Reduction in Reproductive Lifespan of Tissue Inhibitor of Metalloproteinase
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University of California, San Diego
UNIVERSITY OF CALIFORNIA, SAN DIEGO The post-terminal differentiation fate of RNAs revealed by next-generation sequencing A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Biomedical Sciences by Gloria Kuo Lefkowitz Committee in Charge: Professor Benjamin D. Yu, Chair Professor Richard Gallo Professor Bruce A. Hamilton Professor Miles F. Wilkinson Professor Eugene Yeo 2012 Copyright Gloria Kuo Lefkowitz, 2012 All rights reserved. The Dissertation of Gloria Kuo Lefkowitz is approved, and it is acceptable in quality and form for publication on microfilm and electronically: __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ Chair University of California, San Diego 2012 iii DEDICATION Ma and Ba, for your early indulgence and support. Matt and James, for choosing more practical callings. Roy, my love, for patiently sharing the ups and downs of this journey. iv EPIGRAPH It is foolish to tear one's hair in grief, as though sorrow would be made less by baldness. ~Cicero v TABLE OF CONTENTS Signature Page .............................................................................................................. iii Dedication .................................................................................................................... -
Co-Occurrence Based Meta-Analysis of Scientific Texts
Vol. 21 no. 9 2005, pages 2049–2058 BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/bti268 Data and text mining Co-occurrence based meta-analysis of scientific texts: retrieving biological relationships between genes R. Jelier1,∗ G. Jenster2, L. C. J. Dorssers3, C. C. van der Eijk1, E. M. van Mulligen1, B. Mons1 and J. A. Kors1 1Department of Medical Informatics, 2Department of Urology and 3Department of Pathology, Erasmus MC—University Medical Center, Rotterdam, The Netherlands Received on July 15, 2004; revised on December 22, 2004; accepted on January 6, 2005 Advance Access publication January 18, 2005 ABSTRACT are studied, the number of relevant publications will frequently be Motivation: The advent of high-throughput experiments in molecu- prohibitively large. This renders the traditional approach of manu- lar biology creates a need for methods to efficiently extract and use ally searching bibliographic databases for every gene and reading information for large numbers of genes. Recently, the associative scientific articles inadequate. It is therefore an important challenge concept space (ACS) has been developed for the representation of at this time to make the available information both accessible and information extracted from biomedical literature. The ACS is a Euc- interpretable for molecular biologists. lidean space in which thesaurus concepts are positioned and the An interesting current development is the use of annotations of distances between concepts indicates their relatedness. The ACS genes with gene ontology (GO) terms (Ashburner et al., 2000; Camon uses co-occurrence of concepts as a source of information. In this et al., 2004) for the analysis of the results of microarray experiments paper we evaluate how well the system can retrieve functionally (Zhang et al., 2004; Al Shahrour et al., 2004). -
1 Meiotic Sex Chromosome Inactivation Is Disrupted in Sterile
Genetics: Early Online, published on January 10, 2013 as 10.1534/genetics.112.148635 Meiotic sex chromosome inactivation is disrupted in sterile hybrid male house mice Polly Campbell*,1, Jeffrey M. Good§, and Michael W. Nachman* *Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721 §Division of Biological Sciences, University of Montana, Missoula, Montana 59812 1 Copyright 2013. Running head: Disrupted X inactivation in hybrid male mice Keywords: Haldane’s rule, meiosis, postmeiotic sex chromatin, speciation, spermatogenesis 1Corresponding author: Department of Ecology and Evolutionary Biology, Biosciences West 333, 1041 E Lowell St., University of Arizona, Tucson, AZ 85721. E-mail: [email protected] 2 ABSTRACT In male mammals, the