SPEF2 Functions in Microtubule-Mediated Transport in Elongating Spermatids to Ensure Proper Male Germ Cell Differentiation Mari S
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Primepcr™Assay Validation Report
PrimePCR™Assay Validation Report Gene Information Gene Name katanin p80 (WD repeat containing) subunit B 1 Gene Symbol KATNB1 Organism Human Gene Summary Microtubules polymers of alpha and beta tubulin subunits form the mitotic spindle of a dividing cell and help to organize membranous organelles during interphase. Katanin is a heterodimer that consists of a 60 kDa ATPase (p60 subunit A 1) and an 80 kDa accessory protein (p80 subunit B 1). The p60 subunit acts to sever and disassemble microtubules while the p80 subunit targets the enzyme to the centrosome. Katanin is a member of the AAA family of ATPases. Gene Aliases KAT RefSeq Accession No. NC_000016.9, NT_010498.15 UniGene ID Hs.275675 Ensembl Gene ID ENSG00000140854 Entrez Gene ID 10300 Assay Information Unique Assay ID qHsaCIP0026589 Assay Type Probe - Validation information is for the primer pair using SYBR® Green detection Detected Coding Transcript(s) ENST00000379661 Amplicon Context Sequence CACCAAGACAGCCTGGAAGTTGCAAGAGATCGTCGCGCATGCCAGCAACGTGT CCTCACTGGTGCTGGGCAAAGCCTCCGGGCGGCTGCTGGCTACAGGCGGGGAT GACTGCCGCGTCAACCTGTGGTCCATCAACAAGCCCAACTGCATCATGAGCCTG ACG Amplicon Length (bp) 132 Chromosome Location 16:57771173-57778314 Assay Design Intron-spanning Purification Desalted Validation Results Efficiency (%) 100 R2 0.9991 cDNA Cq 21.47 cDNA Tm (Celsius) 89 Page 1/5 PrimePCR™Assay Validation Report gDNA Cq 35.43 Specificity (%) 100 Information to assist with data interpretation is provided at the end of this report. Page 2/5 PrimePCR™Assay Validation Report KATNB1, Human Amplification -
KIAA0556 Is a Novel Ciliary Basal Body Component Mutated in Joubert Syndrome Anna A
Sanders et al. Genome Biology (2015) 16:293 DOI 10.1186/s13059-015-0858-z RESEARCH Open Access KIAA0556 is a novel ciliary basal body component mutated in Joubert syndrome Anna A. W. M. Sanders1†, Erik de Vrieze2,3†, Anas M. Alazami4†, Fatema Alzahrani4, Erik B. Malarkey5, Nasrin Sorusch6, Lars Tebbe6, Stefanie Kuhns1, Teunis J. P. van Dam7, Amal Alhashem8, Brahim Tabarki8, Qianhao Lu9,10, Nils J. Lambacher1, Julie E. Kennedy1, Rachel V. Bowie1, Lisette Hetterschijt2,3, Sylvia van Beersum3,11, Jeroen van Reeuwijk3,11, Karsten Boldt12, Hannie Kremer2,3,11, Robert A. Kesterson13, Dorota Monies4, Mohamed Abouelhoda4, Ronald Roepman3,11, Martijn H. Huynen7, Marius Ueffing12, Rob B. Russell9,10, Uwe Wolfrum6, Bradley K. Yoder5, Erwin van Wijk2,3*, Fowzan S. Alkuraya4,14* and Oliver E. Blacque1* Abstract Background: Joubert syndrome (JBTS) and related disorders are defined by cerebellar malformation (molar tooth sign), together with neurological symptoms of variable expressivity. The ciliary basis of Joubert syndrome related disorders frequently extends the phenotype to tissues such as the eye, kidney, skeleton and craniofacial structures. Results: Using autozygome and exome analyses, we identified a null mutation in KIAA0556 in a multiplex consanguineous family with hallmark features of mild Joubert syndrome. Patient-derived fibroblasts displayed reduced ciliogenesis potential and abnormally elongated cilia. Investigation of disease pathophysiology revealed that Kiaa0556-/- null mice possess a Joubert syndrome-associated brain-restricted phenotype. Functional studies in Caenorhabditis elegans nematodes and cultured human cells support a conserved ciliary role for KIAA0556 linked to microtubule regulation. First, nematode KIAA0556 is expressed almost exclusively in ciliated cells, and the worm and human KIAA0556 proteins are enriched at the ciliary base. -
Dual Proteome-Scale Networks Reveal Cell-Specific Remodeling of the Human Interactome
