DOCSLIB.ORG

Candida Albicans Chromosomal Loci in Conversion to Maintain Centromere

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Candida Albicans Chromosomal Loci in Conversion to Maintain Centromere Downloaded from genome.cshlp.org on March 4, 2013 - Published by Cold Spring Harbor Laboratory Press Efficient neocentromere formation is suppressed by gene conversion to maintain centromere function at native physical chromosomal loci in Candida albicans Jitendra Thakur and Kaustuv Sanyal Genome Res. published online February 25, 2013 Access the most recent version at doi:10.1101/gr.141614.112 P<P Published online February 25, 2013 in advance of the print journal. Creative This article is distributed exclusively by Cold Spring Harbor Laboratory Press Commons for the first six months after the full-issue publication date (see License http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as described at http://creativecommons.org/licenses/by-nc/3.0/. Email alerting Receive free email alerts when new articles cite this article - sign up in the box at the service top right corner of the article or click here Advance online articles have been peer reviewed and accepted for publication but have not yet appeared in the paper journal (edited, typeset versions may be posted when available prior to final publication). Advance online articles are citable and establish publication priority; they are indexed by PubMed from initial publication. Citations to Advance online articles must include the digital object identifier (DOIs) and date of initial publication. To subscribe to Genome Research go to: http://genome.cshlp.org/subscriptions © 2013, Published by Cold Spring Harbor Laboratory Press Downloaded from genome.cshlp.org on March 4, 2013 - Published by Cold Spring Harbor Laboratory Press Research Efficient neocentromere formation is suppressed by gene conversion to maintain centromere function at native physical chromosomal loci in Candida albicans Jitendra Thakur and Kaustuv Sanyal1 Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560 064, India CENPA/Cse4 assembles centromeric chromatin on diverse DNA. CENPA chromatin is epigenetically propagated on unique and different centromere DNA sequences in a pathogenic yeast Candida albicans. Formation of neocentromeres on DNA, nonhomologous to native centromeres, indicates a role of non-DNA sequence determinants in CENPA deposition. Neocentromeres have been shown to form at multiple loci in C. albicans when a native centromere was deleted. However, the process of site selection for CENPA deposition on native or neocentromeres in the absence of defined DNA sequences remains elusive. By systematic deletion of CENPA chromatin-containing regions of variable length of different chromo- somes, followed by mapping of neocentromere loci in C. albicans and its related species Candida dubliniensis, which share similar centromere properties, we demonstrate that the chromosomal location is an evolutionarily conserved primary determinant of CENPA deposition. Neocentromeres on the altered chromosome are always formed close to the site which was once occupied by the native centromere. Interestingly, repositioning of CENPA chromatin from the neocentromere to the native centromere occurs by gene conversion in C. albicans. [Supplemental material is available for this article.] A functional centromere, the chromosomal site where a kineto- Neocentromere formation on a non-native locus takes place chore assembles and attaches to spindle microtubules to facilitate only in the absence of the functional native centromere in a nor- proper chromosome segregation, is formed only once on each mal cell (Ishii et al. 2008; Ketel et al. 2009). The mechanism that monocentric chromosome in normal cells. Occasionally, dicentric suppresses neocentromere loci in the presence of the functional chromosomes are formed in a diseased state such as in cancerous native centromere remains largely unknown. In contrast to short cells that show high genome instability (Shen 2011). The mecha- point centromeres of budding yeast Saccharomyces cerevisiae that nism that assures the presence of only one functional centromere are genetically regulated, repetitive regional centromeres of most in a chromosome is largely unknown. While centromeres perform other eukaryotes including fission yeast Schizosaccharomyces an indispensable function in chromosome segregation, underlying pombe, Drosophila, plants, and