1
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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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2
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Makova KD, Pickett BD, Harris RS, Hartley GA, Cechova M, Pal K, Nurk S, Yoo D, Li Q, Hebbar P, McGrath BC, Antonacci F, Aubel M, Biddanda A, Borchers M, Bomberg E, Bouffard GG, Brooks SY, Carbone L, Carrel L, Carroll A, Chang PC, Chin CS, Cook DE, Craig SJ, de Gennaro L, Diekhans M, Dutra A, Garcia GH, Grady PG, Green RE, Haddad D, Hallast P, Harvey WT, Hickey G, Hillis DA, Hoyt SJ, Jeong H, Kamali K, Kosakovsky Pond SL, LaPolice TM, Lee C, Lewis AP, Loh YHE, Masterson P, McCoy RC, Medvedev P, Miga KH, Munson KM, Pak E, Paten B, Pinto BJ, Potapova T, Rhie A, Rocha JL, Ryabov F, Ryder OA, Sacco S, Shafin K, Shepelev VA, Slon V, Solar SJ, Storer JM, Sudmant PH, Sweetalana, Sweeten A, Tassia MG, Thibaud-Nissen F, Ventura M, Wilson MA, Young AC, Zeng H, Zhang X, Szpiech ZA, Huber CD, Gerton JL, Yi SV, Schatz MC, Alexandrov IA, Koren S, O’Neill RJ, Eichler E, Phillippy AM. The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569198. [PMID: 38077089 PMCID: PMC10705393 DOI: 10.1101/2023.11.30.569198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Apes possess two sex chromosomes-the male-specific Y and the X shared by males and females. The Y chromosome is crucial for male reproduction, with deletions linked to infertility. The X chromosome carries genes vital for reproduction and cognition. Variation in mating patterns and brain function among great apes suggests corresponding differences in their sex chromosome structure and evolution. However, due to their highly repetitive nature and incomplete reference assemblies, ape sex chromosomes have been challenging to study. Here, using the state-of-the-art experimental and computational methods developed for the telomere-to-telomere (T2T) human genome, we produced gapless, complete assemblies of the X and Y chromosomes for five great apes (chimpanzee, bonobo, gorilla, Bornean and Sumatran orangutans) and a lesser ape, the siamang gibbon. These assemblies completely resolved ampliconic, palindromic, and satellite sequences, including the entire centromeres, allowing us to untangle the intricacies of ape sex chromosome evolution. We found that, compared to the X, ape Y chromosomes vary greatly in size and have low alignability and high levels of structural rearrangements. This divergence on the Y arises from the accumulation of lineage-specific ampliconic regions and palindromes (which are shared more broadly among species on the X) and from the abundance of transposable elements and satellites (which have a lower representation on the X). Our analysis of Y chromosome genes revealed lineage-specific expansions of multi-copy gene families and signatures of purifying selection. In summary, the Y exhibits dynamic evolution, while the X is more stable. Finally, mapping short-read sequencing data from >100 great ape individuals revealed the patterns of diversity and selection on their sex chromosomes, demonstrating the utility of these reference assemblies for studies of great ape evolution. These complete sex chromosome assemblies are expected to further inform conservation genetics of nonhuman apes, all of which are endangered species.
