Characterization of NIP2/Centrobin, a Novel Substrate of Nek2, and Its Potential Role in Microtubule Stabilization
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PARSANA-DISSERTATION-2020.Pdf
DECIPHERING TRANSCRIPTIONAL PATTERNS OF GENE REGULATION: A COMPUTATIONAL APPROACH by Princy Parsana A dissertation submitted to The Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland July, 2020 © 2020 Princy Parsana All rights reserved Abstract With rapid advancements in sequencing technology, we now have the ability to sequence the entire human genome, and to quantify expression of tens of thousands of genes from hundreds of individuals. This provides an extraordinary opportunity to learn phenotype relevant genomic patterns that can improve our understanding of molecular and cellular processes underlying a trait. The high dimensional nature of genomic data presents a range of computational and statistical challenges. This dissertation presents a compilation of projects that were driven by the motivation to efficiently capture gene regulatory patterns in the human transcriptome, while addressing statistical and computational challenges that accompany this data. We attempt to address two major difficulties in this domain: a) artifacts and noise in transcriptomic data, andb) limited statistical power. First, we present our work on investigating the effect of artifactual variation in gene expression data and its impact on trans-eQTL discovery. Here we performed an in-depth analysis of diverse pre-recorded covariates and latent confounders to understand their contribution to heterogeneity in gene expression measurements. Next, we discovered 673 trans-eQTLs across 16 human tissues using v6 data from the Genotype Tissue Expression (GTEx) project. Finally, we characterized two trait-associated trans-eQTLs; one in Skeletal Muscle and another in Thyroid. Second, we present a principal component based residualization method to correct gene expression measurements prior to reconstruction of co-expression networks. -
Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino-Like Mouse Models: Tracking the Role of the Hairless Gene
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 5-2006 Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino-like Mouse Models: Tracking the Role of the Hairless Gene Yutao Liu University of Tennessee - Knoxville Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Part of the Life Sciences Commons Recommended Citation Liu, Yutao, "Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino- like Mouse Models: Tracking the Role of the Hairless Gene. " PhD diss., University of Tennessee, 2006. https://trace.tennessee.edu/utk_graddiss/1824 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Yutao Liu entitled "Molecular and Physiological Basis for Hair Loss in Near Naked Hairless and Oak Ridge Rhino-like Mouse Models: Tracking the Role of the Hairless Gene." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the requirements for the degree of Doctor of Philosophy, with a major in Life Sciences. Brynn H. Voy, Major Professor We have read this dissertation and recommend its acceptance: Naima Moustaid-Moussa, Yisong Wang, Rogert Hettich Accepted for the Council: Carolyn R. -
Par6c Is at the Mother Centriole and Controls Centrosomal Protein
860 Research Article Par6c is at the mother centriole and controls centrosomal protein composition through a Par6a-dependent pathway Vale´rian Dormoy, Kati Tormanen and Christine Su¨ tterlin* Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697-2300, USA *Author for correspondence ([email protected]) Accepted 3 December 2012 Journal of Cell Science 126, 860–870 ß 2013. Published by The Company of Biologists Ltd doi: 10.1242/jcs.121186 Summary The centrosome contains two centrioles that differ in age, protein composition and function. This non-membrane bound organelle is known to regulate microtubule organization in dividing cells and ciliogenesis in quiescent cells. These specific roles depend on protein appendages at the older, or mother, centriole. In