On nucleosome positioning

One of the topics I’ve been tracking with some interest lately has been nucleosome positioning. I’m going to briefly highlight some of my recent readings on the subject …

Biophysics of Transcriptional Regulation

I saw a seminar this week by Leonid Mirny, a MIT physicist with a joint appointment in the Harvard–MIT Division of Health Sciences and Technology. It was an interesting talk on how biophysical models concerning how regulatory proteins search for their sites on DNA has interesting implications for genome structure.

Probabilistic Functional Networks

I recently read the Lee et. al. paper “A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans” in Nature Genetics. This is an extension of their previous work on building probabilistic functional networks to a multicellular organism (the worm). (Most of their prior work was in yeast.)

Alignment Uncertainty

Today in Science, Wong et. al. has a brief three page report entitled, “Alignment Uncertainty and Genomic Analysis”. In the same issue (pg 416; doi 10.1126/science.1153156) Rokas writes a perspective on Wong’s report. [Ironically, Rokas' perspective is probably near the same amount of text as Wong's report since Wong includes two large figures.]The report makes a simple assertion, “methods applied to the analysis of genomic data do not account for uncertainty in the sequence alignment.” They then show, by applying seven different popular alignment programs to protein sequences from seven yeast species, that uncertainty in the alignment can lead to problems, including different alignments giving different conclusions.

Structural Variation in the Human Genome

Back in mid December I attended a talk by Evan Eichler entitled, “Structural Variation in the Human Genome”. Evan gave an excellent talk focusing on his lab’s recent work on identifying the regions of the genome which change in structure and content very quickly. In short, identify length variations within the human genome. His talk broke down into two major components:

1. Identify duplicated regions associated with phenotypes
2. Catalog normal structural variation in the genome

I’ll go into more details on both below the fold …