X and Y chromosomes are transcriptionally silenced in primary spermatocytes by meiotic sex chromosome inactivation (MSCI) and remain repressed for the duration of spermatogenesis. Here, we test the longstanding hypothesis that disrupted MSCI might contribute to the preferential sterility of heterogametic hybrid males. We studied a cross between wild-derived inbred strains of Mus musculus musculus and M. m. domesticus in which sterility is asymmetric: F1 males with a M. m. musculus mother are sterile or nearly so while F1 males with a M. m. domesticus mother are normal. In previous work, we discovered widespread over-expression of X-linked genes in the testes of sterile but not fertile F1 males. Here, we ask whether this over-expression is specifically a result of disrupted MSCI. To do this, we isolated cells from different stages of spermatogenesis and measured the expression of several genes using quantitative PCR. We found that X over-expression in sterile F1 primary spermatocytes is coincident with the onset of MSCI and persists in postmeiotic spermatids. -
Early-Life Exposure to the Antidepressant Fluoxetine Induces A
Early-life exposure to the antidepressant fluoxetine induces a male-specific transgenerational disruption of the stress axis and exploratory behavior in adult zebrafish, Danio rerio Marilyn Nohely Vera Chang Thesis submitted to the Faculty of Graduate and Postdoctoral Studies in partial fulfillment of the requirements for the Doctorate in Philosophy degree in Biology with specialization in Chemical and Environmental Toxicology Department of Biology Faculty of Science University of Ottawa © Marilyn Nohely Vera Chang, Ottawa, Canada, 2018 ACKNOWLEDGMENTS Finishing this thesis has been both a challenging and gratifying experience. There are many people whom I must express my sincere gratitude toward as the work presented in this thesis would not have been possible without their contributions and never-ending support. First and foremost, I would like to acknowledge my supervisors, Dr. Vance Trudeau and Dr. Thomas Moon. I want to say how grateful I am for providing me with the opportunity to purse my academic and professional interests. I was first accepted by Tom and I will be forever thankful that he took a shot on me. Also, thanks to you Vance for adopting me when I was lab-less and for believing in my abilities as a scientist. Thank you to both of you for your outstanding guidance, patience and friendship which have given me an amazing experience in these past 6 years, you have been excellent mentors. Your concerns for your student’s well-being and mental health were bonus that I will not soon forget. I don’t think there are enough words to describe how thankful and fortunate I am to have benefit from your supervision not only at the academic and scientific level but also at the personal level, for all my accomplishments during this doctorate, I will forever be indebted to both of you. -
Multiple Routes to Oncogenesis Are Promoted by the Human Papillomavirus–Host Protein Network
Published OnlineFirst September 12, 2018; DOI: 10.1158/2159-8290.CD-17-1018 RESEARCH ARTICLE Multiple Routes to Oncogenesis Are Promoted by the Human Papillomavirus–Host Protein Network Manon Eckhardt 1 , 2 , 3 , Wei Zhang 4 , Andrew M. Gross 4 , John Von Dollen 1 , 3 , Jeffrey R. Johnson 1 , 2 , 3 , Kathleen E. Franks-Skiba1 , 3 , Danielle L. Swaney 1 , 2 , 3 , 5 , Tasha L. Johnson 3 , Gwendolyn M. Jang 1 , 3 , Priya S. Shah1 , 3 , Toni M. Brand 6 , Jacques Archambault 7 , Jason F. Kreisberg 4 , 5 , Jennifer R. Grandis 5 , 6 , Trey Ideker4 , 5 , and Nevan J. Krogan 1 , 2 , 3 , 5 ABSTRACT We have mapped a global network of virus–host protein interactions by purifi cation of the complete set of human papillomavirus (HPV) proteins in multiple cell lines followed by mass spectrometry analysis. Integration of this map with tumor genome atlases shows that the virus targets human proteins frequently mutated in HPV − but not HPV + cancers, providing a unique opportunity to identify novel oncogenic events phenocopied by HPV infection. For example, we fi nd that the NRF2 transcriptional pathway, which protects against oxidative stress, is activated by interaction of the NRF2 regulator KEAP1 with the viral protein E1. We also demonstrate that the L2 HPV protein physically interacts with the RNF20/40 histone ubiquitination complex and promotes tumor cell inva- sion in an RNF20/40-dependent manner. This combined proteomic and genetic approach provides a systematic means to study the cellular mechanisms hijacked by virally induced cancers. SIGNIFICANCE : In this study, we created a protein–protein interaction network between HPV and human proteins. -
