Interaction of Tau with the RNA-Binding Protein TIA1 Regulates Tau Pathophysiology and Toxicity
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Effects of Changes in TIA1 on Stress Granule Formation
Effects of changes in TIA1 on stress granule formation Master’s thesis Lydia Sagath University of Helsinki Faculty of Biological and Environmental Sciences Genetics August 2015 Tiedekunta – Fakultet – Faculty Laitos – Institution– Department Bio- och miljövetenskapliga fakulteten Biovetenskapliga institutionen Tekijä – Författare – Author Lydia Johanna Sagath Työn nimi – Arbetets titel – Title Effects of changes in TIA1 on stress granule formation Oppiaine – Läroämne – Subject Humangenetik Työn laji – Arbetets art – Level Aika – Datum – Month and year Sivumäärä – Sidoantal – Number of pages Pro gradu Augusti 2015 63 Tiivistelmä – Referat – Abstract Welanders distala myopati (WDM) orsakas av mutationen p.E384K i genen TIA1. Mutationen antas vara sjukdomsalstrande på grund av en ökad produktion av protein, som relaterats till formationen av stressgranuler (Hackman et al. 2013). Även omgivningsfaktorer har föreslagits verka i sjukdomens utveckling: en ökad mängd stressgranuler har observerats i celler som behandlats med köldshock jämfört med celler som förvarats i 37°C (Hofmann et al. 2012). I patienter med WDM-liknande symptom som undersökts för förändringar i TIA1 har en p.N357S-förändring noterats förrikad. Denna förändring har tidigare anmälts som en polymorfism. Förändringen i fråga ligger i samma prionliknande domän i exon 5 som WDM-orsakande förändringen p.E384K. Därmed kunde p.N357S-förändringen öka predispositionen till aggregering. Pro gradu –arbetet är uppdelat i två delar: • p.N357S-polymorfismens effekt på stressgranulsbildningen i arsenitbehandle celler • Köldshockens effekt på stressgranulsbildningen Resultaten påvisar, att förändringen p.N357S i TIA1 orsakar en förändring i det translaterade proteinets beteende. I likhet med p.E384K-förändringen orsakar även p.N357S en ökad mängd stressgranuler i arsenitbehandlade celler. Däremot tyder resultaten på att stressgranulerna återbildas snabbare i fluorescence recovery after photobleaching-studier (FRAP) I p.N357S-transfekterade celler än i celler som transfekterats med TIA1 p.E384K och vildtyp. -
Dysregulated Expression of Lipid Storage and Membrane Dynamics Factors in Tia1 Knockout Mouse Nervous Tissue
Neurogenetics DOI 10.1007/s10048-014-0397-x ORIGINAL ARTICLE Dysregulated expression of lipid storage and membrane dynamics factors in Tia1 knockout mouse nervous tissue Melanie Vanessa Heck & Mekhman Azizov & Ta n j a S t e h n i n g & Michael Walter & Nancy Kedersha & Georg Auburger Received: 28 January 2014 /Accepted: 3 March 2014 # The Author(s) 2014. This article is published with open access at Springerlink.com Abstract During cell stress, the transcription and translation decreased levels for Bid and Inca1 transcripts. Novel and sur- of immediate early genes are prioritized, while most other mes- prisingly strong expression alterations were detected for fat stor- senger RNAs (mRNAs) are stored away in stress granules or age and membrane trafficking factors, with prominent +3-fold degraded in processing bodies (P-bodies). TIA-1 is an mRNA- upregulations of Plin4, Wdfy1, Tbc1d24,andPnpla2 vs. a −2.4- binding protein that needs to translocate from the nucleus to seed fold downregulation of Cntn4 transcript, encoding an axonal the formation of stress granules in the cytoplasm. Because other membrane adhesion factor with established haploinsufficiency. stress granule components such as TDP-43, FUS, ATXN2, In comparison, subtle effects on the RNA processing machinery SMN, MAPT, HNRNPA2B1, and HNRNPA1 are crucial for included up to 1.2-fold upregulations of Dcp1b and Tial1.The the motor neuron diseases amyotrophic lateral sclerosis (ALS)/ effect on lipid dynamics factors is noteworthy, since also the gene spinal muscular atrophy (SMA) and for the frontotemporal de- deletion of Ta rd b p (encoding TDP-43) and Atxn2 ledtofat mentia (FTD), here we studied mouse nervous tissue to identify metabolism phenotypes in mouse. -