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Affiliation(s)
| | - Brandon D. Pickett
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Monika Cechova
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - Karol Pal
- Penn State University, University Park, PA, USA
| | - Sergey Nurk
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - DongAhn Yoo
- University of Washington School of Medicine, Seattle, WA, USA
| | - Qiuhui Li
- Johns Hopkins University, Baltimore, MD, USA
| | - Prajna Hebbar
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | | | | | | | | | - Erich Bomberg
- University of Münster, Münster, Germany
- MPI for Developmental Biology, Tübingen, Germany
| | - Gerard G. Bouffard
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shelise Y. Brooks
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lucia Carbone
- Oregon Health & Science University, Portland, OR, USA
- Oregon National Primate Research Center, Hillsboro, OR, USA
| | - Laura Carrel
- Penn State University School of Medicine, Hershey, PA, USA
| | | | | | - Chen-Shan Chin
- Foundation of Biological Data Sciences, Belmont, CA, USA
| | | | | | | | - Mark Diekhans
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - Amalia Dutra
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gage H. Garcia
- University of Washington School of Medicine, Seattle, WA, USA
| | | | | | - Diana Haddad
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Pille Hallast
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Glenn Hickey
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - David A. Hillis
- University of California Santa Barbara, Santa Barbara, CA, USA
| | | | - Hyeonsoo Jeong
- University of Washington School of Medicine, Seattle, WA, USA
| | | | | | | | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | | | - Patrick Masterson
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Karen H. Miga
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | - Evgenia Pak
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Benedict Paten
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | | | - Arang Rhie
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Fedor Ryabov
- Masters Program in National Research University Higher School of Economics, Moscow, Russia
| | | | - Samuel Sacco
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | | | | | - Steven J. Solar
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Sweetalana
- Penn State University, University Park, PA, USA
| | - Alex Sweeten
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Johns Hopkins University, Baltimore, MD, USA
| | | | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Alice C. Young
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Xinru Zhang
- Penn State University, University Park, PA, USA
| | | | | | | | - Soojin V. Yi
- University of California Santa Barbara, Santa Barbara, CA, USA
| | | | | | - Sergey Koren
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Evan Eichler
- University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Adam M. Phillippy
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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3
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Chen C, Tang T, Song QL, He YJ, Cai Y. Confusing finding of quantitative fluorescent polymerase chain reaction analysis in invasive prenatal genetic diagnosis: A case report. World J Clin Cases 2023; 11:6895-6901. [PMID: 37901017 PMCID: PMC10600840 DOI: 10.12998/wjcc.v11.i28.6895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/23/2023] [Accepted: 09/14/2023] [Indexed: 09/25/2023] Open
Abstract
BACKGROUND Quantitative fluorescent polymerase chain reaction (QF-PCR) is a rapid prenatal diagnostic method for abnormalities on chromosomes 21, 18, and 13 and sex chromosomal aneuploidy. However, the value of QF-PCR in diagnosing chromosomal structural abnormalities is limited. In this article, we report a confusing QF-PCR finding in a pregnant woman who underwent amniocentesis. CASE SUMMARY The short tandem repeat marker AMXY (Xp22.2/Yp11.2) located on the sex chromosome exhibited a trisomic biallelic pattern, indicating that the karyotype of the fetus might be 47,XYY. Chromosome analysis performed on cultured amniocytes showed a normal male karyotype of the fetus. Copy number variation sequencing confirmed a 500 kb duplication at Yp11.2-Yp11.2 (chrY:6610001_ 7110000) and a 250 kb duplication at Yp11.2-Yp11.2 (chrY:7110001_7360000). CONCLUSION In conclusion, the comprehensive application of different methods could achieve a higher detection rate and accuracy for the prenatal diagnosis of chromosomal disorders through chromosomal testing.
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Affiliation(s)
- Cui Chen
- Genetic and Prenatal Diagnosis Center, Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
| | - Tao Tang
- Genetic and Prenatal Diagnosis Center, Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
| | - Qi-Ling Song
- Genetic and Prenatal Diagnosis Center, Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
| | - Yong-Jun He
- Genetic and Prenatal Diagnosis Center, Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
| | - Yan Cai
- Genetic and Prenatal Diagnosis Center, Affiliated Hospital of North Sichuan Medical College, Nanchong 637000, Sichuan Province, China
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4
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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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5
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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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6
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Pelzman DL, Hwang K. Genetic testing for men with infertility: techniques and indications. Transl Androl Urol 2021; 10:1354-1364. [PMID: 33850771 PMCID: PMC8039607 DOI: 10.21037/tau-19-725] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Genetic testing is an integral component in the workup of male infertility as genetic conditions may be responsible for up to 15% of all cases. Currently, three genetic tests are commonly performed and recommended by major urologic associations: karyotype analysis (KA), Y-chromosome microdeletion testing, and CFTR mutation testing. Despite widespread adoption of these tests, an etiology for infertility remains elusive in up to 80% of cases. Recent work has identified intriguing new targets for genetic testing which may soon see clinical relevance. This review will discuss the indications and techniques for currently offered genetic tests and briefly explore ongoing research directions within this field.
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Affiliation(s)
- Daniel L Pelzman
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kathleen Hwang
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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7
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Xp;Yq Unbalanced Translocation with Pseudoautosomal Region Aberrations in a Natural Two-Generation Transmission. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4976204. [PMID: 33344636 PMCID: PMC7732387 DOI: 10.1155/2020/4976204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 11/12/2020] [Accepted: 11/23/2020] [Indexed: 12/03/2022]
Abstract
Translocations involving X and Y chromosomes rarely occur in humans and may affect reproductive function. We investigated an Xp:Yq unbalanced translocation with pseudoautosomal region (PAR) aberrations in a natural two-generation transmission. We report the case of an azoospermic male and his fertile mother without any other abnormal clinical phenotypes, except for short stature. Cytogenetic methods, including karyotyping and fluorescence in situ hybridization (FISH), revealed the translocation. Chromosomal microarray comparative genomic hybridization (array-CGH) was used to investigate the regions of Xp partial deletion and Yq partial duplication. Final chromosome karyotypes in the peripheral blood of the infertile male and his mother were 46,Y,der(X)t(X;Y)(p22.33;q11.22) and 46,X,der(X)t(X;Y)(p22.33;q11.22), respectively. Short-stature-homeobox gene deletion was responsible for the short stature in both subjects. PAR aberrations and AZFc duplication may be a direct genetic risk factor for spermatogenesis. This report further supports the use of routine karyotype analysis, FISH-based technology, and array-CGH analysis to identify derivative chromosomes in a complex rearrangement.
