Biology subjects

Puntambekar, S.

Publications and source records attributed to Puntambekar, S..

4 recordsLinked to original sources

bioRxiv2020

Inclusion of processed cell metadata improves single cell sequencing analysis reproducibility and accessibility

Single cell RNA sequencing provides an unprecedented view of cellular diversity of biological systems. Thousands of scRNA-seq datasets have been generated, providing a wealth of biological data on the diversity of cell types across different organisms, developmental stages, and disease states. But while a tremendous number of publications and datasets have been generated using this technology, we found that a minority (< 25%) of studies provide sufficient information to enable direct reuse of their data for further studies. This problem is common across journals, data repositories, and publication dates. The lack of appropriate information not only hinders exploration and knowledge transfer of reported data, but also makes reproducing the original study prohibitively difficult and/or time-consuming. Correcting this problem is not easy but we encourage investigators, reviewers, journals, and data repositories to take steps to improve their standards and ensure proper documentation of these valuable datasets.

bioinformatics↗

bioRxiv2020

Use of short-read RNA-Seq data to identify transcripts that can translate novel ORFs

Identification of as of yet unannotated or undefined novel open reading frames (nORFs) and exploration of their functions in multiple organisms has revealed that vast regions of the genome have remained unexplored or hidden. Present within both protein-coding and noncoding regions, these nORFs signify the presence of a much more diverse proteome than previously expected. Given the need to study nORFs further, proper identification strategies must be in place, especially because they cannot be identified using conventional gene signatures. Although Ribo-Seq and proteogenomics are frequently used to identify and investigate nORFs, in this study, we propose a workflow for identifying nORF containing transcripts using our precompiled database of nORFs with translational evidence, using sample transcript information. Further, we discuss the potential uses of this identification, the caveats involved in such a transcript identification and finally present a few representative results from our analysis of naive mouse B and T cells, human post-mortem brain and cichlid fish transcriptome. Our proposed workflow can identify noncoding transcripts that can potentially translate intronic, intergenic and several other classes of nORFs. One-line summaryA systematic workflow to identify nORF containing transcripts using sample transcript information.

genomics↗

bioRxiv2020

Rapid speciation of cichlids fishes may be explained by evolutionary divergence of novel open reading frames

Novel open reading frames (nORFs) with coding potential may arise from noncoding DNA. Not much is known about their emergence, functional role, fixation in a population or contribution to adaptive radiation. Cichlids fishes exhibit extensive phenotypic diversification and speciation. Encounters with new environments alone are not sufficient to explain this striking diversity of cichlid radiation because other taxa coexistent with the Cichlidae demonstrate lower species richness. Wagner et al analyzed cichlid diversification in 46 African lakes and reported that both extrinsic environmental factors and intrinsic lineage-specific traits related to sexual selection have strongly influenced the cichlid radiation 1, which indicates the existence of unknown molecular mechanisms responsible for rapid phenotypic diversification, such as emergence of novel open reading frames (nORFs). In this study, we integrated transcriptomic and proteomic signatures from two tissues of two cichlids species, identified nORFs and performed evolutionary analysis on these nORF regions. Our results suggest that the time scale of speciation of the two species and evolutionary divergence of these nORF genomic regions are similar and indicate a potential role for these nORFs in speciation of the cichlid fishes.

evolutionary biology↗

bioRxiv2019

Translational products encoded by novel ORFs may form protein-like structures and have biological functions

Translation products encoded by non canonical or novel open reading frame (ORF) genomic regions are generally considered too small to play any significant biological role, and dismissed as inconsequential. In this study, we show that mutations mapping to novel ORFs have significantly higher pathogenicity scores than mutations in protein-coding regions. Importantly, novel ORFs can translate into protein-like structures with putative independent biological functions that can be of relevance in disease states, including cancer. We thus provide strong evidence to support the systematic study of novel ORFs to gain new insights into normal biological and disease processes.\n\nOne Sentence SummaryNon coding regions may encode protein-like products that are important to understand diseases.

genetics↗