humans are epigenetically regulated centromeric sequences are highly divergent (Henikoff et al. 2001). (Black and Cleveland 2011). Many epigenetic determinants of The presence of CENPA, a variant of histone H3, at centromeric centromere function such as RNA interference, H3K9Me2-marked chromatin is a conserved feature of all eukaryotic chromosomes pericentric heterochromatin, and DNA methylation have been (Stimpson and Sullivan 2010; Black and Cleveland 2011). How- identified in several organisms (Lachner et al. 2001; Nakayama ever, the mechanism of CENPA recruitment in yeast to humans et al. 2001; Wong et al. 2006; Folco et al. 2008; Gopalakrishnan may not be universal (Sanyal 2012). et al. 2009; Roy and Sanyal 2011). Two closely related human path- A landmark discovery of neocentromere formation on a locus ogenic budding yeasts, Candida albicans and Candida dubliniensis, nonhomologous to the native centromere in an altered ‘‘acentric’’ carry 3- to 5-kb-long unique centromeres that lack specific sequence chromosome found in a boy with a learning disability provided motifs, characteristics of point centromeres, as well as features as- strong evidence that non-DNA sequence determinants can play sociated with regional centromeres such as repeat elements, DNA a role in centromere specification (Voullaire et al. 1993). Since the methylation, H3K9Me2-mediated heterochromatin, or CENP-B discovery of the first human neocentromere, several neocentro- proteins (Sanyal and Carbon 2002; Sanyal et al. 2004; Baum et al. meres have been identified in humans, and the occurrence of 2006; Padmanabhan et al. 2008). These short regional centromeres neocentromeres has been reported in fungal, animal, and plant of C. albicans have been shown to be regulated epigenetically species as well (Marshall et al. 2008; Marshall and Choo 2009). (Baum et al. 2006). However, the nature of epigenetic factors re- Human neocentromeres also contain most other proteins required mains to be determined. Neocentromere formation at multiple for proper kinetochore formation (Alonso et al. 2007). Thus neo- ectopic loci has been shown to be highly efficient in C. albicans centromere formation provides an excellent model for the study of (Ketel et al. 2009). Thus, the C. albicans neocentromere provides an the determinants of CENPA deposition that forms centromeric attractive system for the study of enigmatic epigenetic regulatory chromatin. factors involved in formation of CENPA chromatin. More interestingly, centromeres of C. albicans have under- gone rapid divergence from C. dubliniensis (they diverged from 1 Corresponding author each other ;20 million years ago) (Padmanabhan et al. 2008). Such E-mail [email protected] Article published online before print. Article, supplemental material, and publi- rapid evolution of centromeres reveals a remarkable plasticity for cation date are at http://www.genome.org/cgi/doi/10.1101/gr.141614.112. DNA sequences in centromere function. A similar divergence in 23:000–000 Ó 2013, Published by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/13; www.genome.org Genome Research 1 www.genome.org Downloaded from genome.cshlp.org on March 4, 2013 - Published by Cold Spring Harbor Laboratory Press Thakur and Sanyal centromeric sequences has been reported in closely related fungal involvement of chromosomal locations in determining centro- (Schizosaccahromyces sp.), plant (Oryza sativa and O. brachyantha), meres’ identity in Candida. and animal (Muscaroli and other mouse species) species, and even in closely related lineages of the Saccharomyces paradoxus (Kipling Formation of centromeric chromatin on a DNA sequence et al. 1995; Lee et al. 2005; Bensasson et al. 2008; Rhind et al. 2011). is context-dependent Asymmetric female meiosis has been proposed to be the drive for selfish centromeres to gain a transmission advantage that leads to To test if a specific chromosomal location per se, irrespective of rapid centromeric evolution (Henikoff et al. 2001). However, the the DNA sequence present, could be an epigenetic determinant for process responsible for the rapid evolution of CENPA-binding centromere formation in Candida, a 1.4-kb URA3 gene sequence regions in lineages of the S. paradoxus with symmetric meio- was integrated into CEN7 (coordinates: Assembly 21 CaChr7, sis (Bensasson et al. 2008) and closely related C. albicans and 427233) in the C. albicans RM1000AH strain (Fig. 1A; Sanyal et al. C. dubliniensis which lack any detectable meiotic cycle remains 2004), and the expected integration was verified by Southern unknown. analysis (Supplemental Fig. S2A). Each homolog of chromosome 7 In the present study, a comprehensive analysis of neo- (Chr7) is marked with a unique marker ARG4 or HIS1 at the same centromere formation identified physical chromosomal location location, unlinked to CEN7 and present ;450 kb away from CEN7 as a novel epigenetic factor that regulates CENPA deposition at on the right arm of Chr7 in RM1000AH. The frequency of chro- Candida centromeres. A comparative analysis revealed that cen- mosome loss was monitored in transformants
