MGAT1 and Complex N-Glycans Regulate ERK Signaling
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Gene Regulation and Speciation in House Mice
Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Research Gene regulation and speciation in house mice Katya L. Mack,1 Polly Campbell,2 and Michael W. Nachman1 1Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, California 94720-3160, USA; 2Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma 74078, USA One approach to understanding the process of speciation is to characterize the genetic architecture of post-zygotic isolation. As gene regulation requires interactions between loci, negative epistatic interactions between divergent regulatory elements might underlie hybrid incompatibilities and contribute to reproductive isolation. Here, we take advantage of a cross between house mouse subspecies, where hybrid dysfunction is largely unidirectional, to test several key predictions about regulatory divergence and reproductive isolation. Regulatory divergence between Mus musculus musculus and M. m. domesticus was charac- terized by studying allele-specific expression in fertile hybrid males using mRNA-sequencing of whole testes. We found ex- tensive regulatory divergence between M. m. musculus and M. m. domesticus, largely attributable to cis-regulatory changes. When both cis and trans changes occurred, they were observed in opposition much more often than expected under a neutral model, providing strong evidence of widespread compensatory evolution. We also found evidence for lineage-specific positive se- lection on a subset of genes related to transcriptional regulation. Comparisons of fertile and sterile hybrid males identified a set of genes that were uniquely misexpressed in sterile individuals. Lastly, we discovered a nonrandom association between these genes and genes showing evidence of compensatory evolution, consistent with the idea that regulatory interactions might contribute to Dobzhansky-Muller incompatibilities and be important in speciation. -
Androgen Receptor Function Is Required in Sertoli Cells for the Terminal Differentiation of Haploid Spermatids Robert W
Research article 459 Androgen receptor function is required in Sertoli cells for the terminal differentiation of haploid spermatids Robert W. Holdcraft and Robert E. Braun* University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA 98195, USA *Author for correspondence (e-mail: [email protected]) Accepted 20 October 2003 Development 131, 459-467 Published by The Company of Biologists 2004 doi:10.1242/dev.00957 Summary Androgen receptor function is required for male embryonic and their release from the seminiferous epithelium is AR sexual differentiation, pubertal development and the dependent and maximally sensitive to AR depletion within regulation of spermatogenesis in mammals. During the testis. Cell-specific disruption of Ar in Sertoli cells of spermatogenesis, this requirement is thought to be hypomorphic animals further shows that progression of mediated by Sertoli cells and its genetic and late-round spermatids to elongating steps is sensitive to loss pharmacological disruption is manifested in spermatocytes of Sertoli cell AR function, but that progression through as meiotic arrest. Through studies of a hypomorphic and meiosis and early-round spermatid differentiation are conditional allele of the androgen receptor (Ar) gene, we surprisingly unaffected. have uncovered a dual post-meiotic requirement for androgen receptor activity during male germ cell Supplemental data available online differentiation. Observations in Ar hypomorphic animals demonstrate that terminal differentiation of spermatids Key words: Androgen receptor, Sertoli, Spermatogenesis, Mouse Introduction function from that resulting from the abdominal positioning Androgen receptor (AR) function is essential in males for of the testes. Mice homozygous for a mutation in the proper sexual differentiation and for the maintenance of normal gonadotrophin releasing hormone gene (Gnrh), which have spermatogenesis. -
Emerging Genetic Alterations Linked to Male Infertility: X-Chromosome Copy Number Variation and Spermatogenesis Regulatory Genes’ Expression
