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 …

In 2006, Segal published a paper in which they attempted to model and predict positioning based purely on localized sequence signals. In the paper, they compared their model to a number of previously published datasets (mostly low resolution or small sized datasets) in order to claim an accuracy of about 50%. In a later paper, Narlikar et. al. (an independent group from the Segal work) showed that using positioning information, the Segal model, can be informative when looking at the regulatory network.

A couple months ago, I saw Jonathan Widom give a talk in which he discussed the initial results of the follow-up work to Segal’s original model. Since the Segal paper, a number of groups have published larger scale and higher resolution mappings of nucleosome positioning, including the Lee et. al. paper (2007). These datasets have provided larger and better datasets which have been used to improve the models of positioning. While I’ve not yet seen the newer model Widom spoke about published, it looked to contain promising improvements to the original.

An entirely different perspective on nucleosomes has to do with histone dynamics. I’ve written before about some elegant work on Histone Turnover, but recently Shivaswamy et. al. took a different approach to the problem. They compared the positioning of nucleosomes in normal versus heat shock conditions and showed some interesting transcription related changes. They also put forth a model in which some nucleosomes are well positioned with neighboring nucleosomes simply pack in around these well defined ones. I know the authors of this paper and they are interested in exploring nucleosome changes in a variety of conditions.

Two additional perspectives are on the horizon: the effects of individual genes on positioning and the pliability of positioning through evolution. Desiree Tillo gave an interesting talk at the recent CSHL Systems Biology meeting on their follow-up work to Lee et. al. (2007). Namely, they are examining nucleosome positioning in a large number of mutant strains (conditional alleles of essentials and deletions of nonessentials) as well as when yeast are challenged with small molecule inhibitors of histone-modifying enzymes. I am aware of at least two groups who are working on the more evolutionary based perspective, but only in the very early stages.

I am definitely NOT an expert in this field, as my current knowledge stems largely from these papers and a few talks. Currently this field is hot and progress is made quickly …. so I’m probably missing several key papers in the area (Suggestions for reading are welcome). Considering the likely influence of nucleosomes on regulation, it is a topic I will continue to follow with some interest.

Segal, E., Fondufe-Mittendorf, Y., Chen, L., Thastrom, A., Field, Y., Moore, I.K., Wang, J.Z., Widom, J. (2006). A genomic code for nucleosome positioning. Nature, 442(7104), 772-778. DOI: 10.1038/nature04979

Lee, W., Tillo, D., Bray, N., Morse, R.H., Davis, R.W., Hughes, T.R., Nislow, C. (2007). A high-resolution atlas of nucleosome occupancy in yeast. Nature Genetics, 39(10), 1235-1244. DOI: 10.1038/ng2117

Narlikar, L., Gordan, R., Hartemink, A.J. (2007). A Nucleosome-Guided Map of Transcription Factor Binding Sites in Yeast. PLoS Computational Biology, 3(11), e215. DOI: 10.1371/journal.pcbi.0030215

Shivaswamy, S., Bhinge, A., Zhao, Y., Jones, S., Hirst, M., Iyer, V.R. (2008). Dynamic Remodeling of Individual Nucleosomes Across a Eukaryotic Genome in Response to Transcriptional Perturbation. PLoS Biology, 6(3), e65. DOI: 10.1371/journal.pbio.0060065

• The May Scientiae Carnival is up. This month’s theme: Career paths, perspective, and changing self-mage. (Hosted by Cat Nap).

• A great piece on the history of the platypus is up over at What You’re Doing is Rather Desperate.

• See Jane Compute has a set of posts on “Is computer science a science?” (See Part 1, Part 1A, Part2, Part 3 is promised soon …)

• I saw Jorge Cham give a talk yesterday. It was an hour lecture on the value of procrastination. While the talk was content-light, it was incredibly funny and entertaining.

• Be sure to get your art break in today by visiting Drawing the Motmot.

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.

Mirny opened by discussing the following paradox … the diffusion rates for a single protein finding a single DNA site within a 3D nucleus is roughly 3X slower than the experimentally measured value. So how does a protein find it’s DNA recognition site faster than diffusion without the consumption of energy?

