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Towards the Understanding of Ccnb1ip1 As a Co-Regulator of Meiotic Crossing-Over in the Mouse
TOWARDS THE UNDERSTANDING OF CCNB1IP1 AS A CO-REGULATOR OF MEIOTIC CROSSING-OVER IN THE MOUSE A Dissertation Presented to the Faculty of the Graduate School of Cornell University In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by Edward Remco Strong January 2014 © 2014 Edward Remco Strong TOWARDS THE UNDERSTANDING OF CCNB1IP1 AS A CO-REGULATOR OF MEIOTIC CROSSING-OVER IN THE MOUSE Edward Remco Strong, Ph. D. Cornell University 2014 It is clear that there are many genes required for meiosis in mammals that are not present in the more tractable model organisms. To identify such genes, our lab has performed forward genetic chemical (ENU) mutagenesis screens for alleles conferring infertility in mice. A novel allele, Ccnb1ip1mei4, generated in these screens is of interest because it is defective in a form of recombination called crossing-over. Ccnb1ip1mei4/mei4 results in male and female infertility of otherwise normal-appearing animals. CCNB1IP1 is finely regulated in both timing and localization to the events of meiotic crossover formations. Towards understanding the molecular functions of CCNB1IP1 and how the defect in Ccnb1ip1me4i/mei4 animals leads to meiotic arrest, studies of CCNB1IP1 within meiocytes implicate a role for CCNB1IP1 in SUMOylation. Remarkably little is understood about SUMO-modification consequences to meiosis. Protein-protein interactions with CCNB1IP1 identify a number of putative targets of SUMOylation, and subsequent in vivo biochemical interrogations reveal the CCNB1IP1-interacting proteins 4930455F23RIK and GGN as targets of posttranslational modification dependent upon a putative SUMO E3 ligase. In totality, these studies support the hypothesis that CCNB1IP1 performs as a meiotic co- regulator, mediating the SUMO-modification of proteins essential to the stabilization and maturation of crossover intermediates. -
Leveraging Mouse Chromatin Data for Heritability Enrichment Informs Common Disease Architecture and Reveals Cortical Layer Contributions to Schizophrenia
Downloaded from genome.cshlp.org on October 5, 2021 - Published by Cold Spring Harbor Laboratory Press Research Leveraging mouse chromatin data for heritability enrichment informs common disease architecture and reveals cortical layer contributions to schizophrenia Paul W. Hook1 and Andrew S. McCallion1,2,3 1McKusick-Nathans Department of Genetic Medicine, 2Department of Comparative and Molecular Pathobiology, 3Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA Genome-wide association studies have implicated thousands of noncoding variants across common human phenotypes. However, they cannot directly inform the cellular context in which disease-associated variants act. Here, we use open chro- matin profiles from discrete mouse cell populations to address this challenge. We applied stratified linkage disequilibrium score regression and evaluated heritability enrichment in 64 genome-wide association studies, emphasizing schizophrenia. We provide evidence that mouse-derived human open chromatin profiles can serve as powerful proxies for difficult to ob- tain human cell populations, facilitating the illumination of common disease heritability enrichment across an array of hu- man phenotypes. We demonstrate that signatures from discrete subpopulations of cortical excitatory and inhibitory neurons are significantly enriched for schizophrenia heritability with maximal enrichment in cortical layer V excitatory neu- rons. We also show that differences between schizophrenia and bipolar disorder are concentrated in excitatory neurons in cortical layers II-III, IV, and V, as well as the dentate gyrus. Finally, we leverage these data to fine-map variants in 177 schiz- ophrenia loci nominating variants in 104/177. We integrate these data with transcription factor binding site, chromatin in- teraction, and validated enhancer data, placing variants in the cellular context where they may modulate risk. -
047605V1.Full.Pdf
