Paulet, D. | Search bioRxiv

bioRxiv2021

RNA-Ribo Explorer: interactive mining and visualisation of Ribosome profiling data

RNA translation has long been thought as a stable and uniform process by which a ribosome produces a protein encoded by the main Open Reading Frame (ORF) of an mRNA. Recently, growing evidence support incomplete correlation between RNA and protein abundance levels, the existence of alternative ORFs in numerous mammalian RNAs, and the involvement of ribosomes in gene expression regulation, thereby challenging previous views of translation. Ribosome profiling (aka Ribo-seq) has renewed the study of translation by enabling the mapping of translating ribosomes on the whole transcriptome using deep-sequencing. Despite increasing use of Ribo-seq, recent review articles conclude that flexible, interactive tools for mining such data are missing. As Ribo-seq protocols still evolve, flexibility is highly desirable for the end-user. Here we describe RNA-Ribo-Explorer (RRE) a stand-alone tool that fills this gap. With RRE, one can explore read-count profiles of RNAs obtained after mapping, compare them between conditions, and visualize the profiles of individual RNAs. Importantly, the user can mine the data by defining queries that combine several criteria to detect interesting subsets of RNAs. For instance, one can ask RRE to find all RNAs whose translation of UTR region compared to that of the main ORF has changed between two conditions. This feature seems useful for finding candidate RNAs whose translation status or processing has changed across conditions. RRE is a platform independent software and is freely available at https://gite.lirmm.fr/rivals/RRE/-/releases.

bioinformatics↗

bioRxiv2018

NF-Y Controls Fidelity of Transcription Initiation at Gene Promoters Through Maintenance of the Nucleosome-Depleted Region

Faithful transcription initiation is critical for accurate gene expression, yet the mechanisms underlying specific transcription start site (TSS) selection in mammals remain unclear. Here, we show that the histone-fold domain protein NF-Y, a ubiquitously expressed transcription factor, controls the fidelity of transcription initiation at gene promoters. We report that NF-Y maintains the region upstream of TSSs in a nucleosome-depleted state while simultaneously protecting this accessible region against aberrant and/or ectopic transcription initiation. We find that loss of NF-Y binding in mammalian cells disrupts the promoter chromatin landscape, leading to nucleosomal encroachment over the canonical TSS. Importantly, this chromatin rearrangement is accompanied by upstream relocation of the transcription preinitiation complex and ectopic transcription initiation. Further, this phenomenon generates aberrant extended transcripts that undergo translation, disrupting gene expression profiles. These results establish NF-Y as a central player in TSS selection in metazoans and highlight the deleterious consequences of inaccurate transcription initiation.

genomics↗