Posts Tagged ‘pseudogenes’

Prehistoric proteins: Raising the dead

June 15, 2018


“The oestrogen receptor achieves this by binding substances that contain a chemical structure called an aromatized A ring. Because oestrogens are the only steroid hormones to have such a ring, that criterion was enough to ensure that the receptor bound only oestrogens for many millions of years. Until, that is, the chemical industry started pumping out hundreds of substances containing such aromatized rings, which the oestrogen receptor unwittingly bound. “The endocrine disrupters are taking advantage, unfortunately, of the promiscuity that is the result of the evolutionary history of receptors,” Thornton says.”

Prehistoric proteins: Raising the dead

Papers for Journal Club

June 7, 2018

Alternative evolutionary histories in the sequence space of an ancient protein Great viz of different potential but not necessarily realized evolutionary trajectories. Quite relevant for molecular #evolution & #pseudogenes

pseudogenes that might have saved us !

March 20, 2017

#Pseudogenes that might have saved us! Interesting link to infectious disease for pseudo-siglecs 13 & 17

“”In a small, restricted population, a single mutation can have a big effect, a rare allele can get to high frequency,” said senior author Ajit Varki, MD, professor of medicine and cellular and molecular medicine and co-director of the Center for Academic Research and Training in Anthropogeny at UC San Diego. “We’ve found two genes that are non-functional in humans, but not in related primates, which could have been targets for bacterial pathogens particularly lethal to newborns and infants. Killing the very young can have a major impact upon reproductive fitness. Species survival can then depend upon either resisting the pathogen or on eliminating the target proteins it uses to gain the upper hand.”

In this case, Varki, who is also director of the UC San Diego Glycobiology Research and Training Center, and colleagues in the United States, Japan and Italy, propose that the latter occurred. Specifically, they point to inactivation of two sialic acid-recognized signaling receptors (siglecs) that modulate immune responses and are part of a larger family of genes believed to have been very active in human evolution.

Working with Victor Nizet, MD, professor of pediatrics and pharmacy, Varki’s group had previously shown that some pathogens can exploit siglecs to alter the host immune responses in favor of the microbe. In the latest study, the scientists found that the gene for Siglec-13 was no longer part of the modern human genome, though it remains intact and functional in chimpanzees, our closest evolutionary cousins. The other siglec gene — for Siglec-17 — was still expressed in humans, but it had been slightly tweaked to make a short, inactive protein of no use to invasive pathogens.”

TP53 copy number expansion is associated with the evolution of increased body size and an enhanced DNA damage response in elephants | eLife

March 4, 2017

TP53 copy number expansion is associated w…enhanced DNA damage response in elephants 18 p53 retro- & pseudo- genes

Integrative analyses reveal a long noncoding RNA-mediated sponge regulatory network in prostate cancer : Nature Communications : Nature Publishing Group

July 2, 2016

lncRNA-mediated sponge regulatory network in prostate cancer Few explicitly noted #pseudogenes besides PTENP1

BMC Genomics | Full text | Pseudogenes transcribed in breast invasive carcinoma show subtype-specific expression and ceRNA potential

July 31, 2015

[440 @GencodeGenes] #Pseudogenes transcribed in breast…carcinoma show subtype-specific expression & ceRNA potential

Comparative genomics reveals insights into avian genome evolution and adaptation

May 16, 2015

Comparative #genomics reveals insights into avian…#evolution Less repeats & dups in birds; woodpecker, an exception

Science 12 December 2014:
Vol. 346 no. 6215 pp. 1311-1320
DOI: 10.1126/science.1251385

Comparative genomics reveals insights into avian genome evolution and adaptation

Guojie Zhang1,2,*,†,
Cai Li1,3,*,
Avian Genome Consortium§,
Erich D. Jarvis20,†,
M. Thomas P. Gilbert3,56,†,
Jun Wang1,55,57,58,59,†

Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators : Nature : Nature Publishing Group

February 21, 2015

Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators Reconstructed #evolution across 8 species

Daniel W. Bellott,
Jennifer F. Hughes,

Richard A. Gibbs,
Richard K. Wilson
& David C. Page

Nature 508, 494–499 (24 April 2014) doi:10.1038/nature13206

Pgenes make proteins

January 24, 2015

Bioinformatics (2015) 31 (1): 33-39. doi: 10.1093/bioinformatics/btu615

Making novel proteins from #pseudogenes Outcomes in 16 cases where one gets stable & functional translated products

PLOS Biology: Where Do Introns Come From?

August 23, 2014

Where Do #Introns Come From? A suggestion: exons with premature stops; has implications for #pseudogene formation

We have proposed a novel hypothesis for the origin of spliceosomal
introns, invoking endogenous production within translatable sequences
(at least in the case of protein-coding genes), facilitated by the
activity of cellular surveillance mechanisms. Despite the mutational
hazard associated with intron presence and proliferation [136], we
argue that, at least initially, introns might represent a favorable
life line for an allele that has acquired an ORF-disrupting mutation.
In this sense, in-frame stop codons need not be dead ends, as often
believed, but rather sequences that occasionally facilitate the
evolution of eukaryotic gene structure, possibly favoring not only
intronization, but also processes such as exonization (following a PTC
loss [137]). Further experimental validation of our hypothesis would
not only support the idea that intron birth/death rates depend on both
the population-genetic [136] and the intracellular environment, but
also shed light on a surprising aspect of the evolution of eukaryotic
gene structure, i.e., the ongoing, stochastic process of mutual
conversion between exons and introns within genes.