bioRxiv preprint doi: https://doi.org/10.1101/047605; this version posted April 8, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Assembly and Activation of Dynein-Dynactin by the Cargo Adaptor Protein Hook3 Courtney M. Schroeder1,2 and Ronald D. Vale1,2 1The Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California, USA 2Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA. Corresponding Author: Ronald D. Vale Dept. of Cellular and Molecular Pharmacology University of California, San Francisco Genentech Hall, MC 2200, Room N312A 600-16th Street San Francisco, CA 94158-2517 E-mail: [email protected] Phone: 415-476-6380 Fax: 415-514-4412 bioRxiv preprint doi: https://doi.org/10.1101/047605; this version posted April 8, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 2 Abstract Metazoan cytoplasmic dynein moves processively along microtubules with the aid of dynactin and an adaptor protein that joins dynein and dynactin into a stable ternary complex. Here, we have examined how Hook3, a cargo adaptor involved in Golgi and endosome transport, forms a motile dynein-dynactin complex. We show that the conserved Hook domain interacts directly with the dynein light intermediate chain 1 (LIC1). -
Transcriptomic and Proteomic Profiling Provides Insight Into
BASIC RESEARCH www.jasn.org Transcriptomic and Proteomic Profiling Provides Insight into Mesangial Cell Function in IgA Nephropathy † † ‡ Peidi Liu,* Emelie Lassén,* Viji Nair, Celine C. Berthier, Miyuki Suguro, Carina Sihlbom,§ † | † Matthias Kretzler, Christer Betsholtz, ¶ Börje Haraldsson,* Wenjun Ju, Kerstin Ebefors,* and Jenny Nyström* *Department of Physiology, Institute of Neuroscience and Physiology, §Proteomics Core Facility at University of Gothenburg, University of Gothenburg, Gothenburg, Sweden; †Division of Nephrology, Department of Internal Medicine and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan; ‡Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya, Japan; |Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden; and ¶Integrated Cardio Metabolic Centre, Karolinska Institutet Novum, Huddinge, Sweden ABSTRACT IgA nephropathy (IgAN), the most common GN worldwide, is characterized by circulating galactose-deficient IgA (gd-IgA) that forms immune complexes. The immune complexes are deposited in the glomerular mesangium, leading to inflammation and loss of renal function, but the complete pathophysiology of the disease is not understood. Using an integrated global transcriptomic and proteomic profiling approach, we investigated the role of the mesangium in the onset and progression of IgAN. Global gene expression was investigated by microarray analysis of the glomerular compartment of renal biopsy specimens from patients with IgAN (n=19) and controls (n=22). Using curated glomerular cell type–specific genes from the published literature, we found differential expression of a much higher percentage of mesangial cell–positive standard genes than podocyte-positive standard genes in IgAN. Principal coordinate analysis of expression data revealed clear separation of patient and control samples on the basis of mesangial but not podocyte cell–positive standard genes. -
Microtubular Dysfunction and Male Infertility
Review Article pISSN: 2287-4208 / eISSN: 2287-4690 World J Mens Health Published online Oct 22, 2018 https://doi.org/10.5534/wjmh.180066 Microtubular Dysfunction and Male Infertility Sezgin Gunes1,7 , Pallav Sengupta2,7 , Ralf Henkel3,7 , Aabed Alguraigari4,7 , Mariana Marques Sinigaglia5,7 , Malik Kayal6,7 , Ahmad Joumah6,7 , Ashok Agarwal7 1Department of Medical Biology, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey, 2Department of Physiology, Faculty of Medicine, MAHSA University, Selangor, Malaysia, 3Department of Medical Bioscience, University of the Western Cape, Bellville, South Africa, 4Batterjee Medical College, Jeddah, Saudi Arabia, 5University of Sao Paulo, Sao Paulo, Brazil, 6Alfaisal University Medical School, Riyadh, Saudi Arabia, 7American Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH, USA Microtubules are the prime component of the cytoskeleton along with microfilaments. Being vital for organelle transport and cellular divisions during spermatogenesis and sperm motility process, microtubules ascertain functional capacity of sperm. Also, microtubule based structures such as axoneme and manchette are crucial for sperm head and tail formation. This review (a) presents a concise, yet detailed structural overview of the microtubules, (b) analyses the role of microtubule structures in various male reproductive functions, and (c) presents the association of microtubular dysfunctions with male infertility. Consid- ering the immense importance of microtubule structures in the formation and maintenance -
