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Xie S, Ma Y, Liu Y, Tao D, Wang Z, Yang Y. Primary azoospermia factor C duplication associated with spermatogenic impariment: a case-control study based on Y-chromosome haplogrouping in a Han Chinese population. Andrology 2024; 12:561-569. [PMID: 37594248 DOI: 10.1111/andr.13510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/22/2023] [Accepted: 08/06/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND Azoospermia factor C (AZFc) in the male-specific region of Y-chromosome (MSY) presents wide structure variation mainly due to frequent non-allele homologous recombination, leading to significant copy number variation of the AZFc-linked coding sequences involving in spermatogenesis. A large number of studies had been conducted to investigate the association between AZFc deletions and male infertility in certain Y chromosome genetic backgrounds, however, the influence of primary AZFc duplication on spermatogenesis remained controversial and the cause of the discrepant outcomes is unknown. METHODS In the present study, a total of 1,102 unrelated Han Chinese males without any detectable AZF deletions were recruited from 2014 to 2019, including 411 controls with normozoospermia and 691 patients with idiopathic spermatogenic failure. Using multiple paralog ratio tests (PRTs), the structure duplications were classified by the copy number of the AZFc-linked amplicons and genes. The Y-chromosome haplogroup (Y-hg) was categorized by genetyping of MSY-linked polymorphism loci. The association of primary AZFc duplication with spermatogenic phenotype was investigated in males with the same Y-hg. RESULTS Within Y-hg O3* group, the frequency of the gr/gr duplication in patients is significantly higher than that of controls (P = 1.29×10-3 , odds ratio (OR) 7.64, 95% confidence interval (CI) 1.79-32.57). Moreover, Y-hg O3* males with the gr/gr duplication presented a significantly lower sperm production compared with non-AZFc duplicated ones (sperm concentration: P = 1.46×10-3 ; total sperm count: P = 1.82 ×10-3 ). The b2/b3 duplication were identified clustered in Y-hg Cα2*, and the significant difference in the distribution was not observed between patients with spermatogenic failure and controls. CONCLUSION The results suggest that, in the Han Chinese population, the gr/gr duplication is a predisposing genetic factor for spermatogenic impairment in males harboring Y-hg O3* . Meanwhile, the b2/b3 duplication may be fixed on a yet-unidentified subbranch of Y-hg Cα2* without significantly deleterious effect on spermatogenesis. Our findings provide evidence that the difference in the Y-hg composition may cause the discrepancy on the association of AZFc duplication with spermatogenic failure among the studied populations.
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Affiliation(s)
- Shengyu Xie
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
| | - Yongyi Ma
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, China
| | - Yunqiang Liu
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
| | - Dachang Tao
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
| | - Zhaokun Wang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
| | - Yuan Yang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
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2
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San Roman AK, Skaletsky H, Godfrey AK, Bokil NV, Teitz L, Singh I, Blanton LV, Bellott DW, Pyntikova T, Lange J, Koutseva N, Hughes JF, Brown L, Phou S, Buscetta A, Kruszka P, Banks N, Dutra A, Pak E, Lasutschinkow PC, Keen C, Davis SM, Lin AE, Tartaglia NR, Samango-Sprouse C, Muenke M, Page DC. The human Y and inactive X chromosomes similarly modulate autosomal gene expression. CELL GENOMICS 2024; 4:100462. [PMID: 38190107 PMCID: PMC10794785 DOI: 10.1016/j.xgen.2023.100462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/15/2023] [Accepted: 11/14/2023] [Indexed: 01/09/2024]
Abstract
Somatic cells of human males and females have 45 chromosomes in common, including the "active" X chromosome. In males the 46th chromosome is a Y; in females it is an "inactive" X (Xi). Through linear modeling of autosomal gene expression in cells from individuals with zero to three Xi and zero to four Y chromosomes, we found that Xi and Y impact autosomal expression broadly and with remarkably similar effects. Studying sex chromosome structural anomalies, promoters of Xi- and Y-responsive genes, and CRISPR inhibition, we traced part of this shared effect to homologous transcription factors-ZFX and ZFY-encoded by Chr X and Y. This demonstrates sex-shared mechanisms by which Xi and Y modulate autosomal expression. Combined with earlier analyses of sex-linked gene expression, our studies show that 21% of all genes expressed in lymphoblastoid cells or fibroblasts change expression significantly in response to Xi or Y chromosomes.
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Affiliation(s)
| | - Helen Skaletsky
- Whitehead Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Alexander K Godfrey
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Neha V Bokil
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Levi Teitz
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Isani Singh
- Whitehead Institute, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | - Julian Lange
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | - Laura Brown
- Whitehead Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Sidaly Phou
- Whitehead Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Ashley Buscetta
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul Kruszka
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole Banks
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amalia Dutra
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Evgenia Pak
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | - Shanlee M Davis
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Angela E Lin
- Medical Genetics, Massachusetts General for Children, Boston, MA 02114, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Nicole R Tartaglia
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA; Developmental Pediatrics, eXtraOrdinarY Kids Program, Children's Hospital Colorado, Aurora, CO 80011, USA
| | - Carole Samango-Sprouse
- Focus Foundation, Davidsonville, MD 21035, USA; Department of Pediatrics, George Washington University, Washington, DC 20052, USA; Department of Human and Molecular Genetics, Florida International University, Miami, FL 33199, USA
| | - Maximilian Muenke
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David C Page
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA.
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3
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Hallast P, Ebert P, Loftus M, Yilmaz F, Audano PA, Logsdon GA, Bonder MJ, Zhou W, Höps W, Kim K, Li C, Hoyt SJ, Dishuck PC, Porubsky D, Tsetsos F, Kwon JY, Zhu Q, Munson KM, Hasenfeld P, Harvey WT, Lewis AP, Kordosky J, Hoekzema K, O'Neill RJ, Korbel JO, Tyler-Smith C, Eichler EE, Shi X, Beck CR, Marschall T, Konkel MK, Lee C. Assembly of 43 human Y chromosomes reveals extensive complexity and variation. Nature 2023; 621:355-364. [PMID: 37612510 PMCID: PMC10726138 DOI: 10.1038/s41586-023-06425-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 07/11/2023] [Indexed: 08/25/2023]
Abstract
The prevalence of highly repetitive sequences within the human Y chromosome has prevented its complete assembly to date1 and led to its systematic omission from genomic analyses. Here we present de novo assemblies of 43 Y chromosomes spanning 182,900 years of human evolution and report considerable diversity in size and structure. Half of the male-specific euchromatic region is subject to large inversions with a greater than twofold higher recurrence rate compared with all other chromosomes2. Ampliconic sequences associated with these inversions show differing mutation rates that are sequence context dependent, and some ampliconic genes exhibit evidence for concerted evolution with the acquisition and purging of lineage-specific pseudogenes. The largest heterochromatic region in the human genome, Yq12, is composed of alternating repeat arrays that show extensive variation in the number, size and distribution, but retain a 1:1 copy-number ratio. Finally, our data suggest that the boundary between the recombining pseudoautosomal region 1 and the non-recombining portions of the X and Y chromosomes lies 500 kb away from the currently established1 boundary. The availability of fully sequence-resolved Y chromosomes from multiple individuals provides a unique opportunity for identifying new associations of traits with specific Y-chromosomal variants and garnering insights into the evolution and function of complex regions of the human genome.