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8
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Hughes JF, Skaletsky H, Pyntikova T, Koutseva N, Raudsepp T, Brown LG, Bellott DW, Cho TJ, Dugan-Rocha S, Khan Z, Kremitzki C, Fronick C, Graves-Lindsay TA, Fulton L, Warren WC, Wilson RK, Owens E, Womack JE, Murphy WJ, Muzny DM, Worley KC, Chowdhary BP, Gibbs RA, Page DC. Sequence analysis in Bos taurus reveals pervasiveness of X-Y arms races in mammalian lineages. Genome Res 2020; 30:1716-1726. [PMID: 33208454 PMCID: PMC7706723 DOI: 10.1101/gr.269902.120] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/28/2020] [Indexed: 12/28/2022]
Abstract
Studies of Y Chromosome evolution have focused primarily on gene decay, a consequence of suppression of crossing-over with the X Chromosome. Here, we provide evidence that suppression of X-Y crossing-over unleashed a second dynamic: selfish X-Y arms races that reshaped the sex chromosomes in mammals as different as cattle, mice, and men. Using super-resolution sequencing, we explore the Y Chromosome of Bos taurus (bull) and find it to be dominated by massive, lineage-specific amplification of testis-expressed gene families, making it the most gene-dense Y Chromosome sequenced to date. As in mice, an X-linked homolog of a bull Y-amplified gene has become testis-specific and amplified. This evolutionary convergence implies that lineage-specific X-Y coevolution through gene amplification, and the selfish forces underlying this phenomenon, were dominatingly powerful among diverse mammalian lineages. Together with Y gene decay, X-Y arms races molded mammalian sex chromosomes and influenced the course of mammalian evolution.
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Affiliation(s)
| | - Helen Skaletsky
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
| | | | | | - Terje Raudsepp
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA
| | - Laura G Brown
- Whitehead Institute, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
| | | | - Ting-Jan Cho
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
| | - Shannon Dugan-Rocha
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ziad Khan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Colin Kremitzki
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Catrina Fronick
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Tina A Graves-Lindsay
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Lucinda Fulton
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Wesley C Warren
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Richard K Wilson
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Elaine Owens
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA
| | - James E Womack
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA
| | - William J Murphy
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Kim C Worley
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Bhanu P Chowdhary
- College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, 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 02142, USA
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9
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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: 12] [Impact Index Per Article: 2.4] [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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10
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Teitz LS, Pyntikova T, Skaletsky H, Page DC. Selection Has Countered High Mutability to Preserve the Ancestral Copy Number of Y Chromosome Amplicons in Diverse Human Lineages. Am J Hum Genet 2018; 103:261-275. [PMID: 30075113 DOI: 10.1016/j.ajhg.2018.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/10/2018] [Indexed: 02/07/2023] Open
Abstract
Amplicons-large, highly identical segmental duplications-are a prominent feature of mammalian Y chromosomes. Although they encode genes essential for fertility, these amplicons differ vastly between species, and little is known about the selective constraints acting on them. Here, we develop computational tools to detect amplicon copy number with unprecedented accuracy from high-throughput sequencing data. We find that one-sixth (16.9%) of 1,216 males from the 1000 Genomes Project have at least one deleted or duplicated amplicon. However, each amplicon's reference copy number is scrupulously maintained among divergent branches of the Y chromosome phylogeny, including the ancient branch A00, indicating that the reference copy number is ancestral to all modern human Y chromosomes. Using phylogenetic analyses and simulations, we demonstrate that this pattern of variation is incompatible with neutral evolution and instead displays hallmarks of mutation-selection balance. We also observe cases of amplicon rescue, in which deleted amplicons are restored through subsequent duplications. These results indicate that, contrary to the lack of constraint suggested by the differences between species, natural selection has suppressed amplicon copy number variation in diverse human lineages.
