• 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)
  • 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)
  • tumor suppr
  • 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)
  • 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)
  • 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)
  • Genes implicated in epigenetic control, like DNMT3A , ASXL1 , EZH2 and TET2 , have been discovered to be mutated in MDS. (mdpi.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)
  • eukaryotes
  • 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)
  • 1998
  • Colgan DJ, McLauchlan A, Wilson GDF et al (1998) Histone H3 and U2 snRNA DNA sequences and arthropod molecular evolution. (springer.com)
  • modifications
  • Histone modifications are modifications made to the amino acid residues in the tails of the histones that either restrict the histone's ability to bind to DNA or boost the histone's ability to bind to DNA. (wikipedia.org)
  • FoxD3 has been associated as a repressor of both B-cell and melanocytic cell differentiation pathways, maintaining repressive histone modifications where bound, that have to be overcome to start differentiation. (wikipedia.org)
  • Pioneer factors can also be associated with recruiting transcription-activating histone modifications. (wikipedia.org)
  • binds
  • When ligand binds to the complex, it induces a conformational change allowing the recruitment of coactivators, histone acetyltransferases, and the basic transcription machinery. (wikipedia.org)
  • The 5' end of the U7 snRNA binds the HDE (Histone Downstream Element), a conserved purine-rich region, located 15 nucleotides downstream the histone mRNA cleavage site. (wikipedia.org)
  • expression
  • Recombination of antigen-receptor loci is regulated both by the developmentally controlled expression of the Rag1 and Rag2 genes and the accessibility of particular loci and their gene segments to recombination. (springer.com)
  • The regulated expression of B-lineage associated genes during B-cell differentiation in bone marrow and fetal liver. (springer.com)
  • Profile gene expression, histone location, replication origin activity etc, and use the data as input to data mining algorithm that tries to find correlations between various aspects of chromosome structure and whatever was profiled. (openwetware.org)
  • Disrupt all occurrences of TF binding sequences that occur in coding sequence (by disrupting the motif but keeping the same amino acid sequence) and then profile gene expression patterns. (openwetware.org)
  • Despite shared aberrations in the MLL gene, expression profiles from MLL -fusion ( MLL -F) and MLL -PTD AMLs display little overlap in gene expression, suggesting distinct molecular origins. (aacrjournals.org)
  • In line with these results, exogenous expression of an MLL fusion gene upregulated LOC100289656 expression in vivo . (aacrjournals.org)
  • Gene expression refers to the transcription of a gene but the RNA produced does not necessarily have to encode a protein product. (wikipedia.org)
  • Transcriptome profiling after deletion of MLL1 in cortical neurons revealed decreased promoter-bound H3K4me3 peaks at 318 genes, with 31 of these having significantly decreased expression and promoter binding. (wikipedia.org)
  • This is important to limit gene expression to specific cell types and has to be removed only when cell differentiation begins. (wikipedia.org)
  • 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)
  • genomic
  • This system is unique and flexible due to its dependence on RNA as the moiety that targets the nuclease to a desired DNA sequence and can be used to induce indel mutations, specific sequence replacements or insertions and large deletions or genomic rearrangements at any desired location in the genome. (diagenode.com)
  • The CRISPR/Cas genome editing system uses a RNA-guided endonuclease technology which allows for inducing indel mutations, specific sequence replacements or insertions and large deletions or genomic rearrangements at any desired location in the genome. (diagenode.com)
  • 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)
  • Mytilus
  • Drabent B, Kim JS, Albig W, Prats E, Cornudella L, Doenecke D (1999) Mytilus edulis histone gene clusters containing only H1 genes. (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)
  • Eirín-López JM, Ruiz MF, González-Tizón AM, Martínez A, Sánchez L, Méndez J (2004) Molecular evolutionary characterization of the mussel Mytilus histone multigene family: first record of a tandemly repeated unit of a five histone genes containing an H1 subtype whit "orphon" features. (springer.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)
  • endogenous
  • 50 genes involved in the pathway and removing all the endogenous copies would be a lot of work, and it's not even clear whether the yeast would still be alive. (openwetware.org)
  • sequences
  • 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)
  • 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)
  • CRISPR/Cas9 genome editing allows for double-stranded DNA breaks at specific sequences to efficiently disrupt, excise, mutate, insert, or replace genes. (diagenode.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
  • Within the MLL -F cohort, recurrent missense mutations were detected in the SPI1 transcription factor gene, and 45% of samples were characterized by mutations in RAS pathway genes, which conferred heightened sensitivity to MEK inhibitors and decreased sensitivity to receptor tyrosine kinase (RTK) inhibitors. (aacrjournals.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)
  • 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)
  • Rearrangements and mutations of chromosome 1 are prevalent in cancer and many other diseases. (wikipedia.org)
  • acute promyelo
  • Acute promyelocytic leukemia can be distinguished from other types of AML based on microscopic examination of the blood film or a bone marrow aspirate or biopsy as well as finding the characteristic rearrangement. (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 myxoid liposarcoma suggests a role in adipogenesis and mesenchymal differentiation. (genetex.com)
  • enzymes
  • 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)
  • downstream
  • 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)
  • 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)
  • 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)
  • fetal
  • These data provide a mechanism for specialization of the fetal thymus for the production of T cells expressing specific Vγ genes. (rupress.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)
  • genome
  • 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)
  • 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)
  • 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)
  • mitotic
  • 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)
  • 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)
  • 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)
  • 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)
  • Humans have four sets of Hox genes, numbering 39 genes altogether, all of which aid in the differentiation of cells by location. (wikipedia.org)