Ardeljan, D. | bioRxiv Science

bioRxiv2018

SQuIRE: Software for Quantifying Interspersed Repeat Elements

Transposable elements are interspersed repeat sequences that make up much of the human genome. Conventional approaches to RNA-seq analysis often exclude these sequences, fail to optimally adjudicate read alignments, or align reads to interspersed repeat consensus sequences without considering these transcripts in their genomic contexts. As a result, repetitive sequence contributions to transcriptomes are not well understood. Here, we present Software for Quantifying Interspersed Repeat Expression (SQuIRE), an RNA-seq analysis pipeline that integrates repeat and genome annotation (RepeatMasker), read alignment (STAR), gene expression (StringTie) and differential expression (DESeq2). SQuIRE uniquely provides a locus-specific picture of interspersed repeat-encoded RNA expression. SQuIRE can be downloaded at (github.com/wyang17/SQuIRE).

bioinformatics↗

bioRxiv2017

Pan-cancer analysis of whole genomes reveals driver rearrangements promoted by LINE-1 retrotransposition in human tumours

About half of all cancers have somatic integrations of retrotransposons. To characterize their role in oncogenesis, we analyzed the patterns and mechanisms of somatic retrotransposition in 2,954 cancer genomes from 37 histological cancer subtypes. We identified 19,166 somatically acquired retrotransposition events, affecting 35% of samples, and spanning a range of event types. L1 insertions emerged as the first most frequent type of somatic structural variation in esophageal adenocarcinoma, and the second most frequent in head-and-neck and colorectal cancers. Aberrant L1 integrations can delete megabase-scale regions of a chromosome, sometimes removing tumour suppressor genes, as well as inducing complex translocations and large-scale duplications. Somatic retrotranspositions can also initiate breakage-fusion-bridge cycles, leading to high-level amplification of oncogenes. These observations illuminate a relevant role of L1 retrotransposition in remodeling the cancer genome, with potential implications in the development of human tumours.

genomics↗