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11
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Cost-effective high-throughput single-haplotype iterative mapping and sequencing for complex genomic structures. Nat Protoc 2018; 13:787-809. [PMID: 29565902 DOI: 10.1038/nprot.2018.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The reference sequences of structurally complex regions can be obtained only through highly accurate clone-based approaches. We and others have successfully used single-haplotype iterative mapping and sequencing (SHIMS) 1.0 to assemble structurally complex regions across the sex chromosomes of several vertebrate species and to allow for targeted improvements to the reference sequences of human autosomes. However, SHIMS 1.0 is expensive and time consuming, requiring resources that only a genome center can provide. Here we introduce SHIMS 2.0, an improved SHIMS protocol that allows even a small laboratory to generate high-quality reference sequence from complex genomic regions. Using a streamlined and parallelized library-preparation protocol, and taking advantage of inexpensive high-throughput short-read-sequencing technologies, a small laboratory with both molecular biology and bioinformatics experience can sequence and assemble 192 large-insert bacterial artificial chromosome (BAC) or fosmid clones in 1 week. In SHIMS 2.0, in contrast to other pooling strategies, each clone is sequenced with a unique barcode, thus enabling clones containing nearly identical sequences to be multiplexed in a single sequencing run and assembled separately. Relative to SHIMS 1.0, SHIMS 2.0 decreases the required cost and time by two orders of magnitude while preserving high sequencing accuracy.
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12
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de Sousa Filho EP, Christofolini DM, Barbosa CP, Glina S, Bianco B. Y chromosome microdeletions and varicocele as aetiological factors of male infertility: A cross-sectional study. Andrologia 2017; 50. [PMID: 29265486 DOI: 10.1111/and.12938] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2017] [Indexed: 02/01/2023] Open
Abstract
The pathogenic mechanisms by which varicocele disrupt spermatogenesis are not clearly understood. Over 30% of male infertility cases resulting from spermatogenic problems are associated with genetic abnormalities, and Y chromosome microdeletions are the second most frequent genetic cause. Here, we aimed to evaluate the frequency of Y chromosome microdeletion in infertile men with varicocele. A cross-sectional study comprising 51 infertile men with varicocele presenting spermatogenesis failures was performed. Y chromosome microdeletion research was made using polymerase chain reaction. Of the 51 men with infertility and varicocele, 35.3% (18/51) had nonobstructive azoospermia and 64.7% had severe oligozoospermia. Y chromosome microdeletion was found in two cases (3.9%): one patient had nonobstructive azoospermia and complete microdeletion of the AZFb and AZFc regions, and another patient had severe oligozoospermia and complete microdeletion of the AZFc region. Although in recent years, a genetic aetiology related to Y chromosome microdeletions has become a major cause of infertility in males with spermatogenesis failures, in this study, the varicocele was the clinical cause of seminal abnormalities that could lead to infertility, suggesting that both varicocele and Y chromosome microdeletion aetiologies can present, alone or combined, as factors of male infertility.
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Affiliation(s)
- E P de Sousa Filho
- Faculdade de Medicina do ABC, Department of Collective Health, Human Reproduction and Genetics Center, Santo André, São Paulo, Brazil
| | - D M Christofolini
- Faculdade de Medicina do ABC, Department of Collective Health, Human Reproduction and Genetics Center, Santo André, São Paulo, Brazil
| | - C P Barbosa
- Faculdade de Medicina do ABC, Department of Collective Health, Human Reproduction and Genetics Center, Santo André, São Paulo, Brazil
| | - S Glina
- Faculdade de Medicina do ABC, Department of Surgery, Discipline of Urology, Santo André, São Paulo, Brazil
| | - B Bianco
- Faculdade de Medicina do ABC, Department of Collective Health, Human Reproduction and Genetics Center, Santo André, São Paulo, Brazil
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13
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García-Souto D, Pérez-García C, Pasantes JJ. Are Pericentric Inversions Reorganizing Wedge Shell Genomes? Genes (Basel) 2017; 8:genes8120370. [PMID: 29215567 PMCID: PMC5748688 DOI: 10.3390/genes8120370] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 11/30/2017] [Accepted: 12/01/2017] [Indexed: 11/27/2022] Open
Abstract
Wedge shells belonging to the Donacidae family are the dominant bivalves in exposed beaches in almost all areas of the world. Typically, two or more sympatric species of wedge shells differentially occupy intertidal, sublittoral, and offshore coastal waters in any given locality. A molecular cytogenetic analysis of two sympatric and closely related wedge shell species, Donax trunculus and Donax vittatus, was performed. Results showed that the karyotypes of these two species were both strikingly different and closely alike; whilst metacentric and submetacentric chromosome pairs were the main components of the karyotype of D. trunculus, 10–11 of the 19 chromosome pairs were telocentric in D. vittatus, most likely as a result of different pericentric inversions. GC-rich heterochromatic bands were present in both species. Furthermore, they showed coincidental 45S ribosomal RNA (rRNA), 5S rRNA and H3 histone gene clusters at conserved chromosomal locations, although D. trunculus had an additional 45S rDNA cluster. Intraspecific pericentric inversions were also detected in both D. trunculus and D. vittatus. The close genetic similarity of these two species together with the high degree of conservation of the 45S rRNA, 5S rRNA and H3 histone gene clusters, and GC-rich heterochromatic bands indicate that pericentric inversions contribute to the karyotype divergence in wedge shells.
