DMRT gene cluster analysis in the platypus: New insights into genomic organization and regulatory regions

Nisrine El-Mogharbel, Matthew Wakefield, J.E. Deakin, Enkhjargal Tsend-Ayush, Frank Grützner, Amber Alsop, T. Ezaz, J.A. Marshall Graves

Research output: Contribution to journalArticle

31 Citations (Scopus)

Abstract

We isolated and characterized a cluster of platypus DMRT genes and compared their arrangement, location, and sequence across vertebrates. The DMRT gene cluster on human 9p24.3 harbors, in order, DMRT1, DMRT3, and DMRT2, which share a DM domain. DMRT1 is highly conserved and involved in sexual development in vertebrates, and deletions in this region cause sex reversal in humans. Sequence comparisons of DMRT genes between species have been valuable in identifying exons, control regions, and conserved nongenic regions (CNGs). The addition of platypus sequences is expected to be particularly valuable, since monotremes fill a gap in the vertebrate genome coverage. We therefore isolated and fully sequenced platypus BAC clones containing DMRT3 and DMRT2 as well as DMRT1 and then generated multispecies alignments and ran prediction programs followed by experimental verification to annotate this gene cluster. We found that the three genes have 58-66% identity to their human orthologues, lie in the same order as in other vertebrates, and colocate on 1 of the 10 platypus sex chromosomes, X5. We also predict that optimal annotation of the newly sequenced platypus genome will be challenging. The analysis of platypus sequence revealed differences in structure and sequence of the DMRT gene cluster. Multispecies comparison was particularly effective for detecting CNGs, revealing several novel potential regulatory regions within DMRT3 and DMRT2 as well as DMRT1. RT-PCR indicated that platypus DMRT1 and DMRT3 are expressed specifically in the adult testis (and not ovary), but DMRT2 has a wider expression profile, as it does for other mammals. The platypus DMRT1 expression pattern, and its location on an X chromosome, suggests an involvement in monotreme sexual development
Original languageUndefined
Pages (from-to)10-21
Number of pages12
JournalGenomics
Volume89
Issue number1
DOIs
Publication statusPublished - 2007
Externally publishedYes

Cite this

El-Mogharbel, N., Wakefield, M., Deakin, J. E., Tsend-Ayush, E., Grützner, F., Alsop, A., ... Marshall Graves, J. A. (2007). DMRT gene cluster analysis in the platypus: New insights into genomic organization and regulatory regions. Genomics, 89(1), 10-21. https://doi.org/10.1016/j.ygeno.2006.07.017
El-Mogharbel, Nisrine ; Wakefield, Matthew ; Deakin, J.E. ; Tsend-Ayush, Enkhjargal ; Grützner, Frank ; Alsop, Amber ; Ezaz, T. ; Marshall Graves, J.A. / DMRT gene cluster analysis in the platypus: New insights into genomic organization and regulatory regions. In: Genomics. 2007 ; Vol. 89, No. 1. pp. 10-21.
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El-Mogharbel, N, Wakefield, M, Deakin, JE, Tsend-Ayush, E, Grützner, F, Alsop, A, Ezaz, T & Marshall Graves, JA 2007, 'DMRT gene cluster analysis in the platypus: New insights into genomic organization and regulatory regions', Genomics, vol. 89, no. 1, pp. 10-21. https://doi.org/10.1016/j.ygeno.2006.07.017

DMRT gene cluster analysis in the platypus: New insights into genomic organization and regulatory regions. / El-Mogharbel, Nisrine; Wakefield, Matthew; Deakin, J.E.; Tsend-Ayush, Enkhjargal; Grützner, Frank; Alsop, Amber; Ezaz, T.; Marshall Graves, J.A.

In: Genomics, Vol. 89, No. 1, 2007, p. 10-21.

Research output: Contribution to journalArticle

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T1 - DMRT gene cluster analysis in the platypus: New insights into genomic organization and regulatory regions

AU - El-Mogharbel, Nisrine

AU - Wakefield, Matthew

AU - Deakin, J.E.

AU - Tsend-Ayush, Enkhjargal

AU - Grützner, Frank

AU - Alsop, Amber

AU - Ezaz, T.

AU - Marshall Graves, J.A.

N1 - cited By 31

PY - 2007

Y1 - 2007

N2 - We isolated and characterized a cluster of platypus DMRT genes and compared their arrangement, location, and sequence across vertebrates. The DMRT gene cluster on human 9p24.3 harbors, in order, DMRT1, DMRT3, and DMRT2, which share a DM domain. DMRT1 is highly conserved and involved in sexual development in vertebrates, and deletions in this region cause sex reversal in humans. Sequence comparisons of DMRT genes between species have been valuable in identifying exons, control regions, and conserved nongenic regions (CNGs). The addition of platypus sequences is expected to be particularly valuable, since monotremes fill a gap in the vertebrate genome coverage. We therefore isolated and fully sequenced platypus BAC clones containing DMRT3 and DMRT2 as well as DMRT1 and then generated multispecies alignments and ran prediction programs followed by experimental verification to annotate this gene cluster. We found that the three genes have 58-66% identity to their human orthologues, lie in the same order as in other vertebrates, and colocate on 1 of the 10 platypus sex chromosomes, X5. We also predict that optimal annotation of the newly sequenced platypus genome will be challenging. The analysis of platypus sequence revealed differences in structure and sequence of the DMRT gene cluster. Multispecies comparison was particularly effective for detecting CNGs, revealing several novel potential regulatory regions within DMRT3 and DMRT2 as well as DMRT1. RT-PCR indicated that platypus DMRT1 and DMRT3 are expressed specifically in the adult testis (and not ovary), but DMRT2 has a wider expression profile, as it does for other mammals. The platypus DMRT1 expression pattern, and its location on an X chromosome, suggests an involvement in monotreme sexual development

AB - We isolated and characterized a cluster of platypus DMRT genes and compared their arrangement, location, and sequence across vertebrates. The DMRT gene cluster on human 9p24.3 harbors, in order, DMRT1, DMRT3, and DMRT2, which share a DM domain. DMRT1 is highly conserved and involved in sexual development in vertebrates, and deletions in this region cause sex reversal in humans. Sequence comparisons of DMRT genes between species have been valuable in identifying exons, control regions, and conserved nongenic regions (CNGs). The addition of platypus sequences is expected to be particularly valuable, since monotremes fill a gap in the vertebrate genome coverage. We therefore isolated and fully sequenced platypus BAC clones containing DMRT3 and DMRT2 as well as DMRT1 and then generated multispecies alignments and ran prediction programs followed by experimental verification to annotate this gene cluster. We found that the three genes have 58-66% identity to their human orthologues, lie in the same order as in other vertebrates, and colocate on 1 of the 10 platypus sex chromosomes, X5. We also predict that optimal annotation of the newly sequenced platypus genome will be challenging. The analysis of platypus sequence revealed differences in structure and sequence of the DMRT gene cluster. Multispecies comparison was particularly effective for detecting CNGs, revealing several novel potential regulatory regions within DMRT3 and DMRT2 as well as DMRT1. RT-PCR indicated that platypus DMRT1 and DMRT3 are expressed specifically in the adult testis (and not ovary), but DMRT2 has a wider expression profile, as it does for other mammals. The platypus DMRT1 expression pattern, and its location on an X chromosome, suggests an involvement in monotreme sexual development

U2 - 10.1016/j.ygeno.2006.07.017

DO - 10.1016/j.ygeno.2006.07.017

M3 - Article

VL - 89

SP - 10

EP - 21

JO - Genomics

JF - Genomics

SN - 0888-7543

IS - 1

ER -