0.3 Gene Regulation Ontology en The cascade of processes by which a signal interacts with a receptor, causing a change in the level or activity of a second messenger or other downstream target, and ultimately effecting a change in the functioning of the cell. [GO:0007165] GO:0007165 signal transduction signaling pathway transcription regulator activity GO:0030528 transcription regulator activity Plays a role in regulating transcription; may bind a promoter or enhancer DNA sequence or interact with a DNA-binding transcription factor. [GO:0030528] protein catabolism The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds. [GO:0030163] GO:0030163 protein catabolic process transcription of stimulon genes The synthesis of RNA on the template of stimulon genes. CHEBI:24846 inositol phosphates inositol phosphate binding of TF to TF binding site of protein Selective interaction of a transcription factor with one or more specific sites on a protein. genetic modification spacer Provides flexibility needed for communication between DNA bound proteins. Not recognized by gene regulatory proteins. A region placed between two or more pieces of sequence features (e.g. genes). eukaryote NCBI Taxonomy ID: 2759 Eukaryota Organism characterized by the presence of a nucleus. Also other organelles such as mitochondria and/or chloroplasts may be present in eukaryotes. Includes all plants, animals, green algae, and fungi. [http://www.knowledgebank.irri.org/glossary/Glossary/E.htm] Selective interaction of a protein with a specific site on DNA which forms a chemical bond. binding of protein to protein binding site of DNA Any process that stops, prevents or reduces the frequency, rate or extent of gene expression. negative regulation of gene expression sigma factor A sigma factor is the promoter specificity subunit of eubacterial-type multisubunit RNA polymerases, those whose core subunit composition is often described as alpha(2)-beta-beta-prime. (This type of multisubunit RNA polymerase complex is known to be found in eubacteria and plant plastids). Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, this binds specifically to promoter sequences, with the sigma factor making sequence specific contacts with the promoter elements. The sigma subunit is released from the elongating form of the polymerase and is thus free to act catalytically for multiple RNA polymerase core enzymes. [GO:0016987] Human serum response factor (SRF) is a ubiquitous nuclear protein important for cell proliferation and differentiation. SRF function is essential for transcriptional regulation of numerous growth-factor-inducible genes, such as c-fos oncogene and muscle-specific actin genes. A core domain of around 90 amino acids is sufficient for the activities of DNA-binding, dimerisation and interaction with accessory factors. Within the core is a DNA-binding region, designated the MADS box, that is highly similar to many eukaryotic regulatory proteins: among these are MCM1, the regulator of cell type-specific genes in fission yeast; DSRF, a Drosophila trachea development factor; the MEF2 family of myocyte-specific enhancer factors; and the Agamous and Deficiens families of plant homeotic proteins. Proteins belonging to the MADS family function as dimers, the primary DNA-binding element of which is an anti-parallel coiled coil of two amphipathic alpha-helices, one from each subunit.! MADS A transcription factor containing the homeobox domain. It is usually involved in the control of gene expression during morphogenesis and development. [PANTHER:MF00038] homeobox transcription factor helix-turn-helix domain transcription factor A transcription factor containing helix-turn-helix domain. The synthesis of RNA on the template of regulon genes. transcription of regulon genes Single-stranded RNA molecules of about 21-23 nucleotides in length, which regulate gene expression. miRNAs are encoded by genes that are transcribed from DNA but not translated into protein (non-coding RNA); instead they are processed from primary transcripts known as pri-miRNA to short stem-loop structures called pre-miRNA and finally to functional miRNA. Mature miRNA molecules are partially complementary to one or more messenger RNA (mRNA) molecules, and their main function is to downregulate gene expression. [http://en.wikipedia.org/wiki/MicroRNA] microRNA miRNA binding The selective, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. [GO:0005488] GO:0005488 binding SMAD NF-1 transcription factor A transcription factor containing SMAD NF-1 domain carbohydrate CHEBI:23008 