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Affiliation(s)
- Daniel García-Souto
- Dpto. Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, E-36310 Vigo, Spain.
| | | | - Juan J Pasantes
- Dpto. Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, E-36310 Vigo, Spain.
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14
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Abstract
The great apes (orangutans, gorillas, chimpanzees, bonobos and humans) descended from a common ancestor around 13 million years ago, and since then their sex chromosomes have followed very different evolutionary paths. While great-ape X chromosomes are highly conserved, their Y chromosomes, reflecting the general lability and degeneration of this male-specific part of the genome since its early mammalian origin, have evolved rapidly both between and within species. Understanding great-ape Y chromosome structure, gene content and diversity would provide a valuable evolutionary context for the human Y, and would also illuminate sex-biased behaviours, and the effects of the evolutionary pressures exerted by different mating strategies on this male-specific part of the genome. High-quality Y-chromosome sequences are available for human and chimpanzee (and low-quality for gorilla). The chromosomes differ in size, sequence organisation and content, and while retaining a relatively stable set of ancestral single-copy genes, show considerable variation in content and copy number of ampliconic multi-copy genes. Studies of Y-chromosome diversity in other great apes are relatively undeveloped compared to those in humans, but have nevertheless provided insights into speciation, dispersal, and mating patterns. Future studies, including data from larger sample sizes of wild-born and geographically well-defined individuals, and full Y-chromosome sequences from bonobos, gorillas and orangutans, promise to further our understanding of population histories, male-biased behaviours, mutation processes, and the functions of Y-chromosomal genes.
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15
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Masoudi R, Mazaheri-Asadi L, Khorasani S. Partial and complete microdeletions of Y chromosome in infertile males from South of Iran. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2016; 5:247-255. [PMID: 28261628 PMCID: PMC5326488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Y chromosome microdeletions are the second genetic cause of male infertility. The incidence of Y chromosome microdeletions can vary considerably depending on several factors, including patient selection criteria, population composition, and diagnostic protocols. They are associated with spermatogenic failure and lead to azoospermia or oligozoospermia. The advance in assisted reproductive technology and intracytoplasmic sperm injection, and the possibility of genetic defect transmission to the next generation make it necessary to improve our knowledge about the various factors leading to spermatogenic impairment. This study was designed to determine the frequency of microdeletions of Y chromosome in a population from South of Iran. 81 infertile males with non-obstructive azoospermia or oligozoospermia were selected. Multiplex PCR using several STS markers was carried out to detect the complete or partial microdeletions. The frequency of both complete and partial microdeletions in men with azoospermia or severe oligozoospermia was 7.4%. All microdeletions were observed in AZFc region. There was 1.25% complete microdeletions and after excluding complete microdeletions, we detected 5% gr/gr and 1.25% b2/b3 microdeletions. In our control group of fertile males, 4% gr/gr microdeletions was detected while there was no b2/b3 microdeletions. We concluded that there is a low frequency of Y chromosome microdeletions in a population of infertile males from South of Iran. b2/b3 microdeletions was detected only in infertile males and not in the control group. Screening a population with larger sample size is necessary to determine the involvement of this partial microdeletion in infertility of this population.
