Global Intersection of Long Non-Coding RNAs with Processed and Unprocessed Pseudogenes in the Human Genome.

ABSTRACT: Pseudogenes are abundant in the human genome and had long been thought of purely as nonfunctional gene fossils. Recent observations point to a role for pseudogenes in regulating genes transcriptionally and post-transcriptionally in human cells. To computationally interrogate the network space of integrated pseudogene and long non-coding RNA regulation in the human transcriptome, we developed and implemented an algorithm to identify all long non-coding RNA (lncRNA) transcripts that overlap the genomic spans, and specifically the exons, of any human pseudogenes in either sense or antisense orientation. As inputs to our algorithm, we imported three public repositories of pseudogenes: GENCODE v17 (processed and unprocessed, Ensembl 72); Retroposed Pseudogenes V5 (processed only), and Yale Pseu

SUBMITTER: Milligan MJ 

PROVIDER: S-EPMC4805607 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature