Intergenic and Repeat Transcription in Human, Chimpanzee and Macaque Brains Measured by RNA-Seq

Download

index.pdf

Date

2010-07-01

Author

Xu, Augix Guohua
He, Liu
Li, Zhongshan
Xu, Ying
Li, Mingfeng
Fu, Xing
Yan, Zheng
Yuan, Yuan
Menzel, Corinna
Li, Na
Somel, Mehmet
Hu, Hao
Chen, Wei
Paabo, Svante
Khaitovich, Philipp

Metadata

Show full item record

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

Item Usage Stats

187
views

75
downloads

Transcription is the first step connecting genetic information with an organism's phenotype. While expression of annotated genes in the human brain has been characterized extensively, our knowledge about the scope and the conservation of transcripts located outside of the known genes' boundaries is limited. Here, we use high-throughput transcriptome sequencing (RNA-Seq) to characterize the total non-ribosomal transcriptome of human, chimpanzee, and rhesus macaque brain. In all species, only 20-28% of non-ribosomal transcripts correspond to annotated exons and 20-23% to introns. By contrast, transcripts originating within intronic and intergenic repetitive sequences constitute 40-48% of the total brain transcriptome. Notably, some repeat families show elevated transcription. In non-repetitive intergenic regions, we identify and characterize 1,093 distinct regions highly expressed in the human brain. These regions are conserved at the RNA expression level across primates studied and at the DNA sequence level across mammals. A large proportion of these transcripts (20%) represents 3'UTR extensions of known genes and may play roles in alternative microRNA-directed regulation. Finally, we show that while transcriptome divergence between species increases with evolutionary time, intergenic transcripts show more expression differences among species and exons show less. Our results show that many yet uncharacterized evolutionary conserved transcripts exist in the human brain. Some of these transcripts may play roles in transcriptional regulation and contribute to evolution of human-specific phenotypic traits.

Subject Keywords

Ecology, Modelling and Simulation, Computational Theory and Mathematics, Genetics, Ecology, Evolution, Behavior and Systematics, Molecular Biology, Cellular and Molecular Neuroscience

URI

https://hdl.handle.net/11511/48233

Journal

PLOS COMPUTATIONAL BIOLOGY

DOI

https://doi.org/10.1371/journal.pcbi.1000843

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...
Evolution of Self-Organized Task Specialization in Robot Swarms Ferrante, Eliseo; Turgut, Ali Emre; Duenez-Guzman, Edgar; Dorigo, Marco; Wenseleers, Tom (Public Library of Science (PLoS), 2015-08-01) Division of labor is ubiquitous in biological systems, as evidenced by various forms of complex task specialization observed in both animal societies and multicellular organisms. Although clearly adaptive, the way in which division of labor first evolved remains enigmatic, as it requires the simultaneous co-occurrence of several complex traits to achieve the required degree of coordination. Recently, evolutionary swarm robotics has emerged as an excellent test bed to study the evolution of coordinated group...
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...
Genetic Structure and Variation of Van Cats ALTUNOK, VAHDETTİN; Yüksek, Nazmi; Berkman, Ceren C.; Agaoglu, Zahid Tevfik; Togan, İnci Zehra (Springer Science and Business Media LLC, 2011-08-01) To determine the genetic structure and variation of Van cats and some other cats, seven enzyme loci were examined using horizontal starch gel electrophoresis. ME bands were observed for the first time in cats. For the enzyme loci CA (1) , SOD, GPI, and GOT, neither the individual Van cats nor the specimens of other cat species exhibited any variation. These enzymes presented identical bands, all of which were homozygous. With respect to the PGD, ME, and ESD loci, however, genetic variation was observed in a...
Early gene expression divergence between allopatric populations of the house mouse (Mus musculus domesticus) Bryk, Jaroslaw; Somel, Mehmet; Lorenc, Anna; Teschke, Meike (Wiley, 2013-03-01) Divergence of gene expression is known to contribute to the differentiation and separation of populations and species, although the dynamics of this process in early stages of population divergence remains unclear. We analyzed gene expression differences in three organs (brain, liver, and testis) between two natural populations of Mus musculus domesticus that have been separated for at most 3000years. We used two different microarray platforms to corroborate the results at a large scale and identified hundr...

Citation Formats

A. G. Xu et al., “Intergenic and Repeat Transcription in Human, Chimpanzee and Macaque Brains Measured by RNA-Seq,” PLOS COMPUTATIONAL BIOLOGY, pp. 0–0, 2010, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/48233.