Large-scale transcriptome sequencing and gene analyses in the crab-eating macaque (Macaca fascicularis) for biomedical research. 2012

Jae-Won Huh, and Young-Hyun Kim, and Sang-Je Park, and Dae-Soo Kim, and Sang-Rae Lee, and Kyoung-Min Kim, and Kang-Jin Jeong, and Ji-Su Kim, and Bong-Seok Song, and Bo-Woong Sim, and Sun-Uk Kim, and Sang-Hyun Kim, and Kyu-Tae Chang
National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Chungbuk 363-883, Republic of Korea.

BACKGROUND As a human replacement, the crab-eating macaque (Macaca fascicularis) is an invaluable non-human primate model for biomedical research, but the lack of genetic information on this primate has represented a significant obstacle for its broader use. RESULTS Here, we sequenced the transcriptome of 16 tissues originated from two individuals of crab-eating macaque (male and female), and identified genes to resolve the main obstacles for understanding the biological response of the crab-eating macaque. From 4 million reads with 1.4 billion base sequences, 31,786 isotigs containing genes similar to those of humans, 12,672 novel isotigs, and 348,160 singletons were identified using the GS FLX sequencing method. Approximately 86% of human genes were represented among the genes sequenced in this study. Additionally, 175 tissue-specific transcripts were identified, 81 of which were experimentally validated. In total, 4,314 alternative splicing (AS) events were identified and analyzed. Intriguingly, 10.4% of AS events were associated with transposable element (TE) insertions. Finally, investigation of TE exonization events and evolutionary analysis were conducted, revealing interesting phenomena of human-specific amplified trends in TE exonization events. CONCLUSIONS This report represents the first large-scale transcriptome sequencing and genetic analyses of M. fascicularis and could contribute to its utility for biomedical research and basic biology.

UI MeSH Term Description Entries
D008252 Macaca fascicularis A species of the genus MACACA which typically lives near the coast in tidal creeks and mangrove swamps primarily on the islands of the Malay peninsula. Burmese Long-Tailed Macaque,Crab-Eating Monkey,Cynomolgus Monkey,M. f. aurea,M. fascicularis,Macaca fascicularis aurea,Monkey, Crab-Eating,Monkey, Cynomolgus,Crab-Eating Macaque,Burmese Long Tailed Macaque,Crab Eating Macaque,Crab Eating Monkey,Crab-Eating Macaques,Crab-Eating Monkeys,Cynomolgus Monkeys,Long-Tailed Macaque, Burmese,Macaque, Burmese Long-Tailed,Macaque, Crab-Eating,Monkey, Crab Eating
D008297 Male Males
D004251 DNA Transposable Elements Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom. DNA Insertion Elements,DNA Transposons,IS Elements,Insertion Sequence Elements,Tn Elements,Transposable Elements,Elements, Insertion Sequence,Sequence Elements, Insertion,DNA Insertion Element,DNA Transposable Element,DNA Transposon,Element, DNA Insertion,Element, DNA Transposable,Element, IS,Element, Insertion Sequence,Element, Tn,Element, Transposable,Elements, DNA Insertion,Elements, DNA Transposable,Elements, IS,Elements, Tn,Elements, Transposable,IS Element,Insertion Element, DNA,Insertion Elements, DNA,Insertion Sequence Element,Sequence Element, Insertion,Tn Element,Transposable Element,Transposable Element, DNA,Transposable Elements, DNA,Transposon, DNA,Transposons, DNA
D005091 Exons The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA. Mini-Exon,Exon,Mini Exon,Mini-Exons
D005260 Female Females
D000818 Animals Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA. Animal,Metazoa,Animalia
D015723 Gene Library A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences. DNA Library,cDNA Library,DNA Libraries,Gene Libraries,Libraries, DNA,Libraries, Gene,Libraries, cDNA,Library, DNA,Library, Gene,Library, cDNA,cDNA Libraries
D017398 Alternative Splicing A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different. RNA Splicing, Alternative,Splicing, Alternative,Alternate Splicing,Nested Transcripts,Alternate Splicings,Alternative RNA Splicing,Alternative RNA Splicings,Alternative Splicings,Nested Transcript,RNA Splicings, Alternative,Splicing, Alternate,Splicing, Alternative RNA,Splicings, Alternate,Splicings, Alternative,Splicings, Alternative RNA,Transcript, Nested,Transcripts, Nested
D017422 Sequence Analysis, DNA A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis. DNA Sequence Analysis,Sequence Determination, DNA,Analysis, DNA Sequence,DNA Sequence Determination,DNA Sequence Determinations,DNA Sequencing,Determination, DNA Sequence,Determinations, DNA Sequence,Sequence Determinations, DNA,Analyses, DNA Sequence,DNA Sequence Analyses,Sequence Analyses, DNA,Sequencing, DNA
D058977 Molecular Sequence Annotation The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record. Gene Annotation,Protein Annotation,Annotation, Gene,Annotation, Molecular Sequence,Annotation, Protein,Annotations, Gene,Annotations, Molecular Sequence,Annotations, Protein,Gene Annotations,Molecular Sequence Annotations,Protein Annotations,Sequence Annotation, Molecular,Sequence Annotations, Molecular