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Affiliation(s)
- Pille Hallast
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Peter Ebert
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- Core Unit Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Mark Loftus
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC, USA
- Center for Human Genetics, Clemson University, Greenwood, SC, USA
| | - Feyza Yilmaz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Peter A Audano
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Marc Jan Bonder
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Weichen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Wolfram Höps
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Kwondo Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Chong Li
- Department of Computer and Information Sciences, Temple University, Philadelphia, PA, USA
| | - Savannah J Hoyt
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Philip C Dishuck
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Fotios Tsetsos
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jee Young Kwon
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Qihui Zhu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Patrick Hasenfeld
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Jennifer Kordosky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Rachel J O'Neill
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- The University of Connecticut Health Center, Farmington, CT, USA
| | - Jan O Korbel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Xinghua Shi
- Department of Computer and Information Sciences, Temple University, Philadelphia, PA, USA
| | - Christine R Beck
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- The University of Connecticut Health Center, Farmington, CT, USA
| | - Tobias Marschall
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Miriam K Konkel
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC, USA
- Center for Human Genetics, Clemson University, Greenwood, SC, USA
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
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4
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Rhie A, Nurk S, Cechova M, Hoyt SJ, Taylor DJ, Altemose N, Hook PW, Koren S, Rautiainen M, Alexandrov IA, Allen J, Asri M, Bzikadze AV, Chen NC, Chin CS, Diekhans M, Flicek P, Formenti G, Fungtammasan A, Garcia Giron C, Garrison E, Gershman A, Gerton JL, Grady PGS, Guarracino A, Haggerty L, Halabian R, Hansen NF, Harris R, Hartley GA, Harvey WT, Haukness M, Heinz J, Hourlier T, Hubley RM, Hunt SE, Hwang S, Jain M, Kesharwani RK, Lewis AP, Li H, Logsdon GA, Lucas JK, Makalowski W, Markovic C, Martin FJ, Mc Cartney AM, McCoy RC, McDaniel J, McNulty BM, Medvedev P, Mikheenko A, Munson KM, Murphy TD, Olsen HE, Olson ND, Paulin LF, Porubsky D, Potapova T, Ryabov F, Salzberg SL, Sauria MEG, Sedlazeck FJ, Shafin K, Shepelev VA, Shumate A, Storer JM, Surapaneni L, Taravella Oill AM, Thibaud-Nissen F, Timp W, Tomaszkiewicz M, Vollger MR, Walenz BP, Watwood AC, Weissensteiner MH, Wenger AM, Wilson MA, Zarate S, Zhu Y, Zook JM, Eichler EE, O'Neill RJ, Schatz MC, Miga KH, Makova KD, Phillippy AM. The complete sequence of a human Y chromosome. Nature 2023; 621:344-354. [PMID: 37612512 PMCID: PMC10752217 DOI: 10.1038/s41586-023-06457-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 07/19/2023] [Indexed: 08/25/2023]
Abstract
The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications1-3. As a result, more than half of the Y chromosome is missing from the GRCh38 reference sequence and it remains the last human chromosome to be finished4,5. Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, showing the complete ampliconic structures of gene families TSPY, DAZ and RBMY; 41 additional protein-coding genes, mostly from the TSPY family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a previous assembly of the CHM13 genome4 and mapped available population variation, clinical variants and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.
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Affiliation(s)
- Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Oxford Nanopore Technologies Inc., Oxford, UK
| | - Monika Cechova
- Faculty of Informatics, Masaryk University, Brno, Czech Republic
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Savannah J Hoyt
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Dylan J Taylor
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Nicolas Altemose
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Paul W Hook
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mikko Rautiainen
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ivan A Alexandrov
- Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- Center for Algorithmic Biotechnology, Saint Petersburg State University, St Petersburg, Russia
- Department of Anatomy and Anthropology and Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Jamie Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Mobin Asri
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Andrey V Bzikadze
- Graduate Program in Bioinformatics and Systems Biology, University of California, San Diego, CA, USA
| | - Nae-Chyun Chen
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Chen-Shan Chin
- GeneDX Holdings Corp, Stamford, CT, USA
- Foundation of Biological Data Science, Belmont, CA, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | | | | | - Carlos Garcia Giron
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ariel Gershman
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jennifer L Gerton
- Stowers Institute for Medical Research, Kansas City, MO, USA
- University of Kansas Medical Center, Kansas City, MO, USA
| | - Patrick G S Grady
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Andrea Guarracino
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Genomics Research Centre, Human Technopole, Milan, Italy
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Reza Halabian
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany
| | - Nancy F Hansen
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Robert Harris
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Gabrielle A Hartley
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Marina Haukness
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Jakob Heinz
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Stephen Hwang
- XDBio Program, Johns Hopkins University, Baltimore, MD, USA
| | - Miten Jain
- Department of Bioengineering, Department of Physics, Northeastern University, Boston, MA, USA
| | - Rupesh K Kesharwani
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Julian K Lucas
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Wojciech Makalowski
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany
| | - Christopher Markovic
- Genome Technology Access Center at the McDonnell Genome Institute, Washington University, St. Louis, MO, USA
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ann M Mc Cartney
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Jennifer McDaniel
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Brandy M McNulty
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Paul Medvedev
- Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
- Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, PA, USA
| | - Alla Mikheenko
- Center for Algorithmic Biotechnology, Saint Petersburg State University, St Petersburg, Russia
- UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Hugh E Olsen
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Nathan D Olson
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Luis F Paulin
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Tamara Potapova
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Fedor Ryabov
- Masters Program in National Research University Higher School of Economics, Moscow, Russia
| | - Steven L Salzberg
- Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MD, USA
| | | | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
| | | | | | - Alaina Shumate
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | | | - Likhitha Surapaneni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Angela M Taravella Oill
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Marta Tomaszkiewicz
- Department of Biology, Pennsylvania State University, University Park, PA, USA
- Department of Biomedical Engineering, Pennsylvania State University, State College, PA, USA
| | - Mitchell R Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Brian P Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Allison C Watwood
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | | | | | - Melissa A Wilson
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Samantha Zarate
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Yiming Zhu
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Justin M Zook
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Investigator, Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Rachel J O'Neill
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
| | - Michael C Schatz
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Karen H Miga
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Kateryna D Makova
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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5
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Hajiesmaeil M, Ravasini F, Risi F, Magnarini G, Olivieri A, D'Atanasio E, Galehdari H, Trombetta B, Cruciani F. High incidence of AZF duplications in clan-structured Iranian populations detected through Y chromosome sequencing read depth analysis. Sci Rep 2023; 13:11857. [PMID: 37481605 PMCID: PMC10363161 DOI: 10.1038/s41598-023-39069-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/19/2023] [Indexed: 07/24/2023] Open
Abstract
The ampliconic region of the human Y chromosome consists of large duplicated sequences that can undergo non-allelic homologous recombination (NAHR), resulting in structural rearrangements that may cause infertility, especially when they occur in the azoospermia factor b/c (AZFb/c) region. Although AZF duplications have long been neglected due to the technical limitations of STS-based studies that focused mainly on deletions, recent next generation sequencing (NGS) technologies provided evidence for their importance in fertility. In this study, a NGS read depth approach was used to detect AZFb/c rearrangements in 87 Iranians from different ethnic groups. The duplication frequency in Iran proved to be twice as high as in the "1000 Genomes" dataset. Interestingly, most duplications were found in patrilineal ethnic groups, possibly as a consequence of their lower male effective population size which can counteract negative selection. Moreover, we found a large 8.0 Mb duplication, resulting in a fourfold increase in the copy number of AZFc genes, which to our knowledge is the largest duplication ever reported in this region. Overall, our results suggest that it is important to consider not only AZF deletions but also duplications to investigate the causes of male infertility, especially in patrilineal clan-based populations.
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Affiliation(s)
- Mogge Hajiesmaeil
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Francesco Ravasini
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Flavia Risi
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Giorgia Magnarini
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Anna Olivieri
- Department of Biology and Biotechnology 'Lazzaro Spallanzani', Pavia University, Pavia, Italy
- NBFC, National Biodiversity Future Center, 90133, Palermo, Italy
| | - Eugenia D'Atanasio
- Institute of Molecular Biology and Pathology (IBPM), CNR, 00185, Rome, Italy
| | - Hamid Galehdari
- Department of Biology, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Beniamino Trombetta
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Fulvio Cruciani
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy.
- Institute of Molecular Biology and Pathology (IBPM), CNR, 00185, Rome, Italy.
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6
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Lucotte EA, Guðmundsdóttir VB, Jensen JM, Skov L, Macià MC, Almstrup K, Schierup MH, Helgason A, Stefansson K. Characterizing the evolution and phenotypic impact of ampliconic Y chromosome regions. Nat Commun 2023; 14:3990. [PMID: 37414752 PMCID: PMC10326017 DOI: 10.1038/s41467-023-39644-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/22/2023] [Indexed: 07/08/2023] Open
Abstract
A major part of the human Y chromosome consists of palindromes with multiple copies of genes primarily expressed in testis, many of which have been claimed to affect male fertility. Here we examine copy number variation in these palindromes based on whole genome sequence data from 11,527 Icelandic men. Using a subset of 7947 men grouped into 1449 patrilineal genealogies, we infer 57 large scale de novo copy number mutations affecting palindrome 1. This corresponds to a mutation rate of 2.34 × 10-3 mutations per meiosis, which is 4.1 times larger than our phylogenetic estimate of the mutation rate (5.72 × 10-4), suggesting that de novo mutations on the Y are lost faster than expected under neutral evolution. Although simulations indicate a selection coefficient of 1.8% against non-reference copy number carriers, we do not observe differences in fertility among sequenced men associated with their copy number genotype, but we lack statistical power to detect differences resulting from weak negative selection. We also perform association testing of a diverse set of 341 traits to palindromic copy number without any significant associations. We conclude that large-scale palindrome copy number variation on the Y chromosome has little impact on human phenotype diversity.