bioRxiv preprint doi: https://doi.org/10.1101/2020.01.19.905109; this version posted January 19, 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. Dual Proteome-scale Networks Reveal Cell-specific Remodeling of the Human Interactome Edward L. Huttlin1*, Raphael J. Bruckner1,3, Jose Navarrete-Perea1, Joe R. Cannon1,4, Kurt Baltier1,5, Fana Gebreab1, Melanie P. Gygi1, Alexandra Thornock1, Gabriela Zarraga1,6, Stanley Tam1,7, John Szpyt1, Alexandra Panov1, Hannah Parzen1,8, Sipei Fu1, Arvene Golbazi1, Eila Maenpaa1, Keegan Stricker1, Sanjukta Guha Thakurta1, Ramin Rad1, Joshua Pan2, David P. Nusinow1, Joao A. Paulo1, Devin K. Schweppe1, Laura Pontano Vaites1, J. Wade Harper1*, Steven P. Gygi1*# 1Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA. 2Broad Institute, Cambridge, MA, 02142, USA. 3Present address: ICCB-Longwood Screening Facility, Harvard Medical School, Boston, MA, 02115, USA. 4Present address: Merck, West Point, PA, 19486, USA. 5Present address: IQ Proteomics, Cambridge, MA, 02139, USA. 6Present address: Vor Biopharma, Cambridge, MA, 02142, USA. 7Present address: Rubius Therapeutics, Cambridge, MA, 02139, USA. 8Present address: RPS North America, South Kingstown, RI, 02879, USA. *Correspondence: [email protected] (E.L.H.), [email protected] (J.W.H.), [email protected] (S.P.G.) #Lead Contact: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.01.19.905109; this version posted January 19, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. -
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Supplementary Figure S1. Results of flow cytometry analysis, performed to estimate CD34 positivity, after immunomagnetic separation in two different experiments. As monoclonal antibody for labeling the sample, the fluorescein isothiocyanate (FITC)- conjugated mouse anti-human CD34 MoAb (Mylteni) was used. Briefly, cell samples were incubated in the presence of the indicated MoAbs, at the proper dilution, in PBS containing 5% FCS and 1% Fc receptor (FcR) blocking reagent (Miltenyi) for 30 min at 4 C. Cells were then washed twice, resuspended with PBS and analyzed by a Coulter Epics XL (Coulter Electronics Inc., Hialeah, FL, USA) flow cytometer. only use Non-commercial 1 Supplementary Table S1. Complete list of the datasets used in this study and their sources. GEO Total samples Geo selected GEO accession of used Platform Reference series in series samples samples GSM142565 GSM142566 GSM142567 GSM142568 GSE6146 HG-U133A 14 8 - GSM142569 GSM142571 GSM142572 GSM142574 GSM51391 GSM51392 GSE2666 HG-U133A 36 4 1 GSM51393 GSM51394 only GSM321583 GSE12803 HG-U133A 20 3 GSM321584 2 GSM321585 use Promyelocytes_1 Promyelocytes_2 Promyelocytes_3 Promyelocytes_4 HG-U133A 8 8 3 GSE64282 Promyelocytes_5 Promyelocytes_6 Promyelocytes_7 Promyelocytes_8 Non-commercial 2 Supplementary Table S2. Chromosomal regions up-regulated in CD34+ samples as identified by the LAP procedure with the two-class statistics coded in the PREDA R package and an FDR threshold of 0.5. Functional enrichment analysis has been performed using DAVID (http://david.abcc.ncifcrf.gov/) -
Detection of a 4 Bp Mutation in the 3'UTR Region of Goat Sox9 Gene
animals Article 0 Detection of a 4 bp Mutation in the 3 UTR Region of Goat Sox9 Gene and Its Effect on the Growth Traits Libang He 1,2, Yi Bi 1,2, Ruolan Wang 1,2, Chuanying Pan 1,2, Hong Chen 1,2, Xianyong Lan 1,2,* and Lei Qu 3,4,* 1 College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China; [email protected] 2 Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling 712100, Shaanxi, China 3 Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin 719000, Shaanxi, China 4 Life Science Research Center, Yulin University, Yulin 719000, Shaanxi, China * Correspondence: [email protected] (X.L.); [email protected] (L.Q.); Tel.: +86-137-7207-1502 (X.L.); +86-189-9226-2688 (L.Q.) Received: 4 March 2020; Accepted: 8 April 2020; Published: 13 April 2020 Simple Summary: The sex determining region Y (SRY)-type high mobility group (HMG) box 9 (Sox9) gene is critically important in the formation and development of cartilage and is considered the “main regulator” of chondrogenesis. Additionally, a large number of studies have shown that mutations in a single allele of human Sox9 can lead to campomelic dysplasia syndrome. Therefore, the mutations of Sox9 have been the subject of increasing interest among researchers. However, no studies to date have examined the association between Sox9 gene variants and growth traits in goats. Here, we detected a 4 bp indel in the 30Untranslated Regions (30UTR) region of Sox9 in Shaanbei white cashmere (SBWC) goats (n = 1109) and studied the association between this indel and growth traits. -
Microtubule-Severing Enzymes at the Cutting Edge