Central Annals of Reproductive Medicine and Treatment Bringing Excellence in Open Access Research Article *Corresponding author Susana Fernandes, Department of Genetics, Faculty of Medicine of University of Porto, Al. Prof. Hernâni Emerging Genetic Alterations Monteiro, 4200 - 319 Porto, Portugal; Tel: 351 22 551 36 47; Email: Submitted: 12 October 2016 Linked to Male Infertility: Accepted: 10 February 2017 Published: 14 February 2017 X-Chromosome Copy Number Copyright © 2017 Fernandes et al. Variation and Spermatogenesis OPEN ACCESS Keywords Regulatory Genes’ Expression • Male infertility • Spermatogenesis Catarina Costa1, Maria João Pinho1,2, Alberto Barros1,2,3, and • DNA copy number variations • Gene expression Susana Fernandes1,2* 1Department of Genetics, Faculty of Medicine of University of Porto, Portugal 2i3S – Instituto de Investigação e Inovação em Saúde, University of Porto, Portugal 3Centre for Reproductive Genetics A Barros, Portugal Abstract The etiopathogenesis of primary testicular failure remains undefined in 50% of cases. Most of these idiopathic cases probably result from genetic mutations/anomalies. Novel causes, like Copy Number Variation and gene expression profile, are being explored thanks to recent advances in the field of genetics. Our aim was to study Copy Number Variation (CNV) 67, a patient-specific CNV related to spermatogenic anomaly and evaluate the expression of regulatory genes AKAP4, responsible for sperm fibrous sheet assembly, and STAG3, essential for sister chromatid cohesion during meiosis. One hundred infertile men were tested for CNV67 with quantitative PCR (qPCR). Quantitative real-time PCR was performed to evaluate gene expression patterns of the two mentioned genes in testicular biopsies from 22 idiopathic infertile patients. CNV67 deletion was found in 2% of patients, with the same semen phenotype described in previous studies. -
Entropy Based Analysis of Vertebrate Sperm Protamines Sequences: Evidence of Potential Dityrosine and Cysteine-Tyrosine Cross-Linking in Sperm Protamines Christian D
Powell et al. BMC Genomics (2020) 21:277 https://doi.org/10.1186/s12864-020-6681-2 RESEARCH ARTICLE Open Access Entropy based analysis of vertebrate sperm protamines sequences: evidence of potential dityrosine and cysteine-tyrosine cross-linking in sperm protamines Christian D. Powell1,2,DanielC.Kirchoff1, Jason E. DeRouchey1 and Hunter N. B. Moseley2,3,4* Abstract Background: Spermatogenesis is the process by which germ cells develop into spermatozoa in the testis. Sperm protamines are small, arginine-rich nuclear proteins which replace somatic histones during spermatogenesis, allowing a hypercondensed DNA state that leads to a smaller nucleus and facilitating sperm head formation. In eutherian mammals, the protamine-DNA complex is achieved through a combination of intra- and intermolecular cysteine cross-linking and possibly histidine-cysteine zinc ion binding. Most metatherian sperm protamines lack cysteine but perform the same function. This lack of dicysteine cross-linking has made the mechanism behind metatherian protamines folding unclear. Results: Protamine sequences from UniProt’s databases were pulled down and sorted into homologous groups. Multiple sequence alignments were then generated and a gap weighted relative entropy score calculated for each position. For the eutherian alignments, the cysteine containing positions were the most highly conserved. For the metatherian alignment, the tyrosine containing positions were the most highly conserved and corresponded to the cysteine positions in the eutherian alignment. Conclusions: High conservation indicates likely functionally/structurally important residues at these positions in the metatherian protamines and the correspondence with cysteine positions within the eutherian alignment implies a similarity in function. One possible explanation is that the metatherian protamine structure relies upon dityrosine cross-linking between these highly conserved tyrosines. -
Relating Sequence Encoded Information to Form and Function of Intrinsically Disordered Proteins
Available online at www.sciencedirect.com ScienceDirect Relating sequence encoded information to form and function of intrinsically disordered proteins Rahul K Das, Kiersten M Ruff and Rohit V Pappu Intrinsically disordered proteins (IDPs) showcase the of archetypal IDPs. CCRs enable the assignments of importance of conformational plasticity and heterogeneity in conformational descriptors and inferences regarding the protein function. We summarize recent advances that connect amplitudes of conformational fluctuations of IDPs. These information encoded in IDP sequences to their conformational insights are relevant because amino acid compositions are properties and functions. We focus on insights obtained often well conserved among orthologs of IDPs even if their through a combination of atomistic simulations and biophysical sequences are poorly conserved [42,43]. measurements that are synthesized into a coherent framework using polymer physics theories. Compositional classes of IDPs Address Amino acid compositions of IDPs are characterized