“Junk” DNA?

The Science News that Shaped 2019

With all the extensive investigations scientists have conducted of the human immune system over the past century, it is astonishing that there are still new cell types to be found.

scientists also reported that humans’ natural killer cells, thought to form the innate immune response, can also keep memories of past encounters with offending antigens, much like the adaptive immune response does.

The discovery challenges the basic dogma of how these cells function—another reminder there is still so much unknown even in our own blood.

Non-coding RNA: what is functional and what is junk?   (2015)

It is clear that the human genome contains a large number of functional ncRNAs. Indeed it is likely that the list of biologically validated ncRNAs, as listed in the LncRNA Database (Quek et al., 2014), will continue to grow. As others have pointed out, even if 10% of current lncRNAs prove to be functional, this would represent a wealth of new biology. However, given our current understanding of biochemistry and evolution, it is likely that most of the RNAs generated from the low levels of pervasive transcription, and likely a substantial number of currently annotated “lncRNAs,” are non-functional.

An atlas of human long non-coding RNAs with accurate 5′ ends   (2017)

we identify 19,175 potentially functional lncRNAs in the human genome.

this study systematically elucidates the diversity of lncRNAs and summarizes the functional relevance of nearly 20,000 lncRNAs as an online resource, which can be further used in prioritizing lncRNA candidates for functional studies.

These observations support the notion that selectively more constrained lncRNAs are more likely to be functional, although it does not exclude the potential functionality of lncRNAs with weaker selective constraints.

Taken together, our analyses provide further evidence of the potential functionality of 69% of the FANTOM CAT lncRNAs (n = 19,175 of 27,919), advancing the current scientific debate on the functional relevance of pervasive transcription from mammalian genomes.

To what extent the remaining 31% represents spurious transcription initiation by RNA polymerase II is still an open question.

Although most of the lncRNAs detected here are likely to originate from genuine TSSs (Supplementary Note 6), additional studies are needed to completely understand their biogenesis and assess their functionality.

To this end, we have summarized their expression patterns, genomic features, conservation and intersection with genetic data into a comprehensive resource (http://fantom.gsc.riken.jp/cat/).

This encompasses a web application to retrieve gene-, trait- and cell-type-based information and ZENBU⁴³ views for visualizing genomic data.

We anticipate wide applications of this resource in prioritizing lncRNA candidates for further elucidation of their functions, which is continuing in the sixth iteration of FANTOM (http://fantom.gsc.riken.jp/6/).