Commentary 2561 Microtubule-severing enzymes at the cutting edge David J. Sharp1,* and Jennifer L. Ross2 1Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA 2Department of Physics, University of Massachusetts-Amherst, 302 Hasbrouck Laboratory, Amherst, MA 01003, USA *Author for correspondence ([email protected]) Journal of Cell Science 125, 2561–2569 ß 2012. Published by The Company of Biologists Ltd doi: 10.1242/jcs.101139 Summary ATP-dependent severing of microtubules was first reported in Xenopus laevis egg extracts in 1991. Two years later this observation led to the purification of the first known microtubule-severing enzyme, katanin. Katanin homologs have now been identified throughout the animal kingdom and in plants. Moreover, members of two closely related enzyme subfamilies, spastin and fidgetin, have been found to sever microtubules and might act alongside katanins in some contexts (Roll-Mecak and McNally, 2010; Yu et al., 2008; Zhang et al., 2007). Over the past few years, it has become clear that microtubule-severing enzymes contribute to a wide range of cellular activities including mitosis and meiosis, morphogenesis, cilia biogenesis and disassembly, and migration. Thus, this group of enzymes is revealing itself to be among the most important of the microtubule regulators. This Commentary focuses on our growing understanding of how microtubule-severing enzymes contribute to the organization and dynamics of diverse microtubule arrays, as well as the structural and biophysical characteristics that afford them the unique capacity to catalyze the removal of tubulin from the interior microtubule lattice. Our goal is to provide a broader perspective, focusing on a limited number of particularly informative, representative and/or timely findings. -
Role of Phytochemicals in Colon Cancer Prevention: a Nutrigenomics Approach
Role of phytochemicals in colon cancer prevention: a nutrigenomics approach Marjan J van Erk Promotor: Prof. Dr. P.J. van Bladeren Hoogleraar in de Toxicokinetiek en Biotransformatie Wageningen Universiteit Co-promotoren: Dr. Ir. J.M.M.J.G. Aarts Universitair Docent, Sectie Toxicologie Wageningen Universiteit Dr. Ir. B. van Ommen Senior Research Fellow Nutritional Systems Biology TNO Voeding, Zeist Promotiecommissie: Prof. Dr. P. Dolara University of Florence, Italy Prof. Dr. J.A.M. Leunissen Wageningen Universiteit Prof. Dr. J.C. Mathers University of Newcastle, United Kingdom Prof. Dr. M. Müller Wageningen Universiteit Dit onderzoek is uitgevoerd binnen de onderzoekschool VLAG Role of phytochemicals in colon cancer prevention: a nutrigenomics approach Marjan Jolanda van Erk Proefschrift ter verkrijging van graad van doctor op gezag van de rector magnificus van Wageningen Universiteit, Prof.Dr.Ir. L. Speelman, in het openbaar te verdedigen op vrijdag 1 oktober 2004 des namiddags te vier uur in de Aula Title Role of phytochemicals in colon cancer prevention: a nutrigenomics approach Author Marjan Jolanda van Erk Thesis Wageningen University, Wageningen, the Netherlands (2004) with abstract, with references, with summary in Dutch ISBN 90-8504-085-X ABSTRACT Role of phytochemicals in colon cancer prevention: a nutrigenomics approach Specific food compounds, especially from fruits and vegetables, may protect against development of colon cancer. In this thesis effects and mechanisms of various phytochemicals in relation to colon cancer prevention were studied through application of large-scale gene expression profiling. Expression measurement of thousands of genes can yield a more complete and in-depth insight into the mode of action of the compounds. -
Katanin-P80 Gene Promoter Characterization and Regulation Via Elk1
Katanin-p80 Gene Promoter Characterization and Regulation via Elk1 Ece Selc¸uk., Koray Kırımtay., Derya Canbaz, Gu¨ her Is¸ık Cesur, Sirin Korulu, Arzu Karabay* Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey Abstract Katanin is an ATPase family member protein that participates in microtubule severing. It has heterodimeric structure consisting of 60 kDa (katanin-p60) and 80 kDa (katanin-p80) subunits encoded by KATNA1 and KATNB1 genes, respectively. Katanin-p60 has the enzymatic activity for microtubule severing, whereas katanin-p80 consists of multiple domains with different functions such as targeting katanin-p60 to the centrosome, augmenting