carbohydrate A class of organic compounds containing carbon, hydrogen and oxygen and having the general formula Cm(H2O)n. They usually serve as a major energy source in the diet of animals. Example: sugar or starch. IMR:0001657 carbohydrate SO:0000165 enhancer A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter. [SO:0000165, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] enhancer A transcription factor containing beta scaffold domain with minor groove contacts beta scaffold domain transcription factor with minor groove contacts downstream regulatory sequence A sequence located in the downstream region of a gene that controls the rate or manner in which the gene is expressed. second messenger IMR:0100022 second messenger The directed movement of proteins into, out of, within or between cells. [GO:0015031] GO:0015031 protein transport protein transport gas The vapor state of matter; nonelastic fluids in which the molecules are in free movement and their mean positions far apart. Gases tend to expand indefinitely, to diffuse and mix readily with other gases, to have definite relations of volume, temperature, and pressure, and to condense or liquefy at low temperatures or under sufficient pressure. [IMR:0001720, MeSH:D005740] IMR:0001720 gas A compact, globular sub-structure of a transcription repressor. structural domain of transcription repressor glia cell missing transcription factors GCM transcription factors are a family of proteins which contain a GCM motif. The GCM motif is a domain that has been identified in proteins belonging to a family of transcriptional regulators involved in fundamental developmental processes which comprise Drosophila melanogaster GCM and its mammalian homologs. IN GCM transcription factors the N-terminal moiety contains a DNA-binding domain of 150 residues. Sequence conservation is highest in this GCM domain. In contrast, the C-terminal moiety contains one or two transactivating regions and is only poorly conserved. The GCM motif has been shown to be a DNA binding domain that recognises preferentially the nonpalindromic octamer 5'-ATGCGGGT-3'. The GCM motif contains many conserved basic amino acid residues, seven cysteine residues, and four histidine residues. The conserved cysteines are involved in shaping the overall conformation of the domain, in the process of DNA binding and in the redox regulation of DNA binding. ! GCM transcription factor A DNA sequence (cis-regulatory element) found in the promoter region of most genes in eukaryotes (also called Goldberg-Hogness box). Considered to be the core promoter sequence, it is the binding site of either transcription factors or histones (the binding of a transcription factor blocks the binding of a histone and vice versa) and is involved in the process of transcription by RNA polymerase. It has the core DNA sequence 5'-TATAAA-3' or a variant, which is usually followed by three or more adenine bases. The TATA box is usually located 25 base pairs upstream to the transcription site. (modified from [http://en.wikipedia.org/wiki/TATA_box]) TATA box plant NCBI Taxonomy ID:3193 Embryophyta Multicellular, eukaryotic life forms of the kingdom Plantae. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions ( MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alteration of haploid and diploid generations. [MESH:D010944] orientation A position or arrangement of points, relative to one another or other specific directions. cold shock domain transcription factor A transcription factor containing cold shock domain. Any of the unicellular prokaryotic organisms, which vary in terms of morphology, oxygen and nutritional requirements and motility and can exist either as independent (free-living) organisms or as parasites (dependent upon another organism for life). NCBI Taxonomy ID: 2 Bacteria bacterium The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure. [GO:0006457] GO:0006457 protein folding protein folding RNA polymerase III promoter A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription. [SO:0000171] SO:0000171 RNApol III promoter fusion of gene with reporter gene The joining of a gene and a reporter gene Any process that modulates the frequency, rate or extent of modification of molecular entity. regulation of modification of molecular entity A domain of a transcription factor that binds DNA. DNA binding domain of transcription factor IMR:0000002 ligand Binding to a specific receptor protein and activating intracellular signaling cascades that alter the behavior of the cell. [IMR:0000002, ISBN:0815340729] ligand