Success and Failure in Human Spermatogenesis as Revealed by Teratozoospermic RNAs Running head: A Sperm's RNA Diagnostic Tail

Adrian E. Platts, David J. Dix, Hector E. Chemes, Kary E. Thompson, Robert Goodrich, John C. Rockett, Vanesa Y. Rawe, Silvina Quintana, Michael P. Diamond, Lillian F. Strader and Stephen A. Krawetz* Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Office of Research and Development, U.S. Environmental Protection Agency, USA, Centro de Investigaciones Endocrinologicas, Argentina Centro de Estudios en Ginecología y Reproducción, Argentina,Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Institue for Scientific Computing, Wayne State University. Submitted to: Human Molecular Genetics HMG-2006D-01086 December, 29, 2006 And in revised form: January 26, 2007 Correspondence to: *Stephen A. Krawetz Charlotte B. Failing Professor of Fetal Therapy and Diagnosis, 253 C.S. Mott Center; 275 East Hancock; Detroit, MI, USA 48201 Laboratory phone: 313-577-0765; Office phone: 313-577-6770; FAX: 313-577-8554 Email: steve@compbio.med.wayne.edu

[1]  S. Krawetz,et al.  Considerations When Using Array Technologies for Male Factor Assessment , 2007 .

[2]  P. Sutovsky,et al.  Differential Expression of Genes Encoding Constitutive and Inducible 20S Proteasomal Core Subunits in the Testis and Epididymis of Theophylline- or 1,3-Dinitrobenzene-Exposed Rats1 , 2007, Biology of reproduction.

[3]  P. Gounon,et al.  RNA-mediated non-mendelian inheritance of an epigenetic change in the mouse , 2006, Nature.

[4]  J. Waring,et al.  GENE EXPRESSION IN HUMAN HEPATOCYTES IN SUSPENSION AFTER ISOLATION IS SIMILAR TO THE LIVER OF ORIGIN, IS NOT AFFECTED BY HEPATOCYTE COLD STORAGE AND CRYOPRESERVATION, BUT IS STRONGLY CHANGED AFTER HEPATOCYTE PLATING , 2006, Drug Metabolism and Disposition.

[5]  G. Gerton,et al.  Proteomic Profiling of Accessory Structures from the Mouse Sperm Flagellum*S , 2006, Molecular & Cellular Proteomics.

[6]  Y. Gur,et al.  Mammalian sperm translate nuclear-encoded proteins by mitochondrial-type ribosomes. , 2006, Genes & development.

[7]  S. Krawetz Paternal contribution: new insights and future challenges , 2005, Nature Reviews Genetics.

[8]  G. Ostermeier,et al.  Toward using stable spermatozoal RNAs for prognostic assessment of male factor fertility. , 2005, Fertility and Sterility.

[9]  S. Krawetz,et al.  RNA in human sperm. , 2005, Asian journal of andrology.

[10]  Claes Wahlestedt,et al.  Considerations when using the significance analysis of microarrays (SAM) algorithm , 2005, BMC Bioinformatics.

[11]  B. N. Day,et al.  Expression and proteasomal degradation of the major vault protein (MVP) in mammalian oocytes and zygotes. , 2005, Reproduction.

[12]  T. Werner,et al.  Linking disease-associated genes to regulatory networks via promoter organization , 2005, Nucleic acids research.

[13]  Dennis B. Troup,et al.  NCBI GEO: mining millions of expression profiles—database and tools , 2004, Nucleic Acids Res..

[14]  Alok J. Saldanha,et al.  Java Treeview - extensible visualization of microarray data , 2004, Bioinform..

[15]  S. Yokota,et al.  Ubiquitin Signals in the Developing Acrosome during Spermatogenesis of Rat Testis: An Immunoelectron Microscopic Study , 2004, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[16]  S. Lambard,et al.  Analysis and significance of mRNA in human ejaculated sperm from normozoospermic donors: relationship to sperm motility and capacitation. , 2004, Molecular human reproduction.