Related Publications

Jae-Won Huh, and Young-Hyun Kim, and Sang-Je Park, and Dae-Soo Kim, and Sang-Rae Lee, and Kyoung-Min Kim, and Kang-Jin Jeong, and Ji-Su Kim, and Bong-Seok Song, and Bo-Woong Sim, and Sun-Uk Kim, and Sang-Hyun Kim, and Kyu-Tae Chang
January 1971, Folia primatologica; international journal of primatology,
Jae-Won Huh, and Young-Hyun Kim, and Sang-Je Park, and Dae-Soo Kim, and Sang-Rae Lee, and Kyoung-Min Kim, and Kang-Jin Jeong, and Ji-Su Kim, and Bong-Seok Song, and Bo-Woong Sim, and Sun-Uk Kim, and Sang-Hyun Kim, and Kyu-Tae Chang
February 2014, Gene,
Jae-Won Huh, and Young-Hyun Kim, and Sang-Je Park, and Dae-Soo Kim, and Sang-Rae Lee, and Kyoung-Min Kim, and Kang-Jin Jeong, and Ji-Su Kim, and Bong-Seok Song, and Bo-Woong Sim, and Sun-Uk Kim, and Sang-Hyun Kim, and Kyu-Tae Chang
December 2020, Neuropsychopharmacology reports,
Jae-Won Huh, and Young-Hyun Kim, and Sang-Je Park, and Dae-Soo Kim, and Sang-Rae Lee, and Kyoung-Min Kim, and Kang-Jin Jeong, and Ji-Su Kim, and Bong-Seok Song, and Bo-Woong Sim, and Sun-Uk Kim, and Sang-Hyun Kim, and Kyu-Tae Chang
December 1985, Laboratory animal science,
Jae-Won Huh, and Young-Hyun Kim, and Sang-Je Park, and Dae-Soo Kim, and Sang-Rae Lee, and Kyoung-Min Kim, and Kang-Jin Jeong, and Ji-Su Kim, and Bong-Seok Song, and Bo-Woong Sim, and Sun-Uk Kim, and Sang-Hyun Kim, and Kyu-Tae Chang
February 1980, Laboratory animal science,
Jae-Won Huh, and Young-Hyun Kim, and Sang-Je Park, and Dae-Soo Kim, and Sang-Rae Lee, and Kyoung-Min Kim, and Kang-Jin Jeong, and Ji-Su Kim, and Bong-Seok Song, and Bo-Woong Sim, and Sun-Uk Kim, and Sang-Hyun Kim, and Kyu-Tae Chang
October 1988, The Anatomical record,
Jae-Won Huh, and Young-Hyun Kim, and Sang-Je Park, and Dae-Soo Kim, and Sang-Rae Lee, and Kyoung-Min Kim, and Kang-Jin Jeong, and Ji-Su Kim, and Bong-Seok Song, and Bo-Woong Sim, and Sun-Uk Kim, and Sang-Hyun Kim, and Kyu-Tae Chang
January 1988, Journal of molecular evolution,
Jae-Won Huh, and Young-Hyun Kim, and Sang-Je Park, and Dae-Soo Kim, and Sang-Rae Lee, and Kyoung-Min Kim, and Kang-Jin Jeong, and Ji-Su Kim, and Bong-Seok Song, and Bo-Woong Sim, and Sun-Uk Kim, and Sang-Hyun Kim, and Kyu-Tae Chang
January 1981, Reproduction, nutrition, developpement,
Jae-Won Huh, and Young-Hyun Kim, and Sang-Je Park, and Dae-Soo Kim, and Sang-Rae Lee, and Kyoung-Min Kim, and Kang-Jin Jeong, and Ji-Su Kim, and Bong-Seok Song, and Bo-Woong Sim, and Sun-Uk Kim, and Sang-Hyun Kim, and Kyu-Tae Chang
July 2018, American journal of physical anthropology,
Jae-Won Huh, and Young-Hyun Kim, and Sang-Je Park, and Dae-Soo Kim, and Sang-Rae Lee, and Kyoung-Min Kim, and Kang-Jin Jeong, and Ji-Su Kim, and Bong-Seok Song, and Bo-Woong Sim, and Sun-Uk Kim, and Sang-Hyun Kim, and Kyu-Tae Chang
January 1972, International journal of fertility,
Copied contents to your clipboard!