Histology and Sperm Retrieval Among Men with Y Chromosome Microdeletions
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Binding Specificities of Human RNA Binding Proteins Towards Structured
bioRxiv preprint doi: https://doi.org/10.1101/317909; this version posted March 1, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Binding specificities of human RNA binding proteins towards structured and linear 2 RNA sequences 3 4 Arttu Jolma1,#, Jilin Zhang1,#, Estefania Mondragón4,#, Teemu Kivioja2, Yimeng Yin1, 5 Fangjie Zhu1, Quaid Morris5,6,7,8, Timothy R. Hughes5,6, Louis James Maher III4 and Jussi 6 Taipale1,2,3,* 7 8 9 AUTHOR AFFILIATIONS 10 11 1Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden 12 2Genome-Scale Biology Program, University of Helsinki, Helsinki, Finland 13 3Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom 14 4Department of Biochemistry and Molecular Biology and Mayo Clinic Graduate School of 15 Biomedical Sciences, Mayo Clinic College of Medicine and Science, Rochester, USA 16 5Department of Molecular Genetics, University of Toronto, Toronto, Canada 17 6Donnelly Centre, University of Toronto, Toronto, Canada 18 7Edward S Rogers Sr Department of Electrical and Computer Engineering, University of 19 Toronto, Toronto, Canada 20 8Department of Computer Science, University of Toronto, Toronto, Canada 21 #Authors contributed equally 22 *Correspondence: [email protected] 23 24 25 SUMMARY 26 27 Sequence specific RNA-binding proteins (RBPs) control many important 28 processes affecting gene expression. They regulate RNA metabolism at multiple 29 levels, by affecting splicing of nascent transcripts, RNA folding, base modification, 30 transport, localization, translation and stability. Despite their central role in most 31 aspects of RNA metabolism and function, most RBP binding specificities remain 32 unknown or incompletely defined. -
DAZ (Z6Q): Sc-100705
SANTA CRUZ BIOTECHNOLOGY, INC. DAZ (Z6Q): sc-100705 BACKGROUND RECOMMENDED SUPPORT REAGENTS Spermatogenesis is the process by which male spermatogonia develop into To ensure optimal results, the following support reagents are recommended: mature spermatozoa. DAZ (deleted in azoospermia) are RNA-binding proteins 1) Western Blotting: use m-IgGk BP-HRP: sc-516102 or m-IgGk BP-HRP (Cruz that play an essential role in spermatogenesis. DAZ proteins influence the Marker): sc-516102-CM (dilution range: 1:1000-1:10000), Cruz Marker™ first stages of spermatogenesis and the maintenance of germ cell populations. Molecular Weight Standards: sc-2035, UltraCruz® Blocking Reagent: DAZ proteins (DAZ1, DAZ2, DAZ3, DAZ4 and DAZ5) are encoded by separate sc-516214 and Western Blotting Luminol Reagent: sc-2048. 2) Immunopre- genes on chromosome Y, each of which contain an AZFc domain in their cod- cipitation: use Protein A/G PLUS-Agarose: sc-2003 (0.5 ml agarose/2.0 ml). ing region. DAZ proteins are localized to the nucleus of spermatogonia, but 3) Immunofluorescence: use m-IgGk BP-FITC: sc-516140 or m-IgGk BP-PE: relocate to the cytoplasm during meiosis. DAZ proteins contain an RRM (RNA sc-516141 (dilution range: 1:50-1:200) with UltraCruz® Mounting Medium: recognition motif) domain that may regulate mRNA translation by binding sc-24941 or UltraCruz® Hard-set Mounting Medium: sc-359850. 4) Immuno- to the 3' UTR. Deletions in the genes encoding DAZ proteins may cause histochemistry: use m-IgGk BP-HRP: sc-516102 with DAB, 50X: sc-24982 azoospermia or oligospermia which can lead to male infertility. -
Partial Azfc Deletions and Duplications: Clinical Correlates in the Italian Population
