Utility of next-generation RNA-sequencing in identifying chimeric transcription involving human endogenous retroviruses.

摘要: Several studies have shown that human endogenous retroviruses and retrovirus-like repeats (here collectively HERVs) impose direct regulation on genes through enhancer promoter motifs present in their long terminal (LTRs). Although chimeric transcription which novel gene isoforms containing retroviral sequence are transcribed from viral promoters commonly associated with disease, by HERVs is beneficial other settings; for example, testis of TP63 induced an ERV9 LTR protect the male germ line upon DNA damage inducing apoptosis, whereas globin locus γ- β-globin switch during normal hematopoiesis mediated complex interactions surrounding sequence. The advent deep sequencing or next-generation (NGS) has revolutionized way researchers solve important scientific questions develop hypotheses relation to genome regulation. We recently applied paired-end RNA-sequencing (RNA-seq) together chromatin immunoprecipitation (ChIP-seq) examine reference cell lines Encyclopedia Elements (ENCODE). This led discovery advanced mechanisms ERV9s across numerous loci including large gene-unannotated genomic regions, as well cooperative multiple non-LTR such Alu elements. In this article, well-established examples reviewed followed a description RNA-seq, its application identifying genome-widely. Based integrative analyses RNA-seq ChIP-seq, data we then tumor suppressor CADM2 SEMA3A, unannotated region. Taken together, article highlights high suitability contemporary methods future biology evolutionary acquired genome.