterochromatin protein 1 | Timing transition region | Embryonic stem cell | HP1 | Fluorescent in situ hybridization | Topological associated domain | MRT | Constant timing region | Mean replication timing | TTR | ESC | TAD | “master” replication origin | FISH | MaOri | CHROMATIN-STRUCTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | NUCLEAR LAMINA INTERACTIONS | EUKARYOTIC DNA-REPLICATION | MAMMALIAN GENOMES | CELL BIOLOGY | HUMAN GENOME | BIOPHYSICS | INTERPHASE CHROMOSOMES | EMBRYONIC STEM-CELLS | GENE-EXPRESSION | FUNCTIONAL-ORGANIZATION | CHROMOSOME CONFORMATION | Chromatin - ultrastructure | Animals | Epigenesis, Genetic | Humans | Regulatory Sequences, Nucleic Acid | Chromatin - physiology | Chromatin Assembly and Disassembly | DNA Replication | Cell Nucleus - ultrastructure | Nucleic Acid Conformation | Cell Nucleus - physiology | Epigenetic inheritance | Analysis | Genomics | Biological Physics | Physics
Chromatin states | Equilibrium and fractal globule models | Replication timing domains | Chromatin conformation | Lamina-associated domains | Topologically associated domains | CTR | heterochromatin protein 1 | Timing transition region | Embryonic stem cell | HP1 | Fluorescent in situ hybridization | Topological associated domain | MRT | Constant timing region | Mean replication timing | TTR | ESC | TAD | “master” replication origin | FISH | MaOri | CHROMATIN-STRUCTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | NUCLEAR LAMINA INTERACTIONS | EUKARYOTIC DNA-REPLICATION | MAMMALIAN GENOMES | CELL BIOLOGY | HUMAN GENOME | BIOPHYSICS | INTERPHASE CHROMOSOMES | EMBRYONIC STEM-CELLS | GENE-EXPRESSION | FUNCTIONAL-ORGANIZATION | CHROMOSOME CONFORMATION | Chromatin - ultrastructure | Animals | Epigenesis, Genetic | Humans | Regulatory Sequences, Nucleic Acid | Chromatin - physiology | Chromatin Assembly and Disassembly | DNA Replication | Cell Nucleus - ultrastructure | Nucleic Acid Conformation | Cell Nucleus - physiology | Epigenetic inheritance | Analysis | Genomics | Biological Physics | Physics
Journal Article