Genomics

Those of you who have been following this blog, as well as Evolution News & Views, for some time, will be aware that I have previously discussed, across multiple articles, the phenomenon of endogenous retroviral inserts into the genomes of primates. Those familiar with the debate over origins will also be familiar with the various arguments for common descent which are based upon these fascinating genetic elements. A friend recently asked me if I would compile my thoughts on the topic into a single article, and hence that is what I intend to do here. Since my previous articles on the topic (and since my progression from undergraduate to postgraduate status), my knowledge of the subject has increased and I Read More ›

In “Exosome Explosion” (The Scientist , July 1, 2011), Clotilde Théry tells us “These small membrane vesicles do much more than clean up a cell’s trash—they also carry signals to distant parts of the body, where they can impact multiple dimensions of cellular life”:

Secreted vesicles known as exosomes were first discovered nearly 30 years ago. But, considered little more than garbage cans whose job was to discard unwanted cellular components, these small vesicles remained little studied for the next decade. Read More ›

All? Some? None?

Clark et al., The Reality of Pervasive Transcription:

Current estimates indicate that only about 1.2% of the mammalian genome codes for amino acids in proteins. However, mounting evidence over the past decade has suggested that the vast majority of the genome is transcribed, well beyond the boundaries of known genes, a phenomenon known as pervasive transcription [1]. Challenging this view, an article published in PLoS Biology by van Bakel et al. concluded that “the genome is not as pervasively transcribed as previously reported” [2] and that the majority of the detected low-level transcription is due to technical artefacts and/or background biological noise. These conclusions attracted considerable publicity [3]–[6]. Here, we present an evaluation of the analysis and conclusions of van Bakel et al. compared to those of others and show that (1) the existence of pervasive transcription is supported by multiple independent techniques; (2) re-analysis of the van Bakel et al. tiling arrays shows that their results are atypical compared to those of ENCODE and lack independent validation; and (3) the RNA sequencing dataset used by van Bakel et al. suffered from insufficient sequencing depth and poor transcript assembly, compromising their ability to detect the less abundant transcripts outside of protein-coding genes. We conclude that the totality of the evidence strongly supports pervasive transcription of mammalian genomes, although the biological significance of many novel coding and noncoding transcripts remains to be explored.

However, van Bakel et al. respond: Read More ›