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Affiliation(s)
- Elise A Lucotte
- Bioinformatics Research Centre, Aarhus University, Dk-8000, Aarhus C., Denmark.
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, 91198, Gif-sur-Yvette, France.
| | - Valdís Björt Guðmundsdóttir
- deCODE genetics/Amgen Inc., 101, Reykjavik, Iceland
- Department of Anthropology, University of Iceland, 101, Reykjavik, Iceland
| | - Jacob M Jensen
- Bioinformatics Research Centre, Aarhus University, Dk-8000, Aarhus C., Denmark
| | - Laurits Skov
- Bioinformatics Research Centre, Aarhus University, Dk-8000, Aarhus C., Denmark
| | - Moisès Coll Macià
- Bioinformatics Research Centre, Aarhus University, Dk-8000, Aarhus C., Denmark
| | - Kristian Almstrup
- Department of Growth and Reproduction, Rigshospitalet, Copenhagen, Denmark
| | - Mikkel H Schierup
- Bioinformatics Research Centre, Aarhus University, Dk-8000, Aarhus C., Denmark
| | - Agnar Helgason
- deCODE genetics/Amgen Inc., 101, Reykjavik, Iceland.
- Department of Anthropology, University of Iceland, 101, Reykjavik, Iceland.
| | - Kari Stefansson
- deCODE genetics/Amgen Inc., 101, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, 101, Reykjavik, Iceland
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7
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San Roman AK, Skaletsky H, Godfrey AK, Bokil NV, Teitz L, Singh I, Blanton LV, Bellott DW, Pyntikova T, Lange J, Koutseva N, Hughes JF, Brown L, Phou S, Buscetta A, Kruszka P, Banks N, Dutra A, Pak E, Lasutschinkow PC, Keen C, Davis SM, Lin AE, Tartaglia NR, Samango-Sprouse C, Muenke M, Page DC. The human Y and inactive X chromosomes similarly modulate autosomal gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543763. [PMID: 37333288 PMCID: PMC10274745 DOI: 10.1101/2023.06.05.543763] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Somatic cells of human males and females have 45 chromosomes in common, including the "active" X chromosome. In males the 46th chromosome is a Y; in females it is an "inactive" X (Xi). Through linear modeling of autosomal gene expression in cells from individuals with zero to three Xi and zero to four Y chromosomes, we found that Xi and Y impact autosomal expression broadly and with remarkably similar effects. Studying sex-chromosome structural anomalies, promoters of Xi- and Y-responsive genes, and CRISPR inhibition, we traced part of this shared effect to homologous transcription factors - ZFX and ZFY - encoded by Chr X and Y. This demonstrates sex-shared mechanisms by which Xi and Y modulate autosomal expression. Combined with earlier analyses of sex-linked gene expression, our studies show that 21% of all genes expressed in lymphoblastoid cells or fibroblasts change expression significantly in response to Xi or Y chromosomes.
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Affiliation(s)
| | - Helen Skaletsky
- Whitehead Institute; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute; Cambridge, MA 02142, USA
| | - Alexander K. Godfrey
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Neha V. Bokil
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Levi Teitz
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Isani Singh
- Whitehead Institute; Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | - Julian Lange
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | | | | | - Laura Brown
- Whitehead Institute; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute; Cambridge, MA 02142, USA
| | - Sidaly Phou
- Whitehead Institute; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute; Cambridge, MA 02142, USA
| | - Ashley Buscetta
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda; MD 20892, USA
| | - Paul Kruszka
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda; MD 20892, USA
| | - Nicole Banks
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda; MD 20892, USA
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health; Bethesda, MD 20892 USA
| | - Amalia Dutra
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD 20892 USA
| | - Evgenia Pak
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD 20892 USA
| | | | | | - Shanlee M. Davis
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Angela E. Lin
- Medical Genetics, Massachusetts General for Children, Boston, MA 02114, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Nicole R. Tartaglia
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Developmental Pediatrics, eXtraOrdinarY Kids Program, Children’s Hospital Colorado, Aurora, CO 80011, USA
| | - Carole Samango-Sprouse
- Focus Foundation, Davidsonville, MD 21035, USA
- Department of Pediatrics, George Washington University, Washington, DC 20052, USA; Department of Human and Molecular Genetics, Florida International University, Miami, FL 33199, USA
| | - Maximilian Muenke
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda; MD 20892, USA
| | - David C. Page
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Whitehead Institute; Cambridge, MA 02142, USA
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8
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Krivega M, Zimmer J, Slezko A, Frank-Herrmann P, Rehnitz J, Hohenfellner M, Bettendorf M, Luzarowski M, Strowitzki T. Genomic instability in individuals with sex determination defects and germ cell cancer. Cell Death Discov 2023; 9:173. [PMID: 37217472 PMCID: PMC10202957 DOI: 10.1038/s41420-023-01470-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/28/2023] [Accepted: 05/12/2023] [Indexed: 05/24/2023] Open
Abstract
The ability to transmit genetic information through generations depends on the preservation of genome integrity. Genetic abnormalities affect cell differentiation, causing tissue specification defects and cancer. We addressed genomic instability in individuals with Differences of Sex Development (DSD), characterized by gonadal dysgenesis, infertility, high susceptibility for different types of cancer, especially Germ Cell Tumors (GCT), and in men with testicular GCTs. Whole proteome analysis of leukocytes, supported by specific gene expression assessment, and dysgenic gonads characterization, uncovered DNA damage phenotypes with altered innate immune response and autophagy. Further examination of DNA damage response revealed a reliance on deltaTP53, which was compromised by mutations in the transactivation domain in DSD-individuals with GCT. Accordingly, drug-induced rescue of DNA damage was achieved by autophagy inhibition but not by stabilization of TP53 in DSD-individuals' blood in vitro. This study elucidates possibilities for prophylactic treatments of DSD-individuals, as well as new diagnostic approaches of GCT.
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Affiliation(s)
- Maria Krivega
- Research Group of Gonadal Differentiation and Embryonic Development, Department of Gynecological Endocrinology & Fertility Disorders, Women Hospital, University of Heidelberg, 69120, Heidelberg, Germany.
| | - Jutta Zimmer
- Research Group of Gonadal Differentiation and Embryonic Development, Department of Gynecological Endocrinology & Fertility Disorders, Women Hospital, University of Heidelberg, 69120, Heidelberg, Germany
| | - Anna Slezko
- Research Group of Gonadal Differentiation and Embryonic Development, Department of Gynecological Endocrinology & Fertility Disorders, Women Hospital, University of Heidelberg, 69120, Heidelberg, Germany
| | - Petra Frank-Herrmann
- Department of Gynecological Endocrinology & Fertility Disorders, Women Hospital, University of Heidelberg, 69120, Heidelberg, Germany
| | - Julia Rehnitz
- Department of Gynecological Endocrinology & Fertility Disorders, Women Hospital, University of Heidelberg, 69120, Heidelberg, Germany
| | - Markus Hohenfellner
- Department of Urology, University Hospital Heidelberg, 69120, Heidelberg, Germany
| | - Markus Bettendorf
- Division of Pediatric Endocrinology, Children's Hospital, University of Heidelberg, 69120, Heidelberg, Germany
| | - Marcin Luzarowski
- Core Facility for Mass Spectrometry & Proteomics, ZMBH, University of Heidelberg, 69120, Heidelberg, Germany
| | - Thomas Strowitzki
- Department of Gynecological Endocrinology & Fertility Disorders, Women Hospital, University of Heidelberg, 69120, Heidelberg, Germany
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9
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Bonito M, Ravasini F, Novelletto A, D'Atanasio E, Cruciani F, Trombetta B. Disclosing complex mutational dynamics at a Y chromosome palindrome evolving through intra- and inter-chromosomal gene conversion. Hum Mol Genet 2023; 32:65-78. [PMID: 35921243 DOI: 10.1093/hmg/ddac144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 01/17/2023] Open
Abstract
The human MSY ampliconic region is mainly composed of large duplicated sequences that are organized in eight palindromes (termed P1-P8), and may undergo arm-to-arm gene conversion. Although the importance of these elements is widely recognized, their evolutionary dynamics are still nuanced. Here, we focused on the P8 palindrome, which shows a complex evolutionary history, being involved in intra- and inter-chromosomal gene conversion. To disclose its evolutionary complexity, we performed a high-depth (50×) targeted next-generation sequencing of this element in 157 subjects belonging to the most divergent lineages of the Y chromosome tree. We found a total of 72 polymorphic paralogous sequence variants that have been exploited to identify 41 Y-Y gene conversion events that occurred during recent human history. Through our analysis, we were able to categorize P8 arms into three portions, whose molecular diversity was modelled by different evolutionary forces. Notably, the outer region of the palindrome is not involved in any gene conversion event and evolves exclusively through the action of mutational pressure. The inner region is affected by Y-Y gene conversion occurring at a rate of 1.52 × 10-5 conversions/base/year, with no bias towards the retention of the ancestral state of the sequence. In this portion, GC-biased gene conversion is counterbalanced by a mutational bias towards AT bases. Finally, the middle region of the arms, in addition to intra-chromosomal gene conversion, is involved in X-to-Y gene conversion (at a rate of 6.013 × 10-8 conversions/base/year) thus being a major force in the evolution of the VCY/VCX gene family.