A definite pathologic process with a characteristic set of signs and symptoms. It may affect the whole body or any of its parts, and its etiology, pathology, and prognosis may be known or unknown. [MeSH:D004194] disease A gene coding for RNA (tRNA, rRNA, etc.). RNA coding gene The use of high-throughput methods (e.g. DNA microarrays) for evaluating the level and timing of gene expression in a biologic sample (a cell or tissue). expression profiling translation initiation complex GO:0003743 translation initiation factor activity; IMR:0000901 translation initiation factor The protein complex that initiates ribosome-mediated translation of mRNA into a polypeptide (modified from [GO:0003743]). A transcription factor containing forkhead/winged-helix domain forkhead/winged-helix transcription factor A transcription factor containing RHR domain RHR transcription factor GO:0045727 positive regulation of protein biosynthetic process Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. [GO:0045727] positive regulation of translation transcription coactivator A transcription cofactor that activates transcription from a RNA polymerase II promoter; it does not bind DNA itself. (modified from [GO:0003713]) GO:0003713 transcription coactivator activity transcription factor gene regulatory protein A transcription factor that binds to a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein (other transcription factors of cofactors) or protein or macromolecular complex. (modified from [GO:0003700]) RNA polymerase III promoter type 2 SO:0000618 RNApol_III_promoter_type_2 A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease. [GO:0042493] GO:0042493 response to drug response to drug sigma factor activity GO:0016987 sigma factor activity Activity of a sigma factor. A sigma factor is the promoter specificity subunit of eubacterial-type multisubunit RNA polymerases, those whose core subunit composition is often described as alpha(2)-beta-beta-prime. (This type of multisubunit RNA polymerase complex is known to be found in eubacteria and plant plastids). Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, this binds specifically to promoter sequences, with the sigma factor making sequence specific contacts with the promoter elements. The sigma subunit is released from the elongating form of the polymerase and is thus free to act catalytically for multiple RNA polymerase core enzymes. [GO:0016987] A virus that infects bacteria. Also called a phage. [www.accessexcellence.org/RC/AB/WYW/wkbooks/SFTS/glossary.html] NCBI Taxonomy ID: 38018 unidentified phage bacteriophage CHEBI:25608 nucleoside phosphates IMR:0001349 nucleotide A nucleotide consists of a nitrogen-containing base, a five-carbon sugar, and one or more phosphate groups. Nucleotides can carry chemical energy (e.g. ATP), form coenzymes (e.g. CoA), be used as specific signaling molecules (e.g. cAMP) in the cell. Nucleotides are the subunits of the nucleic acids. [IMR:0001349, ISBN:0815340729] nucleotide positive regulation of transcription of gene protein coding region Any transcription regulator activity that prevents or downregulates transcription. [GO:0016564] GO:0016564 transcription repressor activity transcription repressor activity A hybrid gene formed from two previously separate genes. It can occur as the result of a translocation, interstitial deletion, or chromosomal inversion. The fusion of two genes is often taken as evidence that these genes have related functions [http://en.wikipedia.org/wiki/Fusion_gene] fusion gene 2 GO:0045182 translation regulator activity Any substance involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome (modified from [GO:0045182]). translation regulator TF binding site of protein A region on a protein that forms a chemical bond with one or more transcription factors. poly-A signal sequence SO:0000551 polyA signal sequence The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA. [SO:0000551, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] transcription repressor Any transcription regulator that prevents or downregulates transcription. transcription inhibitor enzyme A protein that has catalytic activity. heterodimerization GO:0046982 protein heterodimerization activity Interacting selectively with a nonidentical protein to form a heterodimer. [GO:0046982] CHEBI:33696 nucleic acids nucleic acid Macromolecules, the major organic matter of the nuclei of biological cells, made up of nucleotide units, and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. [CHEBI:33696] intron on DNA