FLORE Repository istituzionale dell'Università degli Studi di Firenze Partial AZFc deletions and duplications: clinical correlates in the Italian population. Questa è la Versione finale referata (Post print/Accepted manuscript) della seguente pubblicazione: Original Citation: Partial AZFc deletions and duplications: clinical correlates in the Italian population / Giachini C; Laface I; Guarducci E; Balercia G; Forti G; Krausz C.. - In: HUMAN GENETICS. - ISSN 0340-6717. - STAMPA. - 124(2008), pp. 399-410. Availability: This version is available at: 2158/333113 since: 2019-11-07T18:24:55Z Terms of use: Open Access La pubblicazione è resa disponibile sotto le norme e i termini della licenza di deposito, secondo quanto stabilito dalla Policy per l'accesso aperto dell'Università degli Studi di Firenze (https://www.sba.unifi.it/upload/policy-oa-2016-1.pdf) Publisher copyright claim: (Article begins on next page) 28 September 2021 Hum Genet (2008) 124:399–410 DOI 10.1007/s00439-008-0561-1 ORIGINAL INVESTIGATION Partial AZFc deletions and duplications: clinical correlates in the Italian population Claudia Giachini · Ilaria Laface · Elena Guarducci · Giancarlo Balercia · Gianni Forti · Csilla Krausz Received: 7 August 2008 / Accepted: 9 September 2008 / Published online: 21 September 2008 © Springer-Verlag 2008 Abstract The role of partial AZFc deletions of the Y potential methodological and selection biases were care- chromosome in spermatogenic impairment is currently fully avoided to detect the clinical signiWcance of partial debated. Recently, it was also reported that duplications of AZFc deletions and duplications. Our study provides strong the same region are associated with oligozoospermia in evidence that gr/gr deletion is a risk factor for impaired Han-Chinese men. -
Genetics of Azoospermia
International Journal of Molecular Sciences Review Genetics of Azoospermia Francesca Cioppi , Viktoria Rosta and Csilla Krausz * Department of Biochemical, Experimental and Clinical Sciences “Mario Serio”, University of Florence, 50139 Florence, Italy; francesca.cioppi@unifi.it (F.C.); viktoria.rosta@unifi.it (V.R.) * Correspondence: csilla.krausz@unifi.it Abstract: Azoospermia affects 1% of men, and it can be due to: (i) hypothalamic-pituitary dysfunction, (ii) primary quantitative spermatogenic disturbances, (iii) urogenital duct obstruction. Known genetic factors contribute to all these categories, and genetic testing is part of the routine diagnostic workup of azoospermic men. The diagnostic yield of genetic tests in azoospermia is different in the different etiological categories, with the highest in Congenital Bilateral Absence of Vas Deferens (90%) and the lowest in Non-Obstructive Azoospermia (NOA) due to primary testicular failure (~30%). Whole- Exome Sequencing allowed the discovery of an increasing number of monogenic defects of NOA with a current list of 38 candidate genes. These genes are of potential clinical relevance for future gene panel-based screening. We classified these genes according to the associated-testicular histology underlying the NOA phenotype. The validation and the discovery of novel NOA genes will radically improve patient management. Interestingly, approximately 37% of candidate genes are shared in human male and female gonadal failure, implying that genetic counselling should be extended also to female family members of NOA patients. Keywords: azoospermia; infertility; genetics; exome; NGS; NOA; Klinefelter syndrome; Y chromosome microdeletions; CBAVD; congenital hypogonadotropic hypogonadism Citation: Cioppi, F.; Rosta, V.; Krausz, C. Genetics of Azoospermia. 1. Introduction Int. J. Mol. Sci. -
