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CTCF
Transcriptional repressor CTCF also known as 11-zinc finger protein or CCCTC-binding factor is a transcription factor that in humans is encoded by the ''CTCF'' gene. CTCF is involved in many cellular processes, including transcriptional regulation, insulator activity, V(D)J recombination and regulation of chromatin architecture. Discovery CCCTC-Binding factor or CTCF was initially discovered as a negative regulator of the chicken c-myc gene. This protein was found to be binding to three regularly spaced repeats of the core sequence CCCTC and thus was named CCCTC binding factor. Function The primary role of CTCF is thought to be in regulating the 3D structure of chromatin. CTCF binds together strands of DNA, thus forming chromatin loops, and anchors DNA to cellular structures like the nuclear lamina. It also defines the boundaries between active and heterochromatic DNA. Since the 3D structure of DNA influences the regulation of genes, CTCF's activity influences the expre ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Insulator (genetics)
An insulator is a type of cis-regulatory element known as a long-range regulatory element. Found in multicellular eukaryotes and working over distances from the promoter element of the target gene, an insulator is typically 300 bp to 2000 bp in length. Insulators contain clustered binding sites for sequence specific DNA-binding proteins and mediate intra- and inter- chromosomal interactions. Insulators function either as an enhancer-blocker or a barrier, or both. The mechanisms by which an insulator performs these two functions include loop formation and nucleosome modifications. There are many examples of insulators, including the CTCF insulator, the ''gypsy'' insulator, and the β-globin locus. The CTCF insulator is especially important in vertebrates, while the ''gypsy'' insulator is implicated in '' Drosophila.'' The β-globin locus was first studied in chicken and then in humans for its insulator activity, both of which utilize CTCF. The genetic implications of ins ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Loop Extrusion
Loop extrusion is a major mechanism of Nuclear organization. It is a dynamic process in which structural maintenance of chromosomes (SMC) protein complexes progressively grow loops of DNA or chromatin. In this process, SMC complexes, such as condensin or cohesin, bind to DNA/chromatin, use ATP-driven motor activity to reel in DNA, and as a result, extrude the collected DNA as a loop. Background The organization of DNA presents a remarkable biological challenge: human DNA can reach 2 meters and is packed into the nucleus with the diameter of 5-20 μm. At the same time, the critical cell processes involve complex processes on highly compacted DNA, such as transcription, replication, recombination, DNA repair, and cell division. Loop extrusion is a key mechanism that organizes DNA into loops, enabling its efficient compaction and functional organization. For instance, ''in vitro'' experiments show that cohesin can compact DNA by 80%, while condensin achieves a remarkable 10 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cohesin
Cohesin is a protein complex that mediates Establishment of sister chromatid cohesion, sister chromatid cohesion, homologous recombination, and Topologically associating domain, DNA looping. Cohesin is formed of SMC3, SMC1A, SMC1, RAD21, SCC1 and SCC3 (STAG1, SA1 or STAG2, SA2 in humans). Cohesin holds sister chromatids together after DNA replication until anaphase when removal of cohesin leads to separation of sister chromatids. The complex forms a ring-like structure and it is believed that sister chromatids are held together by entrapment inside the cohesin ring. Cohesin is a member of the SMC proteins, SMC family of protein complexes which includes Condensin, Nucleoid#MukBEF, MukBEF and SMC-ScpAB. Cohesin was separately discovered in budding yeast (''Saccharomyces cerevisiae'') both by Douglas Koshland and Kim Nasmyth in 1997. Structure and subunits Cohesin is a multi-subunit protein complex, made up of SMC1, SMC3, RAD21 and SCC3 (SA1 or SA2). SMC1 and SMC3 are members of ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Topologically Associating Domain
A topologically associating domain (TAD) is a self-interacting genomic region, meaning that DNA sequences within a TAD physically interact with each other more frequently than with sequences outside the TAD. The average size of a topologically associating domain (TAD) is 1000 kb in humans, 880 kb in mouse cells, and 140 kb in fruit flies. Boundaries at both side of these domains are conserved between different mammalian cell types and even across species and are highly enriched with CTCF, CCCTC-binding factor (CTCF) and cohesin. In addition, some types of genes (such as transfer RNA genes and housekeeping genes) appear near TAD boundaries more often than would be expected by chance. The functions of TADs are not fully understood and are still a matter of debate. Most of the studies indicate TADs regulate gene expression by limiting the Enhancer (genetics), enhancer-Promoter (genetics), promoter interaction to each TAD; however, a recent study uncouples TAD organization and gene exp ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chromatin
Chromatin is a complex of DNA and protein found in eukaryote, eukaryotic cells. The primary function is to package long DNA molecules into more compact, denser structures. This prevents the strands from becoming tangled and also plays important roles in reinforcing the DNA during cell division, preventing DNA repair#DNA damage, DNA damage, and regulating gene expression and DNA replication. During mitosis and meiosis, chromatin facilitates proper segregation of the chromosomes in anaphase; the characteristic shapes of chromosomes visible during this stage are the result of DNA being coiled into highly condensed chromatin. The primary protein components of chromatin are histones. An octamer of two sets of four histone cores (Histone H2A, Histone H2B, Histone H3, and Histone H4) bind to DNA and function as "anchors" around which the strands are wound.Maeshima, K., Ide, S., & Babokhov, M. (2019). Dynamic chromatin organization without the 30 nm fiber. ''Current opinion in cell biolog ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Insulin-like Growth Factor 2