Load more

Recommended publications
  • Gene Knockdown of CENPA Reduces Sphere Forming Ability and Stemness of Glioblastoma Initiating Cells
    Neuroepigenetics 7 (2016) 6–18 Contents lists available at ScienceDirect Neuroepigenetics journal homepage: www.elsevier.com/locate/nepig Gene knockdown of CENPA reduces sphere forming ability and stemness of glioblastoma initiating cells Jinan Behnan a,1, Zanina Grieg b,c,1, Mrinal Joel b,c, Ingunn Ramsness c, Biljana Stangeland a,b,⁎ a Department of Molecular Medicine, Institute of Basic Medical Sciences, The Medical Faculty, University of Oslo, Oslo, Norway b Norwegian Center for Stem Cell Research, Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway c Vilhelm Magnus Laboratory for Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Oslo, Norway article info abstract Article history: CENPA is a centromere-associated variant of histone H3 implicated in numerous malignancies. However, the Received 20 May 2016 role of this protein in glioblastoma (GBM) has not been demonstrated. GBM is one of the most aggressive Received in revised form 23 July 2016 human cancers. GBM initiating cells (GICs), contained within these tumors are deemed to convey Accepted 2 August 2016 characteristics such as invasiveness and resistance to therapy. Therefore, there is a strong rationale for targeting these cells. We investigated the expression of CENPA and other centromeric proteins (CENPs) in Keywords: fi CENPA GICs, GBM and variety of other cell types and tissues. Bioinformatics analysis identi ed the gene signature: fi Centromeric proteins high_CENP(AEFNM)/low_CENP(BCTQ) whose expression correlated with signi cantly worse GBM patient Glioblastoma survival. GBM Knockdown of CENPA reduced sphere forming ability, proliferation and cell viability of GICs. We also Brain tumor detected significant reduction in the expression of stemness marker SOX2 and the proliferation marker Glioblastoma initiating cells and therapeutic Ki67.
    [Show full text]
  • Centromere RNA Is a Key Component for the Assembly of Nucleoproteins at the Nucleolus and Centromere
    Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press Letter Centromere RNA is a key component for the assembly of nucleoproteins at the nucleolus and centromere Lee H. Wong,1,3 Kate H. Brettingham-Moore,1 Lyn Chan,1 Julie M. Quach,1 Melisssa A. Anderson,1 Emma L. Northrop,1 Ross Hannan,2 Richard Saffery,1 Margaret L. Shaw,1 Evan Williams,1 and K.H. Andy Choo1 1Chromosome and Chromatin Research Laboratory, Murdoch Childrens Research Institute & Department of Paediatrics, University of Melbourne, Royal Children’s Hospital, Parkville 3052, Victoria, Australia; 2Peter MacCallum Research Institute, St. Andrew’s Place, East Melbourne, Victoria 3002, Australia The centromere is a complex structure, the components and assembly pathway of which remain inadequately defined. Here, we demonstrate that centromeric ␣-satellite RNA and proteins CENPC1 and INCENP accumulate in the human interphase nucleolus in an RNA polymerase I–dependent manner. The nucleolar targeting of CENPC1 and INCENP requires ␣-satellite RNA, as evident from the delocalization of both proteins from the nucleolus in RNase-treated cells, and the nucleolar relocalization of these proteins following ␣-satellite RNA replenishment in these cells. Using protein truncation and in vitro mutagenesis, we have identified the nucleolar localization sequences on CENPC1 and INCENP. We present evidence that CENPC1 is an RNA-associating protein that binds ␣-satellite RNA by an in vitro binding assay. Using chromatin immunoprecipitation, RNase treatment, and “RNA replenishment” experiments, we show that ␣-satellite RNA is a key component in the assembly of CENPC1, INCENP, and survivin (an INCENP-interacting protein) at the metaphase centromere.
