16 March 2010

Last week in Nature: Genomics and Transcriptomics

The brief review presents the most interesting, according to the Genomeweb site reviewer, publications in the Nature series journals.

An international group of scientists working under the leadership of Leif Anderson from Uppsala University in Sweden published on March 10 in the online version of the journal Nature an article Whole-genome sequencing reveals loci under selection during chicken domestication, dedicated to the re-sequencing of the genome of domestic chicken. Pets are convenient to use as models for research on genetic changes underlying the evolution of animal breeds. In the process of adaptation to life in captivity and under the influence of human breeding, domestic animals have acquired hereditary traits underlying the significant changes in morphological, physiological and behavioral characteristics that have arisen. In order to find the genetic changes that play a leading role in the domestication of chickens (Gallus gallus domesticus) and their specialization in broilers and laying hens, scientists analyzed the genomes of 8 different breeds of domestic chickens and their common ancestor, the red jungle chicken (Gallus gallus), using massive parallel sequencing. The researchers found more than 7 million single-nucleotide changes, about 1,300 deleted genome sites and several selective regions of genomes. One of the characteristic genetic traits found in all domestic breeds was the region of the genome encoding the thyroid stimulating hormone receptor (TSHR), which plays a leading role in metabolism and in the way of regulation of reproduction associated with the duration of daylight. In broilers (as expected :), several selective genetic traits were found in genes associated with growth, appetite and metabolic regulation. The conducted research, according to scientists, should attract the attention of researchers to domestic chickens as model organisms for biomedical research. This research may also be useful for breeding new breeds of animals.

In the latest issue of the journal Nature, a group of researchers from the Max Planck Institute of Infectious Biology (Germany) with colleagues from other scientific institutions in Europe and the USA, working under the leadership of Jörg Vogel, published an article The primary transcriptome of the major human pathogen Helicobacter pylori, devoted to the analysis of the transcriptome of Helicobacter pylori (a pathogen found in almost all half of people) using the method of differentiated massive parallel RNA sequencing developed by them (differential massively parallel cDNA sequencing, dRNA-seq), selective at the 5' ends of RNA sequences (the 5' end of RNA corresponds to the beginning of the gene). The new approach allowed scientists to determine the sequences of the Helicobacter pylori genome corresponding to the start signals of RNA synthesis and regulatory elements of the genome, as well as unexpectedly many short regulatory RNA molecules.

(A transcriptome is a collection of all RNA molecules formed as a result of transcription – expression of all coding genes of a cell, a group of cells or an organism, including mRNA and non–coding RNAs.)

In the article Common variants at 5q22 associate with pediatric eosinophilic esophagitis, published in the latest issue of the journal Nature Genetics, an international group of scientists, led by Hakon Hakonarson, identified with the help of an associative large–scale genome study variants of genetic changes characteristic of a painful form of food allergy in children - eosinophilic esophagitis (inflammation of the mucous membrane of the esophagus). It turned out that eosinophilic esophagitis is associated with a section of chromosome 5 that includes two genes. Scientists believe that the disease is associated with changes in the gene of thymic stromal lymphoprotein (thymic stromal lymphopoietin, TSLP), since the amounts of TSLP were increased in children suffering from eosinophilic esophagitis, compared with healthy children. TSLP protein is involved in the regulation of the mechanism of inflammation characteristic of allergic diseases.

Daria Chervyakova
Portal "Eternal Youth" based on Genomeweb materials: This Week in Nature, March 11, 201016.03.2010

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