Posts Tagged ‘pseudogene’

dolphin odorant receptors

June 22, 2014

Perhaps the most interesting, all of the odorant receptors will become pseudogenized in the mammalians aquatically such as dolphins and whales where the nose is demonstrably not used anymore for smelling but becomes the blow hole.

A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics | eLife

June 22, 2014

QT:{{”
We identify an lncRNA pseudogene, Lethe (named after the mythological river of forgetfulness, for its role in negative feedback), which is expressed in response to proinflammatory cytokines TNFα and IL-1β, and the anti-inflammatory agent, dexamthasone, but is not responsive to microbial components, and is primarily found on the chromatin. Lethe is regulated by RelA, independent of pseudogene family members and proximal genes. Additionally, Lethe is dramatically downregulated in aged spleen. Finally, Lethe binds directly to RelA to inhibit NF-κB DNA binding activity. These findings suggest that Lethe may function as a novel negative regulator of NF-κB, to help fine tune the inflammatory response.
“}}

A mammalian #pseudogene #lncRNA at the interface of inflammation… Lethe may down-regulate NF-kB via binding to RelA
http://elifesciences.org/content/2/e00762

No use of Gencode pgenes !

PLOS ONE: Burst of Young Retrogenes and Independent Retrogene Formation in Mammals

April 19, 2014

Burst of Young Retrogenes…in Mammals. Discusses much
retro-transposition ~40 Mya, relevant to proc. #pseudogenes
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0005040

Also, ref #11 provides more detail on this.

age distribution of repeats

March 24, 2014

From the following article:
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium
Nature 409, 860-921(15 February 2001)
doi:10.1038/35057062

Alu age distribution

http://www.nature.com/nature/journal/v409/n6822/fig_tab/409860a0_F18.html

Transcription and translation of pseudogenes

February 23, 2014

http://www.nature.com/nmeth/journal/v11/n1/full/nmeth.2732.html

From the paper:
QT:{{”
2. Pseudogenes represent less than 0.1% of the total search space, yet a surprisingly large number, 36%, of human novel peptides mapped to pseudogenes (Fig. 2b). These findings are supported by recent peptide-level evidence of pseudogenes in mouse6. In humans, the observation of lineage- and cancer-specific expression of pseudogenes at the RNA level indicates biological relevance17. Our data suggest that pseudogenes may be not only transcribed but also translated. An interesting particular example was the pseudogene MYH16, identified by 20 peptides (Fig. 3), which were validated by LC-MS using synthetic peptides (Supplementary Fig. 15). The protein-coding capacity of MYH16 was previously shown to have been lost through double base deletion (resulting in a premature stop codon) during divergence of the human lineage from other primates18. However, our data show that, in the A431 cell line, the MYH16gene is actively encoding a shorter protein isoform with its translation initiation site downstream from the aforementioned double base deletion.
“}}

Kruglyak paper on C. elegans

January 2, 2014

A paper on C. elegans that’s very informative:
http://www.nature.com/ng/journal/v44/n3/full/ng.1050.html
Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity

Most notable of their findings is evidence of recent selective sweeps on chromosomes I, IV, V and (sort of) X. These sweeps have the potential to fix pseudogenes that might have been present at the time.

Pseudogene Vocabulary

August 23, 2013

http://www.ebi.ac.uk/ena/WebFeat/qualifiers/pseudogene.html
http://www.insdc.org/documents/pseudogene-qualifier-vocabulary see here as well
https://www.vectorbase.org/info/website/glossary.html

vs

http://gencodegenes.wordpress.com/toolbox

Also, on unitary pseudogene term “origin” here is the earliest use of the term findable :
http://www.talkorigins.org/faqs/molgen/

Unitary & Processed as in Gencode
Unprocessed = Duplicated
Allelic = Polymorphic

Pseudogene Vocabulary

August 21, 2013

http://www.ebi.ac.uk/ena/WebFeat/qualifiers/pseudogene.html
http://www.insdc.org/documents/pseudogene-qualifier-vocabulary see here as well
https://www.vectorbase.org/info/website/glossary.html

Unitary & Processed as in Gencode
Unprocessed = Duplicated
Allelic = Polymorphic

Extensive Gene Traffic on the Mammalian X Chromosome

June 29, 2013

http://www.sciencemag.org/content/303/5657/537.long

From pseudogenes to proteins

April 19, 2013

Gencode perspective on massspec of pseudogenes
http://www.nature.com/nmeth/journal/v8/n6/full/nmeth0611-448b.html