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Genomic analysis offers insights into the evolution of the bovine TRA/TRD locus.

Connelley TK, Degnan K, Longhi CW, Morrison WI - BMC Genomics (2014)

Bottom Line: Both TRA and TRD selection have contributed to the evolution of the bovine TRAV/TRDV repertoire.However, our data suggest that due to homology unit duplication TRD selection for TRDV1 subgroup expansion may have substantially contributed to the genomic expansion of several TRAV subgroups.Such data demonstrate how integration of genomic and transcript data can provide a more nuanced appreciation of the evolutionary dynamics that have led to the dramatically expanded bovine TRAV/TRDV repertoire.

View Article: PubMed Central - PubMed

Affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian EH25 9RG, Scotland, UK. timothy.connelley@ed.ac.uk.

ABSTRACT

Background: The TRA/TRD locus contains the genes for V(D)J somatic rearrangement of TRA and TRD chains expressed by αβ and γδ T cells respectively. Previous studies have demonstrated that the bovine TRA/TRD locus contains an exceptionally large number of TRAV/TRDV genes. In this study we combine genomic and transcript analysis to provide insights into the evolutionary development of the bovine TRA/TRD locus and the remarkable TRAV/TRDV gene repertoire.

Results: Annotation of the UMD3.1 assembly identified 371 TRAV/TRDV genes (distributed in 42 subgroups), 3 TRDJ, 6 TRDD, 62 TRAJ and single TRAC and TRDC genes, most of which were located within a 3.5 Mb region of chromosome 10. Most of the TRAV/TRDV subgroups have multiple members and several have undergone dramatic expansion, most notably TRDV1 (60 genes). Wide variation in the proportion of pseudogenes within individual subgroups, suggest that differential 'birth' and 'death' rates have been used to form a functional bovine TRAV/TRDV repertoire which is phylogenetically distinct from that of humans and mice. The expansion of the bovine TRAV/TRDV gene repertoire has predominantly been achieved through a complex series of homology unit (regions of DNA containing multiple gene) replications. Frequent co-localisation within homology units of genes from subgroups with low and high pseudogene proportions suggest that replication of homology units driven by evolutionary selection for the former may have led to a 'collateral' expansion of the latter. Transcript analysis was used to define the TRAV/TRDV subgroups available for recombination of TRA and TRD chains and demonstrated preferential usage of different subgroups by the expressed TRA and TRD repertoires, indicating that TRA and TRD selection have had distinct impacts on the evolution of the TRAV/TRDV repertoire.

Conclusion: Both TRA and TRD selection have contributed to the evolution of the bovine TRAV/TRDV repertoire. However, our data suggest that due to homology unit duplication TRD selection for TRDV1 subgroup expansion may have substantially contributed to the genomic expansion of several TRAV subgroups. Such data demonstrate how integration of genomic and transcript data can provide a more nuanced appreciation of the evolutionary dynamics that have led to the dramatically expanded bovine TRAV/TRDV repertoire.

Show MeSH
Conserved synteny of the 3′ end of the bovine, human and murine TRA/TRD loci. A schematic representation shows the conserved inter-species organisation of TR genes and regulatory elements at the 3′ end of the TRA/TRD locus. The approximate positions of TRDD (green lines), TRDJ (orange lines), TRAJ (blue lines), TRDC and TRAC (blue blocks), the single inverted TRDV gene (TRDV3 in bovine and human, TRDV5 in mouse – green block) and regulatory elements (yellow circles) are shown. The regulatory elements represented are – TRA enhancer (Eα), TRD enhancer (Eδ), T early alpha (TEA) and conserved sequence block (CSB). The length of the region is also conserved across the species, with the exception of the area occupied by TRDD genes, which is much greater in the bovine TRA/TRD locus (~80 Kb) than in the mouse or human (~10 Kb). The asterisk indicates the approximate location of the 1 Kb gap between contigs DAAA02028052.1 and DAAAA02028053.1.
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Fig1: Conserved synteny of the 3′ end of the bovine, human and murine TRA/TRD loci. A schematic representation shows the conserved inter-species organisation of TR genes and regulatory elements at the 3′ end of the TRA/TRD locus. The approximate positions of TRDD (green lines), TRDJ (orange lines), TRAJ (blue lines), TRDC and TRAC (blue blocks), the single inverted TRDV gene (TRDV3 in bovine and human, TRDV5 in mouse – green block) and regulatory elements (yellow circles) are shown. The regulatory elements represented are – TRA enhancer (Eα), TRD enhancer (Eδ), T early alpha (TEA) and conserved sequence block (CSB). The length of the region is also conserved across the species, with the exception of the area occupied by TRDD genes, which is much greater in the bovine TRA/TRD locus (~80 Kb) than in the mouse or human (~10 Kb). The asterisk indicates the approximate location of the 1 Kb gap between contigs DAAA02028052.1 and DAAAA02028053.1.

