• proteins
  • In a hypothetical example, the factors A and B might regulate a distinct set of genes from the combination of factors A and C. This combinatorial nature extends to complexes of far more than two proteins, and allows a very small subset (less than 10%) of the genome to control the transcriptional program of the entire cell. (wikipedia.org)
  • Prokaryotic transcription is governed by three main sequence elements: Promoters are elements of DNA that may bind RNA polymerase and other proteins for the successful initiation of transcription directly upstream of the gene. (wikipedia.org)
  • Operators recognize repressor proteins that bind to a stretch of DNA and inhibit the transcription of the gene. (wikipedia.org)
  • Positive control elements that bind to DNA and incite higher levels of transcription While these means of transcriptional regulation also exist in eukaryotes, the transcriptional landscape is significantly more complicated both by the number of proteins involved as well as by the presence of introns and the packaging of DNA into histones. (wikipedia.org)
  • Researchers at the University of Pennsylvania School of Medicine have found that one portion of the MLL protein is an enzyme that 'edits' the so-called histone code, a series of modifications to proteins associated with DNA that influence how and when certain genes are turned on and off. (pennmedicine.org)
  • The theory, which rapidly is gaining acceptance, postulates that expression of certain regions of DNA is turned on and off by modifying portions of histone proteins or DNA. (pennmedicine.org)
  • Domains similar to those with histone modifying activity in MLL are found in other proteins implicated in human tumors including acute leukemia, lymphoma, and prostate cancer and probably have a similar function. (pennmedicine.org)
  • These modifications can either originate from the parental DNA, or can be added to the gene by various proteins and can contribute to differentiation. (wikipedia.org)
  • Processes that alter the epigenetic profile of a gene include production of activating or repressing protein complexes, usage of non-coding RNAs to guide proteins capable of modification, and the proliferation of a signal by having protein complexes attract either another protein complex or more DNA in order to modify other locations in the gene. (wikipedia.org)
  • By making these alterations, proteins, like transcription factors, may bind DNA less or some protein may be inhibited so that it becomes a block in a signaling cascade and certain genes will then not be induced to be expressed. (wikipedia.org)
  • Histone modifications also act as sites for proteins to attach, which then further alter the gene's expression. (wikipedia.org)
  • DNA is, however, supercoiled and wound around "packaging" proteins called histones (in eukaryotes), and both superstructures are vulnerable to the effects of DNA damage. (wikipedia.org)
  • Chromosomes consist of the DNA sequence, and the proteins (such as histones) that are responsible for its packaging into chromosomes. (wikipedia.org)
  • epigenetic
  • Abstract Aberrations in the epigenetic machinery of the genome result in inactivation of critical genes and are important mechanisms in the evolution of malignancies that not only contributes to tumorigenesis but may also precede genetic changes. (springer.com)
  • This review examines the general role of epigenetic changes in the malignant process and focuses on the known changes in gene expression in gliomas due to epigenetic modifications, both in the context of gliomagenesis and in the development of new therapeutic strategies against these malignancies. (springer.com)
  • Dallol A et al (2003) Frequent epigenetic inactivation of the SLIT2 gene in gliomas. (springer.com)
  • Foltz G et al (2006) Genome-wide analysis of epigenetic silencing identifies BEX1 and BEX2 as candidate tumor suppressor genes in malignant glioma. (springer.com)
  • Genes implicated in epigenetic control, like DNMT3A , ASXL1 , EZH2 and TET2 , have been discovered to be mutated in MDS. (mdpi.com)
  • SAC3B, a central component of the mRNA export complex TREX-2, is required for prevention of epigenetic gene silencing in Arabidopsis. (abcam.com)