Molecular Pathogenesis of a Malformation Syndrome Associated with a Pericentric Chromosome 2 Inversion
UNIVERSIDADE DE LISBOA FACULDADE DE CIÊNCIAS DEPARTAMENTO DE BIOLOGIA ANIMAL Molecular pathogenesis of a malformation syndrome associated with a pericentric chromosome 2 inversion Manuela Pinto Cardoso Mestrado em Biologia Humana e do Ambiente Dissertação orientada por: Doutor Dezsö David Doutora Deodália Dias 2017 ACKNOWLEDGEMENTS I would like to say “thank you!” to all the people that contributed in some way to this thesis. First and foremost, I would like to express my deepest gratitude to my supervisor, Dr. Dezsö David, for giving me the opportunity to work in his research group and for everything he taught me. Without his mentorship I would have never learned so much. I am grateful for Prof. Deodália Dias’s encouragement and support in all these years that I have been under her wings. I would like to extent my thanks to everyone at the National Health Institute Dr. Ricardo Jorge, for their continuous help in all stages of this thesis. To the team at Harvard Medical School, thank you for the technical assistance, and in special Dr. Cynthia Morton and Dr. Michael Talkowski. I am also grateful to Dr. Rui Gonçalves and Dr. João Freixo, who accompanied this case study and shared their medical knowledge. Of course, I am grateful for the family members for their involvement in this study. To my lab mates, a shout-out to them all! I really hold them dear for their help and the many laughs we shared every day. Thank you Mariana for being there literally since day one and for playing the role of a more mature counterpart. -
Development of Novel Analysis and Data Integration Systems to Understand Human Gene Regulation
Development of novel analysis and data integration systems to understand human gene regulation Dissertation zur Erlangung des Doktorgrades Dr. rer. nat. der Fakult¨atf¨urMathematik und Informatik der Georg-August-Universit¨atG¨ottingen im PhD Programme in Computer Science (PCS) der Georg-August University School of Science (GAUSS) vorgelegt von Raza-Ur Rahman aus Pakistan G¨ottingen,April 2018 Prof. Dr. Stefan Bonn, Zentrum f¨urMolekulare Neurobiologie (ZMNH), Betreuungsausschuss: Institut f¨urMedizinische Systembiologie, Hamburg Prof. Dr. Tim Beißbarth, Institut f¨urMedizinische Statistik, Universit¨atsmedizin, Georg-August Universit¨at,G¨ottingen Prof. Dr. Burkhard Morgenstern, Institut f¨urMikrobiologie und Genetik Abtl. Bioinformatik, Georg-August Universit¨at,G¨ottingen Pr¨ufungskommission: Prof. Dr. Stefan Bonn, Zentrum f¨urMolekulare Neurobiologie (ZMNH), Referent: Institut f¨urMedizinische Systembiologie, Hamburg Prof. Dr. Tim Beißbarth, Institut f¨urMedizinische Statistik, Universit¨atsmedizin, Korreferent: Georg-August Universit¨at,G¨ottingen Prof. Dr. Burkhard Morgenstern, Weitere Mitglieder Institut f¨urMikrobiologie und Genetik Abtl. Bioinformatik, der Pr¨ufungskommission: Georg-August Universit¨at,G¨ottingen Prof. Dr. Carsten Damm, Institut f¨urInformatik, Georg-August Universit¨at,G¨ottingen Prof. Dr. Florentin W¨org¨otter, Physikalisches Institut Biophysik, Georg-August-Universit¨at,G¨ottingen Prof. Dr. Stephan Waack, Institut f¨urInformatik, Georg-August Universit¨at,G¨ottingen Tag der m¨undlichen Pr¨ufung: der 30. M¨arz2018 -
Hypomethylation of the DAZ3 Promoter in Idiopathic Asthenospermia: a Screening Tool for Liquid Biopsy Shichang Zhang1,3, Li Xu2,3, Mengyao Yu1 & Jiexin Zhang1*
