Advances in analyzing RNA diversity in eukaryotic transcriptomes: peering through the Omics lens

Abstract

Alternative splicing, polyadenylation, and chemical modifications of RNA generate astonishing complexity within eukaryotic transcriptomes. The last decade has brought numerous advances in sequencing technologies that allow biologists to investigate these phenomena with greater depth and accuracy while reducing time and cost. A commensurate development in biochemical techniques for the enrichment and analysis of different RNA variants has accompanied the advancement of global sequencing analysis platforms. Here, we present a detailed overview of the latest biochemical methods, along with bioinformatics pipelines that have aided in identifying different RNA variants. We also highlight the ongoing developments and challenges associated with RNA variant detection and quantification, including sample heterogeneity and isolation, as well as ‘Omics’ big data handling.

Genetic and epigenetic determinants of inter-individual variability in responses to toxicants

“…It may also be impractical as these assays typically require non-trivial amounts of sample material limiting the number of experiments that could be performed, thus requiring an uninformed selection of assays to be made. RNA-seq protocols are able to comprehensively quantify multiple types of RNA transcripts, including protein-coding mRNAs, mircoRNAs (miRNAs), long non-coding RNAs (lncRNAs), enchancer RNAs (eRNAs), and circular RNAs, (circRNAs), and chemical modifications of these molecules [75, 76]. These data are able to characterize variation in transcription generation and RNA processing, including alternative transcript initiation and splicing, providing detailed information about transcriptional outputs that affect cellular function.…”

Tandem Oligonucleotide Probe Annealing and Elongation To Discriminate Viral Sequence

“…Both PCR methods and nearly all NGS methods are burdened by a dependence on enzymatic processes. − In NGS, enzymatic reverse transcription is used to convert the sample RNA to cDNA in library preparation. Then, there is an enzymatic amplification step prior to sequencing to reach a threshold of signal detection .…”