Cargo Specific Regulation of Cytoplasmic Dynein by Effector Proteins
University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2018 Cargo Specific Regulation Of Cytoplasmic Dynein By Effector Proteins Mara Olenick University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Biochemistry Commons, Biophysics Commons, and the Cell Biology Commons Recommended Citation Olenick, Mara, "Cargo Specific Regulation Of Cytoplasmic Dynein By Effector Proteins" (2018). Publicly Accessible Penn Dissertations. 3167. https://repository.upenn.edu/edissertations/3167 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/3167 For more information, please contact [email protected]. Cargo Specific Regulation Of Cytoplasmic Dynein By Effector Proteins Abstract Axonal transport is vital for the development and survival of neurons. The transport of cargo and organelles from the axon to the cell body is driven almost completely by the molecular motor, cytoplasmic dynein. Yet, it remains unclear how dynein is spatially and temporally regulated given the variety of cargo that must be properly localized to maintain cellular function. Previous work has suggested that adaptor proteins provide a mechanism for cargo-specific egulationr of motors. During my thesis work, I have investigated the role of mammalian Hook proteins, Hook1 and Hook3, as potential motor adaptors. Using optogenetic and single molecule assays, I found that Hook proteins interact with both dynein and dynactin, to effectively activate dynein motility, inducing longer run lengths and higher velocities than the previously characterized dynein activator, BICD2. In addition, I found that complex formation requires the N-terminal domain of Hook proteins, which resembles the calponin-homology domain of EB proteins yet cannot bind directly to microtubules. -
Dynein Activators and Adaptors at a Glance Mara A
© 2019. Published by The Company of Biologists Ltd | Journal of Cell Science (2019) 132, jcs227132. doi:10.1242/jcs.227132 CELL SCIENCE AT A GLANCE Dynein activators and adaptors at a glance Mara A. Olenick and Erika L. F. Holzbaur* ABSTRACT ribonucleoprotein particles for BICD2, and signaling endosomes for Cytoplasmic dynein-1 (hereafter dynein) is an essential cellular motor Hook1. In this Cell Science at a Glance article and accompanying that drives the movement of diverse cargos along the microtubule poster, we highlight the conserved structural features found in dynein cytoskeleton, including organelles, vesicles and RNAs. A long- activators, the effects of these activators on biophysical parameters, standing question is how a single form of dynein can be adapted to a such as motor velocity and stall force, and the specific intracellular wide range of cellular functions in both interphase and mitosis. functions they mediate. – Recent progress has provided new insights dynein interacts with a KEY WORDS: BICD2, Cytoplasmic dynein, Dynactin, Hook1, group of activating adaptors that provide cargo-specific and/or Microtubule motors, Trafficking function-specific regulation of the motor complex. Activating adaptors such as BICD2 and Hook1 enhance the stability of the Introduction complex that dynein forms with its required activator dynactin, leading Microtubule-based transport is vital to cellular development and to highly processive motility toward the microtubule minus end. survival. Microtubules provide a polarized highway to facilitate Furthermore, activating adaptors mediate specific interactions of the active transport by the molecular motors dynein and kinesin. While motor complex with cargos such as Rab6-positive vesicles or many types of kinesins drive transport toward microtubule plus- ends, there is only one major form of dynein, cytoplasmic dynein-1, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, which drives the trafficking of a wide array of minus-end-directed USA. -
The Transformation of the Centrosome Into the Basal Body: Similarities and Dissimilarities Between Somatic and Male Germ Cells and Their Relevance for Male Fertility
