Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments, bioRxiv, 2019-03-19

AbstractUnderstanding how gene expression programs are controlled requires identifying regulatory relationships between transcription factors and target genes. Gene regulatory networks are typically constructed from gene expression data acquired following genetic perturbation or environmental stimulus. Single-cell RNA sequencing (scRNAseq) captures the gene expression state of thousands of individual cells in a single experiment, offering advantages in combinatorial experimental design, large numbers of independent measurements, and accessing the interaction between the cell cycle and environmental responses that is hidden by population-level analysis of gene expression. To leverage these advantages, we developed a method for transcriptionally barcoding gene deletion mutants and performing scRNAseq in budding yeast (Saccharomyces cerevisiae). We pooled diverse genotypes in 11 different environmental conditions and determined their expression state by sequencing 38,285 individual cells. We developed, and benchmarked, a framework for learning gene regulatory networks from scRNAseq data that incorporates multitask learning and constructed a global gene regulatory network comprising 12,018 interactions. Our study establishes a general approach to gene regulatory network reconstruction from scRNAseq data that can be employed in any organism.

biorxiv genomics 0-100-users 2019

Ribosome profiling at isoform level reveals an evolutionary conserved impact of differential splicing on the proteome, bioRxiv, 2019-03-19

AbstractThe differential production of transcript isoforms from gene loci is a key cellular mechanism. Yet, its impact in protein production remains an open question. Here, we describe ORQAS (ORF quantification pipeline for alternative splicing) a new pipeline for the translation quantification of individual transcript isoforms using ribosome-protected mRNA fragments (Ribosome profiling). We found evidence of translation for 40-50% of the expressed transcript isoforms in human and mouse, with 53% of the expressed genes having more than one translated isoform in human, 33% in mouse. Differential analysis revealed that about 40% of the splicing changes at RNA level were concordant with changes in translation, with 21.7% of changes at RNA level and 17.8% at translational level conserved between human and mouse. Furthermore, orthologous cassette exons preserving the directionality of the change were found enriched in microexons in a comparison between glia and glioma, and were conserved between human and mouse. ORQAS leverages ribosome profiling to uncover a widespread and evolutionary conserved impact of differential splicing on the translation of isoforms and in particular, of microexon-containing ones. ORQAS is available at <jatsext-link xmlnsxlink=httpwww.w3.org1999xlink ext-link-type=uri xlinkhref=httpsgithub.comcomprnaorqas>httpsgithub.comcomprnaorqas<jatsext-link>

biorxiv genomics 100-200-users 2019

 

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