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Affiliation(s)
- Maria Bonito
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Rome 00185, Italy
| | - Francesco Ravasini
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Rome 00185, Italy
| | - Andrea Novelletto
- Department of Biology, University of Rome Tor Vergata, Rome 00133, Italy
| | - Eugenia D'Atanasio
- Institute of Molecular Biology and Pathology (IBPM), CNR, Rome 00185, Italy
| | - Fulvio Cruciani
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Rome 00185, Italy.,Institute of Molecular Biology and Pathology (IBPM), CNR, Rome 00185, Italy
| | - Beniamino Trombetta
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Rome 00185, Italy
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10
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Castaneda C, Radović L, Felkel S, Juras R, Davis BW, Cothran EG, Wallner B, Raudsepp T. Copy number variation of horse Y chromosome genes in normal equine populations and in horses with abnormal sex development and subfertility: relationship of copy number variations with Y haplogroups. G3 (BETHESDA, MD.) 2022; 12:jkac278. [PMID: 36227030 PMCID: PMC9713435 DOI: 10.1093/g3journal/jkac278] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/08/2022] [Indexed: 11/03/2023]
Abstract
Structural rearrangements like copy number variations in the male-specific Y chromosome have been associated with male fertility phenotypes in human and mouse but have been sparsely studied in other mammalian species. Here, we designed digital droplet PCR assays for 7 horse male-specific Y chromosome multicopy genes and SRY and evaluated their absolute copy numbers in 209 normal male horses of 22 breeds, 73 XY horses with disorders of sex development and/or infertility, 5 Przewalski's horses and 2 kulans. This established baseline copy number for these genes in horses. The TSPY gene showed the highest copy number and was the most copy number variable between individuals and breeds. SRY was a single-copy gene in most horses but had 2-3 copies in some indigenous breeds. Since SRY is flanked by 2 copies of RBMY, their copy number variations were interrelated and may lead to SRY-negative XY disorders of sex development. The Przewalski's horse and kulan had 1 copy of SRY and RBMY. TSPY and ETSTY2 showed significant copy number variations between cryptorchid and normal males (P < 0.05). No significant copy number variations were observed in subfertile/infertile males. Notably, copy number of TSPY and ETSTY5 differed between successive male generations and between cloned horses, indicating germline and somatic mechanisms for copy number variations. We observed no correlation between male-specific Y chromosome gene copy number variations and male-specific Y chromosome haplotypes. We conclude that the ampliconic male-specific Y chromosome reference assembly has deficiencies and further studies with an improved male-specific Y chromosome assembly are needed to determine selective constraints over horse male-specific Y chromosome gene copy number and their relation to stallion reproduction and male biology.
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Affiliation(s)
- Caitlin Castaneda
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA
| | - Lara Radović
- Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
- Vienna Graduate School of Population Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Sabine Felkel
- Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
- Vienna Graduate School of Population Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
- Department of Biotechnology, Institute of Computational Biology, BOKU University of Life Sciences and Natural Resources, Vienna 1190, Austria
| | - Rytis Juras
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA
| | - Ernest Gus Cothran
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA
| | - Barbara Wallner
- Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Terje Raudsepp
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA
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11
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Chernykh VB, Ryzhkova OP, Kuznetsova IA, Kazaryan MS, Sorokina TM, Kurilo LF, Schagina OA, Polyakov AV. Deletions in AZFc Region of Y Chromosome in Russian Fertile Men. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422070043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Bonito M, D’Atanasio E, Ravasini F, Cariati S, Finocchio A, Novelletto A, Trombetta B, Cruciani F. New insights into the evolution of human Y chromosome palindromes through mutation and gene conversion. Hum Mol Genet 2021; 30:2272-2285. [PMID: 34244762 PMCID: PMC8600007 DOI: 10.1093/hmg/ddab189] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 12/16/2022] Open
Abstract
About one-quarter of the euchromatic portion of the male-specific region of the human Y chromosome consists of large duplicated sequences that are organized in eight palindromes (termed P1-P8), which undergo arm-to arm gene conversion, a proposed mechanism for maintaining their sequence integrity. Although the relevance of gene conversion in the evolution of palindromic sequences has been profoundly recognized, the dynamic of this mechanism is still nuanced. To shed light into the evolution of these genomic elements, we performed a high-depth (50×) targeted next-generation sequencing of the palindrome P6 in 157 subjects belonging to the most divergent evolutionary lineages of the Y chromosome. We found 118 new paralogous sequence variants, which were placed into the context of a robust Y chromosome phylogeny based on 7240 SNPs of the X-degenerate region. We mapped along the phylogeny 80 gene conversion events that shaped the diversity of P6 arms during recent human history. In contrast to previous studies, we demonstrated that arm-to-arm gene conversion, which occurs at a rate of 6.01 × 10 -6 conversions/base/year, is not biased toward the retention of the ancestral state of sequences. We also found a significantly lower mutation rate of the arms (6.18 × 10-10 mutations/base/year) compared with the spacer (9.16 × 10-10 mutations/base/year), a finding that may explain the observed higher inter-species conservation of arms, without invoking any bias of conversion. Finally, by formally testing the mutation/conversion balance in P6, we found that the arms of this palindrome reached a steady-state equilibrium between mutation and gene conversion.
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Affiliation(s)
- Maria Bonito
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome 0185, Italy
| | - Eugenia D’Atanasio
- Institute of Molecular Biology and Pathology (IBPM), CNR, Rome 0185, Italy
| | - Francesco Ravasini
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome 0185, Italy
| | - Selene Cariati
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome 0185, Italy
| | - Andrea Finocchio
- Department of Biology, University of Rome Tor Vergata, Rome 0133, Italy
| | - Andrea Novelletto
- Department of Biology, University of Rome Tor Vergata, Rome 0133, Italy
| | - Beniamino Trombetta
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome 0185, Italy
| | - Fulvio Cruciani
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome 0185, Italy
- Institute of Molecular Biology and Pathology (IBPM), CNR, Rome 0185, Italy
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13
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Jackson EK, Bellott DW, Cho TJ, Skaletsky H, Hughes JF, Pyntikova T, Page DC. Large palindromes on the primate X Chromosome are preserved by natural selection. Genome Res 2021; 31:1337-1352. [PMID: 34290043 PMCID: PMC8327919 DOI: 10.1101/gr.275188.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 05/17/2021] [Indexed: 12/27/2022]
Abstract
Mammalian sex chromosomes carry large palindromes that harbor protein-coding gene families with testis-biased expression. However, there are few known examples of sex-chromosome palindromes conserved between species. We identified 26 palindromes on the human X Chromosome, constituting more than 2% of its sequence, and characterized orthologous palindromes in the chimpanzee and the rhesus macaque using a clone-based sequencing approach that incorporates full-length nanopore reads. Many of these palindromes are missing or misassembled in the current reference assemblies of these species' genomes. We find that 12 human X palindromes have been conserved for at least 25 million years, with orthologs in both chimpanzee and rhesus macaque. Insertions and deletions between species are significantly depleted within the X palindromes' protein-coding genes compared to their noncoding sequence, demonstrating that natural selection has preserved these gene families. The spacers that separate the left and right arms of palindromes are a site of localized structural instability, with seven of 12 conserved palindromes showing no spacer orthology between human and rhesus macaque. Analysis of the 1000 Genomes Project data set revealed that human X-palindrome spacers are enriched for deletions relative to arms and flanking sequence, including a common spacer deletion that affects 13% of human X Chromosomes. This work reveals an abundance of conserved palindromes on primate X Chromosomes and suggests that protein-coding gene families in palindromes (most of which remain poorly characterized) promote X-palindrome survival in the face of ongoing structural instability.
