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NOVEL REGULATORY MECHANISMS. "Recent studies, in many cases using quantitative trait loci (QTL)-mapping approaches in cell lines or tissue samples, have provided us with considerable insight into the properties of genetic loci that have regulatory roles. Such studies have uncovered novel biochemical regulatory interactions and led to the identification of previously unrecognized regulatory mechanisms." https://lnkd.in/dFv6Tsi View in LinkedIn

MILLION TIMES EVOLUTION. "Viruses are arguably the fastest-evolving biological entity on this planet. Many of them evolve at a rate in the order of 10(−3) substitutions per site per year (s/n/y). This is approximately a million times faster than the rates of evolution of cellular host organisms, typically around 10(−9) s/n/y.” No mean achievement. http://www.sciencedirect.com/science/article/pii/S0042682215000549 View in LinkedIn

EARLY DAYS. "We still have a limited ability to interpret how genetic variants alter gene regulation. We do not know how to “read the genome” and predict gene regulatory outputs. Our understanding of regulatory mechanisms and biochemical interactions has not yet matured into an ability to “read the code” and fully model transcriptional regulation." https://lnkd.in/dFv6Tsi View in LinkedIn

OPEN ISSUES. "For instance, what types of functional elements in DNA, RNA, or proteins are most often affected by regulatory variants? Which stages of gene regulation are typically altered? How can we predict which variants are most likely to impact regulation in a given cell type?" https://lnkd.in/dFv6Tsi View in LinkedIn

NONCODING REGULATORY VARIANTS. "It is now well established that noncoding regulatory variants play a central role in the genetics of common diseases and in evolution. However, until recently, we have known little about the mechanisms by which most regulatory variants act." https://lnkd.in/dFv6Tsi View in LinkedIn

EPIGENETICS AND NOVELTY. “Our results suggest that DNA methylation may play an important role in the origination and survival of MULE-derived genes through modulation of their stability and expression, which might be a general mechanism for all the TE-derived genes, thereby contributing to the evolution of gene novelty.” (MULEs = Mutator-like transposable elements; TE = transposable element). https://lnkd.in/dPzCkty View in LinkedIn

EPIGENETIC LINKS. “We showed that the methylation level in three cytosine contexts of MULE internal sequences increases and that the CHH context of MULE TIRs decreases over evolutionary time. This result implies that genic-MULEs which acquired potentially functional coding sequences and were maintained in the multiple Oryza species over millions of years might acquire epigenetic marks in their internal and TIR sequences that are needed to maintain their stability in the genome.” (MULEs = Mutator-like transposable elements; TIR = terminated inverted repeats). http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0954-8 View in LinkedIn

CHIMERIC GENES. “More interestingly, MULE-derived putative genes tended to arise from multiple parental sequences, which could potentially form novel chimeric gene structures. This is consistent with our previous discovery that the formation of chimeric ORFs is the general mode of new gene origination in Oryza species.” (MULEs = Mutator-like transposable elements; ORF = open reading frame; Oryza = crop plants). http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0954-8 View in LinkedIn

SO ENDS this first weekend on viruses. These enigmatic and talented creatures have been maligned by biologists who either have only focused on their disease roles, or who have stubbornly refused to drop a Victorian mindset that assumed that they are not alive. Alive they are, in an extreme version of outsourcing. And causing diseases is a minor part of the full spectrum of these creatures. Undoing these two biases is underway but may take decades more to sink into the general consciousness. View in LinkedIn

VERTICAL TREES MISS RELATIONSHIPS. "Phylogenetic trees, however, cannot capture horizontal, or reticulate, events, which occur when distinct clades merge together to form a new hybrid lineage." http://www.pnas.org/content/110/46/18566.full View in LinkedIn