Mentions: The UMD3.1 assembly of the 3′ end of the bovine TRA/TRD locus appears to be essentially complete. All TRAC, TRAJ, TRDC, TRDJ, TRDD genes and the TRDV3 gene (in inverted orientation) are located on 2 large contigs (DAAA02028052.1 – 140 Kb and DAAAA02028053.1 – 114 Kb) separated by a gap of approximately 1 Kb. The organisation of the genes demonstrates a marked syntenic conservation between mouse, human and bovine (Figure 1). Synteny is maintained within the TRAJ repertoire with individual bovine TRAJ genes sharing a conserved order with their murine and human orthologues (Additional file 6). Additionally there is conservation of important regulatory elements at the 3′ end of the TRA/TRD locus, with bovine sequences showing identity with the human/murine TRA enhancer (Eα), TRD enhancer (Eδ), CSB and TEA located in syntenic positions (Figure 1 and Additional file 1 and Additional file 7). In addition to gene content and organisation, the size of the 3′ end of TRA/TRD locus is similar across the 3 species (approximately 100 Kb from TRDJ to TRAC), with the exception of the TRDD region which in bovine is ~80 Kb – approximately 8× the size of the equivalent regions in the mouse and human TRA/TRD loci.Figure 1


Genomic analysis offers insights into the evolution of the bovine TRA/TRD locus.

Connelley TK, Degnan K, Longhi CW, Morrison WI - BMC Genomics (2014)

Conserved synteny of the 3′ end of the bovine, human and murine TRA/TRD loci. A schematic representation shows the conserved inter-species organisation of TR genes and regulatory elements at the 3′ end of the TRA/TRD locus. The approximate positions of TRDD (green lines), TRDJ (orange lines), TRAJ (blue lines), TRDC and TRAC (blue blocks), the single inverted TRDV gene (TRDV3 in bovine and human, TRDV5 in mouse – green block) and regulatory elements (yellow circles) are shown. The regulatory elements represented are – TRA enhancer (Eα), TRD enhancer (Eδ), T early alpha (TEA) and conserved sequence block (CSB). The length of the region is also conserved across the species, with the exception of the area occupied by TRDD genes, which is much greater in the bovine TRA/TRD locus (~80 Kb) than in the mouse or human (~10 Kb). The asterisk indicates the approximate location of the 1 Kb gap between contigs DAAA02028052.1 and DAAAA02028053.1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4289303&req=5

