Emerging Roles of RNA 3'-End Cleavage and Polyadenylation In
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CREB-Binding Protein Regulates Lung Cancer Growth by Targeting MAPK and CPSF4 Signaling Pathway
MOLECULAR ONCOLOGY 10 (2016) 317e329 available at www.sciencedirect.com ScienceDirect www.elsevier.com/locate/molonc CREB-binding protein regulates lung cancer growth by targeting MAPK and CPSF4 signaling pathway Zhipeng Tanga,1, Wendan Yua,1, Changlin Zhangb,1, Shilei Zhaoa, Zhenlong Yua, Xiangsheng Xiaob, Ranran Tanga, Yang Xuana, Wenjing Yanga, Jiaojiao Haoa, Tingting Xua, Qianyi Zhanga, Wenlin Huangb,c, Wuguo Dengb,c,*, Wei Guoa,* aInstitute of Cancer Stem Cell, Dalian Medical University, Dalian, China bSun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China cState Key Laboratory of Targeted Drug for Tumors of Guangdong Province, Guangzhou Double Bioproduct Inc., Guangzhou, China ARTICLE INFO ABSTRACT Article history: CBP (CREB-binding protein) is a transcriptional co-activator which possesses HAT (histone Received 15 September 2015 acetyltransferases) activity and participates in many biological processes, including embry- Accepted 19 October 2015 onic development, growth control and homeostasis. However, its roles and the underlying Available online 5 November 2015 mechanisms in the regulation of carcinogenesis and tumor development remain largely unknown. Here we investigated the molecular mechanisms and potential targets of CBP Keywords: involved in tumor growth and survival in lung cancer cells. Elevated expression of CBP CBP was detected in lung cancer cells and tumor tissues compared to the normal lung cells CPSF4 and tissues. Knockdown of CBP by siRNA or inhibition of its HAT activity using specific hTERT chemical inhibitor effectively suppressed cell proliferation, migration and colony forma- Lung cancer tion and induced apoptosis in lung cancer cells by inhibiting MAPK and activating cyto- chrome C/caspase-dependent signaling pathways. -
Chapter 14: Functional Genomics Learning Objectives
Chapter 14: Functional Genomics Learning objectives Upon reading this chapter, you should be able to: ■ define functional genomics; ■ describe the key features of eight model organisms; ■ explain techniques of forward and reverse genetics; ■ discuss the relation between the central dogma and functional genomics; and ■ describe proteomics-based approaches to functional genomics. Outline : Functional genomics Introduction Relation between genotype and phenotype Eight model organisms E. coli; yeast; Arabidopsis; C. elegans; Drosophila; zebrafish; mouse; human Functional genomics using reverse and forward genetics Reverse genetics: mouse knockouts; yeast; gene trapping; insertional mutatgenesis; gene silencing Forward genetics: chemical mutagenesis Functional genomics and the central dogma Approaches to function; Functional genomics and DNA; …and RNA; …and protein Proteomic approaches to functional genomics CASP; protein-protein interactions; protein networks Perspective Albert Blakeslee (1874–1954) studied the effect of altered chromosome numbers on the phenotype of the jimson-weed Datura stramonium, a flowering plant. Introduction: Functional genomics Functional genomics is the genome-wide study of the function of DNA (including both genes and non-genic regions), as well as RNA and proteins encoded by DNA. The term “functional genomics” may apply to • the genome, transcriptome, or proteome • the use of high-throughput screens • the perturbation of gene function • the complex relationship of genotype and phenotype Functional genomics approaches to high throughput analyses Relationship between genotype and phenotype The genotype of an individual consists of the DNA that comprises the organism. The phenotype is the outward manifestation in terms of properties such as size, shape, movement, and physiology. We can consider the phenotype of a cell (e.g., a precursor cell may develop into a brain cell or liver cell) or the phenotype of an organism (e.g., a person may have a disease phenotype such as sickle‐cell anemia). -
Subcellular RNA Profiling Links Splicing and Nuclear DICER1 to Alternative Cleavage and Polyadenylation
Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation Jonathan Neve1#, Kaspar Burger2#, Wencheng Li3, Mainul Hoque3, Radhika Patel1, Bin Tian3, Monika Gullerova2* and Andre Furger1* Affiliations: 1 Department of Biochemistry, South Parks Road, University of Oxford, OX1 3QU, UK 2 Sir William Dunn School of Pathology, South Parks Road, University of Oxford, OX1 3RE, UK 3Department of Biochemistry and Molecular Biology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA *Corresponding authors: Andre Furger Email: [email protected] Monika Gullerova Email: [email protected] # authors contributed equally Running Title: APA and subcellular fractionation Key words: alternative polyadenylation, mRNA, subcellular fractionation, DICER1 1 Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press ABSTRACT Alternative cleavage and polyadenylation (APA) plays a crucial role in the regulation of gene expression across eukaryotes. Although APA is extensively studied, its regulation within cellular compartments and its physiological impact remains largely enigmatic. Here, we employed a rigorous subcellular fractionation approach to compare APA profiles of cytoplasmic and nuclear RNA fractions from human cell lines. This approach allowed us to extract APA isoforms that are subjected to differential regulation and provided us with a platform to interrogate the molecular regulatory pathways that shape APA profiles in different subcellular locations. Here we show that APA isoforms with shorter 3’UTRs tend to be overrepresented in the cytoplasm and appear to be cell type specific events. -
Differential Analysis of Gene Expression and Alternative Splicing
i bioRxiv preprint doi: https://doi.org/10.1101/2020.08.23.234237; this version posted August 24, 2020. The copyright holder for this preprint i (which was not certified by peer review)“main” is the author/funder, — 2020/8/23 who has — granted 9:38 — bioRxiv page a1 license — #1 to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. i i EmpiReS: Differential Analysis of Gene Expression and Alternative Splicing Gergely Csaba∗, Evi Berchtold*,y, Armin Hadziahmetovic, Markus Gruber, Constantin Ammar and Ralf Zimmer Department of Informatics, Ludwig-Maximilians-Universitat¨ Munchen,¨ 80333, Munich, Germany ABSTRACT to translation. Different transcripts of the same gene are often expressed at the same time, possibly at different abundance, While absolute quantification is challenging in high- yielding a defined mixture of isoforms. Changes to this throughput measurements, changes of features composition are further referred to as differential alternative between conditions can often be determined with splicing (DAS). Various diseases can be linked to DAS high precision. Therefore, analysis of fold changes events (3). Most hallmarks of cancer like tumor progression is the standard method, but often, a doubly and immune escape (4, 5) can be attributed to changes in differential analysis of changes of changes is the transcript composition (6). DAS plays a prominent role required. Differential alternative splicing is an in various types of muscular dystrophy (MD) (7), splicing example of a doubly differential analysis, i.e. fold intervention by targeted exon removal is a therapeutic option changes between conditions for different isoforms in Duchenne MD (8). -
Coupling of Spliceosome Complexity to Intron Diversity
bioRxiv preprint doi: https://doi.org/10.1101/2021.03.19.436190; this version posted March 20, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Coupling of spliceosome complexity to intron diversity Jade Sales-Lee1, Daniela S. Perry1, Bradley A. Bowser2, Jolene K. Diedrich3, Beiduo Rao1, Irene Beusch1, John R. Yates III3, Scott W. Roy4,6, and Hiten D. Madhani1,6,7 1Dept. of Biochemistry and Biophysics University of California – San Francisco San Francisco, CA 94158 2Dept. of Molecular and Cellular Biology University of California - Merced Merced, CA 95343 3Department of Molecular Medicine The Scripps Research Institute, La Jolla, CA 92037 4Dept. of Biology San Francisco State University San Francisco, CA 94132 5Chan-Zuckerberg Biohub San Francisco, CA 94158 6Corresponding authors: [email protected], [email protected] 7Lead Contact 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.03.19.436190; this version posted March 20, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. SUMMARY We determined that over 40 spliceosomal proteins are conserved between many fungal species and humans but were lost during the evolution of S. cerevisiae, an intron-poor yeast with unusually rigid splicing signals. We analyzed null mutations in a subset of these factors, most of which had not been investigated previously, in the intron-rich yeast Cryptococcus neoformans. -
CD56+ T-Cells in Relation to Cytomegalovirus in Healthy Subjects and Kidney Transplant Patients
CD56+ T-cells in Relation to Cytomegalovirus in Healthy Subjects and Kidney Transplant Patients Institute of Infection and Global Health Department of Clinical Infection, Microbiology and Immunology Thesis submitted in accordance with the requirements of the University of Liverpool for the degree of Doctor in Philosophy by Mazen Mohammed Almehmadi December 2014 - 1 - Abstract Human T cells expressing CD56 are capable of tumour cell lysis following activation with interleukin-2 but their role in viral immunity has been less well studied. The work described in this thesis aimed to investigate CD56+ T-cells in relation to cytomegalovirus infection in healthy subjects and kidney transplant patients (KTPs). Proportions of CD56+ T cells were found to be highly significantly increased in healthy cytomegalovirus-seropositive (CMV+) compared to