Structural Insights Into How Prp5 Proofreads the Pre-Mrna Branch Site
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Urabe VK, Et Al. Influences on U2 Snrna Structure U2
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.05.451154; this version posted July 6, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. Urabe VK, et al. Influences on U2 snRNA structure U2 snRNA structure is influenced by SF3A and SF3B proteins but not by SF3B inhibitors Veronica K. Urabe1, Meredith Stevers1, Arun K. Ghosh3 and Melissa S. Jurica1,2 * 1Department of Molecular Cell and Developmental Biology and 2Center for Molecular Biology of RNA, University of California, Santa Cruz, California, United States of America 3Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana United States of America *Corresponding author E-mail: [email protected] (MSJ) bioRxiv preprint doi: https://doi.org/10.1101/2021.07.05.451154; this version posted July 6, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. Urabe VK, et al. Influences on U2 snRNA structure Abstract U2 snRNP is an essential component of the spliceosome. It is responsible for branch point recognition in the spliceosome A-complex via base-pairing of U2 snRNA with an intron to form the branch helix. Small molecule inhibitors target the SF3B component of the U2 snRNP and interfere with A-complex formation during spliceosome assembly. -
SF3B2 Monoclonal Antibody (M01J), Clone 5D2
SF3B2 monoclonal antibody (M01J), clone 5D2 Catalog # : H00010992-M01J 規格 : [ 100 ug ] List All Specification Application Image Product Mouse monoclonal antibody raised against a partial recombinant Western Blot (Cell lysate) Description: SF3B2. Immunogen: SF3B2 (NP_006833, 592 a.a. ~ 645 a.a) partial recombinant protein with GST tag. MW of the GST tag alone is 26 KDa. Sequence: YEGKEFETRLKEKKPGDLSDELRISLGMPVGPNAHKVPPPWLIAMQRYG PPPSY enlarge Western Blot (Cell lysate) Host: Mouse Reactivity: Human, Mouse, Rat Preparation Cell Culture Production Method: (CX Grade Antibody List) enlarge Isotype: IgG2a Kappa Western Blot (Recombinant protein) Quality Control Antibody Reactive Against Recombinant Protein. Immunofluorescence Testing: enlarge Immunohistochemistry (Formalin/PFA-fixed paraffin- embedded sections) Western Blot detection against Immunogen (31.68 KDa) . Storage Buffer: In 1x PBS, pH 7.4 Storage Store at -20°C or lower. Aliquot to avoid repeated freezing and thawing. enlarge Instruction: Sandwich ELISA (Recombinant protein) MSDS: Download Interspecies Mouse (98); Rat (98) Antigen Sequence: Datasheet: Download enlarge ELISA Applications Western Blot (Cell lysate) Page 1 of 3 2021/6/15 SF3B2 monoclonal antibody (M01J), clone 5D2. Western Blot analysis of SF3B2 expression in Hela S3 NE. Protocol Download Western Blot (Cell lysate) SF3B2 monoclonal antibody (M01J), clone 5D2. Western Blot analysis of SF3B2 expression in Jurkat. Protocol Download Western Blot (Recombinant protein) Protocol Download Immunofluorescence enlarge this image Immunofluorescence of monoclonal antibody to SF3B2 on HeLa cell . [antibody concentration 10 ug/ml] Immunohistochemistry (Formalin/PFA-fixed paraffin-embedded sections) enlarge this image Page 2 of 3 2021/6/15 Immunoperoxidase of monoclonal antibody to SF3B2 on formalin-fixed paraffin-embedded human kidney. [antibody concentration 6 ug/ml] Protocol Download Sandwich ELISA (Recombinant protein) Detection limit for recombinant GST tagged SF3B2 is 0.1 ng/ml as a capture antibody. -
SF3B2-Mediated RNA Splicing Drives Human Prostate Cancer Progression
Published OnlineFirst August 20, 2019; DOI: 10.1158/0008-5472.CAN-18-3965 Cancer Molecular Cell Biology Research SF3B2-Mediated RNA Splicing Drives Human Prostate Cancer Progression Norihiko Kawamura1,2, Keisuke Nimura1, Kotaro Saga1, Airi Ishibashi1, Koji Kitamura1,3, Hiromichi Nagano1, Yusuke Yoshikawa4, Kyoso Ishida1,5, Norio Nonomura2, Mitsuhiro Arisawa4, Jun Luo6, and Yasufumi Kaneda1 Abstract Androgen receptor splice variant-7 (AR-V7) is a General RNA splicing SF3B2 complex-mediated alternative RNA splicing constitutively active AR variant implicated in U2 castration-resistant prostate cancers. Here, we show U2 snRNA that the RNA splicing factor SF3B2, identified by 3’ 3’ in silico and CRISPR/Cas9 analyses, is a critical 5’ 3’ splice site 5’ SF3B7 AR-V7 5’ A U2AF2 AGA Exon ? determinant of expression and is correlated SF3B6(p14) SF3B4 SF3B1 SF3B4 SF3B1 with aggressive cancer phenotypes. Transcriptome SF3B5 SF3B2 SF3B3 SF3B2 SF3B3 and PAR-CLIP analyses revealed that SF3B2 con- SF3A3 SF3B2 complex SF3A3 SF3A1 SF3A1 SF3b complex trols the splicing of target genes, including AR, to AR pre-mRNA drive aggressive phenotypes. SF3B2-mediated CE3 aggressive phenotypes in vivo were reversed by AR-V7 mRNA AR mRNA AR-V7 knockout. Pladienolide B, an inhibitor of CE3 a splicing modulator of the SF3b complex, sup- Drive malignancy pressed the growth of tumors addicted to high While the SF3b complex is critical for general RNA splicing, SF3B2 promotes inclusion of the target exon through recognizing a specific RNA motif. SF3B2 expression. These findings support the idea © 2019 American Association for Cancer Research that alteration of the splicing pattern by high SF3B2 expression is one mechanism underlying prostate cancer progression and therapeutic resistance. -
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. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Nuclear PTEN Safeguards Pre-Mrna Splicing to Link Golgi Apparatus for Its Tumor Suppressive Role
ARTICLE DOI: 10.1038/s41467-018-04760-1 OPEN Nuclear PTEN safeguards pre-mRNA splicing to link Golgi apparatus for its tumor suppressive role Shao-Ming Shen1, Yan Ji2, Cheng Zhang1, Shuang-Shu Dong2, Shuo Yang1, Zhong Xiong1, Meng-Kai Ge1, Yun Yu1, Li Xia1, Meng Guo1, Jin-Ke Cheng3, Jun-Ling Liu1,3, Jian-Xiu Yu1,3 & Guo-Qiang Chen1 Dysregulation of pre-mRNA alternative splicing (AS) is closely associated with cancers. However, the relationships between the AS and classic oncogenes/tumor suppressors are 1234567890():,; largely unknown. Here we show that the deletion of tumor suppressor PTEN alters pre-mRNA splicing in a phosphatase-independent manner, and identify 262 PTEN-regulated AS events in 293T cells by RNA sequencing, which are associated with significant worse outcome of cancer patients. Based on these findings, we report that nuclear PTEN interacts with the splicing machinery, spliceosome, to regulate its assembly and pre-mRNA splicing. We also identify a new exon 2b in GOLGA2 transcript and the exon exclusion contributes to PTEN knockdown-induced tumorigenesis by promoting dramatic Golgi extension and secretion, and PTEN depletion significantly sensitizes cancer cells to secretion inhibitors brefeldin A and golgicide A. Our results suggest that Golgi secretion inhibitors alone or in combination with PI3K/Akt kinase inhibitors may be therapeutically useful for PTEN-deficient cancers. 1 Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, China. 2 Institute of Health Sciences, Shanghai Institutes for Biological Sciences of Chinese Academy of Sciences and SJTU-SM, Shanghai 200025, China. -
Transcriptomic Analysis of Short-Fruit 1 (Sf1)
www.nature.com/scientificreports OPEN Transcriptomic analysis of short- fruit 1 (sf1) reveals new insights into the variation of fruit-related Received: 15 November 2016 Accepted: 20 April 2017 traits in Cucumis sativus Published: xx xx xxxx Lina Wang, Chenxing Cao, Shuangshuang Zheng, Haiyang Zhang, Panjing Liu, Qian Ge, Jinrui Li & Zhonghai Ren Fruit size is an important quality trait in different market classes ofCucumis sativus L., an economically important vegetable cultivated worldwide, but the genetic and molecular mechanisms that control fruit size are largely unknown. In this study, we isolated a natural cucumber mutant, short fruit 1 (sf1), caused by a single recessive Mendelian factor, from the North China-type inbred line CNS2. In addition to significantly decreased fruit length, other fruit-related phenotypic variations were also observed in sf1 compared to the wild-type (WT) phenotype, indicating that sf1 might have pleiotropic effects. Microscopic imaging showed that fruit cell size in sf1 was much larger than that in WT, suggesting that the short fruit phenotype in sf1 is caused by decreased cell number. Fine mapping revealed that sf1 was localized to a 174.3 kb region on chromosome 6. Similarly, SNP association analysis of bulked segregant RNA-Seq data showed increased SNP frequency in the same region of chromosome 6. In addition, transcriptomic analysis revealed that sf1 might control fruit length through the fine-tuning of cytokinin and auxin signalling, gibberellin biosynthesis and signal transduction in cucumber fruits. Overall, our results provide important information for further study of fruit length and other fruit-related features in cucumber. Cucumber (Cucumis sativus L., 2n = 14), a member of the family Cucurbitaceae, is one of the most economically important vegetable crops cultivated throughout the world. -