[17]  Zuo-min Zhou,et al.  A spermatogenesis-related gene expression profile in human spermatozoa and its potential clinical applications , 2004, Journal of Molecular Medicine.

[18]  Leszek Rychlewski,et al.  Protein structure prediction for the male-specific region of the human Y chromosome. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[19]  M. Matsui,et al.  In vivo analysis of autophagy in response to nutrient starvation using transgenic mice expressing a fluorescent autophagosome marker. , 2003, Molecular biology of the cell.

[20]  Sergei Egorov,et al.  Pathway studio - the analysis and navigation of molecular networks , 2003, Bioinform..

[21]  V. Rawe,et al.  Sperm pathology: a step beyond descriptive morphology. Origin, characterization and fertility potential of abnormal sperm phenotypes in infertile men. , 2003, Human reproduction update.

[22]  W. Yeung,et al.  Specific Expression of VCY2 in Human Male Germ Cells and Its Involvement in the Pathogenesis of Male Infertility , 2003, Biology of reproduction.

[23]  Brad T. Sherman,et al.  DAVID: Database for Annotation, Visualization, and Integrated Discovery , 2003, Genome Biology.

[24]  P. Sutovsky Ubiquitin‐dependent proteolysis in mammalian spermatogenesis, fertilization, and sperm quality control: Killing three birds with one stone , 2003, Microscopy research and technique.

[25]  D. Barrell,et al.  The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. , 2003, Genome research.

[26]  T. Speed,et al.  Summaries of Affymetrix GeneChip probe level data. , 2003, Nucleic acids research.

[27]  G A Whitmore,et al.  Power and sample size for DNA microarray studies , 2002, Statistics in medicine.

[28]  Wei-Min Liu,et al.  Analysis of high density expression microarrays with signed-rank call algorithms , 2002, Bioinform..

[29]  P. Khatri,et al.  Spermatozoal RNA profiles of normal fertile men , 2002, The Lancet.

[30]  B. Robaire,et al.  Changes in gene expression during aging in the Brown Norway rat epididymis , 2002, Experimental Gerontology.

[31]  A. Oliphant,et al.  BeadArray technology: enabling an accurate, cost-effective approach to high-throughput genotyping. , 2002, BioTechniques.

[32]  C. Lombard,et al.  Predictive value of normal sperm morphology in intrauterine insemination (IUI): a structured literature review. , 2001, Human reproduction update.

[33]  Luming Yin,et al.  Divergent N-terminal Sequences of a Deubiquitinating Enzyme Modulate Substrate Specificity* , 2001, The Journal of Biological Chemistry.

[34]  G. Schatten,et al.  A putative, ubiquitin-dependent mechanism for the recognition and elimination of defective spermatozoa in the mammalian epididymis. , 2001, Journal of cell science.

[35]  G. Schatten,et al.  Ubiquitin-based sperm assay for the diagnosis of male factor infertility , 2001 .

[36]  C. Li,et al.  Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[37]  Alexander Varshavsky,et al.  The ubiquitin system. , 1998, Annual review of biochemistry.

[38]  J. Czyba,et al.  Proteasomes in human spermatozoa. , 2000, International journal of andrology.

[39]  J. Mesirov,et al.  Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. , 1999, Science.

[40]  M. Kurpisz,et al.  Teratozoospermia and its effect on male fertility potential , 1999, Andrologia.

[41]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[42]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[43]  D. Dix,et al.  HSP70-2 is required for desynapsis of synaptonemal complexes during meiotic prophase in juvenile and adult mouse spermatocytes. , 1997, Development.

[44]  J. Malm,et al.  Distribution and tissue expression of semenogelin I and II in man as demonstrated by in situ hybridization and immunocytochemistry. , 1996, Journal of andrology.

[45]  K Tanaka,et al.  Structure and functions of the 20S and 26S proteasomes. , 1996, Annual review of biochemistry.

[46]  W. Ombelet,et al.  Sperm morphology assessment: historical review in relation to fertility. , 1995, Human reproduction update.

[47]  P. J. Rowe,et al.  WHO Manual for the Standardized Investigation and Diagnosis of the Infertile Couple , 1993 .