Fig1: Conserved synteny of the 3′ end of the bovine, human and murine TRA/TRD loci. A schematic representation shows the conserved inter-species organisation of TR genes and regulatory elements at the 3′ end of the TRA/TRD locus. The approximate positions of TRDD (green lines), TRDJ (orange lines), TRAJ (blue lines), TRDC and TRAC (blue blocks), the single inverted TRDV gene (TRDV3 in bovine and human, TRDV5 in mouse – green block) and regulatory elements (yellow circles) are shown. The regulatory elements represented are – TRA enhancer (Eα), TRD enhancer (Eδ), T early alpha (TEA) and conserved sequence block (CSB). The length of the region is also conserved across the species, with the exception of the area occupied by TRDD genes, which is much greater in the bovine TRA/TRD locus (~80 Kb) than in the mouse or human (~10 Kb). The asterisk indicates the approximate location of the 1 Kb gap between contigs DAAA02028052.1 and DAAAA02028053.1.
Mentions: The UMD3.1 assembly of the 3′ end of the bovine TRA/TRD locus appears to be essentially complete. All TRAC, TRAJ, TRDC, TRDJ, TRDD genes and the TRDV3 gene (in inverted orientation) are located on 2 large contigs (DAAA02028052.1 – 140 Kb and DAAAA02028053.1 – 114 Kb) separated by a gap of approximately 1 Kb. The organisation of the genes demonstrates a marked syntenic conservation between mouse, human and bovine (Figure 1). Synteny is maintained within the TRAJ repertoire with individual bovine TRAJ genes sharing a conserved order with their murine and human orthologues (Additional file 6). Additionally there is conservation of important regulatory elements at the 3′ end of the TRA/TRD locus, with bovine sequences showing identity with the human/murine TRA enhancer (Eα), TRD enhancer (Eδ), CSB and TEA located in syntenic positions (Figure 1 and Additional file 1 and Additional file 7). In addition to gene content and organisation, the size of the 3′ end of TRA/TRD locus is similar across the 3 species (approximately 100 Kb from TRDJ to TRAC), with the exception of the TRDD region which in bovine is ~80 Kb – approximately 8× the size of the equivalent regions in the mouse and human TRA/TRD loci.Figure 1

Bottom Line: Both TRA and TRD selection have contributed to the evolution of the bovine TRAV/TRDV repertoire.However, our data suggest that due to homology unit duplication TRD selection for TRDV1 subgroup expansion may have substantially contributed to the genomic expansion of several TRAV subgroups.Such data demonstrate how integration of genomic and transcript data can provide a more nuanced appreciation of the evolutionary dynamics that have led to the dramatically expanded bovine TRAV/TRDV repertoire.

View Article: PubMed Central - PubMed

Affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian EH25 9RG, Scotland, UK. timothy.connelley@ed.ac.uk.

ABSTRACT

Background: The TRA/TRD locus contains the genes for V(D)J somatic rearrangement of TRA and TRD chains expressed by αβ and γδ T cells respectively. Previous studies have demonstrated that the bovine TRA/TRD locus contains an exceptionally large number of TRAV/TRDV genes. In this study we combine genomic and transcript analysis to provide insights into the evolutionary development of the bovine TRA/TRD locus and the remarkable TRAV/TRDV gene repertoire.

Results: Annotation of the UMD3.1 assembly identified 371 TRAV/TRDV genes (distributed in 42 subgroups), 3 TRDJ, 6 TRDD, 62 TRAJ and single TRAC and TRDC genes, most of which were located within a 3.5 Mb region of chromosome 10. Most of the TRAV/TRDV subgroups have multiple members and several have undergone dramatic expansion, most notably TRDV1 (60 genes). Wide variation in the proportion of pseudogenes within individual subgroups, suggest that differential 'birth' and 'death' rates have been used to form a functional bovine TRAV/TRDV repertoire which is phylogenetically distinct from that of humans and mice. The expansion of the bovine TRAV/TRDV gene repertoire has predominantly been achieved through a complex series of homology unit (regions of DNA containing multiple gene) replications. Frequent co-localisation within homology units of genes from subgroups with low and high pseudogene proportions suggest that replication of homology units driven by evolutionary selection for the former may have led to a 'collateral' expansion of the latter. Transcript analysis was used to define the TRAV/TRDV subgroups available for recombination of TRA and TRD chains and demonstrated preferential usage of different subgroups by the expressed TRA and TRD repertoires, indicating that TRA and TRD selection have had distinct impacts on the evolution of the TRAV/TRDV repertoire.

Conclusion: Both TRA and TRD selection have contributed to the evolution of the bovine TRAV/TRDV repertoire. However, our data suggest that due to homology unit duplication TRD selection for TRDV1 subgroup expansion may have substantially contributed to the genomic expansion of several TRAV subgroups. Such data demonstrate how integration of genomic and transcript data can provide a more nuanced appreciation of the evolutionary dynamics that have led to the dramatically expanded bovine TRAV/TRDV repertoire.

Show MeSH