this study, we identified the polarity protein partitioning defective 6 homolog gamma (Par6c) as a novel component of the mother centriole. This specific localization required the Par6c C-terminus, but was independent of intact microtubules, the dynein/dynactin complex and the components of the PAR polarity complex. Par6c depletion resulted in altered centrosomal protein composition, with the loss of a large number of proteins, including Par6a and p150Glued, from the centrosome. As a consequence, there were defects in ciliogenesis, microtubule organization and centrosome reorientation during migration. Par6c interacted with Par3 and aPKC, but these proteins were not required for the regulation of centrosomal protein composition. Par6c also associated with Par6a, which controls protein recruitment to the centrosome through p150Glued. Our study is the first to identify Par6c as a component of the mother centriole and to report a role of a mother centriole protein in the regulation of centrosomal protein composition. -
Cep57, a NEDD1-Binding Pericentriolar Material Component, Is Essential for Spindle Pole Integrity
Cell Research (2012) :1-12. © 2012 IBCB, SIBS, CAS All rights reserved 1001-0602/12 $ 32.00 npg ORIGINAL ARTICLE www.nature.com/cr Cep57, a NEDD1-binding pericentriolar material component, is essential for spindle pole integrity Qixi Wu1, *, Runsheng He1, *, Haining Zhou1, Albert CH Yu2, Bo Zhang1, Junlin Teng1, Jianguo Chen1, 3 1The State Key Laboratory of Biomembrane and Membrane Bioengineering and The Key Laboratory of Cell Proliferation and Dif- ferentiation of Ministry of Education, College of Life Sciences, Peking University, Beijing 100871, China; 2Department of Neurobi- ology, Neuroscience Research Institute, School of Basic Medical Sciences, Peking University, Beijing 100191, China; 3The Center for Theoretical Biology, Peking University, Beijing 100871, China Formation of a bipolar spindle is indispensable for faithful chromosome segregation and cell division. Spindle in- tegrity is largely dependent on the centrosome and the microtubule network. Centrosome protein Cep57 can bundle microtubules in mammalian cells. Its related protein (Cep57R) in Xenopus was characterized as a stabilization factor for microtubule-kinetochore attachment. Here we show that Cep57 is a pericentriolar material (PCM) component. Its interaction with NEDD1 is necessary for the centrosome localization of Cep57. Depletion of Cep57 leads to unaligned chromosomes and a multipolar spindle, which is induced by PCM fragmentation. In the absence of Cep57, cen- trosome microtubule array assembly activity is weakened, and the spindle length and microtubule density decrease. As a spindle microtubule-binding protein, Cep57 is also responsible for the proper organization of the spindle micro- tubule and localization of spindle pole focusing proteins. Collectively, these results suggest that Cep57, as a NEDD1- binding centrosome component, could function as a spindle pole- and microtubule-stabilizing factor for establishing robust spindle architecture. -
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. -
Genomic Discovery of an Evolutionarily Programmed Modality for Small-Molecule Targeting of an Intractable Protein Surface
Genomic discovery of an evolutionarily programmed modality for small-molecule targeting of an intractable protein surface Uddhav K. Shigdela,1,2, Seung-Joo Leea,1,3, Mathew E. Sowaa,1,4, Brian R. Bowmana,1,5, Keith Robisona,6, Minyun Zhoua,7, Khian Hong Puaa,8, Dylan T. Stilesa,6, Joshua A. V. Blodgetta,9, Daniel W. Udwarya,10, Andrew T. Rajczewskia,11, Alan S. Manna,12, Siavash Mostafavia,13, Tara Hardyb, Sukrat Aryab,14, Zhigang Wenga,15, Michelle Stewarta,16, Kyle Kenyona,6, Jay P. Morgensterna,6, Ende Pana,17, Daniel C. Graya,6, Roy M. Pollocka,4, Andrew M. Fryb, Richard D. Klausnerc,18, Sharon A. Townsona,19, and Gregory L. Verdinea,d,e,f,2,18,20 Contributed by Richard D. Klausner, April 21, 2020 (sent for review April 8, 2020; reviewed by Chuan He and Ben Shen) The vast majority of intracellular protein targets are refractory toward small-molecule therapeutic engagement, and additional Author contributions: U.K.S., S.-J.L., M.E.S., B.R.B., K.R., Z.W., M.S., D.C.G., R.M.P., A.M.F., R.D.K., S.A.T., and G.L.V. designed research; U.K.S., S.-J.L., M.E.S., K.R., M.Z., K.H.P., D.T.S., therapeutic modalities are needed to overcome this deficiency. J.A.V.B., D.W.U., A.T.R., A.S.M., S.M., T.H., S.A., K.K., J.P.M., E.P., R.D.K., and G.L.V. performed Here, the identification and characterization of a natural product, research; M.E.S., D.T.S., and A.M.F. -
