Dataset Information

A second TCR? locus in Galliformes uses antibody-like V domains: insight into the evolution of TCR? and TCR? genes in tetrapods.

ABSTRACT: Analyses of the available avian genomes revealed the presence of a second TCR? locus in the Galliformes. This second TCR? locus is nonsyntenic to the conventional TCR?/? and is unusual in that the V genes are more related to IgH V genes (VH) than to TCR V genes. The second TCR? is not found in another avian lineage, the passerine zebra finch. Rather the finch's conventional TCR?/? locus contains VH genes that are expressed with the conventional C? gene, similar to what has been found in amphibians. A comparison between Galliformes and Passeriformes genomic organization suggests an origin of the second TCR? in the former lineage involving gene duplication. Expression of these atypical TCR? transcripts with a VH domain paired with C? was found in lymphoid tissues of both avian lineages. The configuration of the second TCR? in chicken and turkey is reminiscent of the TCR? duplication that is present in nonplacental mammals and provides insight into the origin of the uniquely mammalian TCR? locus.

SUBMITTER: Parra ZE

PROVIDER: S-EPMC3324631 | biostudies-literature | 2012 Apr

REPOSITORIES: biostudies-literature

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A second TCRδ locus in Galliformes uses antibody-like V domains: insight into the evolution of TCRδ and TCRμ genes in tetrapods.

Parra Zuly E ZE Mitchell Kevin K Dalloul Rami A RA Miller Robert D RD

Journal of immunology (Baltimore, Md. : 1950) 20120309 8

Analyses of the available avian genomes revealed the presence of a second TCRδ locus in the Galliformes. This second TCRδ locus is nonsyntenic to the conventional TCRα/δ and is unusual in that the V genes are more related to IgH V genes (VH) than to TCR V genes. The second TCRδ is not found in another avian lineage, the passerine zebra finch. Rather the finch's conventional TCRα/δ locus contains VH genes that are expressed with the conventional Cδ gene, similar to what has been found in amphibia ...[more]

PMID: 22407916

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Project description:Only a minuscule fraction of long non-coding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into their functionality, but comparative analyses have been precluded by our ignorance of lncRNAs in non-model organisms. Here, we use RNA sequencing to identify lncRNAs in eleven tetrapod species and we present the first large-scale evolutionary study of lncRNA repertoires and expression patterns. We identify ~11,000 primate- specific lncRNA families, which show evidence for selective constraint during recent evolution, and ~2,400 highly conserved lncRNAs (including ~400 genes that likely originated more than 300 million years ago). We find that lncRNAs, in particular ancient ones, are generally actively regulated and may predominantly function in embryonic development. lncRNA X-inactivation patterns reveal an extremely female-biased monotreme-specific lncRNA, which may partially compensate X-dosage in this lineage. Most lncRNAs evolve rapidly in terms of sequence and expression levels, but global patterns like tissue specificities are often conserved. We compared expression patterns of homologous lncRNA and protein-coding families across tetrapods to reconstruct an evolutionarily conserved co-expression network. This network, which surprisingly contains many lncRNA hubs, suggests potential functions for lncRNAs in fundamental processes like spermatogenesis or synaptic transmission, but also in more specific mechanisms such as placenta growth suppression through miRNA production. [Batch 1 and 2] To broaden our understanding of lncRNA evolution, we used an extensive RNA-seq dataset to establish lncRNA repertoires and homologous gene families in 11 tetrapod species. We analyzed the poly- adenylated transcriptomes of 8 organs (cortex/whole brain without cerebellum, cerebellum, heart, kidney, liver, placenta, ovary and testis) and 11 species (human, chimpanzee, bonobo, gorilla, orangutan, macaque, mouse, opossum, platypus, chicken and the frog Xenopus tropicalis), which shared a common ancestor ~370 millions of years (MY) ago. Our dataset included 47 strand-specific samples, which allowed us to confirm the orientation of gene predictions and to address the evolution of sense-antisense transcripts. See also GSE43721 (Soumillon et al, Cell Reports, 2013) for three strand-specific samples for mouse brain, liver and testis.

Dataset Information

A second TCR? locus in Galliformes uses antibody-like V domains: insight into the evolution of TCR? and TCR? genes in tetrapods.

Publications

A second TCRδ locus in Galliformes uses antibody-like V domains: insight into the evolution of TCRδ and TCRμ genes in tetrapods.

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