www.nature.com/scientificreports OPEN Hypomethylation of the DAZ3 promoter in idiopathic asthenospermia: a screening tool for liquid biopsy Shichang Zhang1,3, Li Xu2,3, Mengyao Yu1 & Jiexin Zhang1* Given the role of the deleted in azoospermia gene in male infertility, whether the somatic deleted in azoospermia methylation status is associated with idiopathic asthenospermia should be determined. To investigate the methylation levels of the deleted in azoospermia promoter in peripheral white blood cells from idiopathic asthenospermia patients relative to those in normozoospermia controls, 61 ethylene diamine tetraacetic acid anticoagulant blood samples were drawn from all participants for DNA isolation. The deleted in azoospermia promoter methylation ratio was detected by MassARRAY-based methylation quantifcation and confrmed by quantitative methylation-specifc polymerase chain reaction. A MassARRAY-based methylation analysis showed that the deleted in azoospermia 3 promoter (0 to − 2 kbp) was signifcantly hypomethylated in peripheral white blood cells from idiopathic asthenospermia males, specifcally one CpG site (− 246 to − 247). Quantitative methylation-specifc polymerase chain reaction data further confrmed that the methylation level of the deleted in azoospermia 3 promoter region in idiopathic asthenospermia patients was signifcantly lower than that in normozoospermia males. The area under the receiver operating characteristic curve determined by quantitative methylation-specifc polymerase chain reaction was 0.737 (95% confdence interval: 0.552 to 0.924), with a sensitivity of 53.9% and a specifcity of 88.2% at a cut- of level of 74.7%. Therefore, our results suggested that methylation ratio detection of the deleted in azoospermia 3 promoter region by real-time polymerase chain reaction assay is a promising and feasible tool for liquid biopsy in the clinical laboratories. -
Binding Specificities of Human RNA Binding Proteins Towards Structured and Linear RNA Sequences
bioRxiv preprint doi: https://doi.org/10.1101/317909; this version posted May 16, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Binding specificities of human RNA binding proteins towards structured and linear 2 RNA sequences 3 4 Arttu Jolma1,#, Jilin Zhang1,#, Estefania Mondragón4,#, Teemu Kivioja2, Yimeng Yin1, 5 Fangjie Zhu1, Quaid Morris5,6,7,8, Timothy R. Hughes5,6, Louis James Maher III4 and Jussi 6 Taipale1,2,3,* 7 8 9 AUTHOR AFFILIATIONS 10 11 1Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden 12 2Genome-Scale Biology Program, University of Helsinki, Helsinki, Finland 13 3Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom 14 4Department of Biochemistry and Molecular Biology and Mayo Clinic Graduate School of 15 Biomedical Sciences, Mayo Clinic College of Medicine and Science, Rochester, USA 16 5Department of Molecular Genetics, University of Toronto, Toronto, Canada 17 6Donnelly Centre, University of Toronto, Toronto, Canada 18 7Edward S Rogers Sr Department of Electrical and Computer Engineering, University of 19 Toronto, Toronto, Canada 20 8Department of Computer Science, University of Toronto, Toronto, Canada 21 22 #Authors contributed equally 23 *Correspondence: [email protected] 24 25 26 ABSTRACT 27 28 Sequence specific RNA-binding proteins (RBPs) control many important 29 processes affecting gene expression. They regulate RNA metabolism at multiple 30 levels, by affecting splicing of nascent transcripts, RNA folding, base modification, 31 transport, localization, translation and stability. Despite their central role in most 32 aspects of RNA metabolism and function, most RBP binding specificities remain 33 unknown or incompletely defined. -
Molecular Characterization of Some Genetic Factors Controlling Spermatogenesis in Egyptian Patients with Male Infertility