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Affiliation(s)
- Raheleh Masoudi
- Corresponding Author: Department of Biology, College of Sciences, Shiraz University, Shiraz , Iran Tel: +98 71-36137656, Fax:+98 71-32280916, E. mail:
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16
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Pathak D, Yadav SK, Rawal L, Ali S. Mutational landscape of the human Y chromosome-linked genes and loci in patients with hypogonadism. J Genet 2016; 94:677-87. [PMID: 26690523 DOI: 10.1007/s12041-015-0582-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Sex chromosome-related anomalies engender plethora of conditions leading to male infertility. Hypogonadotropic hypogonadism (HH) is a rare but well-known cause of male infertility. Present study was conducted to ascertain possible consensus on the alterations of the Y-linked genes and loci in males representing hypogonadism (H), which in turn culminate in reproductive dysfunction. A total of nineteen 46, XY males, clinically diagnosed with H (11 representative HH adults and eight prepubertal boys suspected of having HH) were included in the study. Sequence-tagged site screening,SRY gene sequencing,fluorescence in situ hybridization mapping (FISH), copy number and relative expression studies by real-time PCR were conducted to uncover the altered status of the Y chromosome in the patients. The result showed random microdeletions within the AZFa (73%)/b (78%) and c(26%) regions. Sequencing of the SRY gene showed nucleotide variations within and outside of the HMG box in four males (21%). FISH uncovered mosaicism for SRY, AMELY,DAZ genes and DYZ1 arrays, structural rearrangement for AMELY (31%) and duplication of DAZ (57%) genes. Copy number variation for seven Y-linked genes (2-8 rounds of duplication), DYZ1 arrays (495-6201 copies) and differential expression of SRY,UTY and VCY in the patients' blood were observed. Present work demonstrates the organizational vulnerability of several Y-linked genes in H males. These results are envisaged to be useful during routine diagnosis of H patients.
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Affiliation(s)
- Deepali Pathak
- Molecular Genetics Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067,India.
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17
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Ghenu AH, Bolker BM, Melnick DJ, Evans BJ. Multicopy gene family evolution on primate Y chromosomes. BMC Genomics 2016; 17:157. [PMID: 26925773 PMCID: PMC4772468 DOI: 10.1186/s12864-015-2187-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 11/02/2015] [Indexed: 12/12/2022] Open
Abstract
Background The primate Y chromosome is distinguished by a lack of inter-chromosomal recombination along most of its length, extensive gene loss, and a prevalence of repetitive elements. A group of genes on the male-specific portion of the Y chromosome known as the “ampliconic genes” are present in multiple copies that are sometimes part of palindromes, and that undergo a form of intra-chromosomal recombination called gene conversion, wherein the nucleotides of one copy are homogenized by those of another. With the aim of further understanding gene family evolution of these genes, we collected nucleotide sequence and gene copy number information for several species of papionin monkey. We then tested for evidence of gene conversion, and developed a novel statistical framework to evaluate alternative models of gene family evolution using our data combined with other information from a human, a chimpanzee, and a rhesus macaque. Results Our results (i) recovered evidence for several novel examples of gene conversion in papionin monkeys and indicate that (ii) ampliconic gene families evolve faster than autosomal gene families and than single-copy genes on the Y chromosome and that (iii) Y-linked singleton and autosomal gene families evolved faster in humans and chimps than they do in the other Old World Monkey lineages we studied. Conclusions Rapid evolution of ampliconic genes cannot be attributed solely to residence on the Y chromosome, nor to variation between primate lineages in the rate of gene family evolution. Instead other factors, such as natural selection and gene conversion, appear to play a role in driving temporal and genomic evolutionary heterogeneity in primate gene families. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2187-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana-Hermina Ghenu
- Biology Department, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada.
| | - Benjamin M Bolker
- Biology Department, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada.,Department of Mathematics & Statistics, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada
| | - Don J Melnick
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, 10th Floor Schermerhorn Extension, New York, 10027, USA
| | - Ben J Evans
- Biology Department, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Canada.
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18
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Recombination between the mouse Y chromosome short arm and an additional Y short arm-derived chromosomal segment attached distal to the X chromosome PAR. Chromosoma 2015; 125:177-88. [PMID: 26596988 PMCID: PMC4830887 DOI: 10.1007/s00412-015-0559-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 11/09/2015] [Accepted: 11/11/2015] [Indexed: 11/02/2022]
Abstract
In a male mouse, meiosis markers of processed DNA double strand breaks (DSBs) such as DMC1 and RAD51 are regularly seen in the non-PAR region of the X chromosome; these disappear late in prophase prior to entry into the first meiotic metaphase. Marker evidence for DSBs occurring in the non-PAR region of the Y chromosome is limited. Nevertheless, historically it has been documented that recombination can occur within the mouse Y short arm (Yp) when an additional Yp segment is attached distal to the X and/or the Y pseudoautosomal region (PAR). A number of recombinants identified among offsprings involved unequal exchanges involving repeated DNA segments; however, equal exchanges will have frequently been missed because of the paucity of markers to differentiate between the two Yp segments. Here, we discuss this historical data and present extensive additional data obtained for two mouse models with Yp additions to the X PAR. PCR genotyping enabled identification of a wider range of potential recombinants; the proportions of Yp exchanges identified among the recombinants were 9.7 and 22.4 %. The frequency of these exchanges suggests that the Yp segment attached to the X PAR is subject to the elevated level of recombinational DSBs that characterizes the PAR.