by Department of Biomedical Engineering and Center for Biological distinct biases [5]. They are deficient in canonical hydro- Systems Engineering, Washington University in St. Louis, One Brookings phobic residues and enriched in polar and charged resi- Drive, Campus Box 1097, St. Louis, MO 63130, USA dues. Accordingly, IDPs fall into three distinct compositional classes that reflect the fraction of charged Corresponding author: Pappu, Rohit V ([email protected]) versus polar residues. The distinct classes are polar tracts, polyampholytes, and polyelectrolytes [41] (see Figure 1). Polar Current Opinion in Structural Biology 2015, 32:102–112 tracts are deficient in charged, hydrophobic, and proline residues. They are enriched in polar amino acids such as This review comes from a themed issue on Sequences and topology Asn, Gly, Gln, His, Ser, and Thr. -
Premature Translation of Protamine 1 Mrna Causes Precocious Nuclear Condensation and Arrests Spermatid Differentiation in Mice KEESOOK LEE*T, HARALD S
Proc. Natl. Acad. Sci. USA Vol. 92, pp. 12451-12455, December 1995 Developmental Biology Premature translation of protamine 1 mRNA causes precocious nuclear condensation and arrests spermatid differentiation in mice KEESOOK LEE*t, HARALD S. HAUGENt, CHRISTOPHER H. CLEGGt, AND ROBERT E. BRAUN*§ *University of Washington, Department of Genetics, Box 357360, Seattle, WA 98195-7360; and tBristol-Myers Squibb Pharmaceutical Research, 3005 First Avenue, Seattle, WA 98121 Communicated by Richard D. Palmiter, University of Washington School of Medicine, Seattle, WA, September 14, 1995 ABSTRACT Translational control is a major form of translational repression, although direct proof that they func- regulating gene expression during gametogenesis and early tion as translational repressors in vivo has not yet been development in many organisms. We sought to determine demonstrated (14, 15). whether the translational repression of the protamine 1 An important and unanswered question in sperm morpho- (Prml) mRNA is necessary for normal spermatid differenti- genesis is whether the temporal expression of the testis nuclear ation in mice. To accomplish this we generated transgenic basic proteins is actually necessary for normal spermatid animals that carry a Prml transgene lacking its normal 3' differentiation. To address the importance of the translational untranslated region. Premature translation of Prml mRNA repression of Prml mRNA, we generated transgenic mice that caused precocious condensation of spermatid nuclear DNA, fail to delay Prml mRNA translation. We show that premature abnormal head morphogenesis, and incomplete processing of translation of Prml mRNA causes precocious condensation of Prm2 protein. Premature accumulation of Prml within syn- nuclear DNA and a failure to complete spermatid differenti- cytial spermatids in mice hemizygous for the transgene caused ation, resulting in sterility. -
© Copyright 2021 Heather Raquel Dahlin
© Copyright 2021 Heather Raquel Dahlin The Structure of Sperm Autoantigenic Protein (SPA17): An R2D2 Protein Critical to Cilia and Implicated in Oncogenesis Heather Raquel Dahlin A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2021 Reading Committee: John D. Scott, Chair Ning Zheng Linda Wordeman Program Authorized to Offer Degree: Pharmacology University of Washington Abstract Structure of SPA17: An R2D2 Protein Critical to Cilia and Implicated in Oncogenesis Heather Raquel Dahlin Chair of the Supervisory Committee: John D. Scott, Ph.D., Edwin G. Krebs- Speights Professor of Cell Signaling and Cancer Biology Pharmacology A-Kinase Anchoring proteins (AKAPs) localize the activity of cyclic AMP (cAMP)-Dependent Protein Kinase (PKA) through interaction of an amphipathic helix that binds to a conserved RIIα docking and dimerization (R2D2) domain on the N-terminus of PKA. Genome analysis indicates that at least thirteen other RIIα superfamily proteins exist in humans, which are not coupled to cyclic nucleotide binding domains and are largely localized to cilia and flagella. The newly reported R2D2 proteins exist in two lineages differing by their similarity to Type I or Type II PKA. Moreover, R2D2 domains bind to AKAPs and can contain extra regulatory sequences conferring novel functions and binding specificity. Here we detail the structure of one such domain comprising the N-terminus of Sperm Autoantigenic Protein 17 (SPA17) resolved to 1.72 Å. The structure of core hydrophobic sites for dimerization and AKAP binding are highly conserved between PKA and SPA17. Additional flanking sequences outside of the core R2D2 domain occlude the AKAP binding site and reduce the affinity for AKAP helices in the absence of heterodimerization with another R2D2 protein, ROPN1L. -
