title: In silico analysis of regulatory and structural motifs of the ovine HSP90AA1 gene.
abstract: Gene promoters are essential regions of DNA where the transcriptional molecular machinery to produce RNA molecules is recruited. In this process, DNA epigenetic modifications can acquire a fundamental role in the regulation of gene expression. Recently, in a previous work of our group, functional features and DNA methylation involved in the ovine HSP90AA1 gene expression regulation have been observed. In this work, we report a combination of methylation analysis by bisulfite sequencing in several tissues and at different developmental stages together with in silico bioinformatic analysis of putative regulating factors in order to identify regulative mechanisms both at the promoter and gene body. Our results show a "hybrid structure" (TATA box + CpG island) of the ovine HSP90AA1 gene promoter both in somatic and non-differentiated germ tissues, revealing the ability of the HSP90AA1 gene to be regulated both in an inducible and constitutive fashion. In addition, in silico analysis showed that several putative alternative spliced regulatory motifs, exonic splicing enhancers (ESEs), and G-quadruplex secondary structures were somehow related to the DNA methylation pattern found. The results obtained here could help explain the differences in cell-type transcripts, tissue expression rate, and transcription silencing mechanisms found in this gene.
authors.affiliation: INIA, Carretera de La Coruña Km. 7.5, 28040, Madrid, Spain.
authors.forename: Carmen
authors.initials: C
authors.lastname: González
authors.affiliation: INIA, Carretera de La Coruña Km. 7.5, 28040, Madrid, Spain. judit.salces-ortiz@univ-lyon1.fr.
authors.forename: Judit
authors.identifier: http://orcid.org/0000-0001-5202-7676
authors.initials: J
authors.lastname: Salces-Ortiz
authors.affiliation: Unidad de Tecnología en Producción Animal, CITA, 59059, Zaragoza, Spain.
authors.forename: Jorge H
authors.initials: JH
authors.lastname: Calvo
authors.affiliation: INIA, Carretera de La Coruña Km. 7.5, 28040, Madrid, Spain.
authors.forename: M Magdalena
authors.initials: MM
authors.lastname: Serrano
mesh_terms: D000818:Animals; D003198:Computer Simulation; D018899:CpG Islands / Q000235:genetics*; D019175:DNA Methylation / Q000235:genetics*; D054856:G-Quadruplexes; D005786:Gene Expression Regulation; D018841:HSP90 Heat-Shock Proteins / Q000737:chemistry / Q000235:genetics*; D011401:Promoter Regions, Genetic; D012756:Sheep; D016385:TATA Box / Q000235:genetics
chemical_list: D018841:HSP90 Heat-Shock Proteins
keywords: HSP90AA1; In silico analysis; Methylation pattern; Regulatory motifs; Sheep; Structural features
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