A non-coding segment of DNA; edited out during the transcription process. [http://library.thinkquest.org/17109/glossary.htm] SO:0000617 RNApol_III_promoter_type_1 RNA polymerase III promoter type 1 The order of nucleotides in RNA or DNA or of amino acids in a polypeptide. [http://www.plantpath.cornell.edu/glossary/Defs_S.htm] sequence gene expression regulator Selective interaction of a transcription factor with an operator binding of transcription factor to operator binding of molecular entity Selective interaction of a molecule entity with other substance. CHEBI:26564 riboses ribose copper-fist domain A domain, similar in structure to metallothionein, undergoing a large conformational change on copper-binding that allows DNA-binding. It contains a conserved array of zinc-binding residues (Cys-X2-Cys-X8-Cys-X-His) and forms a three-stranded antiparallel beta-sheet with two short helical segments that project from one end of the beta-sheet. Conserved residues form a basic patch that may be important for DNA binding. (modified from [InterPro: IPR001083]) unpacked DNA The DNA that is unpacked from the loosen chromatin and hence get easy access to various enzymes like DNA polymerase or RNA polymerase in replication or transcription of gene. C6 zinc cluster transcription factor A transcription factor containing C6 zinc cluster domain The SAND domain (named after Sp100, AIRE-1, NucP41/75, DEAF-1) is a conserved ~80 residue region found in a number of nuclear proteins, many of which function in chromatin-dependent transcriptional control. These include proteins linked to various human diseases, such as the Sp100 (Speckled protein 100 kDa), NUDR (Nuclear DEAF-1 related), GMEB (Glucocorticoid Modulatory Element Binding) proteins and AIRE-1 (Autoimmune regulator 1) proteins. Proteins containing the SAND domain have a modular structure; the SAND domain can be associated with a number of other modules, including the bromodomain, the PHD finger and the MYND finger. Because no SAND domain has been found in yeast, it is thought that the SAND domain could be restricted to animal phyla. Many SAND domain-containing proteins, including NUDR, DEAF-1 (Deformed epidermal autoregulatory factor-1) and GMEB, have been shown to bind DNA sequences specifically. The SAND domain has been proposed to mediate the DNA bindin! SAND domain TF module A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription. [SO:0000169] SO:0000169 RNApol I promoter RNA polymerase I promoter The accidental joining of DNA of two genes, such as can occur in a translocation or inversion. Gene fusions can give rise to hybrid proteins or to the misregulation of the transcription of one gene by the cis regulatory elements (enhancers) of another. [http://www.biochem.northwestern.edu/holmgren/Glossary/Definitions/Def-G/gene_fusion.html] 2 gene fusion deoxynucleoside A molecule composed of a nitrogenous base attached to the five-carbon sugar deoxyribose. [http://cancerweb.ncl.ac.uk/cgi-bin/omd?deoxynucleoside] WRKY domain The WRKY domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger- like motif. The WRKY domain is found in one or two copies in a superfamily of plant transcription factors involved in the regulation of various physiological programs that are unique to plants, including pathogen defense, senescence, trichome development and the biosynthesis of secondary metabolites. The WRKY domain binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core of the W box is essential for function and WRKY binding. Some proteins known to contain a WRKY domain include Arabidopsis thaliana ZAP1 (Zinc-dependent Activator Protein-1) and AtWRKY44/TTG2, a protein involved in trichome development and anthocyanin pigmentation; and wild oat ABF1-2, two proteins involved in the gibberelic acid-induced expression of the alpha-Amy2 gene. Structural stud! histone fold A motif consisting of a core of three helices, where the long middle helix is flanked at each end by shorter ones. Proteins displaying this structure include the nucleosome core histones, which form octomers composed of two copies of each of the four histones, H2A, H2B, H3 and H4; archaeal histone, which possesses only the core domain part of eukaryotic histone; and the TATA-box binding protein (TBP)-associated factors (TAF), where the histone fold is a common motif for mediating TAF-TAF interactions. TAF proteins include TAF(II)18 and TAF(II)28, which form a heterodimer, TAF(II)42 and TAF(II)62, which form a heterotetramer similar to (H3-H4)2, and the negative cofactor 2 (NC2) alpha and beta