TCTE1 Is a Conserved Component of the Dynein Regulatory Complex and Is Required for Motility and Metabolism in Mouse Spermatozoa
TCTE1 is a conserved component of the dynein PNAS PLUS regulatory complex and is required for motility and metabolism in mouse spermatozoa Julio M. Castanedaa,b,1, Rong Huac,d,1, Haruhiko Miyatab, Asami Ojib,e, Yueshuai Guoc,d, Yiwei Chengc,d, Tao Zhouc,d, Xuejiang Guoc,d, Yiqiang Cuic,d, Bin Shenc, Zibin Wangc, Zhibin Huc,f, Zuomin Zhouc,d, Jiahao Shac,d, Renata Prunskaite-Hyyrylainena,g,h, Zhifeng Yua,i, Ramiro Ramirez-Solisj, Masahito Ikawab,e,k,2, Martin M. Matzuka,g,i,l,m,n,2, and Mingxi Liuc,d,2 aDepartment of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030; bResearch Institute for Microbial Diseases, Osaka University, Suita, Osaka 5650871, Japan; cState Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, People’s Republic of China; dDepartment of Histology and Embryology, Nanjing Medical University, Nanjing 210029, People’s Republic of China; eGraduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 5650871, Japan; fAnimal Core Facility of Nanjing Medical University, Nanjing 210029, People’s Republic of China; gCenter for Reproductive Medicine, Baylor College of Medicine, Houston, TX 77030; hFaculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu FI-90014, Finland; iCenter for Drug Discovery, Baylor College of Medicine, Houston, TX 77030; jWellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom; kThe Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 1088639, Japan; lDepartment of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030; mDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030; and nDepartment of Pharmacology, Baylor College of Medicine, Houston, TX 77030 Contributed by Martin M. -
Sex Differences in Response of the Bovine Embryo to Colony
REPRODUCTIONRESEARCH A-kinase anchoring protein 4 has a conserved role in mammalian spermatogenesis Yanqiu Hu, Hongshi Yu, Andrew J Pask, Deborah A O’Brien1, Geoff Shaw and Marilyn B Renfree ARC Centre of Excellence for Kangaroo Genomics, Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia and 1Department of Cell & Developmental Biology, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599-7090, USA Correspondence should be addressed to M B Renfree; Email: [email protected] Abstract A-kinase anchor protein 4 (AKAP4) is an X-linked member of the AKAP family of scaffold proteins that anchor cAMP-dependent protein kinases and play an essential role in fibrous sheath assembly during spermatogenesis and flagellar function in spermatozoa. Marsupial spermatozoa differ in structural organization from those of eutherian mammals but data on the molecular control of their structure and function are limited. We therefore cloned and characterized the AKAP4 gene in a marsupial, the tammar wallaby (Macropus eugenii). The gene structure, sequence, and predicted protein of AKAP4 were highly conserved with that of eutherian orthologues and it mapped to the marsupial X-chromosome. There was no AKAP4 expression detected in the developing young. In the adult, AKAP4 expression was limited to the testis with a major transcript of 2.9 kb. AKAP4 mRNA was expressed in the cytoplasm of round and elongated spermatids while its protein was found on the principal piece of the flagellum in the sperm tail. This is consistent with its expression in other mammals. Thus, AKAP4 appears to have a conserved role in spermatogenesis for at least the last 166 million years of mammalian evolution. -
Evidence for the Evolutionary Origin of Human Chromosome 21 From
Proc. Natl. Acad. Sci. USA Vol. 88, pp. 154-158, January 1991 Genetics Evidence for the evolutionary origin of human chromosome 21 from comparative gene mapping in the cow and mouse (hybrid somatic cell analysis/Bos tarus/Mus musculus) DEBORAH S. THREADGILL*, JAN P. KRAUSt, STEPHEN A. KRAWETZt, AND JAMES E. WOMACK*§ *Department of Veterinary Pathology, Texas A&M University, College Station, TX 77843; tDepartment of Pediatrics and Cellular/Structural Biology, University of Colorado Health Sciences Center, 4200 East Ninth Avenue, Denver, CO 80262; and tDepartment of Molecular Biology and Genetics, School of Medicine, Gordon H. Scott Hall, Wayne State University, 540 East Canfield, Detroit, MI 48202 Communicated by Neal L. First, October 1, 1990 (receivedfor review July 27, 1990) ABSTRACT To determine the extent of conservation be- has not been reported for any species other than the mouse. tween bovine syntenic group U1O, human chromosome 21 In the absence of greater comparative mapping data, the (HSA 21), and mouse chromosome 