August 2011

The JBC unveils thematic minireview series

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The Journal of Biological Chemistry recently published two more thematic minireview series. 

The biochemistry of epigenetics

Shepherded by JBC Associate Editor Joel Gottesfeld of The Scripps Research Institute, the first thematic series contains five minireviews about the mechanisms responsible for epigenetic regulation of gene expression (primarily, the methylation of specific nucleotide bases and post-translational modifications of histone proteins) and the role of small noncoding RNAs in said mechanisms.

In the first review, authors Zhao-xia Chen and Arthur D. Riggs report recent findings about mechanisms of methylation and the maintenance and reversibility of this chemical modification of DNA in mammals. The review addresses links between DNA methyltransferases and chromatin-associated proteins and post-synthetic modifications during cell division and provides evidence for the role of base excision repair in germ cells and early embryos as a mechanism for controlling genomewide demethylation.

A review by Sayyed K. Zaidi, Daniel W. Young, Martin Montecino, Andre J. van Wijnen, Janet L. Stein, Jane B. Lian and Gary S. Stein takes on the question of how DNA methylation states and chromatin structure are coordinated with phases of the cell cycle. The authors also address the role played by small noncoding RNA molecules in the maintenance of epigenetic marks from generation to generation.

In "Combinatorial readout of dual histone modifications by paired chromatin-associated modules," Zhanxin Wang and Dinshaw J. Patel write about the mechanisms by which the cellular machinery reads the epigenetic code so that programs of gene regulation and development are properly orchestrated.

Duane D. Winkler and Karolin Luger review the structural dynamics and biophysical transitions of nucleosome reorganization. Members of the histone chaperone family are implicated in multiple roles linked to epigenetic gene regulation. The two-subunit complex known as FACT, which stands for "facilitates chromatin transcription," is discussed as a histone chaperone of interest, and the authors explore models for FACT function and how FACT allows RNA polymerase to pass through nucleosome-bound DNA.

Computational systems biology

The second thematic minireview series was organized by Arcady Mushegian and JBC Associate Editor Joan W. Conaway, both of Stowers Institute for Medical Research, who conceived of the collection during a 2009 special symposium on systems biology held by the American Society for Biochemistry and Molecular Biology.

The meeting sought to explore how systems-level analyses can both generate and test hypotheses about the molecular features of living systems, the series organizers said, and the minireview collection is intended to feature the promise that such systems approaches hold.

In the first minireview, authors Yan Zhang and Vadim N. Gladyshev focus on approaches to identify new mechanistic and evolutionary pathways that involve metalloenzymes. The genomic representation of enzymes whose activity is trace-element dependent can provide new insights into the exploitation of trace elements by organisms over the course of evolution.

The new science of metabolomics is the focus of a minireview contributed by Guo-Fang Zhang, Sushabhan Sadhukhan, Gregory Tochtrop and Henri Brunengraber. The authors consider the need for bioinformatic strategies to make meaning of amassing data, and they assess the promise of developing biomarkers to follow the complex physiological consequences of the flux of innumerable metabolites within the cell.

In the next review, Oliver Fiehn, Dinesh K. Barupal and Tobias Kind cover how such resources as GenBank and the Protein Data Bank can be used to reveal novel pathways and enzymatic activities that underlie metabolomic activity.

In "Building protein-protein interaction networks with proteomic and informatics tools," Mihaela Sardiu and Michael Washburn survey evolving methodologies for systematically identifying protein-protein interactions as a dimension of functional proteomics. The recent development of protein-interaction networks based on quantitative proteomics data sets is an important step in allowing researchers to consider diverse and subtle levels of protein-protein mechanisms of cellular control.

In the fifth minireview, Hon Nian Chua and Frederick P. Roth present computational methods for mining science literature and data to elucidate the mechanisms of both intended and unintended drug effects. The authors seek to understand the consequences of genetic and chemical perturbations as revealed in genome-wide analyses published from a variety of sources. The investigators illustrate that by evaluating data in a systematic way, research findings from a diversity of experimental settings and models can be marshaled to identify new drugs and drug targets.

The final component, authored by James A. Evans and Andrey Rzhetsky, highlights new strategies for mining the literature "not only to learn what has been reported but also to gain information about how a research area has developed and the history and/or biases that shape the way researchers think about a problem," the organizers write.

Angela Hopp (ahopp@asbmb.org) is managing editor for special projects at ASBMB. 

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