Insulin-like growth factor 2 (IGF-2) is one of three protein hormones that share structural similarity to insulin. The MeSH definition reads: "A well-characterized neutral peptide believed to be secreted by the liver and to circulate in the blood. It has growth-regulating, insulin-like and mitogenic activities. The growth factor has a major, but not absolute, dependence on somatotropin. It is believed to be a major fetal growth factor in contrast to IGF-1, insulin-like growth factor 1 (IGF-1), which is a major growth factor in adults." Gene structure In humans, the gene is located on chromosome 11p15.5, a region which contains numerous Genomic Imprinting, imprinted genes. In mice this Homology (biology), homologous region is found at distal chromosome 7. In both organisms, ''IGF2'' is imprinted, with expression resulting favourably from the paternally inherited allele. However, in some human brain regions a loss of imprinting occurs resulting in both ''IGF2'' and being trans ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
H19 (gene)
H19 is a gene for a long noncoding RNA, found in humans and elsewhere. H19 has a role in the negative regulation (or limiting) of body weight and cell proliferation. This gene also has a role in the formation of some cancers and in the regulation of gene expression. The H19 gene is expressed exclusively on one parental allele in a phenomenon known as imprinting. H19 is only transcribed from the maternally inherited allele; the paternal H19 allele is not expressed. H19 was first named ASM (for Adult Skeletal Muscle) because of its expression in adult skeletal muscle ("ASM") in rats. H19 is also known as BWS because aberrant H19 expression can be involved in Beckwith-Wiedemann Syndrome ("BWS"), as well as Silver-Russell syndrome. Epigenetics deregulations at H19 imprinted gene in sperm have been observed associated with male infertility. Gene characterization The H19 gene contains 3 Sp1 binding sites, however these 3 sites are present in a part of the sequence that has shown ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nucleosome
A nucleosome is the basic structural unit of DNA packaging in eukaryotes. The structure of a nucleosome consists of a segment of DNA wound around eight histone, histone proteins and resembles thread wrapped around a bobbin, spool. The nucleosome is the fundamental subunit of chromatin. Each nucleosome is composed of a little less than two turns of DNA wrapped around a set of eight proteins called histones, which are known as a histone octamer. Each histone octamer is composed of two copies each of the histone proteins Histone H2A, H2A, Histone H2B, H2B, Histone H3, H3, and Histone H4, H4. DNA must be compacted into nucleosomes to fit within the cell nucleus. In addition to nucleosome wrapping, eukaryotic chromatin is further compacted by being folded into a series of more complex structures, eventually forming a chromosome. Each human cell contains about 30 million nucleosomes. Nucleosomes are thought to carry Epigenetics, epigenetically inherited information in the form of coval ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Y Box Binding Protein 1
Y box binding protein 1 also known as Y-box transcription factor or nuclease-sensitive element-binding protein 1 is a protein that in humans is encoded by the ''YBX1'' gene. YBX1 is an RNA binding protein that stabilises messenger RNAs modified with N6-methyladenosine. Clinical significance YBX1 is a potential drug target in cancer therapy. YB-1 helps the replication of adenovirus type 5, a commonly used vector in gene therapy. Thus, YB-1 can cause an "oncolytic" effect in YB-1 positive cancer cells treated with adenoviruses. DNA repair The mitochondria of human cells possess a repair pathway for DNA base pair mismatches that is distinct from the DNA mismatch repair pathway of the nucleus.deSouza-Pinto NC, Mason PA, Hashiguchi K, Weissman L, Tian J, Guay D, Lebel M, Stevnsner TV, Rasmussen LJ, Bohr VA. Novel DNA mismatch-repair activity involving YB-1 in human mitochondria. DNA Repair (Amst). 2009 Jun 4;8(6):704-19. doi: 10.1016/j.dnarep.2009.01.021. Epub 2009 Mar 9. PMID: ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nuclear Lamina
The nuclear lamina is a dense (~30 to 100 nm thick) fibrillar network inside the nucleus of eukaryote cells. It is composed of intermediate filaments and membrane associated proteins. Besides providing mechanical support, the nuclear lamina regulates important cellular events such as DNA replication and cell division. Additionally, it participates in chromatin organization and it anchors the nuclear pore complexes embedded in the nuclear envelope. The nuclear lamina is associated with the inner face of the inner nuclear membrane of the nuclear envelope, whereas the outer face of the outer nuclear membrane is continuous with the endoplasmic reticulum. The nuclear lamina is similar in structure to the nuclear matrix, that extends throughout the nucleoplasm. Structure and composition The nuclear lamina consists of two components, lamins and nuclear lamin-associated membrane proteins. The lamins are type V intermediate filaments which can be categorized as either A-type ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gene Expression
Gene expression is the process (including its Regulation of gene expression, regulation) by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, proteins or non-coding RNA, and ultimately affect a phenotype. These products are often proteins, but in non-protein-coding genes such as Transfer RNA, transfer RNA (tRNA) and Small nuclear RNA, small nuclear RNA (snRNA), the product is a functional List of RNAs, non-coding RNA. The process of gene expression is used by all known life—eukaryotes (including multicellular organisms), prokaryotes (bacteria and archaea), and viruses—to generate the macromolecule, macromolecular machinery for life. In genetics, gene expression is the most fundamental level at which the genotype gives rise to the phenotype, ''i.e.'' observable trait. The genetic information stored in DNA represents the genotype, whereas the phenotype results from the "interpretation" of that informati ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