16 (MMU 16), 11 genes were ancestral relationship of HSA 21 and MMU 16 cannot be physically mapped by segregation analysis in a bovine-hamsuter resolved. Mapping of the loci from HSA 21 and MMU 16 in hybrid somatic cell panel. The genes chosen for study span a third mammalian taxon such as the bovine, however, could MMU 16 and represent virtually the entire q arm of HSA 21. provide important information about the evolution ofHSA 21 Because the somatostatin gene (SST), an HSA 3/MMU 16 and MMU 16 from an ancestral mammalian chromosome. locus, was previously shown tube in U1O, the trnsferrin gene The three species are thought to have been separated from (TF), an HSA 3/MMU 9 marker, was also mapped to deter- each other for 80 million years, and genes syntenic in two of mine whether U10 contains any HSA 3 genes not represented the three species are assumed to represent the ancestral on MMU 16. -
Comparative Genomics Reveals Gene-Specific and Shared Regulatory Sequences in the Spermatid-Expressed Mammalian Odf1, Prm1, Prm2
Genomics 92 (2008) 101–106 Contents lists available at ScienceDirect Genomics journal homepage: www.elsevier.com/locate/ygeno Comparative genomics reveals gene-specific and shared regulatory sequences in the spermatid-expressed mammalian Odf1, Prm1, Prm2, Tnp1, and Tnp2 genes☆ Kenneth C. Kleene ⁎, Jana Bagarova Department of Biology, University of Massachusetts at Boston, Boston, MA 02125, USA ARTICLE INFO ABSTRACT Article history: The comparative genomics of the Odf1, Prm1, Prm2, Tnp1, and Tnp2 genes in 13–21 diverse mammalian Received 6 January 2008 species reveals striking similarities and differences in the sequences that probably function in the Accepted 1 May 2008 transcriptional and translational regulation of gene expression in haploid spermatogenic cells, spermatids. Available online 17 June 2008 The 5′ flanking regions contain putative TATA boxes and cAMP-response elements (CREs), but the TATA boxes and CREs exhibit gene-specific sequences, and an overwhelming majority of CREs differ from the consensus Keywords: ′ ′ fi Comparative genomics sequence. The 5 and 3 UTRs contain highly conserved gene-speci c sequences including canonical and Translational regulation noncanonical poly(A) signals and a suboptimal context for the Tnp2 translation initiation codon. The Spermatid conservation of the 5′ UTR is unexpected because mRNA translation in spermatids is thought to be regulated Protamine primarily by the 3′ UTR. Finally, all of the genes contain a single intron, implying that retroposons are rarely Transition protein created from mRNAs that are expressed in spermatids. Outer dense fiber 1 © 2008 Elsevier Inc. All rights reserved. TATA box CREMτ Noncanonical poly(A) signal Retroposon Introduction [4]. The importance of delaying translation is demonstrated by reports that premature translation of the Prm1 and Tnp2 mRNAs in round The haploid, differentiation phase of spermatogenesis in mammals spermatids in transgenic mice impairs male fertility [5,6]. -
A Yeast Bifc-Seq Method for Genome-Wide Interactome Mapping
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.16.154146; this version posted June 17, 2020. 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 A yeast BiFC-seq method for genome-wide interactome mapping 2 3 Limin Shang1,a, Yuehui Zhang1,b, Yuchen Liu1,c, Chaozhi Jin1,d, Yanzhi Yuan1,e, 4 Chunyan Tian1,f, Ming Ni2,g, Xiaochen Bo2,h, Li Zhang3,i, Dong Li1,j, Fuchu He1,*,k & 5 Jian Wang1,*,l 6 1State Key Laboratory of Proteomics, Beijing Proteome Research Center, National 7 Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, 8 China; 2Department of Biotechnology, Beijing Institute of Radiation Medicine, 9 Beijing 100850, China; 3Department of Rehabilitation Medicine, Nan Lou; 10 Department of Key Laboratory of Wound Repair and Regeneration of PLA, College 11 of Life Sciences, Chinese PLA General Hospital, Beijing 100853, China; 12 Correspondence should be addressed to F.H. ([email protected]) and J.W. 13 ([email protected]). 14 * Corresponding authors. 15 E-mail:[email protected] (Fuchu He),[email protected] (Jian Wang) 16 a ORCID: 0000-0002-6371-1956. 17 b ORCID: 0000-0001-5257-1671 18 c ORCID: 0000-0003-4691-4951 19 d ORCID: 0000-0002-1477-0255 20 e ORCID: 0000-0002-6576-8112 21 f ORCID: 0000-0003-1589-293X 22 g ORCID: 0000-0001-9465-2787 23 h ORCID: 0000-0003-3490-5812 24 i ORCID: 0000-0002-3477-8860 25 j ORCID: 0000-0002-8680-0468 26 k ORCID: 0000-0002-8571-2351 27 l ORCID: 0000-0002-8116-7691 28 Total word counts:4398 (from “Introduction” to “Conclusions”) 29 Total Keywords: 5 bioRxiv preprint doi: https://doi.org/10.1101/2020.06.16.154146; this version posted June 17, 2020.