Polo-Like Kinase 1 Regulates Nlp, a Centrosome Protein Involved in Microtubule Nucleation
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Developmental Cell, Vol. 5, 113–125, July, 2003, Copyright 2003 by Cell Press Polo-like Kinase 1 Regulates Nlp, a Centrosome Protein Involved in Microtubule Nucleation Martina Casenghi,1,2 Patrick Meraldi,1,2,3 Rieder, 1999; Palazzo et al., 2000). Although centrosome Ulrike Weinhart,1 Peter I. Duncan,1,4 maturation is important for mitotic spindle formation, the Roman Ko¨ rner,1 and Erich A. Nigg1,* underlying mechanisms remain largely unknown. Two 1Department of Cell Biology protein kinases, Polo-like kinase 1 (Plk1; Lane and Nigg, Max Planck Institute of Biochemistry 1996; Sunkel and Glover, 1988) and Aurora-A (Berdnik Am Klopferspitz 18a and Knoblich, 2002; Hannak et al., 2001), as well as D-82152 Martinsried protein phosphatase 4 (Helps et al., 1998; Sumiyoshi Germany et al., 2002), have been implicated in the regulation of centrosome maturation, but the substrates of these en- zymes await identification. Also acting at the G2/M tran- sition, the protein kinase Nek2 and a member of the Summary phosphatase 1 family contribute to regulate centrosome separation, in part through phosphorylation of the centri- In animal cells, most microtubules are nucleated at ole-associated protein C-Nap1 (Fry et al., 1998b; Helps centrosomes. At the onset of mitosis, centrosomes et al., 2000; Mayor et al., 2000). undergo a structural reorganization, termed matura- The discovery of ␥-tubulin and ␥-tubulin-containing tion, which leads to increased microtubule nucleation multiprotein complexes has greatly advanced our un- activity. -
Centriole Overduplication Is the Predominant Mechanism Leading to Centrosome Amplification in Melanoma
Published OnlineFirst January 12, 2018; DOI: 10.1158/1541-7786.MCR-17-0197 Oncogenes and Tumor Suppressors Molecular Cancer Research Centriole Overduplication is the Predominant Mechanism Leading to Centrosome Amplification in Melanoma Ryan A. Denu1,2, Maria Shabbir3, Minakshi Nihal3, Chandra K. Singh3, B. Jack Longley3,4,5, Mark E. Burkard2,4, and Nihal Ahmad3,4,5 Abstract Centrosome amplification (CA) is common in cancer and can evaluated. PLK4 is significantly overexpressed in melanoma com- arise by centriole overduplication or by cell doubling events, pared with benign nevi and in a panel of human melanoma cell including the failure of cell division and cell–cell fusion. To assess lines (A375, Hs294T, G361, WM35, WM115, 451Lu, and SK-MEL- the relative contributions of these two mechanisms, the number of 28) compared with normal human melanocytes. Interestingly, centrosomes with mature/mother centrioles was examined by although PLK4 expression did not correlate with CA in most cases, immunofluorescence in a tissue microarray of human melanomas treatment of melanoma cells with a selective small-molecule PLK4 and benign nevi (n ¼ 79 and 17, respectively). The centrosomal inhibitor (centrinone B) significantly decreased cell proliferation. protein 170 (CEP170) was used to identify centrosomes with The antiproliferative effects of centrinone B were also accompa- mature centrioles; this is expected to be present in most centro- nied by induction of apoptosis. somes with cell doubling, but on fewer centrosomes with over- duplication. Using this method, it was determined that the major- Implications: This study demonstrates that centriole overdupli- ity of CA in melanoma can be attributed to centriole overduplica- cation is the predominant mechanism leading to centrosome tion rather than cell doubling events. -