University of California, San Diego
UC San Diego UC San Diego Electronic Theses and Dissertations Title The post-terminal differentiation fate of RNAs revealed by next-generation sequencing Permalink https://escholarship.org/uc/item/7324r1rj Author Lefkowitz, Gloria Kuo Publication Date 2012 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO The post-terminal differentiation fate of RNAs revealed by next-generation sequencing A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Biomedical Sciences by Gloria Kuo Lefkowitz Committee in Charge: Professor Benjamin D. Yu, Chair Professor Richard Gallo Professor Bruce A. Hamilton Professor Miles F. Wilkinson Professor Eugene Yeo 2012 Copyright Gloria Kuo Lefkowitz, 2012 All rights reserved. The Dissertation of Gloria Kuo Lefkowitz is approved, and it is acceptable in quality and form for publication on microfilm and electronically: __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ Chair University of California, San Diego 2012 iii DEDICATION Ma and Ba, for your early indulgence and support. Matt and James, for choosing more practical callings. Roy, my love, for patiently sharing the ups and downs -
Histone Variants and Their Post-Translational Modifications in Primary Human Fat Cells
Linköping University Post Print Histone Variants and Their Post-Translational Modifications in Primary Human Fat Cells Asa Jufvas, Peter Strålfors and Alexander Vener N.B.: When citing this work, cite the original article. Original Publication: Asa Jufvas, Peter Strålfors and Alexander Vener, Histone Variants and Their Post- Translational Modifications in Primary Human Fat Cells, 2011, PLOS ONE, (6), 1. http://dx.doi.org/10.1371/journal.pone.0015960 Licensee: Public Library of Science (PLoS) http://www.plos.org/ Postprint available at: Linköping University Electronic Press http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-65933 Histone Variants and Their Post-Translational Modifications in Primary Human Fat Cells A˚ sa Jufvas, Peter Stra˚lfors, Alexander V. Vener* Department of Clinical and Experimental Medicine, Linko¨ping University, Linko¨ping, Sweden Abstract Epigenetic changes related to human disease cannot be fully addressed by studies of cells from cultures or from other mammals. We isolated human fat cells from subcutaneous abdominal fat tissue of female subjects and extracted histones from either purified nuclei or intact cells. Direct acid extraction of whole adipocytes was more efficient, yielding about 100 mg of protein with histone content of 60% –70% from 10 mL of fat cells. Differential proteolysis of the protein extracts by trypsin or ArgC-protease followed by nanoLC/MS/MS with alternating CID/ETD peptide sequencing identified 19 histone variants. Four variants were found at the protein level for the first time; particularly HIST2H4B was identified besides the only H4 isoform earlier known to be expressed in humans. Three of the found H2A potentially organize small nucleosomes in transcriptionally active chromatin, while two H2AFY variants inactivate X chromosome in female cells. -
A Multiprotein Occupancy Map of the Mrnp on the 3 End of Histone