    [Show full text]
  • PDF Output of CLIC (Clustering by Inferred Co-Expression)
    PDF Output of CLIC (clustering by inferred co-expression) Dataset: Num of genes in input gene set: 13 Total number of genes: 16493 CLIC PDF output has three sections: 1) Overview of Co-Expression Modules (CEMs) Heatmap shows pairwise correlations between all genes in the input query gene set. Red lines shows the partition of input genes into CEMs, ordered by CEM strength. Each row shows one gene, and the brightness of squares indicates its correlations with other genes. Gene symbols are shown at left side and on the top of the heatmap. 2) Details of each CEM and its expansion CEM+ Top panel shows the posterior selection probability (dataset weights) for top GEO series datasets. Bottom panel shows the CEM genes (blue rows) as well as expanded CEM+ genes (green rows). Each column is one GEO series dataset, sorted by their posterior probability of being selected. The brightness of squares indicates the gene's correlations with CEM genes in the corresponding dataset. CEM+ includes genes that co-express with CEM genes in high-weight datasets, measured by LLR score. 3) Details of each GEO series dataset and its expression profile: Top panel shows the detailed information (e.g. title, summary) for the GEO series dataset. Bottom panel shows the background distribution and the expression profile for CEM genes in this dataset. Overview of Co-Expression Modules (CEMs) with Dataset Weighting Scale of average Pearson correlations Num of Genes in Query Geneset: 13. Num of CEMs: 1. 0.0 0.2 0.4 0.6 0.8 1.0 Cenpk Cenph Cenpp Cenpu Cenpn Cenpq Cenpl Apitd1
    [Show full text]
  • The Genetic Program of Pancreatic Beta-Cell Replication in Vivo
    Page 1 of 65 Diabetes The genetic program of pancreatic beta-cell replication in vivo Agnes Klochendler1, Inbal Caspi2, Noa Corem1, Maya Moran3, Oriel Friedlich1, Sharona Elgavish4, Yuval Nevo4, Aharon Helman1, Benjamin Glaser5, Amir Eden3, Shalev Itzkovitz2, Yuval Dor1,* 1Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel 2Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel. 3Department of Cell and Developmental Biology, The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel 4Info-CORE, Bioinformatics Unit of the I-CORE Computation Center, The Hebrew University and Hadassah, The Institute for Medical Research Israel- Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel 5Endocrinology and Metabolism Service, Department of Internal Medicine, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel *Correspondence: [email protected] Running title: The genetic program of pancreatic β-cell replication 1 Diabetes Publish Ahead of Print, published online March 18, 2016 Diabetes Page 2 of 65 Abstract The molecular program underlying infrequent replication of pancreatic beta- cells remains largely inaccessible. Using transgenic mice expressing GFP in cycling cells we sorted live, replicating beta-cells and determined their transcriptome. Replicating beta-cells upregulate hundreds of proliferation- related genes, along with many novel putative cell cycle components. Strikingly, genes involved in beta-cell functions, namely glucose sensing and insulin secretion were repressed. Further studies using single molecule RNA in situ hybridization revealed that in fact, replicating beta-cells double the amount of RNA for most genes, but this upregulation excludes genes involved in beta-cell function.
    [Show full text]
  • Genome-Wide Screening Identifies Genes and Biological Processes
    Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 10-12-2018 Genome-Wide Screening Identifies Genes and Biological Processes Implicated in Chemoresistance and Oncogene-Induced Apoptosis Tengyu Ko Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Part of the Cancer Biology Commons, Cell Biology Commons, and the Genomics Commons Recommended Citation Ko, Tengyu, "Genome-Wide Screening Identifies Genes and Biological Processes Implicated in Chemoresistance and Oncogene- Induced Apoptosis" (2018). LSU Doctoral Dissertations. 4715. https://digitalcommons.lsu.edu/gradschool_dissertations/4715 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. GENOME-WIDE SCREENING IDENTIFIES GENES AND BIOLOGICAL PROCESSES IMPLICATED IN CHEMORESISTANCE AND ONCOGENE- INDUCED APOPTOSIS A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical and Veterinary Medical Sciences through the Department of Comparative Biomedical Sciences by Tengyu Ko B.S., University of California, Santa Barbara 2010 December 2018 ACKNOWLEDGEMENTS I would like to express my sincerest gratitude to my major supervisor Dr. Shisheng Li for giving me the opportunity to join his team and the freedom to pursue projects. I appreciate all of his thoughts and efforts. Truly, none of these findings would be possible without his supervisions, supports, insightful discussions, and patience.