The classical answer to this problem is the idea of facilitated diffusion … ie. that DNA binding proteins can bind non-specifically and reduce the 3D diffusion problem to a 1D problem by “sliding” along DNA searching. Proteins must therefore balance time spent in 1D (facilitated diffusion) versus 3D (diffusion) search modes. Mirny shows how measured values for the affinity of a protein to non-specific DNA indicates that the system is far from optimal, spending too much time on the DNA (in 1D mode). Consequently, estimated search times far are too long for most bacterial systems and facilitated diffusion is insufficient!

There are two ways to overcome the problem. The first is a concentration effect … make so much transcription factor that each molecule is responsible for only a small portion of the search space. The second is to utilize co-localization … imposing constraints on the search space which favor the transcription factor finding it’s DNA site. Mirny then claims that this second strategy is used in prokaryotes for “local” regulators … so that the transcription factor’s genomic location is nearby to the genes it will eventually regulate. Recall that in prokaryotes transcription and translation occur in rapid succession … even simultaneously. Therefore the protein is produce nearby to where it is expected to bind. Regulators with lots of DNA targets, “global” regulators, do not show these patterns.

The majority of Mirny’s talk was over work published in PNAS last year:

Kolesov, G., Wunderlich, Z., Laikova, O.N., Gelfand, M.S., Mirny, L.A. (2007). How gene order is influenced by the biophysics of transcription regulation. Proceedings of the National Academy of Sciences, 104(35), 13948-13953. DOI: 10.1073/pnas.0700672104

Courtesy PhD Comics:

I’ve worked in Red Brick Wonderland, Modernist “It cost HOW much?”, Gothic Envyist and Neo-Penal at different times during my career already!

Last year Kathryn O’Donnell and Jef Boeke published a review in Cell on Piwis and their role in maintaining transposon silencing in the germline genome. Together with an additional short review by Seto et. al. on Piwi proteins, a compelling picture of Piwis is just beginning to emerge … In brief,

“.. the recent characterization of the molecular function of Piwis (P element-induced wimpy testes) proteins, a novel form of control for mobile elements has emerged involving small RNAs in germ line.”

A small number of specific loci in Drosophilia produce large numbers of piRNAs (Piwi interacting RNAs) which direct Piwi proteins to cleave transposon targets. There appears to be a self-reinforcing amplification cycle induced by the cleave event, as cleaved transposons result in sense piRNAs which direct cleavage of the original genomic piRNA cluster. Unanswered questions exist concerning how the cycle is initiated and what prevents constitutive autoamplification (perhaps cellular localization) still exist. Nevertheless, the proposed piRNA mechanism opens yet another chapter in the saga that is non-coding RNAs as regulators.

While the conservation of the mechanism is yet to be established, Piwi orthologs are being studied in at least flies, mice, and zebrafish. Piwi proteins exist in a number of organisms (including ciliates and slime molds) implying that their function may also be conserved. Furthermore, there are some lines of evidence suggesting that the mammalian Piwis may have acquired additional germline-specific functions besides regulating repetitive elements. Piwi proteins may serve an epigenetic role in nuclear surveillance, but currently this is unclear as there is evidence both for and against this hypothesis. So, we are still at the very early stages of understanding piRNAs and their function. Therefore this is an area of research with many open questions.

But the use of piRNAs as a defense mechanism against runaway selfish elements (transposons) is an attractive idea. It also implies that some regions of the genome, containing apparent graveyards of transposable elements, may in fact be storage banks necessary for defensive surveillance. Repeat elements comprise the majority of animal genomes, therefore cells must effectively deal with this complex and poorly understood bulk sequence. A deeper understanding of Piwi proteins and piRNAs has implications on understanding fertility, stem cell development, evolution of genomes, and regulation.

ODONNELL, K., BOEKE, J. (2007). Mighty Piwis Defend the Germline against Genome Intruders. Cell, 129(1), 37-44. DOI: 10.1016/j.cell.2007.03.028

SETO, A., KINGSTON, R., LAU, N. (2007). The Coming of Age for Piwi Proteins. Molecular Cell, 26(5), 603-609. DOI: 10.1016/j.molcel.2007.05.021