PMC:2725788 / 19087-21550 JSONTXT

{"project":"2_test","denotations":[{"id":"19561344-15507602-25963813","span":{"begin":333,"end":335},"obj":"15507602"},{"id":"19561344-16176588-25963814","span":{"begin":336,"end":338},"obj":"16176588"},{"id":"19561344-14757826-25963815","span":{"begin":1849,"end":1851},"obj":"14757826"}],"text":"3.1.1. Description of the investigated HERV-W LTRs\nERVWE1/Syncytin-1 (Ch7q21.2; AC007566) transcription is regulated by two distinct elements, i.e. the ERVWE1 5′LTR U3 promoter region and an adjacent upstream TSE. This enhancer is located within a MaLR solo LTR within which the ERVWE1 provirus integrated ∼25–40 millions years ago.43,46 We chose to analyze together the methylation status of these two co-opted but unrelated LTRs involved in Syncytin-1 regulation, further referred to as MaLR[LTR]–ERVWE1[5′LTR]. As a minimal model to test the family related methylation process hypothesis, three other HERV-W LTRs were studied: ERVWE1[3′LTR], HW_4[5′LTR] and HW_12[solo LTR]. ERVWE1[3′LTR] is the 3′LTR of ERVWE1 provirus and represents topographically and phylogenetically the closest HERV-W LTR relative to ERVWE1[5′LTR]. HW_4[5′LTR] is an another functional (data not shown) 5′LTR belonging to a HERV-W provirus located on chromosome 4 (Ch4p13; AC024 022). HW_12[solo LTR] is a full-length solitary HERV-W LTR localized on chromosome 12 (Chr12q24.32; AC005868), and a cDNA overlapping the 51 bp at the 3′ end of the U5 region was found to have 100% identity with this part of the U5 region (BC038735). These HERV-W LTRs exhibit common but also specific CpG sites. An alignment of the investigated LTR U3 regions with highlighted CpG location is presented in Fig. 1. About 200 bp of the upstream env region from the ERVWE1[3′LTR] and ∼100 bp of the upstream region from the HW_4[5′LTR], which contains a MER110 type LTR, were co-amplified with the respective HERV-W LTRs as controls of genomic environment methylation.\nFigure 1 Alignment of HERV-W LTR U3 promoter. ERVWE1[5′LTR] and ERVWE1[3′LTR] U3 region allelic forms were previously determined on DNA amplified from 24 individuals (e.g. -132A. individual 132, allele A), i.e. 48 sequences.45 HW_12[solo LTR] and HW_4[5′LTR] allelic forms derive from the annotated genome sequence (-A, reference allele; -B, alternative allele; SNP ID, rs6489086). Proportion of each allelic form is given in hooks (e.g. [3], 3 of the 48 sequences hold this allelic form; [nd], not determined). CAAT box, TATA box and transcription binding sites are indicated. Effective transcription factor binding sites are underlined; putative transcription factor binding sites are marked by interrupted lines. CpG sites are indicated by gray background, their position in the U3 region is given relative to ERVWE1 5′LTR sequence.\n\n3"}