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Affiliation(s)
- Emily K Jackson
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | - Ting-Jan Cho
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
| | - Helen Skaletsky
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
| | | | | | - David C Page
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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14
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Structural and numerical Y chromosomal variations in elderly men identified through multiplex ligation-dependent probe amplification. J Hum Genet 2021; 66:1181-1184. [PMID: 34108640 DOI: 10.1038/s10038-021-00943-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/09/2021] [Accepted: 05/27/2021] [Indexed: 11/08/2022]
Abstract
Human Y chromosomes frequently acquire structural and numerical alterations. Known alterations include germline copy-number variations (CNVs) in the azoospermia factor (AZF) region and somatic mosaic loss of the Y chromosome (mLOY). Here, we explored Y chromosomal variations in 160 Japanese men aged 75-90 years. Multiplex ligation-dependent probe amplification (MLPA) identified ten types of AZF-linked CNVs in 77 men and mLOY of various degrees in 37. Seventeen men carried both a CNV and mLOY. MLOY levels estimated by MLPA were closely correlated with those determined by droplet digital PCR. No association was found between AZF-linked CNVs and the frequency or levels of mLOY. These results emphasize the high frequency and large inter-individual variability of AZF-linked CNVs and mLOY, and demonstrate the usefulness of MLPA in the detection of these variations. More importantly, this study provides the first evidence that AZF-linked CNVs do not increase the risk of aging-related mLOY.
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15
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Improved Models of Coalescence Ages of Y-DNA Haplogroups. Genes (Basel) 2021; 12:genes12060862. [PMID: 34200049 PMCID: PMC8228294 DOI: 10.3390/genes12060862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/27/2021] [Accepted: 06/02/2021] [Indexed: 11/19/2022] Open
Abstract
Databases of commercial DNA-testing companies now contain more customers with sequenced DNA than any completed academic study, leading to growing interest from academic and forensic entities. An important result for both these entities and the test takers themselves is how closely two individuals are related in time, as calculated through one or more molecular clocks. For Y-DNA, existing interpretations of these clocks are insufficiently accurate to usefully measure relatedness in historic times. In this article, I update the methods used to calculate coalescence ages (times to most-recent common ancestor, or TMRCAs) using a new, probabilistic statistical model that includes Y-SNP, Y-STR and ancilliary historical data, and provide examples of its use.
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16
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Clifton BD, Jimenez J, Kimura A, Chahine Z, Librado P, Sánchez-Gracia A, Abbassi M, Carranza F, Chan C, Marchetti M, Zhang W, Shi M, Vu C, Yeh S, Fanti L, Xia XQ, Rozas J, Ranz JM. Understanding the Early Evolutionary Stages of a Tandem Drosophilamelanogaster-Specific Gene Family: A Structural and Functional Population Study. Mol Biol Evol 2021; 37:2584-2600. [PMID: 32359138 PMCID: PMC7475035 DOI: 10.1093/molbev/msaa109] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Gene families underlie genetic innovation and phenotypic diversification. However, our understanding of the early genomic and functional evolution of tandemly arranged gene families remains incomplete as paralog sequence similarity hinders their accurate characterization. The Drosophila melanogaster-specific gene family Sdic is tandemly repeated and impacts sperm competition. We scrutinized Sdic in 20 geographically diverse populations using reference-quality genome assemblies, read-depth methodologies, and qPCR, finding that ∼90% of the individuals harbor 3-7 copies as well as evidence of population differentiation. In strains with reliable gene annotations, copy number variation (CNV) and differential transposable element insertions distinguish one structurally distinct version of the Sdic region per strain. All 31 annotated copies featured protein-coding potential and, based on the protein variant encoded, were categorized into 13 paratypes differing in their 3' ends, with 3-5 paratypes coexisting in any strain examined. Despite widespread gene conversion, the only copy present in all strains has functionally diverged at both coding and regulatory levels under positive selection. Contrary to artificial tandem duplications of the Sdic region that resulted in increased male expression, CNV in cosmopolitan strains did not correlate with expression levels, likely as a result of differential genome modifier composition. Duplicating the region did not enhance sperm competitiveness, suggesting a fitness cost at high expression levels or a plateau effect. Beyond facilitating a minimally optimal expression level, Sdic CNV acts as a catalyst of protein and regulatory diversity, showcasing a possible evolutionary path recently formed tandem multigene families can follow toward long-term consolidation in eukaryotic genomes.
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Affiliation(s)
- Bryan D Clifton
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Jamie Jimenez
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Ashlyn Kimura
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Zeinab Chahine
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Pablo Librado
- Laboratoire AMIS CNRS UMR 5288, Faculté de Médicine de Purpan, Université Paul Sabatier, Toulouse, France
| | - Alejandro Sánchez-Gracia
- Departament de Genètica, Microbiologia i Estadistica, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
| | - Mashya Abbassi
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Francisco Carranza
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Carolus Chan
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Marcella Marchetti
- Istituto Pasteur Italia, Fondazione Cenci-Bolognetti, Rome, Italy.,Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Wanting Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Mijuan Shi
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Christine Vu
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
| | - Shudan Yeh
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA.,Department of Life Sciences, National Central University, Taoyuan City, Zhongli District, Taiwan
| | - Laura Fanti
- Istituto Pasteur Italia, Fondazione Cenci-Bolognetti, Rome, Italy.,Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Xiao-Qin Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, China
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadistica, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
| | - José M Ranz
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA
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17
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Ravasini F, D'Atanasio E, Bonito M, Bonucci B, Della Rocca C, Berti A, Trombetta B, Cruciani F. Sequence Read Depth Analysis of a Monophyletic Cluster of Y Chromosomes Characterized by Structural Rearrangements in the AZFc Region Resulting in DYS448 Deletion and DYF387S1 Duplication. Front Genet 2021; 12:669405. [PMID: 33936180 PMCID: PMC8085532 DOI: 10.3389/fgene.2021.669405] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/29/2021] [Indexed: 12/26/2022] Open
Abstract
The azoospermia factor c region (AZFc), located in the long arm of the human Y chromosome, is frequently involved in chromosome rearrangements, mainly due to non-allelic homologous recombination events that occur between the nearly identical sequences (amplicon) that comprises it. These rearrangements may have major phenotypic effects like spermatogenic failure or other pathologies linked to male infertility. Moreover, they may also be relevant in forensic genetics, since some of the Y chromosome short tandem repeats (Y-STRs) commonly used in forensic analysis are located in amplicons or in inter-amplicon sequences of the AZFc. In a previous study, we identified four phylogenetically related samples with a null allele at DYS448 and a tetrallelic pattern at DYF387S1, two Y-STRs located in the AZFc. Through NGS read depth analysis, we found that the unusual Y-STR pattern may be due to a 1.6 Mb deletion arising concurrently or after a 3.5 Mb duplication event. The observed large genomic rearrangement results in copy number reduction for the RBMY gene family as well as duplication of other AZFc genes. Based on the diversity of 16 additional Y-STRs, we estimated that the duplication/deletion event occurred at least twenty generations ago, suggesting that it has not been affected by negative selection.