  • This protein belongs to the group of histone-modifying enzymes comprising transactivation domain 9aaTAD and is involved in the epigenetic maintenance of transcriptional memory. (wikipedia.org)
  • Genes on the other hand, refer only to the DNA sequence (hereditary unit) and it is not necessary that they will be expressed once epigenetic factors are taken into account. (wikipedia.org)
  • tumor suppr
  • However, in some cases mutations, like in oncogenes or tumor suppressor genes, may occur that allow the cell to bypass apoptosis and to survive. (mdpi.com)
  • While this constitutes only 0.000165% of the human genome's approximately 6 billion bases (3 billion base pairs), unrepaired lesions in critical genes (such as tumor suppressor genes) can impede a cell's ability to carry out its function and appreciably increase the likelihood of tumor formation and contribute to tumour heterogeneity. (wikipedia.org)
  • promyelocytic leukem
  • Eight other rare gene rearrangements have been described in APL fusing RARA to promyelocytic leukemia zinc finger (PLZF also known as ZBTB16), nucleophosmin(NPM1), nuclear matrix associated (NUMA1), signal transducer and activator of transcription 5b (STAT5B), protein kinase A regulatory subunit 1α (PRKAR1A), factor interacting with PAPOLA and CPSF1 (FIP1L1), BCL6 corepressor (BCOR) or oligonucleotide/oligosaccharide-binding fold containing 2A (OBFC2A also known as NABP1) genes. (wikipedia.org)
  • 1998
  • Colgan DJ, McLauchlan A, Wilson GDF et al (1998) Histone H3 and U2 snRNA DNA sequences and arthropod molecular evolution. (springer.com)
  • protein
  • High-mobility group AT-hook 2, also known as HMGA2, is a protein that, in humans, is encoded by the HMGA2 gene. (wikipedia.org)
  • The let-7a miRNA normally represses the HMGA2 gene, and in normal adult tissues, almost no HMGA2 protein is present. (wikipedia.org)
  • Zinc finger and BTB domain-containing protein 16 is a protein that in humans is encoded by the ZBTB16 gene. (wikipedia.org)
  • This gene is a member of the Krueppel C2H2-type zinc-finger protein family and encodes a zinc finger transcription factor that contains nine Kruppel-type zinc finger domains at the carboxyl terminus. (wikipedia.org)
  • Zinc finger MYM-type protein 2 is a protein that in humans is encoded by the ZMYM2 gene. (wikipedia.org)
  • Histone acetyltransferase p300 also known as p300 HAT or E1A-associated protein p300 (where E1A = adenovirus early region 1A) also known as EP300 or p300 is an enzyme that, in humans, is encoded by the EP300 gene. (wikipedia.org)
  • EP300 is closely related to another gene, CREB binding protein, which is found on human chromosome 16. (wikipedia.org)
  • It mediates cAMP-gene regulation by binding specifically to phosphorylated CREB protein. (wikipedia.org)
  • These mutations result in the loss of one copy of the gene in each cell, which reduces the amount of p300 protein by half. (wikipedia.org)
  • Some mutations lead to the production of a very short, nonfunctional version of the p300 protein, while others prevent one copy of the gene from making any protein at all. (wikipedia.org)
  • Although researchers do not know how a reduction in the amount of p300 protein leads to the specific features of Rubinstein-Taybi syndrome, it is clear that the loss of one copy of the EP300 gene disrupts normal development. (wikipedia.org)
  • In cancer cells, EP300 mutations prevent the gene from producing any functional protein. (wikipedia.org)
  • These fragments then assemble into different multi-protein complexes that regulate the transcription of specific target genes, including many of the HOX genes. (wikipedia.org)
  • So CCDS's gene number prediction represents a lower bound on the total number of human protein-coding genes. (wikipedia.org)
  • enzyme
  • A vitamin B12-dependent enzyme catalyzes rearrangement of L-methylmalonyl-CoA to succinyl-CoA, which is an intermediate of the citric acid cycle and can be readily incorporated there. (wikipedia.org)
  • molecular
  • Canapa A, Schiaparelli S, Marota I, Barucca M (2003) Molecular data from the 16S rRNA gene for the phylogeny of Veneridae. (springer.com)
  • Eirín-López JM, González-Tizón AM, Martínez A, Méndez J (2002) Molecular and evolutionary analysis of mussel histone genes ( Mytilus spp): possible evidence of an "orphon origin" for H1 histone genes. (springer.com)
