Genome-wide expression analysis of a new class of lncRNAs driven by SINE B2

Jinjiang Fan; Daniel B Martinez-Arguelles; Vassilios Papadopoulos

doi:10.1016/j.gene.2020.145332

Genome-wide expression analysis of a new class of lncRNAs driven by SINE B2

Gene. 2021 Feb 5:768:145332. doi: 10.1016/j.gene.2020.145332. Epub 2020 Dec 3.

Authors

Jinjiang Fan¹, Daniel B Martinez-Arguelles², Vassilios Papadopoulos³

Affiliations

¹ The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada; Department of Medicine, McGill University, Montreal, Quebec, Canada.
² The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada.
³ The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada; Department of Medicine, McGill University, Montreal, Quebec, Canada; Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, United States. Electronic address: vpapadop@usc.edu.

PMID: 33278552
DOI: 10.1016/j.gene.2020.145332

Abstract

Repetitive short interspersed elements B2 (SINE B2) have been shown to possess two promoters: polymerase III promoter for producing short B2-S RNAs and polymerase II promoter for driving the expression of long non-coding RNA (B2-AS lncRNAs). Using a B2-antisense (B2-AS) transcript sequence from the SINE B2 resident in mitochondrial translocator protein gene (Tspo) locus, we constructed a B2-AS specific RNA library and identified 96,862 sequences encoding potential B2-mediated lncRNAs, of which 55,592 lncRNAs with more than 390 nt in length possess a feature of potential genomic locus-specific effect. In addition, small RNA-Northern hybridization showed that the new B2-AS lncRNAs are constantly degraded by the Dicer1 enzyme, a finding further confirmed by in vitro Dicer1 enzyme digestion. B2-AS lncRNAs regulate the expression of target genes in a different fashion than B2-S RNAs. Genome-wide cross-comparison with mRNA mapping showed a total of 904 mRNA loci directly targeted by B2-AS lncRNAs, suggesting a locus-specific effect of the B2-AS lncRNAs and a general effect of B2-S RNAs.

Keywords: B2-AS lncRNA; RNA-seq; SINE B2; TSPO.

MeSH terms

Animals
Chromosome Mapping
Exome Sequencing / methods*
Gene Expression Profiling
High-Throughput Nucleotide Sequencing
Humans
Mice
Promoter Regions, Genetic
RNA Stability
RNA, Long Noncoding / chemistry*
RNA, Long Noncoding / genetics*
Receptors, GABA / genetics
Ribonuclease III / metabolism
Short Interspersed Nucleotide Elements*
Transcription, Genetic

Substances

RNA, Long Noncoding
Receptors, GABA
Ribonuclease III