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19
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Hipp LE, Mohnach LH, Wei S, Thomas IH, Elhassan ME, Sandberg DE, Quint EH, Keegan CE. Isodicentric Y mosaicism involving a 46, XX cell line: Implications for management. Am J Med Genet A 2015; 170A:233-8. [PMID: 26407917 DOI: 10.1002/ajmg.a.37403] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 09/08/2015] [Indexed: 01/14/2023]
Abstract
Carriers of isodicentric Y (idicY) mosaicism exhibit a wide range of clinical features, including short stature, gonadal abnormalities, and external genital anomalies. However, the phenotypic spectrum for individuals carrying an idicY and a 46, XX cell line is less clearly defined. A more complete description of the phenotype related to idicY is thus essential to guide management related to pubertal development, fertility, and gonadoblastoma risk in mosaic carriers. Findings from the evaluation of twin females with an abnormal karyotype, 48, XX, +idic(Yq) x2/47, XX, +idic(Yq)/46, XX, are presented to highlight the importance of interdisciplinary care in the management of multifaceted disorders of sex development.
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Affiliation(s)
- Lauren E Hipp
- Department of Internal Medicine, Molecular Medicine & Genetics, University of Michigan, Ann Arbor, Michigan
| | - Lauren H Mohnach
- Department of Obstetrics & Gynecology, University of Michigan, Ann Arbor, Michigan.,Department of Urology, University of Michigan, Ann Arbor, Michigan
| | - Sainan Wei
- Department of Pediatrics and Human Development, Michigan State University, East Lansing, Michigan
| | - Inas H Thomas
- Division of Endocrinology, Department of Pediatrics, University of Michigan, Ann Arbor, Michigan
| | - Maha E Elhassan
- Division of Endocrinology, Department of Pediatrics, University of Michigan, Ann Arbor, Michigan
| | - David E Sandberg
- Division of Pediatric Psychology and Child Health Evaluation & Research (CHEAR) Unit, Department of Pediatrics, University of Michigan, Ann Arbor, Michigan
| | - Elisabeth H Quint
- Department of Obstetrics & Gynecology, University of Michigan, Ann Arbor, Michigan
| | - Catherine E Keegan
- Division of Genetics, Department of Pediatrics, University of Michigan, Ann Arbor, Michigan.,Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
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20
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FISH and array CGH characterization of de novo derivative Y chromosome (Yq duplication and partial Yp deletion) in an azoospermic male. Reprod Biomed Online 2015; 31:217-24. [PMID: 26096031 DOI: 10.1016/j.rbmo.2015.04.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 04/17/2015] [Accepted: 04/21/2015] [Indexed: 12/12/2022]
Abstract
This study presents a 28-year-old infertile male who was referred to the cytogenetic laboratory for chromosomal analysis after 4 years of regular unprotected intercourse in whom non-obstructive azoospermia was revealed. Standard cytogenetic G-banding was performed on metaphase spreads and a de-novo karyotype 46,X,der(Y)(q11.22;p11.3) was identified. This analysis was followed by flourescence in-situ hybridization(FISH) and array comparative genomic hybridization (aCGH). Finally, the patient's karyotype was identified as 46,X,der(Y)(qter→q11.221::p11.31→qter).ish der(Y) (qter+,pter-,SHOX+,SRY+,Ycen+,DYZ3+;DYZ1+,qter+).arrYq11.221q12(14,448,863-59,288,511) x2, Yp11.32p11.31(104,062-266,388) x0. It is proposed that de-novo derivative monocentric Y chromosome with duplicated region Y qter→q11.221::p11.31→qter with partial deletion of Yp PAR1 region most probably can perturb the conjugation of sex chromosomes during first meiotic division of spermatogenic arrested differentiation (development).