    [Show full text]
  • Molecular Studies in Horses with Sry-Positive Xy Sex Reversal
    MOLECULAR STUDIES IN HORSES WITH SRY-POSITIVE XY SEX REVERSAL SYNDROME A Thesis by ERICA FANG Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE December 2011 Major Subject: Genetics Molecular Studies in Horses with SRY-positive XY Sex Reversal Syndrome Copyright 2011 Erica Fang MOLECULAR STUDIES IN HORSES WITH SRY-POSITIVE XY SEX REVERSAL SYNDROME A Thesis by ERICA FANG Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Approved by: Co-Chairs of Committee, Terje Raudsepp Bhanu Chowdhary Committee Member, Penny Riggs Intercollegiate Faculty Chair, Craig Coates December 2011 Major Subject: Genetics iii ABSTRACT Molecular Studies in Horses with SRY-positive XY Sex Reversal Syndrome. (December 2011) Erica Fang, B.S., Texas A&M University Co-Chairs of Advisory Committee, Dr. Terje Raudsepp Dr. Bhanu Chowdhary Sex determination in mammals is regulated by the sex-determining region on the Y chromosome (SRY); the presence of SRY activates the male developmental pathway and suppresses the gene network necessary for female gonad development. Mutations in sex determination genes lead to various abnormal sexual phenotypes, including sex reversal syndrome in which the genetic and phenotypic sex do not match. Sex reversal syndrome has been reported in humans, mouse, and several domestic species. In horses, SRY-negative XY sex reversal syndrome has been well described and is caused by deletions on the Y chromosome. However, the molecular causes of the SRY-positive condition in horses and other mammals are not known.
    [Show full text]
  • Supplemental Solier
    Supplementary Figure 1. Importance of Exon numbers for transcript downregulation by CPT Numbers of down-regulated genes for four groups of comparable size genes, differing only by the number of exons. Supplementary Figure 2. CPT up-regulates the p53 signaling pathway genes A, List of the GO categories for the up-regulated genes in CPT-treated HCT116 cells (p<0.05). In bold: GO category also present for the genes that are up-regulated in CPT- treated MCF7 cells. B, List of the up-regulated genes in both CPT-treated HCT116 cells and CPT-treated MCF7 cells (CPT 4 h). C, RT-PCR showing the effect of CPT on JUN and H2AFJ transcripts. Control cells were exposed to DMSO. β2 microglobulin (β2) mRNA was used as control. Supplementary Figure 3. Down-regulation of RNA degradation-related genes after CPT treatment A, “RNA degradation” pathway from KEGG. The genes with “red stars” were down- regulated genes after CPT treatment. B, Affy Exon array data for the “CNOT” genes. The log2 difference for the “CNOT” genes expression depending on CPT treatment was normalized to the untreated controls. C, RT-PCR showing the effect of CPT on “CNOT” genes down-regulation. HCT116 cells were treated with CPT (10 µM, 20 h) and CNOT6L, CNOT2, CNOT4 and CNOT6 mRNA were analysed by RT-PCR. Control cells were exposed to DMSO. β2 microglobulin (β2) mRNA was used as control. D, CNOT6L down-regulation after CPT treatment. CNOT6L transcript was analysed by Q- PCR. Supplementary Figure 4. Down-regulation of ubiquitin-related genes after CPT treatment A, “Ubiquitin-mediated proteolysis” pathway from KEGG.
