Whole-genome expression analysis of mammalian-wide interspersed repeat elements in human cell lines.
DNA Res
; 24(1): 59-69, 2017 Feb 01.
Article
em En
| MEDLINE
| ID: mdl-28028040
ABSTRACT
With more than 500,000 copies, mammalian-wide interspersed repeats (MIRs), a sub-group of SINEs, represent â¼2.5% of the human genome and one of the most numerous family of potential targets for the RNA polymerase (Pol) III transcription machinery. Since MIR elements ceased to amplify â¼130 myr ago, previous studies primarily focused on their genomic impact, while the issue of their expression has not been extensively addressed. We applied a dedicated bioinformatic pipeline to ENCODE RNA-Seq datasets of seven human cell lines and, for the first time, we were able to define the Pol III-driven MIR transcriptome at single-locus resolution. While the majority of Pol III-transcribed MIR elements are cell-specific, we discovered a small set of ubiquitously transcribed MIRs mapping within Pol II-transcribed genes in antisense orientation that could influence the expression of the overlapping gene. We also identified novel Pol III-transcribed ncRNAs, deriving from transcription of annotated MIR fragments flanked by unique MIR-unrelated sequences, and confirmed the role of Pol III-specific internal promoter elements in MIR transcription. Besides demonstrating widespread transcription at these retrotranspositionally inactive elements in human cells, the ability to profile MIR expression at single-locus resolution will facilitate their study in different cell types and states including pathological alterations.
Palavras-chave
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Sequências Repetitivas Dispersas
Limite:
Humans
Idioma:
En
Revista:
DNA Res
Assunto da revista:
BIOLOGIA MOLECULAR
/
GENETICA
Ano de publicação:
2017
Tipo de documento:
Article
País de afiliação:
Itália