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Affiliation(s)
- Francesco Ravasini
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | - Eugenia D'Atanasio
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Maria Bonito
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | - Biancamaria Bonucci
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | - Chiara Della Rocca
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | - Andrea Berti
- Sezione di Biologia, Reparto CC Investigazioni Scientifiche di Roma, Rome, Italy
| | - Beniamino Trombetta
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | - Fulvio Cruciani
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy.,Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy
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18
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Hallast P, Kibena L, Punab M, Arciero E, Rootsi S, Grigorova M, Flores R, Jobling MA, Poolamets O, Pomm K, Korrovits P, Rull K, Xue Y, Tyler-Smith C, Laan M. A common 1.6 mb Y-chromosomal inversion predisposes to subsequent deletions and severe spermatogenic failure in humans. eLife 2021; 10:65420. [PMID: 33781384 PMCID: PMC8009663 DOI: 10.7554/elife.65420] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/15/2021] [Indexed: 12/19/2022] Open
Abstract
Male infertility is a prevalent condition, affecting 5–10% of men. So far, few genetic factors have been described as contributors to spermatogenic failure. Here, we report the first re-sequencing study of the Y-chromosomal Azoospermia Factor c (AZFc) region, combined with gene dosage analysis of the multicopy DAZ, BPY2, and CDYgenes and Y-haplogroup determination. In analysing 2324 Estonian men, we uncovered a novel structural variant as a high-penetrance risk factor for male infertility. The Y lineage R1a1-M458, reported at >20% frequency in several European populations, carries a fixed ~1.6 Mb r2/r3 inversion, destabilizing the AZFc region and predisposing to large recurrent microdeletions. Such complex rearrangements were significantly enriched among severe oligozoospermia cases. The carrier vs non-carrier risk for spermatogenic failure was increased 8.6-fold (p=6.0×10−4). This finding contributes to improved molecular diagnostics and clinical management of infertility. Carrier identification at young age will facilitate timely counselling and reproductive decision-making.
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Affiliation(s)
- Pille Hallast
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.,Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Laura Kibena
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Margus Punab
- Andrology Unit, Tartu University Hospital, Tartu, Estonia.,Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Elena Arciero
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Siiri Rootsi
- Institute of Genomics, Estonian Biocentre, University of Tartu, Tartu, Estonia
| | - Marina Grigorova
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Rodrigo Flores
- Institute of Genomics, Estonian Biocentre, University of Tartu, Tartu, Estonia
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Olev Poolamets
- Andrology Unit, Tartu University Hospital, Tartu, Estonia
| | - Kristjan Pomm
- Andrology Unit, Tartu University Hospital, Tartu, Estonia
| | - Paul Korrovits
- Andrology Unit, Tartu University Hospital, Tartu, Estonia
| | - Kristiina Rull
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.,Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Women's Clinic, Tartu University Hospital, Tartu, Estonia
| | - Yali Xue
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Chris Tyler-Smith
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Maris Laan
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
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19
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Vogt PH, Bender U, Deibel B, Kiesewetter F, Zimmer J, Strowitzki T. Human AZFb deletions cause distinct testicular pathologies depending on their extensions in Yq11 and the Y haplogroup: new cases and review of literature. Cell Biosci 2021; 11:60. [PMID: 33766143 PMCID: PMC7995748 DOI: 10.1186/s13578-021-00551-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/06/2021] [Indexed: 02/07/2023] Open
Abstract
Genomic AZFb deletions in Yq11 coined “classical” (i.e. length of Y DNA deletion: 6.23 Mb) are associated with meiotic arrest (MA) of patient spermatogenesis, i.e., absence of any postmeiotic germ cells. These AZFb deletions are caused by non-allelic homologous recombination (NAHR) events between identical sequence blocks located in the proximal arm of the P5 palindrome and within P1.2, a 92 kb long sequence block located in the P1 palindrome structure of AZFc in Yq11. This large genomic Y region includes deletion of 6 protein encoding Y genes, EIFA1Y, HSFY, PRY, RBMY1, RPS4Y, SMCY. Additionally, one copy of CDY2 and XKRY located in the proximal P5 palindrome and one copy of BPY1, two copies of DAZ located in the P2 palindrome, and one copy of CDY1 located proximal to P1.2 are included within this AZFb microdeletion. It overlaps thus distally along 2.3 Mb with the proximal part of the genomic AZFc deletion. However, AZFb deletions have been also reported with distinct break sites in the proximal and/or distal AZFb breakpoint intervals on the Y chromosome of infertile men. These so called “non-classical” AZFb deletions are associated with variable testicular pathologies, including meiotic arrest, cryptozoospermia, severe oligozoospermia, or oligoasthenoteratozoospermia (OAT syndrome), respectively. This raised the question whether there are any specific length(s) of the AZFb deletion interval along Yq11 required to cause meiotic arrest of the patient’s spermatogenesis, respectively, whether there is any single AZFb Y gene deletion also able to cause this “classical” AZFb testicular pathology? Review of the literature and more cases with “classical” and “non-classical” AZFb deletions analysed in our lab since the last 20 years suggests that the composition of the genomic Y sequence in AZFb is variable in men with distinct Y haplogroups especially in the distal AZFb region overlapping with the proximal AZFc deletion interval and that its extension can be “polymorphic” in the P3 palindrome. That means this AZFb subinterval can be rearranged or deleted also on the Y chromosome of fertile men. Any AZFb deletion observed in infertile men with azoospermia should therefore be confirmed as “de novo” mutation event, i.e., not present on the Y chromosome of the patient’s father or fertile brother before it is considered as causative agent for man’s infertility. Moreover, its molecular length in Yq11 should be comparable to that of the “classical” AZFb deletion, before meiotic arrest is prognosed as the patient’s testicular pathology.
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Affiliation(s)
- P H Vogt
- Division of Reproduction Genetics, Department of Gynaecol. Endocrinology & Infertility Disorders, Women Hospital, University of Heidelberg, Im Neuenheimer Feld 440, 69120, Heidelberg, Germany.
| | - U Bender
- Division of Reproduction Genetics, Department of Gynaecol. Endocrinology & Infertility Disorders, Women Hospital, University of Heidelberg, Im Neuenheimer Feld 440, 69120, Heidelberg, Germany
| | - B Deibel
- Division of Reproduction Genetics, Department of Gynaecol. Endocrinology & Infertility Disorders, Women Hospital, University of Heidelberg, Im Neuenheimer Feld 440, 69120, Heidelberg, Germany
| | - F Kiesewetter
- Department of Andrology, University Clinic of Dermatology, Erlangen, Germany
| | - J Zimmer
- Division of Reproduction Genetics, Department of Gynaecol. Endocrinology & Infertility Disorders, Women Hospital, University of Heidelberg, Im Neuenheimer Feld 440, 69120, Heidelberg, Germany
| | - T Strowitzki
- Department of Gynaecol. Endocrinology & Infertility Disorders, Women Hospital, University of Heidelberg, Heidelberg, Germany
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20
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Suppression of Non-Random Fertilization by MHC Class I Antigens. Int J Mol Sci 2020; 21:ijms21228731. [PMID: 33227981 PMCID: PMC7699254 DOI: 10.3390/ijms21228731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 11/22/2022] Open
Abstract
Hermaphroditic invertebrates and plants have a self-recognition system on the cell surface of sperm and eggs, which prevents their self-fusion and enhances non-self-fusion, thereby contributing to genetic variation. However, the system of sperm–egg recognition in mammals is under debate. To address this issue, we explored the role of major histocompatibility complex class I (MHC class I, also known as histocompatibility 2-Kb or H2-Kb and H2-Db in mice) antigens by analyzing H2-Kb-/-H2-Db-/-β2-microglobulin (β2M)-/- triple-knockout (T-KO) male mice with full fertility. T-KO sperm exhibited an increased sperm number in the perivitelline space of wild-type (WT) eggs in vitro. Moreover, T-KO sperm showed multiple fusion with zona pellucida (ZP)-free WT eggs, implying that the ability of polyspermy block for sperm from T-KO males was weakened in WT eggs. When T-KO male mice were intercrossed with WT female mice, the percentage of females in progeny increased. We speculate that WT eggs prefer fusion with T-KO sperm, more specifically X-chromosome-bearing sperm (X sperm), suggesting the presence of preferential (non-random) fertilization in mammals, including humans.
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21
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The Y Chromosome: A Complex Locus for Genetic Analyses of Complex Human Traits. Genes (Basel) 2020; 11:genes11111273. [PMID: 33137877 PMCID: PMC7693691 DOI: 10.3390/genes11111273] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/19/2020] [Accepted: 10/26/2020] [Indexed: 12/29/2022] Open
Abstract
The Human Y chromosome (ChrY) has been demonstrated to be a powerful tool for phylogenetics, population genetics, genetic genealogy and forensics. However, the importance of ChrY genetic variation in relation to human complex traits is less clear. In this review, we summarise existing evidence about the inherent complexities of ChrY variation and their use in association studies of human complex traits. We present and discuss the specific particularities of ChrY genetic variation, including Y chromosomal haplogroups, that need to be considered in the design and interpretation of genetic epidemiological studies involving ChrY.
