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Open Access Research article

On the quest for selective constraints shaping the expressivity of the genes casting retropseudogenes in human

Kamalika Sen, Soumita Podder and Tapash C Ghosh*

Author Affiliations

Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata- 700 054, India

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BMC Genomics 2011, 12:401  doi:10.1186/1471-2164-12-401

Published: 8 August 2011

Abstract

Background

Pseudogenes, the nonfunctional homologues of functional genes are now coming to light as important resources regarding the study of human protein evolution. Processed pseudogenes arising by reverse transcription and reinsertion can provide molecular record on the dynamics and evolution of genomes. Researches on the progenitors of human processed pseudogenes delved out their highly expressed and evolutionarily conserved characters. They are reported to be short and GC-poor indicating their high efficiency for retrotransposition. In this article we focused on their high expressivity and explored the factors contributing for that and their relevance in the milieu of protein sequence evolution.

Results

We here, analyzed the high expressivity of these genes configuring processed or retropseudogenes by their immense connectivity in protein-protein interaction network, an inclination towards alternative splicing mechanism, a lower rate of mRNA disintegration and a slower evolutionary rate. While the unusual trend of the upraised disorder in contrast with the high expressivity of the proteins encoded by processed pseudogene ancestors is accredited by a predominance of hub-protein encoding genes, a high propensity of repeat sequence containing genes, elevated protein stability and the functional constraint to perform the transcription regulatory jobs. Linear regression analysis demonstrates mRNA decay rate and protein intrinsic disorder as the influential factors controlling the expressivity of these retropseudogene ancestors while the latter one is found to have the most significant regulatory power.

Conclusions

Our findings imply that, the affluence of disordered regions elevating the network attachment to be involved in important cellular assignments and the stability in transcriptional level are acting as the prevailing forces behind the high expressivity of the human genes configuring processed pseudogenes.

Keywords:
Expressivity; Protein intrinsic disorder; Connectivity; Alternative splicing; Protein stability; mRNA decay rate; Evolutionary rate