Skip to content

Research at St Andrews

Amphioxus SYCP1: a case of retrogene replacement and co-option of regulatory elements adjacent to the ParaHox cluster

Research output: Contribution to journalArticle

Abstract

Retrogenes are formed when an mRNA is reverse transcribed and re-inserted into the genome in a location unrelated to the original locus. If this retrocopy inserts into a transcriptionally favourable locus and is able to carry out its original function, it can, in rare cases, lead to retrogene replacement. This involves the original, often multi-exonic, parental copy being lost whilst the newer single-exon retrogene copy ‘replaces’ the role of the ancestral parent gene. One example of this is amphioxus SYCP1, a gene that encodes a protein used in synaptonemal complex formation during meiosis, and which offers the opportunity to examine how a retrogene evolves after the retrogene replacement event. SYCP1 genes exist as large multi-exonic genes in most animals. AmphiSYCP1, however, contains a single coding exon of ~3200bp and has inserted next to the ParaHox cluster of amphioxus, whilst the multi-exonic ancestral parental copy has been lost. Here, we show that AmphiSYCP1 has not only replaced its parental copy, but has evolved additional regulatory function by co- opting a bidirectional promoter from the nearby AmphiCHIC gene. AmphiSYCP1 has also evolved a de novo, multi-exonic 5’untranslated region that displays distinct regulatory states, in the form of two different isoforms, and has evolved novel expression patterns during amphioxus embryogenesis in addition to its ancestral role in meiosis. Absence of ParaHox-like expression of AmphiSYCP1, despite its proximity to the ParaHox cluster, also suggests this gene is not influenced by any potential pan-cluster regulatory mechanisms, which are seemingly restricted to only the ParaHox genes themselves.
Close

Details

Original languageEnglish
Pages (from-to)13-30
Number of pages18
JournalDevelopment Genes and Evolution
Volume228
Issue number1
Early online date2 Jan 2018
DOIs
StatePublished - Jan 2018

    Research areas

  • Amphioxus, ParaHox, Retrogene replacement, SYCPI, Synaptonemal complex, CHIC genes

Discover related content
Find related publications, people, projects and more using interactive charts.

View graph of relations

Related by author

  1. Two more Posterior Hox genes and Hox cluster dispersal in echinoderms

    Szabó, R. & Ferrier, D. E. K. 27 Dec 2018 In : BMC Evolutionary Biology. 18, 13 p., 203

    Research output: Contribution to journalArticle

  2. Transcriptional regulation of the Ciona Gsx gene in the neural plate

    Hudson, C., Esposito, R., Palladino, A., Staiano, L., Ferrier, D., Faure, E., Lemaire, P., Yasuo, H. & Spagnuolo, A. 21 Dec 2018 In : Developmental Biology. In press

    Research output: Contribution to journalArticle

  3. Amphioxus functional genomics and the origins of vertebrate gene regulation

    Marletaz, F. , Firbas, P. , Maeso, I. , Tena, J. , Bogdanovic, O. , Perry, M. , Wyatt, C. , de la Calle-Mustienes, E. , Bertrand, S. , Burguera, D. , Acemel, R. , van Heeringen, S. , Naranjo, S. , Herrera-Ubeda, C. , Skvortsova, K. , Jimenez-Gancedo, S. , Aldea, D. , Marquez, Y. , Buono, L. , Kozmikova, I. & 41 others Permanyer, J., Louis, A., Albuixech-Crespo, B., Le Petillon, Y., Leon Florian, A., Subirana, L., Balwierz, P. J., Duckett, P., Farahani, E., Aury, J. M., Mangenot, S., Wincker, P., Albalat, R., Benito-Gutierrez, E., Canestro, C., Castro, F., D'Aniello, S., Ferrier, D. E. K., Huang, S., Laudet, V., Marais, G., Pontarotti, P., Schubert, M., Seitz, H., Somorjai, I. M. L., Takahashi, T., Mirabeau, O., Xu, A., Yu, J-K., Carninci, P., Martinez-Morales, J., Crollius, H., Kozmik, Z., Weirauch, M., Garcia-Fernandez, J., Lister, R., Lenhard, B., Holland, P., Escriva, H., Gomez-Skarmeta, J. L. & Irimia, M. 21 Nov 2018 In : Nature. 564, 7734, p. 64-70 29 p.

    Research output: Contribution to journalArticle

  4. Horizons in evolutionary genomics: an interview with David Ferrier

    Ferrier, D. E. K. 1 Nov 2018 In : BMC Biology. 16, 3 p., 124

    Research output: Contribution to journalArticle

  5. Genome biology: unconventional DNA repair in an extreme genome

    Ferrier, D. E. K. & Sogabe, S. 22 Oct 2018 In : Current Biology. 28, 20, p. R1208-R1210

    Research output: Contribution to journalReview article

Related by journal

  1. Comprehensive survey and classification of homeobox genes in the genome of amphioxus, Branchiostoma floridae.

    Takatori, N., Butts, T., Candiani, S., Pestariono, M., Ferrier, D. E. K., Saiga, H. & Holland, P. W. H. Dec 2008 In : Development Genes and Evolution. 218, p. 579-590 12 p.

    Research output: Contribution to journalArticle

  2. Evolution of follistatin in teleosts revealed through phylogenetic, genomic and expression analyses

    Johnston, I. A. & MacQueen, D. J. Jan 2008 In : Development Genes and Evolution. 218, 1, p. 1-14 14 p.

    Research output: Contribution to journalArticle

  3. The Mnx homeobox class defined by HB9, MNR2 and amphioxus AmphiMnx.

    Ferrier, D. E. K., Brooke, N. M., Panopoulou, G. & Holland, P. W. H. Feb 2001 In : Development Genes and Evolution. 211, p. 103-107 5 p.

    Research output: Contribution to journalArticle

ID: 251735763