Posts Tagged ‘pseudogene’

BRAF pseudogene and cancer development

April 17, 2015

BRAF #Pseudogene Functions as a Competitive Endogenous RNA; [Shows it] induces Lymphoma [after alteration, in mice]
http://www.cell.com/cell/abstract/S0092-8674(15)00244-5

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.

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

Circle of life

November 15, 2014

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

DOI: http://dx.doi.org/10.1016/j.cub.2014.02.016

Myosin gene mutation correlates with anatomical changes in the human lineage : Abstract : Nature

July 23, 2014

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.

“}}

http://www.nature.com/nature/journal/v428/n6981/abs/nature02358.html

Pseudogene expression in TCGA data

July 11, 2014

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

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.
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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.