  • The histone demethylase PHF8 is a molecular safeguard of the IFN? (abcam.com)
  • rRNA
  • These data provide evidence that different evolutionary forces act at the heterochromatin and the 45S rDNA loci compared to the 5S rRNA and histone H3 genes during the evolution of the Scarabainae karyotypes. (biomedcentral.com)
  • multiple genes
  • Dong SM et al (2001) Concurrent hypermethylation of multiple genes is associated with grade of oligodendroglial tumors. (springer.com)
  • Gonzalez-Gomez P et al (2003) Promoter hypermethylation of multiple genes in astrocytic gliomas. (springer.com)
  • specific genes
  • Pioneer factors are involved in initiating cell differentiation and activation of cell-specific genes. (wikipedia.org)
  • Patterns of sequence variation reveal signals of recent selection in specific genes that may contribute to human fitness, and also in regions where no function is evident. (wikipedia.org)
  • mutations
  • Daughter cells that inherit these wrong bases carry mutations from which the original DNA sequence is unrecoverable (except in the rare case of a back mutation, for example, through gene conversion). (wikipedia.org)
  • Mutations in the EP300 gene are responsible for a small percentage of cases of Rubinstein-Taybi syndrome. (wikipedia.org)
  • Mutations in the EP300 gene have been identified in several other types of cancer. (wikipedia.org)
  • Somatic mutations in the EP300 gene have been found in a small number of solid tumors, including cancers of the colon and rectum, stomach, breast, and pancreas. (wikipedia.org)
  • Rearrangements and mutations of chromosome 1 are prevalent in cancer and many other diseases. (wikipedia.org)
  • recruitment
  • The binding of the HDE region by the U7 snRNA, through complementary base-pairing, is an important step for the future recruitment of cleavage factors during histone pre-mRNA processing. (wikipedia.org)
  • deletion
  • Identification of the deletion, amplification, and rearrangement of this gene that are associated with lipomas suggests a role in adipogenesis and mesenchymal differentiation. (wikipedia.org)
  • cell's
  • Modified histones and DNA attract the cell's gene-reading machinery via specific interactions with these elements of the histone code. (pennmedicine.org)
  • Many of these lesions cause structural damage to the DNA molecule and can alter or eliminate the cell's ability to transcribe the gene that the affected DNA encodes. (wikipedia.org)
  • Enzymes
  • Some examples of this include producing the mRNA that encode enzymes to adapt to a change in a food source, producing the gene products involved in cell cycle specific activities, and producing the gene products responsible for cellular differentiation in higher eukaryotes, as studied in evolutionary developmental biology. (wikipedia.org)
  • Pioneer factors can play a role in this by binding specific enhancers and flagging histone modification enzymes to that specific gene. (wikipedia.org)
  • nucleosome
  • Whereas point centromeres are defined by sequence, regional and holocentromeres are epigenetically defined by where a specific type of nucleosome (the one containing the centromeric histone H3) is located. (wikipedia.org)
  • Cells
  • Tracking individual cells, we show that the cells migrate in two phases that differ in speed, direction and amount of cellular rearrangement. (biologists.org)
  • Evidence such as tumour specific aneuploidy, presence of aneuploidy in various preneoplastic conditions, increased frequency of genetic instability in aneuploid cell lines compared with diploid cells, and mutation of mitotic checkpoint genes suggests that aneuploidy possibly plays an active role in carcinogenesis. (bmj.com)
  • The Vγ3 and Vγ4 genes, located downstream in the TCRγ Cγ1 gene cluster, are expressed by the earliest waves of developing TCRγδ + T cells in the fetal thymus, destined for intraepithelial locations. (rupress.org)
  • Upstream Vγ2 and Vγ5 genes are expressed in later waves in the adult and constitute most TCRγδ + T cells in secondary lymphoid tissue. (rupress.org)
  • These data provide a mechanism for specialization of the fetal thymus for the production of T cells expressing specific Vγ genes. (rupress.org)
