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Comprehensive characterization of transcript diversity at the human NODAL locus

Scott D Findlay, Lynne-Marie Postovit

Preprint posted on January 25, 2018 https://www.biorxiv.org/content/early/2018/01/25/254409

A comprehensive quantitative analysis led to the identification of multiple transcripts derived from a single locus, allowing the identification of previously unreported alternative splice-variants in sub-populations of the same cell line.

Selected by Christian Ramos

Summary:

A novel strategy based on a comprehensive quantitative analysis of transcripts led to the identification of multiple transcripts derived from a single locus, allowing the identification of previously unreported alternative splice-variants in sub-populations of the same cell line.

How do these discoveries help the progress of science?

The “strangeness” of the original data the authors were looking at, and the willingness to understand it, brings us this very interesting work:

their realization that gene expression levels within the same cell line shows dramatic variations, using ddPCR (for sure, this could have been overlooked using less sensitive methods) enabled the characterization and quantification of known and novel transcript isoforms.

This work thus proposes very detailed approach to investigate possible factors that may influence transcript levels: the effects of different cell culture media were tested and the exact composition of transcripts related to the presence of single nucleotide polymorphisms eliciting the alternative splicing, complemented with “old-school” and very robust 5’- and 3’-RACE assays. Whereas these methods are not new per se  and generally are not used combined, they deliver very interesting data when they are employed as a sequential approach, as done here,.The authors highlight the fact that gene expression can vary a great deal within sub-populations of the same cell line (using state-of-the-art gene expression quantification methods), and that, besides the effects of previously unreported alternatively spliced transcripts, the presence of circular RNAs and natural anti-sense transcripts should be taken into account.

Therefore, this work fits the bigger picture of RNA biology mostly by acknowledging the presence of diverse transcripts that result from within the same locus, which might confound the interpretation of data, thereby moving the field forward.

How will the reported finding impact past and future research?

One very common problem encountered by the community when looking at eukaryotic transcription deals with the discrepancies in alternatively spliced transcripts between databases. Furthermore, few studies incorporate data regarding the specific origin of the sample (cell type and/or tissue) or the experimental conditions in which the data were obtained (age and/or time of day and/or assay used). This might therefore impede a more detailed exploration of publicly available data.

This report prompts for database curators to include such information when available, for the authors of the data deposited to update it, and for future work to include such critical details.

If this is accomplished, the community will benefit from this increase in data accuracy.

Tags: alternative splicing, anti-sense transcription, gene expression

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