Evolutionary direction of processed pseudogenes

Liu, Guoqing; Cui, Xiangjun; Liang, Hong; Cai, Liang

doi:10.1007/s11427-016-5074-x

Cited by 6 publications

(2 citation statements)

References 67 publications

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“…Using our computational model, we obtained distribution patterns of nucleosome occupancy around both ends of pseudogenes in the human genome [39], which are in agreement with the experimental results. Analyses based on the model also indicated that processed pseudogenes show a decreased ability to form nucleosomes during evolution [40]. Possible applications of the model in the prediction of nucleosome free energy and nucleosome sliding were discussed [41].…”

Section: Introductionmentioning

confidence: 99%

DNA physical properties outperform sequence compositional information in classifying nucleosome-enriched and -depleted regions

Liu

Tan

et al. 2019

Genomics

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The nucleosome is the fundamental structural unit of eukaryotic chromatin and plays an essential role in the epigenetic regulation of cellular processes, such as DNA replication, recombination, and transcription. Hence, it is important to identify nucleosome positions in the genome. Our previous model based on DNA deformation energy, in which a set of DNA physical descriptors was used, performed well in predicting nucleosome dyad positions and occupancy. In this study, we established a machine-learning model for predicting nucleosome occupancy in order to further verify the physical descriptors. Results showed that (1) our model outperformed several other sequence compositional information-based models, indicating a stronger dependence of nucleosome positioning on DNA physical properties; (2) nucleosome-enriched and -depleted regions have distinct features in terms of DNA physical descriptors like sequence-dependent flexibility and equilibrium structure parameters; (3) gene transcription start sites and termination sites can be well characterized with the distribution patterns of the physical descriptors, indicating the regulatory role of DNA physical properties in gene transcription. In addition, we developed a web server for the model, which is freely accessible at http://lin-group.cn/server/iNuc-force/.

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Section: Introductionmentioning

confidence: 99%

DNA physical properties outperform sequence compositional information in classifying nucleosome-enriched and -depleted regions

Liu

Tan

et al. 2019

Genomics

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“…In the absence of selective pressure for their retention, TFBMs degenerate over evolutionary time. [ 91 ] Under selection, processed pseudogenes could evolve promoter activity and profoundly impact the coding sequences of nearby genes or host genes. For example, some pseudogene transcripts are embedded with alternative downstream transcriptional start sites inherited from parental transcripts that can evolve promoter activity.…”

Section: Pseudogenes Can Evolve Proto‐promoter Activity and Influence Proximal Genesmentioning

confidence: 99%

Processed pseudogenes: A substrate for evolutionary innovation

2021

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Processed pseudogenes may serve as a genetic reservoir for evolutionary innovation. Here, we argue that through the activity of long interspersed element-1 retrotransposons, processed pseudogenes disperse coding and noncoding sequences rich with regulatory potential throughout the human genome. While these sequences may appear to be non-functional, a lack of contemporary function does not prohibit future development of biological activity. Here, we discuss the dynamic evolution of certain processed pseudogenes into coding and noncoding genes and regulatory elements, and their implication in wide-ranging biological and pathological processes. Also see the

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