Transcriptome Reconstruction and Annotation of Cynomolgus and African Green Monkey

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2014 Oct 4

PMID 25277458

Citations 10

Authors

Albert Lee

Hossein Khiabanian

Jeffrey Kugelman

Oliver Elliott

Elyse Nagle

Guo-Yun Yu

Travis Warren

Gustavo Palacios

Raul Rabadan

Affiliations

Soon will be listed here.

Abstract

Background: Non-human primates (NHPs) and humans share major biological mechanisms, functions, and responses due to their close evolutionary relationship and, as such, provide ideal animal models to study human diseases. RNA expression in NHPs provides specific signatures that are informative of disease mechanisms and therapeutic modes of action. Unlike the human transcriptome, the transcriptomes of major NHP animal models are yet to be comprehensively annotated.

Results: In this manuscript, employing deep RNA sequencing of seven tissue samples, we characterize the transcriptomes of two commonly used NHP animal models: Cynomolgus macaque (Macaca fascicularis) and African green monkey (Chlorocebus aethiops). We present the Multi-Species Annotation (MSA) pipeline that leverages well-annotated primate species and annotates 99.8% of reconstructed transcripts. We elucidate tissue-specific expression profiles and report 13 experimentally validated novel transcripts in these NHP animal models.

Conclusion: We report comprehensively annotated transcriptomes of two non-human primates, which we have made publically available on a customized UCSC Genome Browser interface. The MSA pipeline is also freely available.

Citing Articles

The epitranscriptome of Vero cells infected with SARS-CoV-2 assessed by direct RNA sequencing reveals m6A pattern changes and DRACH motif biases in viral and cellular RNAs.

Campos J, Alves G, Maricato J, Braconi C, Antoneli F, Janini L Front Cell Infect Microbiol. 2022; 12:906578.

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Signature MicroRNA expression profile is associated with lipid metabolism in African green monkey.

Zhou X, Wang J, Ye H, Fa Y Lipids Health Dis. 2019; 18(1):55.

PMID: 30819205 PMC: 6396449. DOI: 10.1186/s12944-019-0999-2.

Improved Macaca fascicularis gene annotation reveals evolution of gene expression profiles in multiple tissues.

Tan T, Xia L, Tu K, Tang J, Yin S, Dai L BMC Genomics. 2018; 19(1):787.

PMID: 30382841 PMC: 6211470. DOI: 10.1186/s12864-018-5183-y.

Successful application of human-based methyl capture sequencing for methylome analysis in non-human primate models.

Lee J, Ryu D, Park S, Choe S, Cho H, Lee S BMC Genomics. 2018; 19(1):267.

PMID: 29669513 PMC: 5907189. DOI: 10.1186/s12864-018-4666-1.

A conserved transcriptional response to intranasal Ebola virus exposure in nonhuman primates prior to onset of fever.

Speranza E, Bixler S, Altamura L, Arnold C, Pratt W, Taylor-Howell C Sci Transl Med. 2018; 10(434).

PMID: 29593102 PMC: 9986849. DOI: 10.1126/scitranslmed.aaq1016.

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