Coordination of Centrosome Homeostasis and DNA Repair Is Intact in MCF-7 and Disrupted in MDA-MB 231 Breast Cancer Cells
Published OnlineFirst April 13, 2010; DOI: 10.1158/0008-5472.CAN-09-3800 Tumor and Stem Cell Biology Cancer Research Coordination of Centrosome Homeostasis and DNA Repair Is Intact in MCF-7 and Disrupted in MDA-MB 231 Breast Cancer Cells Ilie D. Acu1, Tieju Liu1,3, Kelly Suino-Powell1,4, Steven M. Mooney1, Antonino B. D'Assoro1, Nicholas Rowland1, Alysson R. Muotri5, Ricardo G. Correa6, Yun Niu3, Rajiv Kumar1,2, and Jeffrey L. Salisbury1 Abstract When cells encounter substantial DNA damage, critical cell cycle events are halted while DNA repair mechanisms are activated to restore genome integrity. Genomic integrity also depends on proper assembly and function of the bipolar mitotic spindle, which is required for equal chromosome segregation. Failure to execute either of these processes leads to genomic instability, aging, and cancer. Here, we show that following DNA damage in the breast cancer cell line MCF-7, the centrosome protein centrin2 moves from the cytoplasm and accumulates in the nucleus in a xeroderma pigmentosum complementation group C protein (XPC)– dependent manner, reducing the available cytoplasmic pool of this key centriole protein and preventing cen- trosome amplification. MDA-MB 231 cells do not express XPC and fail to move centrin into the nucleus following DNA damage. Reintroduction of XPC expression in MDA-MB 231 cells rescues nuclear centrin2 sequestration and reestablishes control against centrosome amplification, regardless of mutant p53 status. Importantly, the capacity to repair DNA damage was also dependent on the availability of centrin2 in the nucleus. These observations show that centrin and XPC cooperate in a reciprocal mechanism to coordinate centrosome homeostasis and DNA repair and suggest that this process may provide a tractable target to develop treatments to slow progression of cancer and aging. -
CENTROSOME NUMBER HOMEOSTASIS: LESSONS from CEP135 ISOFORM DYSREGULATION in BREAST CANCER by DIVYA GANAPATHI SANKARAN Bachelor
CENTROSOME NUMBER HOMEOSTASIS: LESSONS FROM CEP135 ISOFORM DYSREGULATION IN BREAST CANCER By DIVYA GANAPATHI SANKARAN Bachelor of Technology, Anna University, India, 2013 A thesis submitted to the Faculty of the Graduate School of the University of Colorado in partial fulfillment of the requirements for the degree of Doctor of Philosophy Cancer Biology Program 2019 This thesis for the Doctor of Philosophy degree by Divya Ganapathi Sankaran has been approved for the Cancer Biology Program By Rytis Prekeris, Chair Jeffrey Moore David Bentley Heide Ford Mary Reyland Chad G Pearson, Advisor Date: 05/17/2019 ii Ganapathi Sankaran, Divya (Ph.D., Cancer Biology) Centrosome Number Homeostasis: Lessons from CEP135 Isoform Dysregulation in Breast Cancer Thesis Directed by Associate Professor Chad G. Pearson ABSTRACT The centrosome, comprised of two centrioles surrounded by pericentriolar material, is the cell’s central microtubule organizing center. Centrosome duplication is coupled with the cell cycle such that centrosomes duplicate once in S phase. Loss of such coupling produces supernumerary centrosomes, a condition called centrosome amplification (CA). CA can promote hallmarks of tumorigenesis. In this thesis, I investigate the contribution of centriole overduplication to CA and its consequences on microtubule organization and genomic stability in breast cancer cells. CEP135, a centriole assembly protein, is dysregulated in some breast cancers. We previously identified a short isoform of CEP135, CEP135mini that represses centriole duplication. CEP135mini represses centriole duplication by limiting the localization of essential proteins required for centriole duplication. Interestingly, the relative level of CEP135full to CEP135mini (the CEP135full:mini ratio) is higher in centrosome amplified breast cancer cell lines. -