microtubule severing by katanin-p60, and even suppressing microtubule severing. Despite the various important functions of katanin-p80, its transcriptional regulation has not been studied yet. Elk1 transcription factor has been shown to interact with microtubules and regulate the transcription of another microtubule severing protein, spastin. In spite of katanin’s importance, and structural and functional similarities to spastin, there is no study on the transcriptional regulation of katanin yet. In this study, we aimed to characterize KATNB1 promoter and analyze the effects of Elk1 on katanin-p80 expression. We identified a 518- bp TATA-less promoter including a critical CpG island and GC boxes as an optimal promoter, and sequential deletion of CpG island and the GC elements gradually decreased the KATNB1 promoter activity. In addition, we showed Elk1 binding on the KATNB1 promoter by EMSA. We found that Elk1 activated KATNB1 promoter, and increased both mRNA and protein levels of katanin- p80 in SH-SY5Y cells. On the other hand, KCl treatment increasing SUMOylation decreased KATNB1 promoter activity. -
Supplemental Information
Supplemental information Dissection of the genomic structure of the miR-183/96/182 gene. Previously, we showed that the miR-183/96/182 cluster is an intergenic miRNA cluster, located in a ~60-kb interval between the genes encoding nuclear respiratory factor-1 (Nrf1) and ubiquitin-conjugating enzyme E2H (Ube2h) on mouse chr6qA3.3 (1). To start to uncover the genomic structure of the miR- 183/96/182 gene, we first studied genomic features around miR-183/96/182 in the UCSC genome browser (http://genome.UCSC.edu/), and identified two CpG islands 3.4-6.5 kb 5’ of pre-miR-183, the most 5’ miRNA of the cluster (Fig. 1A; Fig. S1 and Seq. S1). A cDNA clone, AK044220, located at 3.2-4.6 kb 5’ to pre-miR-183, encompasses the second CpG island (Fig. 1A; Fig. S1). We hypothesized that this cDNA clone was derived from 5’ exon(s) of the primary transcript of the miR-183/96/182 gene, as CpG islands are often associated with promoters (2). Supporting this hypothesis, multiple expressed sequences detected by gene-trap clones, including clone D016D06 (3, 4), were co-localized with the cDNA clone AK044220 (Fig. 1A; Fig. S1). Clone D016D06, deposited by the German GeneTrap Consortium (GGTC) (http://tikus.gsf.de) (3, 4), was derived from insertion of a retroviral construct, rFlpROSAβgeo in 129S2 ES cells (Fig. 1A and C). The rFlpROSAβgeo construct carries a promoterless reporter gene, the β−geo cassette - an in-frame fusion of the β-galactosidase and neomycin resistance (Neor) gene (5), with a splicing acceptor (SA) immediately upstream, and a polyA signal downstream of the β−geo cassette (Fig. -
Chromosome Substitution Strain Assessment of a Huntington's
Mamm Genome DOI 10.1007/s00335-014-9552-9 Chromosome substitution strain assessment of a Huntington’s disease modifier locus Eliana Marisa Ramos • Marina Kovalenko • Jolene R. Guide • Jason St. Claire • Tammy Gillis • Jayalakshmi S. Mysore • Jorge Sequeiros • Vanessa C. Wheeler • Isabel Alonso • Marcy E. MacDonald Received: 26 August 2014 / Accepted: 3 December 2014 Ó The Author(s) 2015. This article is published with open access at Springerlink.com Abstract Huntington’s disease (HD) is a dominant neu- with the human 6q23–24 region, is derived from the A/J rodegenerative disorder that is due to expansion of an (AJ) strain. Crosses were performed to assess the possi- unstable HTT CAG repeat for which genome-wide genetic bility of dominantly acting chr10 AJ-B6J variants of strong scans are now revealing chromosome regions that contain effect that may modulate CAG-dependent HdhQ111/? phe- disease-modifying genes. We have explored a novel notypes. Testing of F1 progeny confirmed that a single AJ human–mouse cross-species functional prioritisation chromosome had a significant effect on the rate of body approach, by evaluating the HD modifier 6q23–24 linkage weight gain and in HdhQ111 mice the AJ chromosome was interval. This unbiased strategy employs C57BL/6J (B6J) associated subtle alterations in somatic CAG instability in HdhQ111 knock-in mice, replicates of the HD mutation, and the liver and the formation of intra-nuclear inclusions, as the C57BL/6J-chr10A/J/NaJ chromosome substitution strain well as DARPP-32 levels, in the striatum. These findings in (CSS10), in which only chromosome 10 (chr10), in synteny relatively small cohorts are suggestive of dominant chr10 AJ-B6 variants that may modify effects of the CAG expansion, and encourage a larger study with CSS10 and sub-strains. -