Downloaded from rnajournal.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press A multiprotein occupancy map of the mRNP on the 3′ end of histone mRNAs LIONEL BROOKS III,1 SHAWN M. LYONS,2 J. MATTHEW MAHONEY,1 JOSHUA D. WELCH,3 ZHONGLE LIU,1 WILLIAM F. MARZLUFF,2 and MICHAEL L. WHITFIELD1 1Department of Genetics, Dartmouth Geisel School of Medicine, Hanover, New Hampshire 03755, USA 2Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA 3Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599, USA ABSTRACT The animal replication-dependent (RD) histone mRNAs are coordinately regulated with chromosome replication. The RD-histone mRNAs are the only known cellular mRNAs that are not polyadenylated. Instead, the mature transcripts end in a conserved stem– loop (SL) structure. This SL structure interacts with the stem–loop binding protein (SLBP), which is involved in all aspects of RD- histone mRNA metabolism. We used several genomic methods, including high-throughput sequencing of cross-linked immunoprecipitate (HITS-CLIP) to analyze the RNA-binding landscape of SLBP. SLBP was not bound to any RNAs other than histone mRNAs. We performed bioinformatic analyses of the HITS-CLIP data that included (i) clustering genes by sequencing read coverage using CVCA, (ii) mapping the bound RNA fragment termini, and (iii) mapping cross-linking induced mutation sites (CIMS) using CLIP-PyL software. These analyses allowed us to identify specific sites of molecular contact between SLBP and its RD-histone mRNA ligands. We performed in vitro crosslinking assays to refine the CIMS mapping and found that uracils one and three in the loop of the histone mRNA SL preferentially crosslink to SLBP, whereas uracil two in the loop preferentially crosslinks to a separate component, likely the 3′hExo. -
Acetyl-Histone H4-K12 Pab Cat
Acetyl-Histone H4-K12 pAb Cat. No.: 15-437 Acetyl-Histone H4-K12 pAb Immunohistochemistry of paraffin- embedded rat ovary using Acetyl-Histone Immunohistochemistry of paraffin-embedded mouse testis using H4-K12 antibody (15-437) at dilution of 1:200 Acetyl-Histone H4-K12 antibody (15-437) at dilution of 1:200 (40x lens). (40x lens). Immunohistochemistry of paraffin- Immunofluorescence analysis of C6 cells using Acetyl-Histone H4-K12 embedded mouse spinal cord using Acetyl- antibody (15-437) at dilution of 1:100.C6 cells were treated by TSA (1 Histone H4-K12 antibody (15-437) at dilution uM) at 37? for 18 hours. Blue: DAPI for nuclear staining. of 1:200 (40x lens). September 27, 2021 1 https://www.prosci-inc.com/acetyl-histone-h4-k12-pab-15-437.html Immunofluorescence analysis of NIH/3T3 cells using Acetyl-Histone H4-K12 antibody (15-437) at dilution of 1:100.NIH/3T3 cells were treated by TSA (1 uM) at 37? for 18 hours. Blue: DAPI for nuclear staining. Specifications HOST SPECIES: Rabbit SPECIES REACTIVITY: Human, Mouse IMMUNOGEN: A synthetic acetylated peptide around K12 of human Histone H4 (NP_001029249.1). TESTED APPLICATIONS: IF, IHC, WB WB: ,1:500 - 1:2000 APPLICATIONS: IHC: ,1:50 - 1:200 IF: ,1:50 - 1:200 Properties PURIFICATION: Affinity purification CLONALITY: Polyclonal ISOTYPE: IgG CONJUGATE: Unconjugated PHYSICAL STATE: Liquid BUFFER: PBS with 0.02% sodium azide, 50% glycerol, pH7.3. STORAGE CONDITIONS: Store at -20˚C. Avoid freeze / thaw cycles. Additional Info OFFICIAL SYMBOL: H4K12ac September 27, 2021 2 https://www.prosci-inc.com/acetyl-histone-h4-k12-pab-15-437.html H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, ALTERNATE NAMES: H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4, Histone H4H4FA GENE ID: 8366 USER NOTE: Optimal dilutions for each application to be determined by the researcher. -
Research Article Common Expression Quantitative Trait Loci Shared by Histone Genes
Hindawi International Journal of Genomics Volume 2017, Article ID 6202567, 14 pages https://doi.org/10.1155/2017/6202567 Research Article Common Expression Quantitative Trait Loci Shared by Histone Genes Hanseol Kim, Yujin Suh, and Chaeyoung Lee Department of Bioinformatics and Life Science, Soongsil University, Seoul, Republic of Korea Correspondence should be addressed to Chaeyoung Lee; [email protected] Received 29 May 2017; Revised 26 July 2017; Accepted 2 August 2017; Published 27 August 2017 Academic Editor: Marco Gerdol Copyright © 2017 Hanseol Kim et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. A genome-wide association study (GWAS) was conducted to examine expression quantitative trait loci (eQTLs) for histone genes. We examined common eQTLs