Following our spectacular special issue on plant genomics (which you can re-live here), July brought another set of amazing articles with a broad, if unintentional, underlying RNA-esque theme.
All tissues, all ages
We kicked off with a study from Alvis Brazma and colleagues, who analyze gene expression across 21 different human tissues and cell lines, finding that the majority of genes have only one dominant transcript. It seems that news about the death of the ‘one gene = one protein’ paradigm was greatly exaggerated.
The topic of tissue-specific expression returned in work from Nadav Ahituv and Katherine Pollard’s labs, in which the authors perform a smart in vivo screen of all 4,096 unique 6-mer sequences packed neatly into 184 15-bp long constructs. 27 of these constructs produce consistent expression patterns – most of them in one tissue only. Thus, the authors not only provide an impressive compendium of functional tissue-specific enhancer motifs, but also show how to effectively optimize synthetic biology approaches.
In the last of our tissue-specific articles this month, Tim Spector from King’s College leads a large consortium of researchers in the study of age-related gene expression changes in a number of human tissues. This analysis of nearly 900 individuals shows that most age-related expression changes happen in skin.
To code or not to code
A decent chunk of July’s issue comprises articles dedicated to a number of different non-coding RNAs. Phillip Kapranov and colleagues publish a study in which they identify over 2,000 vlincRNAs (very long intergenic non-coding RNAs). As it turns out, these vlincRNAs – previously found in tumors – cover 10% of our genome and are also present in perfectly normal cells. Interestingly, the number of vlincRNAs expressed from endogenous retroviral promoters correlates with pluripotency and cancerous transformations. The authors even go so far as to speculate that vlincRNAs are the genome’s ‘dark matter’ (a term that has recently gained surprising popularity in life sciences).
To all microRNA scientists working hard on the identification of microRNA targets, Ralf Zimmer’s group brings PARma: a new software tool that does just that and does it more accurately than other approaches.
Still on the subject of microRNAs: a group of German researchers reports, in their quite spectacular study, a method for early diagnosis of Alzheimer’s disease. By looking at microRNAs in the blood of Alzheimer’s disease patients, the authors manage to identify some 140 mature microRNAs with significantly altered expression. They choose 12 to construct a diagnostic panel, which yields a staggering 93% of accuracy in distinguishing between Alzheimer’s patients and healthy controls.
Odd(s) one out
In other articles published in July in Genome Biology:
– Karina Sampath’s group uses a combinatorial action of TALENs and ZFNs (the Holy Grails of genome engineering) to generate targeted and heritable chromosomal deletion in zebrafish. This simple, inexpensive strategy can be easily used to generate disease models;
– Neil Hall and colleagues describe the genome and transcriptome of Entamoeba invadens – a close relative of the nasty E. hystolytica and a model organism for studies of encystation. You can read more on this study in our other blog post;
– Steve Brown and colleagues look at the phenotypic and genomic differences between two common lab mouse strains, C57BL/6J and C57BL/6N. Taking into account a recent shift from the 6J to 6N strain, it might be very much worth just having a look – and the differences aren’t just nominal.
For these – and more (because we wouldn’t want to spoil the surprise for you completely!) articles from our July issue, please click here.