Application to Neuroimaging Biomarkers in Alzheimer's
The Author(s) BMC Medical Informatics and Decision Making 2017, 17(Suppl 1):61 DOI 10.1186/s12911-017-0454-0 RESEARCH Open Access Knowledge-driven binning approach for rare variant association analysis: application to neuroimaging biomarkers in Alzheimer’s disease Dokyoon Kim1,2, Anna O. Basile2, Lisa Bang1, Emrin Horgusluoglu4, Seunggeun Lee3, Marylyn D. Ritchie1,2, Andrew J. Saykin4 and Kwangsik Nho4* From The 6th Translational Bioinformatics Conference Je Ju Island, Korea. 15-17 October 2016 Abstract Background: Rapid advancement of next generation sequencing technologies such as whole genome sequencing (WGS) has facilitated the search for genetic factors that influence disease risk in the field of human genetics. To identify rare variants associated with human diseases or traits, an efficient genome-wide binning approach is needed. In this study we developed a novel biological knowledge-based binning approach for rare-variant association analysis and then applied the approach to structural neuroimaging endophenotypes related to late-onset Alzheimer’sdisease(LOAD). Methods: For rare-variant analysis, we used the knowledge-driven binning approach implemented in Bin-KAT, an automated tool, that provides 1) binning/collapsing methods for multi-level variant aggregation with a flexible, biologically informed binning strategy and 2) an option of performing unified collapsing and statistical rare variant analyses in one tool. A total of 750 non-Hispanic Caucasian participants from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) cohort who had both WGS data and magnetic resonance imaging (MRI) scans were used in this study. Mean bilateral cortical thickness of the entorhinal cortex extracted from MRI scans was used as an AD-related neuroimaging endophenotype. -
Classification and Evolution of P-Loop Gtpases and Related Atpases Detlefd.Leipe,Yurii.Wolf,Eugenev.Koonin*Andl.Aravind
doi:10.1006/jmbi.2001.5378availableonlineathttp://www.idealibrary.comon J. Mol. Biol. (2002) 317, 41±72 Classification and Evolution of P-loop GTPases and Related ATPases DetlefD.Leipe,YuriI.Wolf,EugeneV.Koonin*andL.Aravind National Center for Sequences and available structures were compared for all the widely dis- Biotechnology Information tributed representatives of the P-loop GTPases and GTPase-related pro- National Library of Medicine teins with the aim of constructing an evolutionary classi®cation for this National Institutes of Health superclass of proteins and reconstructing the principal events in their Bethesda, MD 20894, USA evolution. The GTPase superclass can be divided into two large classes, each of which has a unique set of sequence and structural signatures (synapomorphies). The ®rst class, designated TRAFAC (after translation factors) includes enzymes involved in translation (initiation, elongation, and release factors), signal transduction (in particular, the extended Ras- like family), cell motility, and intracellular transport. The second class, designated SIMIBI (after signal recognition particle, MinD, and BioD), consists of signal recognition particle (SRP) GTPases, the assemblage of MinD-like ATPases, which are involved in protein localization, chromo- some partitioning, and membrane transport, and a group of metabolic enzymes with kinase or related phosphate transferase activity. These two classes together contain over 20 distinct families that are further subdi- vided into 57 subfamilies (ancient lineages) on the basis of conserved sequence motifs, shared structural features, and domain architectures. Ten subfamilies show a universal phyletic distribution compatible with presence in the last universal common ancestor of the extant life forms (LUCA). These include four translation factors, two OBG-like GTPases, the YawG/YlqF-like GTPases (these two subfamilies also consist of pre- dicted translation factors), the two signal-recognition-associated GTPases, and the MRP subfamily of MinD-like ATPases.