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22
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Wilson J, Staley JM, Wyckoff GJ. Extinction of chromosomes due to specialization is a universal occurrence. Sci Rep 2020; 10:2170. [PMID: 32034231 PMCID: PMC7005762 DOI: 10.1038/s41598-020-58997-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 01/20/2020] [Indexed: 11/09/2022] Open
Abstract
The human X and Y chromosomes evolved from a pair of autosomes approximately 180 million years ago. Despite their shared evolutionary origin, extensive genetic decay has resulted in the human Y chromosome losing 97% of its ancestral genes while gene content and order remain highly conserved on the X chromosome. Five 'stratification' events, most likely inversions, reduced the Y chromosome's ability to recombine with the X chromosome across the majority of its length and subjected its genes to the erosive forces associated with reduced recombination. The remaining functional genes are ubiquitously expressed, functionally coherent, dosage-sensitive genes, or have evolved male-specific functionality. It is unknown, however, whether functional specialization is a degenerative phenomenon unique to sex chromosomes, or if it conveys a potential selective advantage aside from sexual antagonism. We examined the evolution of mammalian orthologs to determine if the selective forces that led to the degeneration of the Y chromosome are unique in the genome. The results of our study suggest these forces are not exclusive to the Y chromosome, and chromosomal degeneration may have occurred throughout our evolutionary history. The reduction of recombination could additionally result in rapid fixation through isolation of specialized functions resulting in a cost-benefit relationship during times of intense selective pressure.
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Affiliation(s)
- Jason Wilson
- University of Missouri-Kansas City School of Medicine, Department of Biomedical and Health Informatics, Kansas City, 64108, Missouri, USA.
| | - Joshua M Staley
- Kansas State University College of Veterinary Medicine, Department of Diagnostic Medicine/Pathobiology, Olathe, 66061, Kansas, USA
| | - Gerald J Wyckoff
- University of Missouri-Kansas City School of Medicine, Department of Biomedical and Health Informatics, Kansas City, 64108, Missouri, USA.,Kansas State University College of Veterinary Medicine, Department of Diagnostic Medicine/Pathobiology, Olathe, 66061, Kansas, USA.,University of Missouri-Kansas City School of Biological and Chemical Sciences, Department of Molecular Biology and Biochemistry, Kansas City, 64108, Missouri, USA
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23
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The Role of Number of Copies, Structure, Behavior and Copy Number Variations (CNV) of the Y Chromosome in Male Infertility. Genes (Basel) 2019; 11:genes11010040. [PMID: 31905733 PMCID: PMC7016774 DOI: 10.3390/genes11010040] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/17/2019] [Accepted: 12/23/2019] [Indexed: 12/11/2022] Open
Abstract
The World Health Organization (WHO) defines infertility as the inability of a sexually active, non-contracepting couple to achieve spontaneous pregnancy within one year. Statistics show that the two sexes are equally at risk. Several causes may be responsible for male infertility; however, in 30–40% of cases a diagnosis of idiopathic male infertility is made in men with normal urogenital anatomy, no history of familial fertility-related diseases and a normal panel of values as for endocrine, genetic and biochemical markers. Idiopathic male infertility may be the result of gene/environment interactions, genetic and epigenetic abnormalities. Numerical and structural anomalies of the Y chromosome represent a minor yet significant proportion and are the topic discussed in this review. We searched the PubMed database and major search engines for reports about Y-linked male infertility. We present cases of Y-linked male infertility in terms of (i) anomalies of the Y chromosome structure/number; (ii) Y chromosome misbehavior in a normal genetic background; (iii) Y chromosome copy number variations (CNVs). We discuss possible explanations of male infertility caused by mutations, lower or higher number of copies of otherwise wild type, Y-linked sequences. Despite Y chromosome structural anomalies are not a major cause of male infertility, in case of negative results and of normal DNA sequencing of the ascertained genes causing infertility and mapping on this chromosome, we recommend an analysis of the karyotype integrity in all cases of idiopathic fertility impairment, with an emphasis on the structure and number of this chromosome.
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24
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Shi W, Massaia A, Louzada S, Handsaker J, Chow W, McCarthy S, Collins J, Hallast P, Howe K, Church DM, Yang F, Xue Y, Tyler-Smith C. Birth, expansion, and death of VCY-containing palindromes on the human Y chromosome. Genome Biol 2019; 20:207. [PMID: 31610793 PMCID: PMC6790999 DOI: 10.1186/s13059-019-1816-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/04/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Large palindromes (inverted repeats) make up substantial proportions of mammalian sex chromosomes, often contain genes, and have high rates of structural variation arising via ectopic recombination. As a result, they underlie many genomic disorders. Maintenance of the palindromic structure by gene conversion between the arms has been documented, but over longer time periods, palindromes are remarkably labile. Mechanisms of origin and loss of palindromes have, however, received little attention. RESULTS Here, we use fiber-FISH, 10x Genomics Linked-Read sequencing, and breakpoint PCR sequencing to characterize the structural variation of the P8 palindrome on the human Y chromosome, which contains two copies of the VCY (Variable Charge Y) gene. We find a deletion of almost an entire arm of the palindrome, leading to death of the palindrome, a size increase by recruitment of adjacent sequence, and other complex changes including the formation of an entire new palindrome nearby. Together, these changes are found in ~ 1% of men, and we can assign likely molecular mechanisms to these mutational events. As a result, healthy men can have 1-4 copies of VCY. CONCLUSIONS Gross changes, especially duplications, in palindrome structure can be relatively frequent and facilitate the evolution of sex chromosomes in humans, and potentially also in other mammalian species.
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Affiliation(s)
- Wentao Shi
- The Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
- Department of Genetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Andrea Massaia
- The Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
- Present address: National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - Sandra Louzada
- The Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Juliet Handsaker
- The Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - William Chow
- The Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Shane McCarthy
- The Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
- Present address: Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Joanna Collins
- The Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Pille Hallast
- The Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
- Institute of Biomedicine and Translational Medicine, University of Tartu, 51011, Tartu, Estonia
| | - Kerstin Howe
- The Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Deanna M Church
- 10x Genomics, 7068 Koll Center Parkway, Suite 401, Pleasanton, CA, 94566, USA
- Present address: Inscripta Inc., 5500 Central Avenue #220, Boulder, CO, 80301, USA
| | - Fengtang Yang
- The Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Yali Xue
- The Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK.
| | - Chris Tyler-Smith
- The Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK.
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25
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Vegesna R, Tomaszkiewicz M, Medvedev P, Makova KD. Dosage regulation, and variation in gene expression and copy number of human Y chromosome ampliconic genes. PLoS Genet 2019; 15:e1008369. [PMID: 31525193 PMCID: PMC6772104 DOI: 10.1371/journal.pgen.1008369] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 10/01/2019] [Accepted: 08/13/2019] [Indexed: 12/28/2022] Open
Abstract
The Y chromosome harbors nine multi-copy ampliconic gene families expressed exclusively in testis. The gene copies within each family are >99% identical to each other, which poses a major challenge in evaluating their copy number. Recent studies demonstrated high variation in Y ampliconic gene copy number among humans. However, how this variation affects expression levels in human testis remains understudied. Here we developed a novel computational tool Ampliconic Copy Number Estimator (AmpliCoNE) that utilizes read sequencing depth information to estimate Y ampliconic gene copy number per family. We applied this tool to whole-genome sequencing data of 149 men with matched testis expression data whose samples are part of the Genotype-Tissue Expression (GTEx) project. We found that the Y ampliconic gene families with low copy number in humans were deleted or pseudogenized in non-human great apes, suggesting relaxation of functional constraints. Among the Y ampliconic gene families, higher copy number leads to higher expression. Within the Y ampliconic gene families, copy number does not influence gene expression, rather a high tolerance for variation in gene expression was observed in testis of presumably healthy men. No differences in gene expression levels were found among major Y haplogroups. Age positively correlated with expression levels of the HSFY and PRY gene families in the African subhaplogroup E1b, but not in the European subhaplogroups R1b and I1. We also found that expression of five Y ampliconic gene families is coordinated with that of their non-Y (i.e. X or autosomal) homologs. Indeed, five ampliconic gene families had consistently lower expression levels when compared to their non-Y homologs suggesting dosage regulation, while the HSFY family had higher expression levels than its X homolog and thus lacked dosage regulation.
