the "circle of life"
http://www.sciencedirect.com/science/article/pii/S0960982214001547#
Volume 24, Issue 6, pR238–R240, 17 March 2014
Evolution: Dynamics of De Novo Gene Emergence
Rafik Neme
Diethard Tautz
From S Caroll, “Many approaches are being taken, and a few intriguing associations of candidate genes and the evolution of particular traits have been discovered, such as the…MYH16 muscle-specific myosin pseudogene and the evolutionary reduction of the masticatory apparatus.”
QT:{{”
Powerful masticatory muscles are found in most primates, including chimpanzees and gorillas…. In contrast, masticatory muscles are considerably smaller in both modern and fossil members of Homo. …Here, we show that the gene encoding the predominant myosin heavy chain (MYH) expressed in these muscles was inactivated by a
frameshifting mutation after the lineages leading to humans and chimpanzees diverged. Loss of this protein isoform is associated with marked size reductions in individual muscle fibres and entire masticatory muscles. Using the coding sequence for the myosin rod domains as a molecular clock, we estimate that this mutation appeared approximately 2.4 million years ago.
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http://www.nature.com/nature/journal/v428/n6981/abs/nature02358.html
http://www.nature.com/ncomms/2014/140707/ncomms4963/full/ncomms4963.html
The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant tumour subtypes
Leng Han
Yuan Yuan
Siyuan Zheng
Yang Yang
Jun Li
Mary E. Edgerton
Lixia Diao
Yanxun Xu
Roeland G. W. Verhaak
Han Liang
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.
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.
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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 !
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.
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
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.
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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.
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