Biology subjects

Singh, B.

Publications and source records attributed to Singh, B..

93 records · Page 6Linked to original sources

bioRxiv2017

Combined analysis of genome sequencing and RNA-motifs reveals novel damaging non-coding mutations in human tumors

A major challenge in cancer research is to determine the biological and clinical significance of somatic mutations in non-coding regions. This has been studied in terms of recurrence, functional impact, and association to individual regulatory sites, but the combinatorial contribution of mutations to common RNA regulatory motifs has not been explored. We developed a new method, MIRA, to perform the first comprehensive study of significantly mutated regions (SMRs) affecting binding sites for RNA-binding proteins (RBPs) in cancer. Extracting signals related to RNA-related selection processes and using RNA sequencing data from the same samples we identified alterations in RNA expression and splicing linked to mutations on RBP binding sites. We found SRSF10 and MBNL1 motifs in introns, HNRPLL motifs at 5 UTRs, as well as 5 and 3 splice-site motifs, among others, with specific mutational patterns that disrupt the motif and impact RNA processing. MIRA facilitates the integrative analysis of multiple genome sites that operate collectively through common RBPs and can aid in the interpretation of non-coding variants in cancer. MIRA is available at https://github.com/comprna/mira.

cancer biology↗

bioRxiv2017

Enhanced neuronal regeneration in the CAST/Ei mouse strain is linked to expression of differentiation markers after injury

Peripheral nerve regeneration after injury requires a broad program of transcriptional changes. We investigated the basis for the enhanced nerve regenerative capacity of the CAST/Ei mouse strain relative to C57BL/6 mice. RNA sequencing of dorsal root ganglia (DRG) showed a CAST/Ei specific upregulation of Ascl1 after injury. Ascl1 overexpression in C57BL/6 mice DRG neurons enhanced their neurite outgrowth. Ascl1 is regulated by miR-7048-3p, which is down-regulated in CAST/Ei mice. Inhibition of miR-7048-3p enhances neurite outgrowth. Following injury, CAST/Ei neurons largely retained their mature neuronal profile as determined by single cell RNAseq, whereas the C57BL/6 neurons acquired an immature profile. These findings suggest that one facet of the enhanced regenerative phenotype is preservation of neuronal identity in response to injury.

molecular biology↗

bioRxiv2016

Fast and accurate differential splicing analysis across multiple conditions with replicates

Multiple approaches have been proposed to study differential splicing from RNA sequencing (RNA-seq) data1, including the analysis of transcript isoforms2,3, clusters of splice-junctions4,5, alternative splicing events6-8 and exonic regions9. However, many challenges remain unsolved, including the limitation in speed, the computing capacity and storage requirements, the constraints in the number of reads needed to achieve sufficient accuracy, and the lack of robust methods to account for variability between replicates and for analyses across multiple conditions. We present here a significant extension of SUPPA8 to enable streamlined analysis of differential splicing across multiple conditions, taking into account biological variability. We show that SUPPA differential splicing analysis achieves high accuracy using extensive experimental and simulated data compared to other methods; and shows higher accuracy at low sequencing depth, with short read lengths, and using replicas with unbalanced depth, which has important implications for the cost-effective use of RNA-seq data for splicing analysis. We also validate the analysis of multiple conditions with SUPPA by studying differential splicing during iPS-cell to neuron differentiation and during erythroblast differentiation, providing support for the applicability of SUPPA for the robust analysis of differential splicing beyond binary comparisons.

bioinformatics↗