NSDHL-Containing Duplication at Xq28 in a Male Patient with Autism
Hu et al. BMC Medical Genetics (2018) 19:192 https://doi.org/10.1186/s12881-018-0705-7 CASEREPORT Open Access NSDHL-containing duplication at Xq28 in a male patient with autism spectrum disorder: a case report Chun-Chun Hu1, Yun-Jun Sun2*, Chun-xue Liu1, Bing-rui Zhou1, Chun-yang Li1, Qiong Xu1 and Xiu Xu1* Abstract Background: Autism spectrum disorder (ASD) is a neurodevelopmental disorder in which genetics plays a key aetiological role. The gene encoding NAD(P)H steroid dehydrogenase-like protein (NSDHL) is expressed in developing cortical neurons and glia, and its mutation may result in intellectual disability or congenital hemidysplasia. Case presentation: An 8-year-old boy presented with a 260-kb NSDHL-containing duplication at Xq28 (151,868,909 – 152,129,300) inherited from his mother. His clinical features included defects in social communication and interaction, restricted interests, attention deficit, impulsive behaviour, minor facial anomalies and serum free fatty acid abnormality. Conclusion: This is the first report of an ASD patient with a related NSDHL-containing duplication at Xq28. Further studies and case reports are required for genetic research to demonstrate that duplication as well as mutation can cause neurodevelopmental diseases. Keywords: Xq28 duplication, NSDHL, Autism, CNV Background 300005), located at Xq28, causing severe X-linked intellec- Autism spectrum disorder (ASD) is a neurodevelopmental tual disability (XLID) [10], and its loss of function causes disorder that is defined in DSM-5 [1] as persistent deficits Rett syndrome (OMIM: 613454) [11, 12]. Duplication of in social communication and social interaction across chromosome 15q11–13, which includes a series of im- multiple contexts in conjunction with restricted, repetitive printing and non-imprinting genes, results in the recur- patterns, interests, or activities as manifested by at least rent cytogenetic abnormalities associated with ASD and two prototypically inflexible behaviours [2]. -
S41467-019-10037-Y.Pdf
ARTICLE https://doi.org/10.1038/s41467-019-10037-y OPEN Feedback inhibition of cAMP effector signaling by a chaperone-assisted ubiquitin system Laura Rinaldi1, Rossella Delle Donne1, Bruno Catalanotti 2, Omar Torres-Quesada3, Florian Enzler3, Federica Moraca 4, Robert Nisticò5, Francesco Chiuso1, Sonia Piccinin5, Verena Bachmann3, Herbert H Lindner6, Corrado Garbi1, Antonella Scorziello7, Nicola Antonino Russo8, Matthis Synofzik9, Ulrich Stelzl 10, Lucio Annunziato11, Eduard Stefan 3 & Antonio Feliciello1 1234567890():,; Activation of G-protein coupled receptors elevates cAMP levels promoting dissociation of protein kinase A (PKA) holoenzymes and release of catalytic subunits (PKAc). This results in PKAc-mediated phosphorylation of compartmentalized substrates that control central aspects of cell physiology. The mechanism of PKAc activation and signaling have been largely characterized. However, the modes of PKAc inactivation by regulated proteolysis were unknown. Here, we identify a regulatory mechanism that precisely tunes PKAc stability and downstream signaling. Following agonist stimulation, the recruitment of the chaperone- bound E3 ligase CHIP promotes ubiquitylation and proteolysis of PKAc, thus attenuating cAMP signaling. Genetic inactivation of CHIP or pharmacological inhibition of HSP70 enhances PKAc signaling and sustains hippocampal long-term potentiation. Interestingly, primary fibroblasts from autosomal recessive spinocerebellar ataxia 16 (SCAR16) patients carrying germline inactivating mutations of CHIP show a dramatic dysregulation of PKA signaling. This suggests the existence of a negative feedback mechanism for restricting hormonally controlled PKA activities. 1 Department of Molecular Medicine and Medical Biotechnologies, University Federico II, 80131 Naples, Italy. 2 Department of Pharmacy, University Federico II, 80131 Naples, Italy. 3 Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, A-6020 Innsbruck, Austria.