Saturday, December 14, 2013

Science - Exonic Transcription Factor Binding

M. Madan Babu, PhD
MRC Laboratory of Molecular Biology, Cambridge, UK
image Madan homepage

Science reports:

The Hidden Codes That Shape Protein Evolution

Despite redundancy in the genetic code, the choice of codons used is highly biased in some proteins, suggesting that additional constraints operate in certain protein-coding regions of the genome. This suggests that the preference for particular codons, and therefore amino acids in specific regions of the protein, is often determined by factors unrelated to protein structure or function. On page 1367 in this issue, Stergachis et al. reveal that transcription factors bind within protein-coding regions (in addition to nearby noncoding regions) in a large number of human genes. Thus, a transcription factor “binding code” may influence codon choice and, consequently, protein evolution. This “binding” code joins other “regulatory” codes that govern chromatin organization, enhancers, mRNA structure, mRNA splicing, microRNA target sites, translational efficiency, and cotranslational folding, all of which have been proposed to constrain codon choice, and thus protein evolution.

See also Nature World News:  DNA has Secret Code for Gene Control, Scientists say

Now this is what I call significant news on the study of DNA and evolution. Not only amino acid sequences and replicating proteins but a second, previously hidden coding mechanism, that guides the DNA an shows what an incredibly efficient storage system of information it is.

Sooner or later someone will seriously start to ask where the information written in such wondrously powerful ways into the DNA comes in the first place.

Sooner or later.

Friday, February 8, 2013

Placental mammals DNA

Project: (P561) Morphological and molecular evidence
converge upon a robust phylogeny of the
megadiverse Holometabola
Image Morphobank
BBC Science and Environment James Palmer reports on recent advances in the research on the evolutionary origins of placental mammals
Placental mammals - as opposed to the kind that lay eggs, such as the platypus, or carry young in pouches, such as the kangaroo - are an extraordinarily diverse group of animals with more than 5,000 species today. They include examples that fly, swim and run, and range in weight from a couple of grams to hundreds of tonnes.

A wealth of fossil evidence had pointed to the notion that the group, or clade, grew in an "explosion" of species shortly after the dinosaurs' end about 65 million years ago.

But a range of genetic studies that look for fairly regular changes in genetic makeup suggested that the group arose as long as 100 million years ago, with mammals such as early rodents sharing the Earth with the dinosaurs.
To build the database, the team gathered more than 4,500 details of phenotype - diet, lengths of limbs, shapes of teeth, length of fur if any, and so on - from 86 different species that are around today, and from 40 fossils of extinct animals.

To that they added some 12,000 detailed images and genetic information for all of the current species, putting all the data into what Dr O'Leary called "a supermatrix - essentially like a spreadsheet, filled with observations and images, to create a really rich description of mammals we'd sampled".

"That really wasn't possible until we developed this software called Morphobank. Our experts in China or Brazil or Canada or the US or just across the hall could all be working in one place at the same time," Dr O'Leary said.
Read the entire article in BBC News Science and Environment

Wednesday, January 23, 2013

Evolution of dogs

BBC Science correspondent Jonathan Amos has written with his usual clarity and expertise an interesting overview of current research on the possible impact of genes on the domestication of dogs

Dog evolved `on the waste dump'

Check also the article with much nicer title written by Virginia Hughes in National Geographic

People and dogs: A Genetic Love Story

Both articles are inspired by the work of Erik Axelsson and his team in the Biomedical Centre of Uppsala University, Sweden

The genomic signature of dog domestication reveals adaptation to a starch-rich diet

published online in Nature January 23, 2013