chains, which form a heterodimer. (modified from [InterPro:IPR009072]) A ligand-dependent receptor found in the nucleus of the cell. [GO:0004879] GO:0004879 ligand-dependent nuclear receptor activity nuclear receptor transcription factor primary structure (Wikipedia, en:) The primary structure of a biological molecule is the exact specification of its atomic composition and the chemical bonds connecting those atoms (including stereochemistry). For a typical unbranched, un-crosslinked biopolymer (such as a molecule of DNA, RNA or typical intracellular protein), the primary structure is equivalent to specifying the sequence of its monomeric subunits, e.g., the nucleotide or peptide sequence. mutant regulatory DNA protein maturation GO:0051604 protein maturation The process leading to the attainment of the full functional capacity of a protein. [GO:0051604] Protein that has transcription regulator activity. transcription regulator Any process that modulates the frequency, rate or extent of transcription by protein components involved in a system responding to environmental changes characterized usually by a sensor kinase in the cell membrane that phosphorylates itself in response to a signal and a response regulator to which the phosphoryl group is transferred. regulation of transcriptin by two component regulatory system Identification of motifs using the experimental and computational techniques. motif identification DNA binding domain of protein Any protein motif that binds to double- or single-stranded DNA with affinity to a specific sequence or set thereof or a general affinity to DNA. [http://en.wikipedia.org/wiki/DNA-binding_domain] This domain is found in a number of transcription factors, including p53, NFATC, TonEBP, STAT-1, and NFkappaB, where it is responsible for DNA-binding. These transcription factors play diverse roles in the regulation of cellular functions: the p53 tumour suppressor upregulates the expression of genes involved in cell cycle arrest and apoptosis; NFATC regulates the production of effector proteins involved in coordinating the immune response; TonEBP regulates gene expression induced by osmotic stress and helps regulate intracellular volume during cell growth; STAT-1 plays an important role in B lymphocyte growth and function; and NFkappaB is involved in the inflammatory response. The DNA-binding domain acts to clamp, or in the case of TonEBP, encircle the DNA target in order to stabilize the protein-DNA complex. Protein interactions may also serve to stabilize the protein-DNA complex, for example in the STAT-1 dimer the SH2 (Src homology 2) domain in each monomer is coup! p 53 like A slime layer that develops naturally when bacteria congregate on surfaces. [publications.nigms.nih.gov/thenewgenetics/glossary.htm] biofilm tissue A group of similar cells, specialized to perform a particular function (or functions). Examples of tissue include, heart mucslce, skin, bone etc.[http://medicineworld.org/cancer/descriptions.html] The process by which a methyl group is covalently attached to a molecule. [GO:0032259] GO:0032259 methylation methylation A transcription factor containing WRKY domain. WRKY transcription factor Any process involved in mediating the movement of discrete segments of DNA between nonhomolgous sites. [GO:0032196] GO:0032196 transposition transposition A transcription factor that contains a basic region mediating sequence-specific DNA-binding, followed by a leucine zipper region for protein dimerization. bZIP transcription factor substrate A molecule upon which an enzyme acts. Enzymes catalyze chemical reactions involving the substrate(s). The substrate binds with the enzyme's active site, and an enzyme-substrate complex is formed. The substrate is broken down into a product and is released from the active site. The active site is now free to accept another substrate molecule. [http://en.wikipedia.org/wiki/Substrate_%28biochemistry%29] A domain defined as the minimal region within the T-box protein that is both necessary and sufficient for sequence-specific DNA binding, all members of the family bind to the DNA consensus sequence TCACACCT. Transcription factors of the T-box family are required both for early cell-fate decisions, such as those necessary for formation of the basic vertebrate body plan, and for differentiation and organogenesis. (modified from [InterPro:IPR001699] T box domain A genetic process by which, in eukaryotic cells, primary transcript RNA is converted into mature RNA. The three main modifications are 5' capping, 3' polyadenylation, and