    [Show full text]
  • Centromere RNA Is a Key Component for the Assembly of Nucleoproteins at the Nucleolus and Centromere
    Downloaded from genome.cshlp.org on February 1, 2016 - Published by Cold Spring Harbor Laboratory Press Letter Centromere RNA is a key component for the assembly of nucleoproteins at the nucleolus and centromere Lee H. Wong,1,3 Kate H. Brettingham-Moore,1 Lyn Chan,1 Julie M. Quach,1 Melissa A. Anderson,1 Emma L. Northrop,1 Ross Hannan,2 Richard Saffery,1 Margaret L. Shaw,1 Evan Williams,1 and K.H. Andy Choo1 1Chromosome and Chromatin Research Laboratory, Murdoch Childrens Research Institute & Department of Paediatrics, University of Melbourne, Royal Children’s Hospital, Parkville 3052, Victoria, Australia; 2Peter MacCallum Research Institute, St. Andrew’s Place, East Melbourne, Victoria 3002, Australia The centromere is a complex structure, the components and assembly pathway of which remain inadequately defined. Here, we demonstrate that centromeric ␣-satellite RNA and proteins CENPC1 and INCENP accumulate in the human interphase nucleolus in an RNA polymerase I–dependent manner. The nucleolar targeting of CENPC1 and INCENP requires ␣-satellite RNA, as evident from the delocalization of both proteins from the nucleolus in RNase-treated cells, and the nucleolar relocalization of these proteins following ␣-satellite RNA replenishment in these cells. Using protein truncation and in vitro mutagenesis, we have identified the nucleolar localization sequences on CENPC1 and INCENP. We present evidence that CENPC1 is an RNA-associating protein that binds ␣-satellite RNA by an in vitro binding assay. Using chromatin immunoprecipitation, RNase treatment, and “RNA replenishment” experiments, we show that ␣-satellite RNA is a key component in the assembly of CENPC1, INCENP, and survivin (an INCENP-interacting protein) at the metaphase centromere.
    [Show full text]
  • PDF Output of CLIC (Clustering by Inferred Co-Expression)
    PDF Output of CLIC (clustering by inferred co-expression) Dataset: Num of genes in input gene set: 6 Total number of genes: 16493 CLIC PDF output has three sections: 1) Overview of Co-Expression Modules (CEMs) Heatmap shows pairwise correlations between all genes in the input query gene set. Red lines shows the partition of input genes into CEMs, ordered by CEM strength. Each row shows one gene, and the brightness of squares indicates its correlations with other genes. Gene symbols are shown at left side and on the top of the heatmap. 2) Details of each CEM and its expansion CEM+ Top panel shows the posterior selection probability (dataset weights) for top GEO series datasets. Bottom panel shows the CEM genes (blue rows) as well as expanded CEM+ genes (green rows). Each column is one GEO series dataset, sorted by their posterior probability of being selected. The brightness of squares indicates the gene's correlations with CEM genes in the corresponding dataset. CEM+ includes genes that co-express with CEM genes in high-weight datasets, measured by LLR score. 3) Details of each GEO series dataset and its expression profile: Top panel shows the detailed information (e.g. title, summary) for the GEO series dataset. Bottom panel shows the background distribution and the expression profile for CEM genes in this dataset. Overview of Co-Expression Modules (CEMs) with Dataset Weighting Scale of average Pearson correlations Num of Genes in Query Geneset: 6. Num of CEMs: 1. 0.0 0.2 0.4 0.6 0.8 1.0 Cenph Cenpn Cenpu Cenpm Cenpt Cenpc1 Cenph Cenpn
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2016/0312305 A1 KENNEDY Et Al
    US 2016.0312305A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2016/0312305 A1 KENNEDY et al. (43) Pub. Date: Oct. 27, 2016 (54) METHODS AND COMPOSITIONS OF (60) Provisional application No. 61/199,585, filed on Nov. MOLECULAR PROFLING FOR DISEASE 17, 2008, provisional application No. 61/270.812, DAGNOSTICS filed on Jul. 13, 2009. (71) Applicant: VERACYTE, INC., South San Francisco, CA (US) Publication Classification (72) Inventors: Giulia C. KENNEDY, San Francisco, (51) Int. Cl. CA (US); Bonnie H. ANDERSON, CI2O I/68 (2006.01) Half Moon Bay, CA (US); Darya I. G06F 9/20 (2006.01) CHUDOVA, San Jose, CA (US); Eric (52) U.S. Cl. T. WANG, Milpitas, CA (US); Hui CPC ............. CI2O 1/6886 (2013.01); G06F 19/20 WANG, San Bruno, CA (US); (2013.01); C12O 2600/158 (2013.01); C12O Moraima PAGAN, San Francisco, CA 2600/178 (2013.01); C12O 2600/112 (2013.01) (US); Nusrat RABBEE, South San Francisco, CA (US); Jonathan I. WILDE, Burlingame, CA (US) (57) ABSTRACT (21) Appl. No.: 15/164,217 The present invention relates to compositions, kits, and (22) Filed: May 25, 2016 methods for molecular profiling and cancer diagnostics, including but not limited to gene expression product mark Related U.S. Application Data ers, alternative exon usage markers, and DNA polymor (63) Continuation of application No. 13/589,022, filed on phisms associated with cancer. In particular, the present Aug. 17, 2012, which is a continuation of application invention provides molecular profiles associated with thy No. 12/592,065, filed on Nov. 17, 2009, now Pat.