cells Review The Transformation of the Centrosome into the Basal Body: Similarities and Dissimilarities between Somatic and Male Germ Cells and Their Relevance for Male Fertility Constanza Tapia Contreras and Sigrid Hoyer-Fender * Göttingen Center of Molecular Biosciences, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology-Developmental Biology, Faculty of Biology and Psychology, Georg-August University of Göttingen, 37077 Göttingen, Germany; [email protected] * Correspondence: [email protected] Abstract: The sperm flagellum is essential for the transport of the genetic material toward the oocyte and thus the transmission of the genetic information to the next generation. During the haploid phase of spermatogenesis, i.e., spermiogenesis, a morphological and molecular restructuring of the male germ cell, the round spermatid, takes place that includes the silencing and compaction of the nucleus, the formation of the acrosomal vesicle from the Golgi apparatus, the formation of the sperm tail, and, finally, the shedding of excessive cytoplasm. Sperm tail formation starts in the round spermatid stage when the pair of centrioles moves toward the posterior pole of the nucleus. The sperm tail, eventually, becomes located opposed to the acrosomal vesicle, which develops at the anterior pole of the nucleus. The centriole pair tightly attaches to the nucleus, forming a nuclear membrane indentation. An Citation: Tapia Contreras, C.; articular structure is formed around the centriole pair known as the connecting piece, situated in the Hoyer-Fender, S. The Transformation neck region and linking the sperm head to the tail, also named the head-to-tail coupling apparatus or, of the Centrosome into the Basal in short, HTCA. -
Bioinformatic Analysis Reveals the Importance of Epithelial-Mesenchymal Transition in the Development of Endometriosis
www.nature.com/scientificreports OPEN Bioinformatic analysis reveals the importance of epithelial- mesenchymal transition in the development of endometriosis Meihong Chen1,6, Yilu Zhou2,3,6, Hong Xu4, Charlotte Hill2, Rob M. Ewing2,3, Deming He1, Xiaoling Zhang1 ✉ & Yihua Wang2,3,5 ✉ Background: Endometriosis is a frequently occurring disease in women, which seriously afects their quality of life. However, its etiology and pathogenesis are still unclear. Methods: To identify key genes/ pathways involved in the pathogenesis of endometriosis, we recruited 3 raw microarray datasets (GSE11691, GSE7305, and GSE12768) from Gene Expression Omnibus database (GEO), which contain endometriosis tissues and normal endometrial tissues. We then performed in-depth bioinformatic analysis to determine diferentially expressed genes (DEGs), followed by gene ontology (GO), Hallmark pathway enrichment and protein-protein interaction (PPI) network analysis. The fndings were further validated by immunohistochemistry (IHC) staining in endometrial tissues from endometriosis or control patients. Results: We identifed 186 DEGs, of which 118 were up-regulated and 68 were down-regulated. The most enriched DEGs in GO functional analysis were mainly associated with cell adhesion, infammatory response, and extracellular exosome. We found that epithelial-mesenchymal transition (EMT) ranked frst in the Hallmark pathway enrichment. EMT may potentially be induced by infammatory cytokines such as CXCL12. IHC confrmed the down-regulation of E-cadherin (CDH1) and up-regulation of CXCL12 in endometriosis tissues. Conclusions: Utilizing bioinformatics and patient samples, we provide evidence of EMT in endometriosis. Elucidating the role of EMT will improve the understanding of the molecular mechanisms involved in the development of endometriosis. Endometriosis is a frequently occurring gynaecological disease characterised by chronic pelvic pain, dysmenor- rhea and infertility1. -
Dynein Activator Hook1 Is Required for Trafficking of BDNF-Signaling Endosomes in Neurons
ARTICLE Dynein activator Hook1 is required for trafficking of BDNF-signaling endosomes in neurons Mara A. Olenick2,3,4, Roberto Dominguez1,2,3, and Erika L.F. Holzbaur1,2,3 Axonal transport is required for neuronal development and survival. Transport from the axon to the soma is driven by the molecular motor cytoplasmic dynein, yet it remains unclear how dynein is spatially and temporally regulated. We find that the dynein effector Hook1 mediates transport of TrkB–BDNF-signaling endosomes in primary hippocampal neurons. Hook1 comigrates with a subpopulation of Rab5 endosomes positive for TrkB and BDNF, which exhibit processive retrograde motility with faster velocities than the overall Rab5 population. Knockdown of Hook1 significantly reduced the motility of