Congratulations to Alex for winning the Best Research Presentation Award at the recent Gordon Human Genetics and Genomics Conference! Her presentation, “Are Genetic Interactions Influencing Gene Expression Evidence for Biological Epistasis or Statistical Artifacts?”, is the culmination of her hard work to evaluate the conflicting evidence for and against epistatic gene regulatory interactions in humans.

If you are interested, check out the bioRxiv preprint:
Are Genetic Interactions Influencing Gene Expression Evidence for Biological Epistasis or Statistical Artifacts?
http://biorxiv.org/content/early/2015/06/05/020479

We are very happy to welcome BSCI graduate student Ling Chen to the group. Ling has a B.S. in Biology from Nankai University. She is interested in studying gene regulation and epigenetic dynamics.

Congratulations to Corinne Simonti for winning a $2,000 travel award to present a talk at this year’s Society for Molecular Biology and Evolution meeting in Vienna!

RNA pol II is highly post-translationally modified, and we recently helped to show that a newly discovered acetylation modification of the C-terminal domain (CTD) of its RPB1 subunit regulates transcription in mammals. In this study we trace the evolution of the RPBI CTD and show that the potential for acetylation arose in the early history of animals, and that potential for CTD acetylation expanded in specific developmentally complex metazoan lineages. Functional analysis of genes regulated by acetylation of RPB1 highlight functions involved in the origin of and diversification of complex Metazoa. This suggests that acetylation of RPB1 may have played a role in the success of animals.

Evolution of lysine acetylation in the RNA polymerase II C-terminal domain
http://www.biomedcentral.com/1471-2148/15/35

Our paper on using machine learning to extrapolate genome-wide histone modification data across tissues, developmental stages, and species is out in BMC Genomics:

Extrapolating histone marks across developmental stages, tissues, and species: an enhancer prediction case study
http://www.biomedcentral.com/1471-2164/16/104/abstract

Check it out!

The Capra Lab has received an Innovation Catalyst grant from the March of Dimes to study the influence of non-coding genetic variants on the risk of preterm birth. We are very grateful to the March of Dimes for their support.

The paper describing our collaboration with Nasim Sabouri and Ginger Zakian to understand the role of the Pfh1 helicase in resolving G-quadruplex motifs to prevent DNA damage in fission yeast just appeared in BMC Biology:

The essential Schizosaccharomyces pombe Pfh1 DNA helicase promotes fork movement past G-quadruplex motifs to prevent DNA damage

I’ve been thinking about how and when it is justified to use functional genomics data (e.g., histone modifications, DNA methylation, DNaseI hypersensitivity, etc.) collected in one cellular context for an analysis in a different context.  I performed a case study of this question for H3K27ac and H3K4me1 marks across developmental stages, tissues, and species. Check out the manuscript for the results:

Extrapolating histone marks across developmental stages, tissues, and species: an enhancer prediction case study [bioRxiv]

Congratulations to Vir Patel for being selected as a semifinalist in the 2014 Siemens Competition in Math, Science & Technology for his work with our group this summer. See the press release for more information.

We have been collaborating with Stephen Altschul’s group at the NIH to develop a more statistically sound way to represent DNA and protein sequence patterns using sequence logos. The paper describing our results just appeared in Bioinformatics:
Log-Odds Sequence Logos

If you’ve got some sequences you want to summarize, we highly recommend that you use the new tool (both web and command line versions are available):
LogOddsLogo