Clustering of DNA Sequences in Human Promoters (original) (raw)
Related papers
2004
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Identification and Characterization of the Potential Promoter Regions of 1031 Kinds of Human Genes
To understand the mechanism of transcriptional regulation, it is essential to identify and characterize thepromoter, which is located proximal to the mRNA start site. To identify the promoters from the large volumesof genomic sequences, we used mRNA start sites determined by a large-scale sequencing of the cDNA librariesconstructed by the “oligo-capping” method. We aligned the mRNA start sites with the genomic sequences andretrieved adjacent sequences as potential promoter regions (PPRs) for 1031 genes. The PPR sequences weresearched to determine the frequencies of major promoter elements. Among 1031 PPRs, 329 (32%) containedTATA boxes, 872 (85%) contained initiators, 999 (97%) contained GC box, and 663 (64%) contained CAATbox. Furthermore, 493 (48%) PPRs were located in CpG islands. This frequency of CpG islands was reduced inTATA+/Inr+ PPRs and in the PPRs of ubiquitously expressed genes. In the PPRs of the CGM2 gene, the DRAgene, and the TM30pl genes, which showed highly colon specific expression patterns, the consensus sequences ofE boxes were commonly observed. The PPRs were also useful for exploring promoter SNPs. (PDF) ERRATUM Identification and characterization of the potential promoter regions of 1031 kinds of human genes. Available from: https://www.researchgate.net/publication/222101688\_ERRATUM\_Identification\_and\_characterization\_of\_the\_potential\_promoter\_regions\_of\_1031\_kinds\_of\_human\_genes#fullTextFileContent [accessed May 17 2023].
MS#005 Hobson G Genomics 29 704 711 1995
The MEF2 genes belong to the MADS box family of regulated genes (Pollock and Treisman, 1991; Chamtranscription factors and encode proteins that bind as bers et al., 1992; homo-and heterodimers to a consensus CTA(T/ Martin et al., , 1994; McDermott A) 4 TAG/A sequence, which is present in the regulatory et al., 1993). This TA-rich sequence has been shown by regions of numerous muscle-specific and growth-inmutation analysis to play a role in muscle-specific gene ducible genes. Sequence analysis of human MEF2 regulation, as well as gene regulation in nonmuscle cDNA clones suggests that they arose from alternacells ; Horlick tively spliced transcripts of four different genes, termed MEF2A-D. We have mapped the MEF2 genes Molkentin and Markham, 1993). to human chromosomal regions by identifying unique The MEF2 proteins belong to the MADS box family of sequences in the MEF2 cDNA clones and using these transcription factors. The MADS box is a 49-amino-acid sequences as PCR primers on the DNA of human -roregion of homology that has been shown to function dent hybrid clone panels that are informative for difas a DNA binding and dimerization domain (Schwarzferent regions of the human genome. PCR primers Sommer et al., 1990;. The were also used to identify individual YAC clones for diversity of species that have transcription factors that two of the genes, MEF2A and MEF2C, and a PCR prodshare this domain is illustrated by the factors for which uct was used to identify cosmid clones for MEF2B. Gethe MADS box was named: the yeast mating-type spenetic and physical mapping information available cific factor, MCM1, the flowering plant homeotic genes, from genome databases on markers contained within AG and DEF A, and the mammalian serum response YAC and cosmid clones provided independent assignfactor, SRF (Schwarz-Sommer et al., 1990). In addition ments for those genes. Inter-Alu PCR painting probes of YAC clones were used as probes for high-resolution to the MADS box, the MEF2 proteins have a 29-aminochromosomal regional assignment by fluorescence in acid region of homology, termed the MEF2 domain, situ hybridization. The localization of MEF2A to chrowhich is directly carboxy-terminal to the MADS box mosome 15q26, MEF2B to 19p12, MEF2C to 5q14, and . The function of this domain is un-MEF2D to 1q12-q23 verifies the existence of at least known. four distinct loci for members of this gene family. MEF2 cDNA clones have been isolated from several ᭧ 1995 Academic Press, Inc.
BMC Molecular Biology BioMed Central
2007
Research article Two non-homologous brain diseases-related genes, SERPINI1 and PDCD10, are tightly linked by an asymmetric bidirectional promoter in an evolutionarily conserved manner
GENE-36664-15-feb-2010-Romero-PradoMMJ.pdf
The metabolic conditions affecting placental development depend on nutritional state, genetic constitution and other external factors. The secretion of human placental growth hormone (hGH-V) had shown to be dependent of glucose, but the regulatory effects of this metabolite on hGH-V promoter activity and gene expression in presence of 5-azacytidine had not been studied. In this work we compared the hGH-V promoter activity and the endogenous mRNA expression in human placental choriocarcinoma cell line JAR in the presence of glucose and demethylating genome conditions. High glucose concentration in culture medium diminished hGH-V mRNA endogenous levels in JAR cells whereas the expression of hGH-V from transfected PACs was slightly higher; but in the presence of 5azaC a higher hGH-V gene expression from both the endogenous and the transfected ones was obtained. A drastic diminution of promoter analysis was shown when cells had no glucose (J0 cells) or in presence of 5azaC; the placental transcription factors that showed modified binding capacity were HES-2, PPAR-γ, H4TF-1 and OCT-1. Our results suggest that in vitro suppressive glucose effect dictates a metabolic context to hGH-V gene expression and promoter regulation whereas a genomic methylation-dependent background is necessary to maintain placental transcription factors able to bind and regulate proximal promoter region of hGH-V in placental cells.
Via the Transcription Factors NF-IL6 and NF-�B in
2013
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