Friday, June 7, 2013

Location and timing control of Pol2 promoter-proximal pausing

Kinetic Competition between Elongation Rate and Binding of NELF Controls Promoter-Proximal Pausing
Jian Li, Yingyun Liu, Ho Sung Rhee, Saikat Kumar B. Ghosh, Lu Bai, B. Franklin Pugh, David S. Gilmour

Several significant conclusions: 
First, core promoters of protein-coding genes throughout theDrosophila genome contain little or no open Pol II promoter complexes. Thus immediately after assembly of the transcription complex at the core promoter, Pol II rapidly initiates and elongates into a paused state that precludes assembly of a second polymerase into an initiation complex. snRNA genes encoding components of the spliceosome and the induced heat shock genes are exceptional in that open Pol II promoter complexes are evident on these genes. 
Second, the location of the pause can be altered by perturbing the kinetics of elongation or the levels of pausing factors, suggesting that the location of the pause depends on a kinetic competition between elongation and the binding of these factors. 
Third, GAF tips this kinetic competition in favor of pausing by recruiting NELF to the promoter.

Wednesday, May 22, 2013

DNA methylome changes along the maternal-to-zygotic transition

In this issue of Cell, two studies from Jiang et al. (pp. 773–784) and Potok et al. (pp. 759–772) generate genome-wide methylome maps of zebrafish gametes and early embryos. Surprisingly, the sperm methylome remains largely unchanged until zygotic genome activation, and the oocyte undergoes a series of methylation-demethylation reprogramming cycles to ultimately match the patterns of sperm.

Question: How the piRNA dynamics co-incide with the methylation dynamics during MZT?

Reprogramming the Maternal Zebrafish Genome after Fertilization to Match the Paternal Methylation Pattern p759
Magdalena E. Potok, David A. Nix, Timothy J. Parnell, Bradley R. Cairns
In Brief | Summary | Full Text
Sperm, but Not Oocyte, DNA Methylome Is Inherited by Zebrafish Early Embryos p773
Lan Jiang, Jing Zhang, Jing-Jing Wang, Lu Wang, Li Zhang, Guoqiang Li, Xiaodan Yang, Xin Ma, Xin Sun, Jun Cai, Jun Zhang, Xingxu Huang, Miao Yu, Xuegeng Wang, Feng Liu, Chung-I Wu, Chuan He, Bo Zhang, Weimin Ci, Jiang Liu
In Brief | Summary | Full Text