Producing Cells of the Testis, Ovary and Adrenal Gland F
RESEARCH ARTICLE 4561 Development 139, 4561-4570 (2012) doi:10.1242/dev.087247 © 2012. Published by The Company of Biologists Ltd In vivo evidence for the crucial role of SF1 in steroid- producing cells of the testis, ovary and adrenal gland F. William Buaas1,*, Jennifer R. Gardiner1, Sally Clayton1, Pierre Val2 and Amanda Swain1,‡ SUMMARY Adrenal and gonadal steroids are essential for life and reproduction. The orphan nuclear receptor SF1 (NR5A1) has been shown to regulate the expression of enzymes involved in steroid production in vitro. However, the in vivo role of this transcription factor in steroidogenesis has not been elucidated. In this study, we have generated steroidogenic-specific Cre-expressing mice to lineage mark and delete Sf1 in differentiated steroid-producing cells of the testis, the ovary and the adrenal gland. Our data show that SF1 is a regulator of the expression of steroidogenic genes in all three organs. In addition, Sf1 deletion leads to a radical change in cell morphology and loss of identity. Surprisingly, sexual development and reproduction in mutant animals were not compromised owing, in part, to the presence of a small proportion of SF1-positive cells. In contrast to the testis and ovary, the mutant adult adrenal gland showed a lack of Sf1-deleted cells and our studies suggest that steroidogenic adrenal cells during foetal stages require Sf1 to give rise to the adult adrenal population. This study is the first to show the in vivo requirements of SF1 in steroidogenesis and provides novel data on the cellular consequences of the loss of this protein specifically within steroid-producing cells. -
Possible Misdiagnosis of 46,XX Testicular Disorders of Sex
Int. J. Med. Sci. 2020, Vol. 17 1136 Ivyspring International Publisher International Journal of Medical Sciences 2020; 17(9): 1136-1141. doi: 10.7150/ijms.46058 Research Paper Possible misdiagnosis of 46,XX testicular disorders of sex development in infertile males Tong Chen1,2†, Linlin Tian1,3†, Xianlong Wang1, Demin Fan4, Gang Ma1, Rong Tang1, Xujun Xuan1,5 1. Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics; The Key Laboratory for Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250021, P.R. China 2. Department of Pediatric Surgery, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, 200062, P.R. China 3. Department of microbiology, Faculty of Basic Medical Sciences, Guilin Medical University, Guilin, Guangxi 541004, P.R. China 4. Department of Urology, Shandong Provincial Qianfoshan Hospital, Jinan, Shandong 250002, P.R. China 5. Department of Andrology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, P.R. China. †Tong Chen and Linlin Tian contributed equally to this study. Corresponding author: Xujun Xuan, Department of Andrology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, P.R. China. E-mail: [email protected] © The author(s). This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/). See http://ivyspring.com/terms for full terms and conditions. Received: 2020.03.16; Accepted: 2020.04.23; Published: 2020.05.11 Abstract Objectives: The 46,XX disorders of sex development (DSD) is a rare genetic cause of male infertility and possible misdiagnosis of this condition has never been reported. -
Identification of Tat-SF1 Cellular Targets by Exon Array Analysis Reveals Dual Roles in Transcription and Splicing