for multiple histone genes in 373 European lymphoblastoid cell lines (LCLs). A linear regression model was employed to identify single-nucleotide polymorphisms (SNPs) associated with expression of the histone genes, and the number of eQTLs was determined by linkage disequilibrium analysis. Additional associations of the identified eQTLs with other genes were also examined. We identified 31 eQTLs for 29 histone genes through genome-wide analysis using 29 histone genes (P <297 × 10−10). Among them, 12 eQTLs were associated with the expression of multiple histone genes. Transcriptome- wide association analysis using the identified eQTLs showed their associations with additional 80 genes (P <475 × 10−6). In particular, expression of RPPH1, SCARNA2, and SCARNA7 genes was associated with 26, 25, and 23 eQTLs, respectively. -
Ernas and Superenhancer Lncrnas Are Functional in Human Prostate Cancer
Hindawi Disease Markers Volume 2020, Article ID 8847986, 17 pages https://doi.org/10.1155/2020/8847986 Research Article eRNAs and Superenhancer lncRNAs Are Functional in Human Prostate Cancer Xiaona Zhang,1,2,3 Panpan Pang,2,3,4 Min Jiang,1,2,3 Qunfa Cao,2,3 Huili Li,2,3 Yi Xu,5 Yao Li ,4 Xue Chen ,1 and Junsong Han 2,3 1Department of Pathology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China 2National Engineering Center for Biochip at Shanghai, Shanghai, China 3Shanghai Biochip Corporation, Shanghai, China 4Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Science, Fudan University, Shanghai, China 5Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Chinese Medicine, Shanghai, China Correspondence should be addressed to Yao Li; [email protected], Xue Chen; [email protected], and Junsong Han; [email protected] Received 23 June 2020; Revised 27 July 2020; Accepted 14 August 2020; Published 24 September 2020 Academic Editor: Mingjun Shi Copyright © 2020 Xiaona Zhang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Prostate cancer (PCa) is one of the most commonly diagnosed cancers in males worldwide. lncRNAs (long noncoding RNAs) play a significant role in the occurrence and development of PCa. eRNAs (enhancer RNAs) and SE-lncRNAs (superenhancer lncRNAs) are important elements of lncRNAs, but the role of eRNAs and SE-lncRNAs in PCa remains largely unclear. In this work, we identified 681 eRNAs and 292 SE-lncRNAs that were expressed differentially in PCa using a microarray. -
Supplemental Data.Pdf
Supplementary material -Table of content Supplementary Figures (Fig 1- Fig 6) Supplementary Tables (1-13) Lists of genes belonging to distinct biological processes identified by GREAT analyses to be significantly enriched with UBTF1/2-bound genes Supplementary Table 14 List of the common UBTF1/2 bound genes within +/- 2kb of their TSSs in NIH3T3 and HMECs. Supplementary Table 15 List of gene identified by microarray expression analysis to be differentially regulated following UBTF1/2 knockdown by siRNA Supplementary Table 16 List of UBTF1/2 binding regions overlapping with histone genes in NIH3T3 cells Supplementary Table 17 List of UBTF1/2 binding regions overlapping with histone genes in HMEC Supplementary Table 18 Sequences of short interfering RNA oligonucleotides Supplementary Table 19 qPCR primer sequences for qChIP experiments Supplementary Table 20 qPCR primer sequences for reverse transcription-qPCR Supplementary Table 21 Sequences of primers used in CHART-PCR Supplementary Methods Supplementary Fig 1. (A) ChIP-seq analysis of UBTF1/2 and Pol I (POLR1A) binding across mouse rDNA. UBTF1/2 is enriched at the enhancer and promoter regions and along the entire transcribed portions of rDNA with little if any enrichment in the intergenic spacer (IGS), which separates the rDNA repeats. This enrichment coincides with the distribution of the largest subunit of Pol I (POLR1A) across the rDNA. All sequencing reads were mapped to the published complete sequence of the mouse rDNA repeat (Gene bank accession number: BK000964). The graph represents the frequency of ribosomal sequences enriched in UBTF1/2 and Pol I-ChIPed DNA expressed as fold change over those of input genomic DNA.