Biology subjects

Burns, K. H.

Publications and source records attributed to Burns, K. H..

3 recordsLinked to original sources

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

Dissection of purified LINE-1 reveals distinct nuclear and cytoplasmic intermediates

1.Long Interspersed Nuclear Element-1 (LINE-1, L1) is a mobile genetic element active in human genomes. L1-encoded ORF1 and ORF2 proteins bind L1 RNAs, forming ribonucleoproteins (RNPs). These RNPs interact with diverse host proteins, some repressive and others required for the L1 lifecycle. Using differential affinity purifications and quantitative mass spectrometry, we have characterized the proteins associated with distinctive L1 macromolecular complexes. Our findings support the presence of multiple L1-derived retrotransposition intermediates in vivo. Among them, we describe a cytoplasmic intermediate that we hypothesize to be the canonical ORF1p/ORF2p/L1-RNA-containing RNP, and we describe a nuclear population containing ORF2p, but lacking ORF1p, which likely contains host factors participating in template-primed reverse transcription.

molecular biology↗

bioRxiv2017

Towards the human cellular microRNAome

microRNAs are short RNAs that serve as master regulators of gene expression and are essential components of normal development as well as modulators of disease. MicroRNAs generally act cell autonomously and thus their localization to specific cell types is needed to guide our understanding of microRNA activity. Current tissue-level data has caused considerable confusion and comprehensive cell-level data does not yet exist. Here we establish the landscape of human cell-specific microRNA expression. This project evaluated 8 billion small RNA-seq reads from 46 primary cell types, 42 cancer or immortalized cell lines, and 26 tissues. It identified both specific and ubiquitous patterns of expression that strongly correlate with adjacent super-enhancer activity. Analysis of unaligned RNA reads uncovered 207 unknown minor strand (passenger) microRNAs of known microRNA loci and 2,632 novel putative microRNA loci. Although cancer cell lines generally recapitulated the expression patterns of matched primary cells, their isomiR sequence families exhibited increased disorder suggesting Drosha and Dicer-dependent microRNA processing variability. Cell-specific patterns of microRNA expression were used to deconvolute variable cellular composition of adipose tissue samples highlighting one use of this cell-specific microRNA expression data. Characterization of cellular microRNA expression across a wide variety of cell types provides a new understanding of this critical regulatory RNA species.

genomics↗