Posts Tagged ‘pseudogene’

Mystery RNA spawns gene-activating peptides : Nature News

Saturday, March 2nd, 2019


It should be possible to scan the genome for sequences encoding peptides shorter than 100 amino acids, says Mark Gerstein, a computational biologist at Yale University in New Haven, Connecticut, but sorting through the many ‘hits’ to determine which are functional is likely to be much more difficult.

Meanwhile, Gerstein notes that the polished rice peptides could also have implications for how we view pseudogenes, which have long been thought to be defunct relics of protein-coding genes. Pseudogenes often contain many signals that would stop protein synthesis and, as a result, could only encode short amino-acid chains. “Maybe this would provide a new way for pseudogenes to have some sort of function,” he says.

Jim Simons, the Numbers King

Sunday, January 28th, 2018

Jim Simons, the Numbers King Highlights the new @FlatironInst & one of its new hires, Nick Carriero, who co-wrote the original Yale pseudogene pipeline, PseudoPipe ( HT @Anne_Churchland

“Our discussion turned to the Flatiron Institute. Renaissance’s computer infrastructure, he said, had been a central part of its success. At universities, Simons said, coding tends to be an erratic process. He said of the graduate students and postdocs who handled such work, “Some of them are pretty good code writers, and some of them are not so good. But then they leave, and there’s no one to maintain that code.” For the institute, he has hired two esteemed coders from academia: Carriero, who had led my tour, had been recruited from Yale, where he had developed the university’s high-performance computing capabilities for the life sciences; Ian Fisk had worked at cern, the particle-physics laboratory outside Geneva. Simons offered them greater authority and high salaries. “They’re the best of the breed,” he said. Carriero and Fisk sometimes consult with their counterparts at Renaissance about technical matters.

Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element. – PubMed – NCBI

Tuesday, October 31st, 2017

Comparative…3D chromosomal architecture identifies a novel fetal Hb reg. element #Pseudogene shifts v. promotor

Genome expansion via lineage splitting and genome reduction in the cicada endosymbiont Hodgkinia

Tuesday, February 14th, 2017

Genome expansion via lineage splitting…in the cicada endosymbiont Hodgkinia Host lifecycle partially enables split

Eat, Pray, Latin – The New Yorker

Friday, August 19th, 2016

Eat, pray, #Latin “An undead language, a ghost shadowing…our words, a zombie…in sentences,” viz pseudolanguage!

Pseudoenzyme – Proteopedia, life in 3D

Sunday, August 2nd, 2015

Pseudoenzymes are proteins that cannot catalyze chemical reactions despite being clearly related structurally to functioning enzymes. Many enzyme families contain inactive members. For example, a number of human kinases lack at least one of the key amino acids necessary for catalysis of phosphate transfer [1]. Often pseudoenzymes still have biological roles, albeit non-catalytic. Some assist true enzymes in obtaining functional folds, some server as platforms for other proteins to interact, and some are escorts for proteins [2][3]. “}}

New lives for old: evolution of pseudoenzyme function illustrated by iRhoms : Abstract : Nature Reviews Molecular Cell Biology

Sunday, August 2nd, 2015

– pseudoenzyme

Genome-wide identification of pseudogenes capable of disease-causing gene conversion. – PubMed – NCBI

Sunday, August 2nd, 2015

The structure, function and evolution of proteins that bind DNA and RNA : Nature Reviews Molecular Cell Biology : Nature Publishing Group

Wednesday, June 10th, 2015

William H. Hudson
& Eric A. Ortlund
Nature Reviews Molecular Cell Biology 15, 749–760 (2014) doi:10.1038/nrm3884

BRAF pseudogene and cancer development

Friday, April 17th, 2015

BRAF #Pseudogene Functions as a Competitive Endogenous RNA; [Shows it] induces Lymphoma [after alteration, in mice]

Cell. 2015 Apr 9;161(2):319-32. doi: 10.1016/j.cell.2015.02.043. Epub 2015 Apr 2.

Karreth FA1, Reschke M1, Ruocco A1, Ng C1, Chapuy B2, Léopold V1, Sjoberg M3, Keane TM3, Verma A4, Ala U1, Tay Y1, Wu D5, Seitzer N1, Velasco-Herrera Mdel C3, Bothmer A1, Fung J1, Langellotto F6, Rodig SJ7, Elemento O4, Shipp MA2, Adams DJ3, Chiarle R8, Pandolfi PP9.

Research over the past decade has suggested important roles for pseudogenes in physiology and disease. In vitro experiments
demonstrated that pseudogenes contribute….