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MESH Headings
- Animals
- Chromosomes, Human, Y/genetics
- Chromosomes, Human, Y/physiology
- DNA Copy Number Variations/genetics
- Databases, Genetic
- Dosage Compensation, Genetic/genetics
- Dosage Compensation, Genetic/physiology
- Epigenesis, Genetic/genetics
- Gene Dosage/genetics
- Gene Expression/genetics
- Gene Expression Regulation/genetics
- Genes, Y-Linked/genetics
- Genes, Y-Linked/physiology
- Heat Shock Transcription Factors/genetics
- Heat Shock Transcription Factors/metabolism
- Humans
- Male
- Multigene Family/genetics
- Sequence Analysis, DNA/methods
- Testis/metabolism
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Affiliation(s)
- Rahulsimham Vegesna
- Bioinformatics and Genomics Graduate Program, The Huck Institutes for the Life Sciences, Pennsylvania State University, University Park, PA, United States of America
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, United States of America
| | - Marta Tomaszkiewicz
- Department of Biology, Pennsylvania State University, University Park, PA, United States of America
| | - Paul Medvedev
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, United States of America
- Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA, United States of America
- Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, PA, United States of America
- Center for Medical Genomics, Pennsylvania State University, University Park, PA, United States of America
| | - Kateryna D. Makova
- Bioinformatics and Genomics Graduate Program, The Huck Institutes for the Life Sciences, Pennsylvania State University, University Park, PA, United States of America
- Department of Biology, Pennsylvania State University, University Park, PA, United States of America
- Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, PA, United States of America
- Center for Medical Genomics, Pennsylvania State University, University Park, PA, United States of America
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26
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Shi W, Louzada S, Grigorova M, Massaia A, Arciero E, Kibena L, Ge XJ, Chen Y, Ayub Q, Poolamets O, Tyler-Smith C, Punab M, Laan M, Yang F, Hallast P, Xue Y. Evolutionary and functional analysis of RBMY1 gene copy number variation on the human Y chromosome. Hum Mol Genet 2019; 28:2785-2798. [PMID: 31108506 PMCID: PMC6687947 DOI: 10.1093/hmg/ddz101] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/10/2019] [Accepted: 05/11/2019] [Indexed: 01/17/2023] Open
Abstract
Human RBMY1 genes are located in four variable-sized clusters on the Y chromosome, expressed in male germ cells and possibly associated with sperm motility. We have re-investigated the mutational background and evolutionary history of the RBMY1 copy number distribution in worldwide samples and its relevance to sperm parameters in an Estonian cohort of idiopathic male factor infertility subjects. We estimated approximate RBMY1 copy numbers in 1218 1000 Genomes Project phase 3 males from sequencing read-depth, then chose 14 for valid ation by multicolour fibre-FISH. These fibre-FISH samples provided accurate calibration standards for the entire panel and led to detailed insights into population variation and mutational mechanisms. RBMY1 copy number worldwide ranged from 3 to 13 with a mode of 8. The two larger proximal clusters were the most variable, and additional duplications, deletions and inversions were detected. Placing the copy number estimates onto the published Y-SNP-based phylogeny of the same samples suggested a minimum of 562 mutational changes, translating to a mutation rate of 2.20 × 10-3 (95% CI 1.94 × 10-3 to 2.48 × 10-3) per father-to-son Y-transmission, higher than many short tandem repeat (Y-STRs), and showed no evidence for selection for increased or decreased copy number, but possible copy number stabilizing selection. An analysis of RBMY1 copy numbers among 376 infertility subjects failed to replicate a previously reported association with sperm motility and showed no significant effect on sperm count and concentration, serum follicle stimulating hormone (FSH), luteinizing hormone (LH) and testosterone levels or testicular and semen volume. These results provide the first in-depth insights into the structural rearrangements underlying RBMY1 copy number variation across diverse human lineages.
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Affiliation(s)
- Wentao Shi
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Department of Genetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Sandra Louzada
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Marina Grigorova
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu 50411, Estonia
| | - Andrea Massaia
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK
| | - Elena Arciero
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Laura Kibena
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu 50411, Estonia
| | - Xiangyu Jack Ge
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Faculty of Biology, Medicine and Health, School of Biological Science, Division of Musculoskeletal and Dermatological Science, University of Manchester, Manchester M13 9PL, UK
| | - Yuan Chen
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Qasim Ayub
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Monash University Malaysia Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia
| | - Olev Poolamets
- Andrology Unit, Tartu University Hospital, Tartu 50406, Estonia
| | - Chris Tyler-Smith
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Margus Punab
- Andrology Unit, Tartu University Hospital, Tartu 50406, Estonia
| | - Maris Laan
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu 50411, Estonia
| | - Fengtang Yang
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Pille Hallast
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu 50411, Estonia
| | - Yali Xue
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
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27
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Moreno-Mendoza D, Casamonti E, Paoli D, Chianese C, Riera-Escamilla A, Giachini C, Fino MG, Cioppi F, Lotti F, Vinci S, Magini A, Ars E, Sanchez-Curbelo J, Ruiz-Castane E, Lenzi A, Lombardo F, Krausz C. gr/gr deletion predisposes to testicular germ cell tumour independently from altered spermatogenesis: results from the largest European study. Eur J Hum Genet 2019; 27:1578-1588. [PMID: 31053779 DOI: 10.1038/s41431-019-0420-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 03/26/2019] [Accepted: 04/13/2019] [Indexed: 11/09/2022] Open
Abstract
The association between impaired spermatogenesis and TGCT has stimulated research on shared genetic factors. Y chromosome-linked partial AZFc deletions predispose to oligozoospermia and were also studied in TGCT patients with controversial results. In the largest study reporting the association between gr/gr deletion and TGCT, sperm parameters were unknown. Hence, it remains to be established whether this genetic defect truly represents a common genetic link between TGCT and impaired sperm production. Our aim was to explore the role of the following Y chromosome-linked factors in the predisposition to TGCT: (i) gr/gr deletion in subjects with known sperm parameters; (ii) other partial AZFc deletions and, for the first time, the role of partial AZFc duplications; (iii) DAZ gene dosage variation. 497 TGCT patients and 2030 controls from two Mediterranean populations with full semen/andrological characterization were analyzed through a series of molecular genetic techniques. Our most interesting finding concerns the gr/gr deletion and DAZ gene dosage variation (i.e., DAZ copy number is different from the reference sequence), both conferring TGCT susceptibility. In particular, the highest risk was observed when normozoospermic TGCT and normozoospermic controls were compared (OR = 3.7; 95% CI = 1.5-9.1; p = 0.006 for gr/gr deletion and OR = 1.8; 95% CI = 1.1-3.0; p = 0.013 for DAZ gene dosage alteration). We report in the largest European study population the predisposing effect of gr/gr deletion to TGCT as an independent risk factor from impaired spermatogenesis. Our finding implies regular tumour screening/follow-up in male family members of TGCT patients with gr/gr deletion and in infertile gr/gr deletion carriers.
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Affiliation(s)
- Daniel Moreno-Mendoza
- Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - Elena Casamonti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Centre of Excellence DeNothe, University of Florence, Florence, Italy
| | - Donatella Paoli
- Laboratory of Seminology-Sperm Bank "Loredana Gandini", Department of Experimental Medicine "Sapienza", University of Rome, Rome, Italy
| | - Chiara Chianese
- Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - Antoni Riera-Escamilla
- Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - Claudia Giachini
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Centre of Excellence DeNothe, University of Florence, Florence, Italy
| | - Maria Grazia Fino
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Centre of Excellence DeNothe, University of Florence, Florence, Italy
| | - Francesca Cioppi
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Centre of Excellence DeNothe, University of Florence, Florence, Italy
| | - Francesco Lotti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Centre of Excellence DeNothe, University of Florence, Florence, Italy
| | - Serena Vinci
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Centre of Excellence DeNothe, University of Florence, Florence, Italy
| | - Angela Magini
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Centre of Excellence DeNothe, University of Florence, Florence, Italy
| | - Elisabet Ars
- Molecular Biology Laboratory, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB Sant Pau), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Josvany Sanchez-Curbelo
- Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - Eduard Ruiz-Castane
- Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - Andrea Lenzi
- Laboratory of Seminology-Sperm Bank "Loredana Gandini", Department of Experimental Medicine "Sapienza", University of Rome, Rome, Italy
| | - Francesco Lombardo
- Laboratory of Seminology-Sperm Bank "Loredana Gandini", Department of Experimental Medicine "Sapienza", University of Rome, Rome, Italy
| | - Csilla Krausz
- Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Spain. .,Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Centre of Excellence DeNothe, University of Florence, Florence, Italy.
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