RNA splicing. (modified from [http://en.wikipedia.org/wiki/Post-transcriptional_modification]) posttranscriptional modification A permanent change in the DNA sequence of a gene that alters the genetic message carried by that gene. mutation cell differentiation GO:0030154 cell differentiation The process whereby relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate. [GO:0030154] TEA domain transcription factor Transcriptional enhancer activators are nuclear proteins that contain a TEA/ATTS domain, a DNA-binding region of 66-68 amino acids. The TEA/ATTS domain is found in the N-termini of certain gene regulatory proteins, such as the Simian virus 40 (SV40) enhancer factor TEF-1, yeast trans-acting factor TEC-1 (which is required for TY1 enhancer activity), and the Aspergillus abaA regulatory gene product. SV40 and retroviral enhancers, and those to which TEF-1, TEC-1 and abaA proteins bind, contain GT-IIC sites: the TEA/ATTS domain may therefore recognise and bind such sites. Secondary structure predictions suggest the presence of 3 helices, but have not confirmed the presence of the helix-turn-helix motif characteristic of many DNA-binding proteins: DNA-binding may therefore be effected by a different mechanism. [InterPro: IPR000818] GO:0006350 transcription The synthesis of either RNA on a template of DNA or DNA on a template of RNA. [GO:0006350] transcription of gene intron on RNA The parts that are transcribed along with the exons but are removed from the primary gene transcript (pre-RNA) by RNA SPLICING to leave mature RNA. The specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death. [GO:0008219] GO:0008219 cell death cell death regulatory sequence regulatory DNA region regulatory DNA A DNA sequence that controls the expression of a gene. [SO:0005836, http://www.genpromag.com/scripts/glossary.asp?LETTER=R] Typically binding sites for proteins required for transcription, such as gene regulatory proteins and polymerases. SO:0005836 regulatory region DM-domain-containing transcription factor A transcription factor containing DM domain. gene expression The process by which the information encoded in a gene is converted into protein or some form of RNA. The DNA sequence is first transcribed into RNA and then usually translated into protein. [http://www.homepages.indiana.edu/120800/text/glossary.html] positive polarity The positive direction. metabolic pathway GO:0008152 metabolic process Processes that cause many of the chemical changes in living organisms, including anabolism and catabolism. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. [GO:0008152] A process of producing a protein from its gene via transcription and translation in eukaryotes. It is usually controlled at various points in the sequence leading to protein synthesis. eukaryotic gene expression GO:0006605 protein targeting The process of targeting specific proteins to particular membrane-bound subcellular organelles. Usually requires an organelle specific protein sequence motif. [GO:0006605] protein targeting Any process that activates or increases the frequency, rate or extent of transcription. [GO:0045941] GO:0045941 positive regulation of transcription positive regulation of transcription E.coli Escherichia coli NCBI Taxonomy ID: 562 Escherichia coli feedback loop The regulatory circuits whereby some proportion of the output signal of a system is passed (fed back) to the input. e.g. repressor and activator proteins in genetic operons are used to create feedback loop. The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide. [GO:0016310] GO:0016310 phosphorylation phosphorylation A DNA region that encodes one or more proteins.. protein coding DNA region locus control region A region that enhances the expression of linked genes to physiological levels in a tissue-specific and copy number-dependent manner at ectopic chromatin sites. It is required for normal regulation of expression of some genes. SO:0000037 locus control region LCR open reading frame The inframe interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER. [SO:0000236] SO:0000236 ORF ORF The directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells.[GO:0006810] GO:0006810 transport transport A helix-span-helix domain in the C-terminal region of activator protein-2 (AP-2) transcription factors, which mediates dimerisation and site-specific DNA binding. (modified from [InterPro:IPR013854]) b HSH transcription of operon The synthesis of RNA on a DNA template of operon. A transcription regulator required for initiation of transcription. transcription activator cellular developmental process A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition. [GO:0048869] GO:0048869 cellular developmental process Heat shock factor (HSF) is a transcriptional activator of heat shock genes: it binds specifically to heat shock promoter elements, which are palindromic sequences rich with repetitive purine and pyrimidine motifs. Under normal conditions, HSF is a homo-trimeric cytoplasmic protein, but heat shock activation results in relocalisation to the nucleus. Each HSF monomer contains one C-terminal and three N-terminal leucine zipper repeats. Point mutations in these regions result in disruption of cellular localisation, rendering the protein constitutively nuclear. Two sequences flanking the N-terminal zippers fit the consensus of a bi- partite nuclear localisation signal (NLS). Interaction between the N- and C-terminal zippers may result in a structure that masks the NLS sequences: following activation of HSF, these may then be unmasked, resulting in relocalisation of the protein to the nucleus. The DNA-binding component of HSF lies to the N-terminus of the first NLS region, a! HSF domain p53-like transcription factor A transcription factor containing p53-like domain. RNA coding region GO:0003674 molecular function gene product function formation of transcription factor complex The joining of transcription factors Any process that modulates the frequency, rate or extent of gene expression. regulation of gene expression GO:0009452 RNA capping The sequence of enzymatic reactions by which the 5' cap structure, an inverted 7-methylguanosine linked via a 5'-5' triphosphate bridge (m7G(5')ppp(5')X) to the first transcribed residue, is added to a nascent RNA polymerase II transcript. [GO:0009452] 5' capping GO:0032993 protein-DNA complex A macromolecular complex containing both protein and DNA molecules. [GO:0032993] complex of protein and DNA reporter gene construction Construction of any gene that encodes an easily assayed product that is used to monitor gene expression under different conditions; usually to test the activity of a promoter. protein binding site of protein A region on a protein that forms a chemical bond (protein ligands) with other proteins. GO:0003899 DNA-directed RNA polymerase activity GO:0003968 RNA-directed RNA polymerase activity An enzyme that catalyses the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA or RNA template (modified from [GO:0003899, GO:0003968]). RNA polymerase A physical continuant is an entity that has spatial dimension. It can either have mass (such as a protein) or no mass (such as DNA minor groove). physical continuant intron A segment of DNA that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it. [SO: 0000188, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html] SO:0000188 intron euchromatin Transcriptionally active form of chromatin. double strand DNA Double stranded DNA molecules structural domain of transcription activator A compact, globular sub-structure of a transcription activator. GO:0017148 negative regulation of protein biosynthetic process Any process that stops, prevents or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA. [GO:0017148] negative regulation of translation sequence homology analysis An analytic procedure that compares the similarity of a sequence with other sequences. rRNA SO:0000252 rRNA RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity. [SO:0000252, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732] A sequence feature of nucleic acids. nucleic acid region molecular interaction Interaction of a molecule with another molecule. The helix-loop-helix (HLH) DNA-binding domain consists of a closed bundle of four helices in a left-handed twist with two crossover connections. The HLH domain directs dimerisation, and is juxtaposed to basic regions to create a DNA interaction interface surface that recognises specific DNA sequences. Basic region/HLH (bHLH) proteins regulate diverse biological pathways. bHLH proteins include MyoD, SREBPs (sterol regulatory element binding proteins), and yeast Pho4 (phosphatase system). In certain proteins the bHLH domain contains a leucine-zipper motif. The bHLH/leucine zipper (bHLHZip) domain specifies dimerisation within a network of proteins and determines sequence-specific DNA binding. bHLHZip domains occur in the transcription factors Myc, Mad, Max and Usf. [InterPro: IPR011598] b HLH A process is a collection of molecular events with a defined beginning and end. [GO:0008150] GO:0008150 biological process