BDNF-signaling endosomes without affecting the motility of other organelles. In microfluidic chambers, Hook1 depletion resulted in a significant decrease in the flux and processivity of BDNF-Qdots along the mid-axon, an effect specific for Hook1 but not Hook3. Hook1 depletion inhibited BDNF trafficking to the soma and blocked downstream BDNF- and TrkB-dependent signaling to the nucleus. Together, these studies support a model in which differential association with cargo-specific effectors efficiently regulates dynein in neurons. Introduction Axonal transport is vital for the maintenance and survival of dynactin has been suggested to play a role in cargo interaction neurons. Axons have a uniformly polarized microtubule array (Zhang et al., 2011; Yeh et al., 2012), adaptor and scaffolding pro- in which the faster-growing plus ends of microtubules are ori- teins are required to link cargo to the dynein–dynactin motor ented toward the distal terminal. -
Sperm Differentiation
International Journal of Molecular Sciences Review Sperm Differentiation: The Role of Trafficking of Proteins Maria E. Teves 1,* , Eduardo R. S. Roldan 2,*, Diego Krapf 3 , Jerome F. Strauss III 1 , Virali Bhagat 4 and Paulene Sapao 5 1 Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, VA 23298, USA; [email protected] 2 Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (CSIC), 28006 Madrid, Spain 3 Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, CO 80523, USA; [email protected] 4 Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, VA 23298, USA; [email protected] 5 Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA; [email protected] * Correspondence: [email protected] (M.E.T.); [email protected] (E.R.S.R.) Received: 4 March 2020; Accepted: 20 May 2020; Published: 24 May 2020 Abstract: Sperm differentiation encompasses a complex sequence of morphological changes that takes place in the seminiferous epithelium. In this process, haploid round spermatids undergo substantial structural and functional alterations, resulting in highly polarized sperm. Hallmark changes during the differentiation process include the formation of new organelles, chromatin condensation and nuclear shaping, elimination of residual cytoplasm, and assembly of the sperm flagella. To achieve these transformations, spermatids have unique mechanisms for protein trafficking that operate in a coordinated fashion. Microtubules and filaments of actin are the main tracks used to facilitate the transport mechanisms, assisted by motor and non-motor proteins, for delivery of vesicular and non-vesicular cargos to specific sites. -
Gene- and Tissue-Level Interactions in Normal Gastrointestinal Development and Hirschsprung Disease
Gene- and tissue-level interactions in normal gastrointestinal development and Hirschsprung disease Sumantra Chatterjeea,b,1, Priyanka Nandakumara,1, Dallas R. Auera,b, Stacey B. Gabrielc, and Aravinda Chakravartia,b,2 aCenter for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205; bCenter for Human Genetics and Genomics, New York University School of Medicine, New York, NY 10016; and cGenomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142 Contributed by Aravinda Chakravarti, November 1, 2019 (sent for review May 21, 2019; reviewed by William J. Pavan and Tatjana Sauka-Spengler) The development of the gut from endodermal tissue to an organ between the longitudinal and circular muscles, and the sub- with multiple distinct structures and functions occurs over a mucosal (Meissner’s) plexus, between the circular muscle and prolonged time during embryonic days E10.5–E14.5 in the mouse. the submucosal layer. The myenteric and submucoal plexuses During this process, one major event is innervation of the gut by provide motor innervation to both muscular layers of the gut, enteric neural crest cells (ENCCs) to establish the enteric nervous and secretomotor innervation of the mucosa nearest the lumen system (ENS). To understand the molecular processes underpinning of the gut, respectively (6). gut and ENS development, we generated RNA-sequencing profiles The many stages of gut development require numerous initiat- from wild-type mouse guts at E10.5, E12.5, and E14.5 from both ing signaling events activating transcription factors (TFs) targeting sexes. We also generated these profiles from homozygous Ret null diverse genes and pathways varying across development (7, 8).