Thursday, July 8, 2010

All yeasts are not equal.. The chromatin regulation differs for peroxisome genes.

Recent paper from PLoS Biology
The Role of Nucleosome Positioning in the Evolution of Gene Regulation
Tsankov AM, Thompson DA, Socha A, Regev A, Rando OJ (2010)
PLoS Biol 8(7): e1000414. doi:10.1371/journal.pbio.1000414

Following is the reproduction of peroxisome specific data and figures from the above paper.
The data is reproduced here for academic purposes of researchers interested in peroxisome research. 
The blog readers are thankful to PLoS publishers for providing the free access to the articles.

Peroxisome genes are highly expressed in D. hansenii, C. albicans, and Y. lipolytica, where they are packaged with long (but not deep) NFRs, despite no enrichment for Poly(dA:dT) tracts.

Changes in GRFs Contribute to Chromatin Divergence Between Species in Peroxisomal Genes
In some cases, the gain or loss of binding sites for GRFs can contribute to divergence in chromatin organization, coupled to phenotypic changes. Most notably, peroxisomal genes are associated with wider NFRs in Y. lipolytica, C. albicans, and D. hansenii, and shorter NFRs in subsequently divergent species (Figures 3E and S15F), but are not associated with intrinsic anti-nucleosomal poly(dA:dT) tracts in any of the 12 species. Instead, we find that these genes' promoters are enriched for PolyG and Rsc3/30-like sites in Y. lipolytica, C. albicans, and D. hansenii, but not in other species. This suggests an evolutionary scenario where either a Rsc-like motif or PolyG-based nucleosome depletion was the ancestral mechanism controlling peroxisomal genes, and was subsequently lost in the LCA of the clade spanning S. kluyverii and S. cerevisiae. This scenario is consistent with the higher expression of peroxisomal genes in Y. lipolytica (where peroxisomes are particularly central for carbon metabolism) and C. albicans (where peroxisomes play a key role in virulence).

(Note - I tried to understand the chromatin biology of peroxisome genes, but i need to read more about basic concepts. So I will come up with detailed article about this paper later..)

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