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21
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Federici F, Mulugeta E, Schoenmakers S, Wassenaar E, Hoogerbrugge JW, van der Heijden GW, van Cappellen WA, Slotman JA, van IJcken WFJ, Laven JSE, Grootegoed JA, Baarends WM. Incomplete meiotic sex chromosome inactivation in the domestic dog. BMC Genomics 2015; 16:291. [PMID: 25884295 PMCID: PMC4399420 DOI: 10.1186/s12864-015-1501-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/30/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In mammalian meiotic prophase, homologous chromosome recognition is aided by formation and repair of programmed DNA double-strand breaks (DSBs). Subsequently, stable associations form through homologous chromosome synapsis. In male mouse meiosis, the largely heterologous X and Y chromosomes synapse only in their short pseudoautosomal regions (PARs), and DSBs persist along the unsynapsed non-homologous arms of these sex chromosomes. Asynapsis of these arms and the persistent DSBs then trigger transcriptional silencing through meiotic sex chromosome inactivation (MSCI), resulting in formation of the XY body. This inactive state is partially maintained in post-meiotic haploid spermatids (postmeiotic sex chromatin repression, PSCR). For the human, establishment of MSCI and PSCR have also been reported, but X-linked gene silencing appears to be more variable compared to mouse. To gain more insight into the regulation and significance of MSCI and PSCR among different eutherian species, we have performed a global analysis of XY pairing dynamics, DSB repair, MSCI and PSCR in the domestic dog (Canis lupus familiaris), for which the complete genome sequence has recently become available, allowing a thorough comparative analyses. RESULTS In addition to PAR synapsis between X and Y, we observed extensive self-synapsis of part of the dog X chromosome, and rapid loss of known markers of DSB repair from that part of the X. Sequencing of RNA from purified spermatocytes and spermatids revealed establishment of MSCI. However, the self-synapsing region of the X displayed higher X-linked gene expression compared to the unsynapsed area in spermatocytes, and was post-meiotically reactivated in spermatids. In contrast, genes in the PAR, which are expected to escape MSCI, were expressed at very low levels in both spermatocytes and spermatids. Our comparative analysis was then used to identify two X-linked genes that may escape MSCI in spermatocytes, and 21 that are specifically re-activated in spermatids of human, mouse and dog. CONCLUSIONS Our data indicate that MSCI is incomplete in the dog. This may be partially explained by extensive, but transient, self-synapsis of the X chromosome, in association with rapid completion of meiotic DSB repair. In addition, our comparative analysis identifies novel candidate male fertility genes.
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Affiliation(s)
- Federica Federici
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Eskeatnaf Mulugeta
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands. .,Present address: Institut Curie, Genetics and Developmental Biology, Unit 11 et 13 rue Pierre et Marie Curie, 75248, Paris, Cedex 05, France.
| | - Sam Schoenmakers
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands. .,Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Evelyne Wassenaar
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Jos W Hoogerbrugge
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Godfried W van der Heijden
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands. .,Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Wiggert A van Cappellen
- Department of Pathology, Erasmus Optical Imaging Centre, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Johan A Slotman
- Department of Pathology, Erasmus Optical Imaging Centre, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Wilfred F J van IJcken
- Erasmus Center for Biomics, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
| | - Joop S E Laven
- Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - J Anton Grootegoed
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Willy M Baarends
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
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White MA, Kitano J, Peichel CL. Purifying Selection Maintains Dosage-Sensitive Genes during Degeneration of the Threespine Stickleback Y Chromosome. Mol Biol Evol 2015; 32:1981-95. [PMID: 25818858 DOI: 10.1093/molbev/msv078] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Sex chromosomes are subject to unique evolutionary forces that cause suppression of recombination, leading to sequence degeneration and the formation of heteromorphic chromosome pairs (i.e., XY or ZW). Although progress has been made in characterizing the outcomes of these evolutionary processes on vertebrate sex chromosomes, it is still unclear how recombination suppression and sequence divergence typically occur and how gene dosage imbalances are resolved in the heterogametic sex. The threespine stickleback fish (Gasterosteus aculeatus) is a powerful model system to explore vertebrate sex chromosome evolution, as it possesses an XY sex chromosome pair at relatively early stages of differentiation. Using a combination of whole-genome and transcriptome sequencing, we characterized sequence evolution and gene expression across the sex chromosomes. We uncovered two distinct evolutionary strata that correspond with known structural rearrangements on the Y chromosome. In the oldest stratum, only a handful of genes remain, and these genes are under strong purifying selection. By comparing sex-linked gene expression with expression of autosomal orthologs in an outgroup, we show that dosage compensation has not evolved in threespine sticklebacks through upregulation of the X chromosome in males. Instead, in the oldest stratum, the genes that still possess a Y chromosome allele are enriched for genes predicted to be dosage sensitive in mammals and yeast. Our results suggest that dosage imbalances may have been avoided at haploinsufficient genes by retaining function of the Y chromosome allele through strong purifying selection.
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Affiliation(s)
- Michael A White
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Catherine L Peichel
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
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