IJIFM 10.5005/jp-journals-10016-1045 RESEARCHMolecular ARTICLECharacterization of Some Genetic Factors Controlling Spermatogenesis in Egyptian Patients with Male Infertility Molecular Characterization of Some Genetic Factors Controlling Spermatogenesis in Egyptian Patients with Male Infertility Alaaeldin Gamal Fayez, Amr Saad El-Sayed, Mohamed Ali El-Desouky, Waheba Ahmed Zarouk, Alaa Khalil Kamel, Ibrahim Mohamed Fahmi, Mona Omar El-Ruby ABSTRACT frequencies of Y chromosome microdeletion, definitely in Men with severe infertility suffer a high risk of Y chromosome azoospermia factor (AZF), in Egyptian nonobstructive deletion, hence screening for these cases is recommended prior azoospermic (NOA) infertile men. Furthermore, the present to treatment with assisted reproduction. Our study aimed to study was designed to determine the frequency of copy investigate and detect the azoospermia factor (AZF) region number variations of one of testis specific genes named deletion, rearrangement and deleted azoospermia (DAZ) gene deleted azoospermia (DAZ) gene that is confirmed by AZFc copy number variations in Egyptian azoospermic infertile men. This was tested on 54 Egyptian nonobstructive azoospermic rearrangement. (NOA) infertile men, with age ranged from 21 to 45 years (mean: 31.4 ± 6.1 years), by STS ± multiplex PCR using a set of MATERIALS AND METHODS 14 sequence tagged sites (STSs) from three different regions of the Y chromosome: AZFa, AZFb, AZFc and sY587/DraI PCR- Male subjects with primary infertility attending the clinical RFLP assay to determine DAZ copy number variations. The genetics clinic at the National Research Centre (NRC) and results revealed a significant prevalence of AZFc subtypes andrology clinic at the Kasr Al Ainy Hospital, Cairo deletion and reduced DAZ gene dosage in Egyptian University (Egypt), were enrolled in the present study after azoospermic cases affecting Y chromosome deletions. -
Rabbit Anti-DAZ4/FITC Conjugated Antibody
SunLong Biotech Co.,LTD Tel: 0086-571- 56623320 Fax:0086-571- 56623318 E-mail:[email protected] www.sunlongbiotech.com Rabbit Anti-DAZ4/FITC Conjugated antibody SL13609R-FITC Product Name: Anti-DAZ4/FITC Chinese Name: FITC标记的无精症缺失基因4抗体 Alias: DAZ4; Deleted in azoospermia 4; Deleted in azoospermia protein 4; DAZ4_HUMAN. Organism Species: Rabbit Clonality: Polyclonal React Species: Human,Mouse,Rat,Dog,Pig,Cow,Horse,Sheep, ICC=1:50-200IF=1:50-200 Applications: not yet tested in other applications. optimal dilutions/concentrations should be determined by the end user. Molecular weight: 65kDa Form: Lyophilized or Liquid Concentration: 1mg/ml immunogen: KLH conjugated synthetic peptide derived from human DAZ4 Lsotype: IgG Purification: affinity purified by Protein A Storage Buffer: 0.01M TBS(pH7.4) with 1% BSA, 0.03% Proclin300 and 50% Glycerol. Store at -20 °C for one year. Avoid repeated freeze/thaw cycles. The lyophilized antibodywww.sunlongbiotech.com is stable at room temperature for at least one month and for greater than a year Storage: when kept at -20°C. When reconstituted in sterile pH 7.4 0.01M PBS or diluent of antibody the antibody is stable for at least two weeks at 2-4 °C. background: Spermatogenesis is the process by which male spermatogonia develop into mature spermatozoa. DAZ (deleted in azoospermia) are RNA-binding proteins that play an essential role in spermatogenesis. DAZ proteins influence the first stages of spermatogenesis and the maintenance of germ cell populations. DAZ proteins (DAZ1, Product Detail: DAZ2, DAZ3, DAZ4 and DAZ5) are encoded by separate genes on chromosome Y, each of which contain an AZFc domain in their coding region. -
DMRTC2, PAX7, BRACHYURY/T and TERT Are Implicated in Male Germ Cell Development Following Curative Hormone Treatment for Cryptorchidism-Induced Infertility