    [Show full text]
  • Rnai Pathway Participates Into Chromosome Segregation In
    OPEN Citation: Cell Discovery (2015) 1, 15029; doi:10.1038/celldisc.2015.29 ARTICLE www.nature.com/celldisc RNAi pathway participates in chromosome segregation in mammalian cells Chuan Huang, Xiaolin Wang, Xu Liu, Shuhuan Cao, Ge Shan School of Life Sciences, CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, China The RNAi machinery is a mighty regulator in a myriad of life events. Despite lines of evidence that small RNAs and components of the RNAi pathway may be associated with structure and behavior of mitotic chromosomes in diverse organisms, a direct role of the RNAi pathway in mammalian mitotic chromosome segregation remains elusive. Here we report that Dicer and AGO2, two central components of the mammalian RNAi pathway, participate in the chromosome segregation. Knockdown of Dicer or AGO2 results in a higher incidence of chromosome lagging, and this effect is independent from microRNAs as examined with DGCR8 knockout cells. Further investigation has revealed that α-satellite RNA, a noncoding RNA derived from centromeric repeat region, is managed by AGO2 under the guidance of endogenous small interference RNAs (ASAT siRNAs) generated by Dicer. Furthermore, the slicer activity of AGO2 is essential for the chromosome segregation. Level and distribution of chromosome-associated α-satellite RNA have crucial regulatory effect on the localization of centromeric proteins such as centromere protein C1 (CENPC1). With these results, we also provide a paradigm in which the RNAi pathway
    [Show full text]
  • Efficient Neocentromere Formation Is Suppressed by Gene Conversion to Maintain Centromere Function at Native Physical Chromosomal Loci in Candida Albicans
    Downloaded from genome.cshlp.org on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press Research Efficient neocentromere formation is suppressed by gene conversion to maintain centromere function at native physical chromosomal loci in Candida albicans Jitendra Thakur and Kaustuv Sanyal1 Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560 064, India CENPA/Cse4 assembles centromeric chromatin on diverse DNA. CENPA chromatin is epigenetically propagated on unique and different centromere DNA sequences in a pathogenic yeast Candida albicans. Formation of neocentromeres on DNA, nonhomologous to native centromeres, indicates a role of non-DNA sequence determinants in CENPA deposition. Neocentromeres have been shown to form at multiple loci in C. albicans when a native centromere was deleted. However, the process of site selection for CENPA deposition on native or neocentromeres in the absence of defined DNA sequences remains elusive. By systematic deletion of CENPA chromatin-containing regions of variable length of different chromo- somes, followed by mapping of neocentromere loci in C. albicans and its related species Candida dubliniensis, which share similar centromere properties, we demonstrate that the chromosomal location is an evolutionarily conserved primary determinant of CENPA deposition. Neocentromeres on the altered chromosome are always formed close to the site which was once occupied by the native centromere. Interestingly, repositioning of CENPA chromatin from the neocentromere to the native centromere occurs by gene conversion in C. albicans. [Supplemental material is available for this article.] A functional centromere, the chromosomal site where a kineto- Neocentromere formation on a non-native locus takes place chore assembles and attaches to spindle microtubules to facilitate only in the absence of the functional native centromere in a nor- proper chromosome segregation, is formed only once on each mal cell (Ishii et al.
    [Show full text]