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Genome Biol Evol. 2019 Sep 1;11(9):2678-2690. doi: 10.1093/gbe/evz163.

Gene Fusions Derived by Transcriptional Readthrough are Driven by Segmental Duplication in Human.

Author information

1
Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Ireland.
2
Computational and Molecular Evolutionary Biology Group, School of Biology, Faculty of Biological Sciences, The University of Leeds, United Kingdom.
3
Institute for Global Food Security, Queens University Belfast, United Kingdom.
4
Teagasc Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, County Meath, Ireland.
5
School of Biological Sciences, University of Auckland, New Zealand.
6
School of Fundamental Sciences, Massey University, New Zealand.
7
Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, 08003 Barcelona, Spain.
8
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom.
9
Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, United Kingdom.
10
School of Molecular and Cellular Biology, Faculty of Biological Sciences, The University of Leeds, United Kingdom.
11
Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, M13 9PL, United Kingdom.
12
School of Life Sciences, Faculty of Medicine and Health Sciences, The University of Nottingham, NG7 2RD, United Kingdom.
13
Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain.
14
NAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.
15
Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/ Columnes s/n, 08193 Cerdanyola del Vallés, Barcelona, Spain.

Abstract

Gene fusion occurs when two or more individual genes with independent open reading frames becoming juxtaposed under the same open reading frame creating a new fused gene. A small number of gene fusions described in detail have been associated with novel functions, for example, the hominid-specific PIPSL gene, TNFSF12, and the TWE-PRIL gene family. We use Sequence Similarity Networks and species level comparisons of great ape genomes to identify 45 new genes that have emerged by transcriptional readthrough, that is, transcription-derived gene fusion. For 35 of these putative gene fusions, we have been able to assess available RNAseq data to determine whether there are reads that map to each breakpoint. A total of 29 of the putative gene fusions had annotated transcripts (9/29 of which are human-specific). We carried out RT-qPCR in a range of human tissues (placenta, lung, liver, brain, and testes) and found that 23 of the putative gene fusion events were expressed in at least one tissue. Examining the available ribosome foot-printing data, we find evidence for translation of three of the fused genes in human. Finally, we find enrichment for transcription-derived gene fusions in regions of known segmental duplication in human. Together, our results implicate chromosomal structural variation brought about by segmental duplication with the emergence of novel transcripts and translated protein products.

KEYWORDS:

Great Ape Comparative genomics; mechanisms of protein-coding evolution; novel genes; segmental duplication; sequence similarity networks; transcriptional readthrough

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