G C A T T A C G G C A T genes Article DMRTC2, PAX7, BRACHYURY/T and TERT Are Implicated in Male Germ Cell Development Following Curative Hormone Treatment for Cryptorchidism-Induced Infertility Katharina Gegenschatz-Schmid 1, Gilvydas Verkauskas 2, Philippe Demougin 3, Vytautas Bilius 2, Darius Dasevicius 4, Michael B. Stadler 5,6 and Faruk Hadziselimovic 1,* 1 Cryptorchidism Research Institute, Kindermedizinisches Zentrum Liestal, 4410 Liestal, Switzerland; [email protected] 2 Children’s Surgery Centre, Faculty of Medicine, Vilnius of University, 01513 Vilnius, Lithuania; [email protected] (G.V.); [email protected] (V.B.) 3 Biozentrum, Life Sciences Training Facility, University of Basel, 4001 Basel, Switzerland; [email protected] 4 Institute for Pathology, National Centre of Pathology, Affiliate of Vilnius University Hospital Santariskiu Klinikos, 08406 Vilnius, Lithuania; [email protected] 5 Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; [email protected] 6 Swiss Institute of Bioinformatics, Basel, Switzerland * Correspondence: [email protected]; Tel.: +41-61-927-9090; Fax: +41-61-927-9099 Academic Editor: Paolo Cinelli Received: 18 August 2017; Accepted: 5 October 2017; Published: 11 October 2017 Abstract: Defective mini-puberty results in insufficient testosterone secretion that impairs the differentiation of gonocytes into dark-type (Ad) spermatogonia. The differentiation of gonocytes into Ad spermatogonia can be induced by administration of the gonadotropin-releasing hormone agonist, GnRHa (Buserelin, INN)). Nothing is known about the mechanism that underlies successful GnRHa treatment in the germ cells. Using RNA-sequencing of testicular biopsies, we recently examined RNA profiles of testes with and without GnRHa treatment. -
Genetic Landscape of Nonobstructive Azoospermia and New Perspectives for the Clinic
Journal of Clinical Medicine Review Genetic Landscape of Nonobstructive Azoospermia and New Perspectives for the Clinic Miriam Cerván-Martín 1,2, José A. Castilla 2,3,4, Rogelio J. Palomino-Morales 2,5 and F. David Carmona 1,2,* 1 Departamento de Genética e Instituto de Biotecnología, Universidad de Granada, Centro de Investigación Biomédica (CIBM), Parque Tecnológico Ciencias de la Salud, Av. del Conocimiento, s/n, 18016 Granada, Spain; [email protected] 2 Instituto de Investigación Biosanitaria ibs.GRANADA, Av. de Madrid, 15, Pabellón de Consultas Externas 2, 2ª Planta, 18012 Granada, Spain; [email protected] (J.A.C.); [email protected] (R.J.P.-M.) 3 Unidad de Reproducción, UGC Obstetricia y Ginecología, HU Virgen de las Nieves, Av. de las Fuerzas Armadas 2, 18014 Granada, Spain 4 CEIFER Biobanco—NextClinics, Calle Maestro Bretón 1, 18004 Granada, Spain 5 Departamento de Bioquímica y Biología Molecular I, Universidad de Granada, Facultad de Ciencias, Av. de Fuente Nueva s/n, 18071 Granada, Spain * Correspondence: [email protected]; Tel.: +34-958-241-000 (ext 20170) Received: 29 December 2019; Accepted: 16 January 2020; Published: 21 January 2020 Abstract: Nonobstructive azoospermia (NOA) represents the most severe expression of male infertility, involving around 1% of the male population and 10% of infertile men. This condition is characterised by the inability of the testis to produce sperm cells, and it is considered to have an important genetic component. During the last two decades, different genetic anomalies, including microdeletions of the Y chromosome, karyotype defects, and missense mutations in genes involved in the reproductive function, have been described as the primary cause of NOA in many infertile men.