Evolution of Primate Gene Expression: Drift and Corrective Sweeps?

Download

index.pdf

Date

2008-11-01

Author

Chaix, R.
Somel, Mehmet
Kreil, D. P.
Khaitovich, P.
Lunter, G. A.

Metadata

Show full item record

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Item Usage Stats

114
views

0
downloads

Changes in gene expression play an important: role in species' evolution. Earlier studies uncovered evidence that the effect of mutations on expression levels within the primate order is skewed, with many small downregulations balanced by fewer but larger upregulations. In addition, brain-expressed genes appeared to show an increased rate of evolution on the branch leading to human. However, the lack of a mathematical model adequately describing the evolution of gene expression precluded the rigorous establishment of these observations. Here, we develop mathematical tools that allow us to revisit these earlier observations in a model-testing and inference framework. We introduce a model for skewed gene-expression evolution within a phylogenetic tree and use a separate model to account for biological or experimental outliers. A Bayesian Markov chain Monte Carlo inference procedure allows its to infer the phylogeny and other evolutionary parameters, while quantifying the confidence in these inferences. Our results support previous observations; in particular, we find strong evidence for a sustained positive skew in the distribution of gene-expression changes in primate evolution. We propose a "corrective sweep" scenario to explain this phenomenon.

Subject Keywords

Genetics

URI

https://hdl.handle.net/11511/45997

Journal

GENETICS

DOI

https://doi.org/10.1534/genetics.108.089623

Collections

Department of Biology, Article

Suggestions

OpenMETU
Core

Evolution of Neuronal and Endothelial Transcriptomes in Primates Giger, Thomas; Khaitovich, Philipp; Somel, Mehmet; Lorenc, Anna; Lizano, Esther; Harris, Laura W.; Ryan, Margaret M.; Lan, Martin; Wayland, Matthew T.; Bahn, Sabine; Paeaebo, Svante (Oxford University Press (OUP), 2010-01-01) The study of gene expression evolution in vertebrates has hitherto focused on the analysis of transcriptomes in tissues of different species. However, because a tissue is made up of different cell types, and cell types differ with respect to their transcriptomes, the analysis of tissues offers a composite picture of transcriptome evolution. The isolation of individual cells from tissue sections opens up the opportunity to study gene expression evolution at the cell type level. We have stained neurons and en...
Functional characterization of microrna-125b expression in MCF7 breast cancer cell line Tuna, Serkan; Erson Bensan, Ayşe Elif; Department of Biology (2010) microRNA dependent gene expression regulation has roles in diverse processes such as differentiation, proliferation and apoptosis. Therefore, deregulated miRNA expression has functional importance for various diseases, including cancer. miR-125b is among the commonly downregulated miRNAs in breast cancer cells . Therefore we aimed to characterize the effects of miR-125b expression in MCF7 breast cancer cell line (BCCL) to better understand its roles in tumorigenesis. Here, we investigated mir-125 family mem...
USP32 is an active, membrane-bound ubiquitin protease overexpressed in breast cancers AKHAVANTABASI, Shiva; AKMAN, Hesna B.; SAPMAZ, Aysegul; Keller, Jennifer; Petty, Elizabeth M.; Erson Bensan, Ayşe Elif (Springer Science and Business Media LLC, 2010-08-01) USP32, on chromosomal band 17q23.1-17q23.2, is a highly conserved but uncharacterized gene that gave rise during evolution to a well-known hominoid-specific proto-oncogene, USP6. We investigated the expression profile of USP32 in human tissues and examined its functions to gain insight into this novel member of the well-conserved ubiquitination system. We detected ubiquitous USP32 expression across tissues and confirmed the predicted deubiquitination function owing to the presence of conserved peptidase sig...
Identification and analysis of genomic regions with large between-population differentiation in humans Myles, S.; Tang, K.; Somel, Mehmet; Green, R. E.; Kelso, J.; Stoneking, M. (Wiley, 2008-01-01) The primary aim of genetic association and linkage studies is to identify genetic variants that contribute to phenotypic variation within human populations. Since the overwhelming majority of human genetic variation is found within populations, these methods are expected to be effective and can likely be extrapolated from one human population to another. However, they may lack power in detecting the genetic variants that contribute to phenotypes that differ greatly between human populations. Phenotypes that...
Transcriptomic insights into human brain evolution: acceleration, neutrality, heterochrony Somel, Mehmet; Liu, Xiling (Elsevier BV, 2014-12-01) Primate brain transcriptome comparisons within the last 12 years have yielded interesting but contradictory observations on how the transcriptome evolves, and its adaptive role in human cognitive evolution. Since the human-chimpanzee common ancestor, the human prefrontal cortex transcriptome seems to have evolved more than that of the chimpanzee. But at the same time, most expression differences among species, especially those observed in adults, appear as consequences of neutral evolution at cis-regulatory...

Citation Formats

R. Chaix, M. Somel, D. P. Kreil, P. Khaitovich, and G. A. Lunter, “Evolution of Primate Gene Expression: Drift and Corrective Sweeps?,” GENETICS, pp. 1379–1389, 2008, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/45997.