Identification of Tat-SF1 cellular targets by exon array analysis reveals dual roles in transcription and splicing HEATHER B. MILLER,1,2,7 TIMOTHY J. ROBINSON,1,2,3,4 RALUCA GORDAˆ N,5,8 ALEXANDER J. HARTEMINK,5 and MARIANO A. GARCIA-BLANCO1,2,6 1Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA 2Center for RNA Biology, Duke University Medical Center, Durham, North Carolina 27710, USA 3Medical Scientist Training Program, Duke University Medical Center, Durham, North Carolina 27710, USA 4Program in Molecular Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA 5Department of Computer Science, Duke University, Durham, North Carolina 27708, USA 6Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA ABSTRACT Tat specific factor 1 (Tat-SF1) interacts with components of both the transcription and splicing machineries and has been classified as a transcription-splicing factor. Although its function as an HIV-1 dependency factor has been investigated, relatively little is known about the cellular functions of Tat-SF1. To identify target genes of Tat-SF1, we utilized a combination of RNAi and exon-specific microarrays. These arrays, which survey genome-wide changes in transcript and individual exon levels, revealed 450 genes with transcript level changes upon Tat-SF1 depletion. Strikingly, 98% of these target genes were down-regulated upon depletion, indicating that Tat-SF1 generally activates gene expression. We also identified 89 genes that showed differential exon level changes after Tat-SF1 depletion. The 89 genes showed evidence of many different types of alternative exon use consistent with the regulation of transcription initiation sites and RNA processing. -
Primepcr™Assay Validation Report
PrimePCR™Assay Validation Report Gene Information Gene Name splicing factor 3b, subunit 2, 145kDa Gene Symbol SF3B2 Organism Human Gene Summary This gene encodes subunit 2 of the splicing factor 3b protein complex. Splicing factor 3b together with splicing factor 3a and a 12S RNA unit forms the U2 small nuclear ribonucleoproteins complex (U2 snRNP). The splicing factor 3b/3a complex binds pre-mRNA upstream of the intron's branch site in a sequence-independent manner and may anchor the U2 snRNP to the pre-mRNA. Splicing factor 3b is also a component of the minor U12-type spliceosome. Subunit 2 associates with pre-mRNA upstream of the branch site at the anchoring site. Subunit 2 also interacts directly with subunit 4 of the splicing factor 3b complex. Subunit 2 is a highly hydrophilic protein with a proline-rich N-terminus and a glutamate-rich stretch in the C-terminus. Gene Aliases Cus1, SAP145, SF3B145, SF3b1, SF3b150 RefSeq Accession No. NC_000011.9, NT_167190.1 UniGene ID Hs.406423 Ensembl Gene ID ENSG00000087365 Entrez Gene ID 10992 Assay Information Unique Assay ID qHsaCEP0049827 Assay Type Probe - Validation information is for the primer pair using SYBR® Green detection Detected Coding Transcript(s) ENST00000566339, ENST00000301717, ENST00000542440, ENST00000267197, ENST00000528302, ENST00000322535, ENST00000524627, ENST00000533595, ENST00000530322, ENST00000524475, ENST00000483722, ENST00000545968, ENST00000399249, ENST00000256993, ENST00000381569, ENST00000265801, ENST00000538941, ENST00000563290, ENST00000324767, ENST00000356924, -
The RNA Splicing Response to DNA Damage
Biomolecules 2015, 5, 2935-2977; doi:10.3390/biom5042935 OPEN ACCESS biomolecules ISSN 2218-273X www.mdpi.com/journal/biomolecules/ Review The RNA Splicing Response to DNA Damage Lulzim Shkreta and Benoit Chabot * Département de Microbiologie et d’Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-819-821-8000 (ext. 75321); Fax: +1-819-820-6831. Academic Editors: Wolf-Dietrich Heyer, Thomas Helleday and Fumio Hanaoka Received: 12 August 2015 / Accepted: 16 October 2015 / Published: 29 October 2015 Abstract: The number of factors known to participate in the DNA damage response (DDR) has expanded considerably in recent years to include splicing and alternative splicing factors. While the binding of splicing proteins and ribonucleoprotein complexes to nascent transcripts prevents genomic instability by deterring the formation of RNA/DNA duplexes, splicing factors are also recruited to, or removed from, sites of DNA damage. The first steps of the DDR promote the post-translational modification of splicing factors to affect their localization and activity, while more downstream DDR events alter their expression. Although descriptions of molecular mechanisms remain limited, an emerging trend is that DNA damage disrupts the coupling of constitutive and alternative splicing with the transcription of genes involved in DNA repair, cell-cycle control and apoptosis. A better understanding of how changes in splice site selection are integrated into the DDR may provide new avenues to combat cancer and delay aging.