  • The apparent function of HMGA2 in proliferation and differentiation of cells during development is supported by the observation that mice with mutant HMGA2 genes are unusually small (pygmy phenotype), and genome-wide association studies linking HMGA2-associated SNPs to variation in human height. (wikipedia.org)
  • In some leukemias MLL is rearranged so that the cells are unable to turn off Hox genes. (pennmedicine.org)
  • Humans have four sets of Hox genes, numbering 39 genes altogether, all of which aid in the differentiation of cells by location. (wikipedia.org)
  • downstream
  • This developmental pattern is caused in part by a preference for rearrangements of the downstream Vγ3 and Vγ4 genes in the early fetal stage, which switches to a preference for rearrangements of the upstream Vγ2 and Vγ5 gene rearrangements in the adult. (rupress.org)
  • Our gene targeting studies show that the downstream Vγ genes rearrange preferentially in the early fetal thymus because of their downstream location, independent of promoter or recombination signal sequences and unrelated to the extent of germline transcription. (rupress.org)
  • Gene targeting approach to insert a second downstream copy of the Vγ2 gene and delete the downstream Vγ4 and Vγ3 genes. (rupress.org)
  • In the fetal period, all of the genes are in an open configuration, and the closer Vγ3 and Vγ4 genes enjoy an advantage in rearrangement because of their downstream location proximal to Jγ1 . (rupress.org)
  • genome
  • Because researchers use different approaches to genome annotation their predictions of the number of genes on each chromosome varies (for technical details, see gene prediction). (wikipedia.org)
  • nuclear
  • Retinoic acid receptor alpha (RAR-α), also known as NR1B1 (nuclear receptor subfamily 1, group B, member 1) is a nuclear receptor that in humans is encoded by the RARA gene. (wikipedia.org)
  • sequences
  • Much of this diversity is caused by a great potential variability in CDR3 sequences in the TCR δ chain, but there is also diversity in the number of V, J, and (in the case of δ) D gene segments. (rupress.org)
  • Promoter
  • Fukushima T et al (2005) Promoter hypermethylation of mismatch repair gene hMLH1 predicts the clinical response of malignant astrocytomas to nitrosourea. (springer.com)
  • The transcription of a basic prokaryotic gene is dependent on the strength of its promoter and the presence of activators or repressors. (wikipedia.org)
  • subtype
  • RAR-α/PLZF gene fusion produces a subtype of APL that is unresponsive to tretinoin therapy and less responsive to standard anthracycline chemotherapy hence leading to poorer long-term outcomes in this subset of patients. (wikipedia.org)
  • Cell
  • Two other types of cell stacks that participate in ovary morphogenesis, the basal stalks and interfollicular stalks, also form by cell rearrangement utilizing a convergence and extension mechanism. (biologists.org)
  • 1994 ) A putative cell signal encoded by the folded gastrulation gene coordinates cell shape changes during Drosophila gastrulation. (biologists.org)
  • 1989 ) Local shifts in position and polarized motility drive cell rearrangement during sea urchin gastrulation. (biologists.org)
  • This contrasts with other developing epithelia, such as the wing imaginal disc and the embryonic germband in Drosophila , where oriented mitoses and local cell rearrangements appear to direct morphogenesis. (biologists.org)
  • The hallmark of B-cell development is the ordered recombination of immunoglobulin (Ig) genes. (springer.com)
  • Sigma factors act as mediators of sequence-specific transcription, such that a single sigma factor can be used for transcription of all housekeeping genes or a suite of genes the cell wishes to express in response to some external stimuli such as stress. (wikipedia.org)
  • This is a mechanism for the cell to switch a gene on was observed with glucocorticoid receptor recruiting modification factors that then modify the site to bind activated estrogen receptor which was coined as a "bait and switch" mechanism. (wikipedia.org)
  • These factors act, at least partly, by changing the genes of a cell. (wikipedia.org)
  • tandem
  • Childs G, Maxson R, Cohn RH, Kedes L (1981) Orphons: dispersed genetic elements derived from tandem repetitive genes of eucaryotes. (springer.com)
  • Histone recognition by tandem modules and modulation by multiple PTMs. (mskcc.org)