Biology subjects

Bitton, D. A.

Publications and source records attributed to Bitton, D. A..

3 recordsLinked to original sources

bioRxiv2018

Fitness Landscape of the Fission Yeast Genome

BackgroundNon-protein-coding regions of eukaryotic genomes remain poorly understood. Diversity studies, comparative genomics and biochemical outputs of genomic sites can be indicators of functional elements, but none produce fine-scale genome-wide descriptions of all functional elements.\n\nResultsTowards the generation of a comprehensive description of functional elements in the haploid Schizosaccharomyces pombe genome, we generated transposon mutagenesis libraries to a density of one insertion per 13 nucleotides of the genome. We applied a five-state hidden Markov model (HMM) to characterise insertion-depleted regions at nucleotide-level resolution. HMM-defined functional constraint was consistent with genetic diversity, comparative genomics, gene-expression data and genome annotation.\n\nConclusionsWe infer that transposon insertions lead to fitness consequences in 90% of the genome, including 80% of the non-protein-coding regions, reflecting the presence of numerous non-coding elements in this compact genome that have functional roles. Display of this data in genome browsers provides fine-scale views of structure-function relationships within specific genes.

genomics↗

bioRxiv2017

Cdk9, Spt5 and histone H2B mono-ubiquitylation cooperate to ensure antisense suppression by the Clr6-CII/Rpd3S HDAC complex

Cyclin-dependent kinase 9 (Cdk9) and histone H2B monoubiquitylation (H2Bub1) are both implicated in elongation by RNA polymerase II (RNAPII). In fission yeast, Cdk9 and H2Bub1 regulate each other through a feedback loop involving phosphorylation of the elongation factor Spt5. Conversely, genetic interactions suggest opposing functions of H2Bub1 and Cdk9 through an Spt5-independent pathway. To understand these interactions, we performed RNA-seq analysis after H2Bub1 loss, Cdk9 inhibition, or both. Either Cdk9 inhibition or H2Bub1 loss increased levels of antisense transcription initiating within coding regions of distinct subsets of genes; ablation of both pathways led to antisense derepression affecting over half the genome. Cdk9 and H2Bub1 cooperate to suppress antisense transcription by promoting function of the Clr6-CII histone deacetylase (HDAC) complex. H2Bub1 plays a second role, in opposition to Clr6-CII, to promote sense transcription in subtelomeric regions. Therefore, functional genomics revealed both collaborative and antagonistic functions of H2Bub1 and Cdk9.

molecular biology↗

bioRxiv2017

Long non-coding RNA repertoire and regulation by nuclear exosome, cytoplasmic exonuclease and RNAi in fission yeast

Transcriptomes feature pervasive, but poorly defined long non-coding RNAs (lncRNAs). We identify 5775 novel lncRNAs in Schizosaccharomyces pombe, nearly 4-times the previously annotated lncRNAs. Most lncRNAs become derepressed under genetic and physiological perturbations, especially during late meiosis. These lncRNAs are targeted by three RNA-processing pathways: the nuclear exosome, cytoplasmic exonuclease and RNAi, with substantial coordination and redundancy among pathways. We classify lncRNAs into cryptic unstable transcripts (CUTs), Xrn1-sensitive unstable transcripts (XUTs), and Dicer-sensitive unstable transcripts (DUTs). XUTs and DUTs are enriched for antisense lncRNAs, while CUTs are often bidirectional and actively translated. The cytoplasmic exonuclease and RNAi repress thousands of meiotically induced RNAs. Antisense lncRNA and sense mRNA expression often negatively correlate in the physiological, but not the genetic conditions. Intergenic and bidirectional lncRNAs emerge from nucleosome-depleted regions, upstream of positioned nucleosomes. This broad survey of the S. pombe lncRNA repertoire and characteristics provides a rich resource for functional analyses.

genomics↗