cytomegalovirus-seronegative (CMV-) subjects (8.38% ± 0.33 versus 3.29%± 0.33; P < 0.0001). In donor CMV-/recipient CMV- (D-/R-)- KTPs levels of CD56+ T cells were 1.9% ±0.35 versus 5.42% ±1.01 in D+/R- patients and 5.11% ±0.69 in R+ patients (P 0.0247 and < 0.0001 respectively). CD56+ T cells in both healthy CMV+ subjects and KTPs expressed markers of effector memory- RA T-cells (TEMRA) while in healthy CMV- subjects and D-/R- KTPs the phenotype was predominantly that of naïve T-cells. Other surface markers, CD8, CD4, CD58, CD57, CD94 and NKG2C were expressed by a significantly higher proportion of CD56+ T-cells in healthy CMV+ than CMV- subjects. Functional studies showed levels of pro-inflammatory cytokines IFN-γ and TNF-α, as well as granzyme B and CD107a were significantly higher in CD56+ T-cells from CMV+ than CMV- subjects following stimulation with CMV antigens. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Anti-CSTF1 (C-Terminal) (C2372)
Anti-CSTF1 (C-terminal) produced in rabbit, affinity isolated antibody Product Number C2372 Product Description Reagent Anti-CSTF1 (C-terminal) is produced in rabbit using as Supplied as a solution in 0.01 M phosphate buffered the immunogen a synthetic peptide corresponding to a saline, pH 7.4, containing 15 mM sodium azide as a sequence at the C-terminal of human CSTF1 (GeneID: preservative. 1477) conjugated to KLH. The corresponding sequence is identical in mouse and rat. The antibody is affinity- Antibody concentration: 1.0 mg/mL purified using the immunizing peptide immobilized on agarose. Precautions and Disclaimer For R&D use only. Not for drug, household, or other Anti-CSTF1 (C-terminal) specifically recognizes human uses. Please consult the Safety Data Sheet for CSTF1 (also known as Cleavage stimulation factor, information regarding hazards and safe handling 3 pre-RNA, subunit 1, 50 kDa, CSF-50 subunit). The practices. antibody may be used in several immunochemical techniques including immunoblotting (48 kDa) and Storage/Stability immunoprecipitation. Detection of the CSTF1 band by Store at –20 C. For continuous use, the product may immunoblotting is specifically inhibited with the be stored at 2–8 C for up to one month. For extended immunizing peptide. storage, freeze in working aliquots at –20 C. Repeated freezing and thawing, or storage in “frost-free” freezers, mRNA precursors are processed 3-ends in a two-step is not recommended. If slight turbidity occurs upon reaction; endonucleolytic cleavage at the poly(A) site prolonged storage, clarify the solution by centrifugation followed by the addition of adenylate residues to form a before use. -
Nuclear Expression of a Group II Intron Is Consistent with Spliceosomal Intron Ancestry
Downloaded from genesdev.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press Nuclear expression of a group II intron is consistent with spliceosomal intron ancestry Venkata R. Chalamcharla, M. Joan Curcio, and Marlene Belfort1 Center for Medical Sciences, Wadsworth Center, New York State Department of Health, Albany, New York 12208, USA; and School of Public Health, State University of New York at Albany, Albany, New York 12201, USA Group II introns are self-splicing RNAs found in eubacteria, archaea, and eukaryotic organelles. They are mechanistically similar to the metazoan nuclear spliceosomal introns; therefore, group II introns have been invoked as the progenitors of the eukaryotic pre-mRNA introns. However, the ability of group II introns to function outside of the bacteria-derived organelles is debatable, since they are not found in the nuclear genomes of eukaryotes. Here, we show that the Lactococcus lactis Ll.LtrB group II intron splices accurately and efficiently from different pre-mRNAs in a eukaryote, Saccharomyces cerevisiae. However, a pre-mRNA harboring a group II intron is spliced predominantly in the cytoplasm and is subject to nonsense-mediated mRNA decay (NMD), and the mature mRNA from which the group II intron is spliced is poorly translated. In contrast, a pre-mRNA bearing the Tetrahymena group I intron or the yeast spliceosomal ACT1 intron at the same location is not subject to NMD, and the mature mRNA is translated efficiently. Thus, a group II intron can splice from a nuclear transcript, but RNA instability and translation defects would have favored intron loss or evolution into protein-dependent spliceosomal introns, consistent with the bacterial group II intron ancestry hypothesis. -
Essential Genes and Their Role in Autism Spectrum Disorder
University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2017 Essential Genes And Their Role In Autism Spectrum Disorder Xiao Ji University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Bioinformatics Commons, and the Genetics Commons Recommended Citation Ji, Xiao, "Essential Genes And Their Role In Autism Spectrum Disorder" (2017). Publicly Accessible Penn Dissertations. 2369. https://repository.upenn.edu/edissertations/2369 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/2369 For more information, please contact [email protected]. Essential Genes And Their Role In Autism Spectrum Disorder Abstract Essential genes (EGs) play central roles in fundamental cellular processes and are required for the survival of an organism. EGs are enriched for human disease genes and are under strong purifying selection. This intolerance to deleterious mutations, commonly observed haploinsufficiency and the importance of EGs in pre- and postnatal development suggests a possible cumulative effect of deleterious variants in EGs on complex neurodevelopmental disorders. Autism spectrum disorder (ASD) is a heterogeneous, highly heritable neurodevelopmental syndrome characterized by impaired social interaction, communication and repetitive behavior. More and more genetic evidence points to a polygenic model of ASD and it is estimated that hundreds of genes contribute to ASD. The central question addressed in this dissertation is whether genes with a strong effect on survival and fitness (i.e. EGs) play a specific oler in ASD risk. I compiled a comprehensive catalog of 3,915 mammalian EGs by combining human orthologs of lethal genes in knockout mice and genes responsible for cell-based essentiality. -
RNA Components of the Spliceosome Regulate Tissue- and Cancer-Specific Alternative Splicing
Downloaded from genome.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press Research RNA components of the spliceosome regulate tissue- and cancer-specific alternative splicing Heidi Dvinge,1,2,4 Jamie Guenthoer,3 Peggy L. Porter,3 and Robert K. Bradley1,2 1Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; 2Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; 3Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA Alternative splicing of pre-mRNAs plays a pivotal role during the establishment and maintenance of human cell types. Characterizing the trans-acting regulatory proteins that control alternative splicing has therefore been the focus of much research. Recent work has established that even core protein components of the spliceosome, which are required for splicing to proceed, can nonetheless contribute to splicing regulation by modulating splice site choice. We here show that the RNA components of the spliceosome likewise influence alternative splicing decisions. Although these small nuclear RNAs (snRNAs), termed U1, U2, U4, U5, and U6 snRNA, are present in equal stoichiometry within the spliceosome, we found that their relative levels vary by an order of magnitude during development, across tissues, and across cancer samples. Physiologically relevant perturbation of individual snRNAs drove widespread gene-specific differences in alternative splic- ing but not transcriptome-wide splicing failure. Genes that were particularly sensitive to variations in snRNA abundance in a breast cancer cell line model were likewise preferentially misspliced within a clinically diverse cohort of invasive breast ductal carcinomas. -
The Reciprocal Regulation Between Splicing and 3-End Processing
Advanced Review The reciprocal regulation between splicing and 30-end processing Daisuke Kaida* Most eukaryotic precursor mRNAs are subjected to RNA processing events, including 50-end capping, splicing and 30-end processing. These processing events were historically studied independently; however, since the early 1990s tremendous efforts by many research groups have revealed that these processing factors interact with each other to control each other’s functions. U1 snRNP and its components negatively regulate polyadenylation of precursor mRNAs. Impor- tantly, this function is necessary for protecting the integrity of the transcriptome and for regulating gene length and the direction of transcription. In addition, physical and functional interactions occur between splicing factors and 30-end processing factors across the last exon. These interactions activate or inhibit spli- cing and 30-end processing depending on the context. Therefore, splicing and 30- end processing are reciprocally regulated in many ways through the complex protein–protein interaction network. Although interesting questions remain, future studies will illuminate the molecular mechanisms underlying the recipro- cal regulation. © 2016 The Authors. WIREs RNA published by Wiley Periodicals, Inc. How to cite this article: WIREs RNA 2016, 7:499–511. doi: 10.1002/wrna.1348 INTRODUCTION regulate each other on the transcription apparatus. In addition, because these events are carried out co- n eukaryotic cells, most precursor mRNAs (pre- transcriptionally in most cases, such factors can exist ImRNAs) consist of protein-coding regions, exons, on pre-mRNA just after synthesis of the binding sites 1,2 and intervening regions, introns. The pre-mRNAs of processing factors, suggesting that the factors are subjected to splicing to remove introns and to affect each other on the pre-mRNA.