Supplementary Materials
Supplementary Materials COMPARATIVE ANALYSIS OF THE TRANSCRIPTOME, PROTEOME AND miRNA PROFILE OF KUPFFER CELLS AND MONOCYTES Andrey Elchaninov1,3*, Anastasiya Lokhonina1,3, Maria Nikitina2, Polina Vishnyakova1,3, Andrey Makarov1, Irina Arutyunyan1, Anastasiya Poltavets1, Evgeniya Kananykhina2, Sergey Kovalchuk4, Evgeny Karpulevich5,6, Galina Bolshakova2, Gennady Sukhikh1, Timur Fatkhudinov2,3 1 Laboratory of Regenerative Medicine, National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of Ministry of Healthcare of Russian Federation, Moscow, Russia 2 Laboratory of Growth and Development, Scientific Research Institute of Human Morphology, Moscow, Russia 3 Histology Department, Medical Institute, Peoples' Friendship University of Russia, Moscow, Russia 4 Laboratory of Bioinformatic methods for Combinatorial Chemistry and Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia 5 Information Systems Department, Ivannikov Institute for System Programming of the Russian Academy of Sciences, Moscow, Russia 6 Genome Engineering Laboratory, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia Figure S1. Flow cytometry analysis of unsorted blood sample. Representative forward, side scattering and histogram are shown. The proportions of negative cells were determined in relation to the isotype controls. The percentages of positive cells are indicated. The blue curve corresponds to the isotype control. Figure S2. Flow cytometry analysis of unsorted liver stromal cells. Representative forward, side scattering and histogram are shown. The proportions of negative cells were determined in relation to the isotype controls. The percentages of positive cells are indicated. The blue curve corresponds to the isotype control. Figure S3. MiRNAs expression analysis in monocytes and Kupffer cells. Full-length of heatmaps are presented. -
U1 Snrnp Regulates Chromatin Retention of Noncoding Rnas
bioRxiv preprint doi: https://doi.org/10.1101/310433; this version posted April 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. U1 snRNP regulates chromatin retention of noncoding RNAs Yafei Yin,1,* J. Yuyang Lu,1 Xuechun Zhang,1 Wen Shao,1 Yanhui Xu,1 Pan Li,1,2 Yantao Hong,1 Qiangfeng Cliff Zhang,2 and Xiaohua Shen 1,3,* 1 Tsinghua-Peking Center for Life Sciences, School of Medicine and School of Life Sciences, Tsinghua University, Beijing 100084, China 2 MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China 3 Lead Contact *Correspondence: [email protected] (Y.Y.), [email protected] (X.S.) Running title: U1 snRNP regulates ncRNA-chromatin retention Keywords: RNA-chromatin localization, U1 snRNA, lncRNA, PROMPTs and eRNA, splicing 1 bioRxiv preprint doi: https://doi.org/10.1101/310433; this version posted April 29, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Thousands of noncoding transcripts exist in mammalian genomes, and they preferentially localize to chromatin. Here, to identify cis-regulatory elements that control RNA-chromatin association, we developed a high-throughput method named RNA element for subcellular localization by sequencing (REL-seq). Coupling REL-seq with random mutagenesis (mutREL-seq), we discovered a key 7-nt U1 recognition motif in chromatin-enriched RNA elements. -
Anti-TIA1 Antibody (ARG58772)
Product datasheet [email protected] ARG58772 Package: 100 μl anti-TIA1 antibody Store at: -20°C Summary Product Description Rabbit Polyclonal antibody recognizes TIA1 Tested Reactivity Hu, Ms Tested Application IHC-P, WB Host Rabbit Clonality Polyclonal Isotype IgG Target Name TIA1 Antigen Species Human Immunogen Synthetic peptide from Human TIA1. Conjugation Un-conjugated Alternate Names T-cell-restricted intracellular antigen-1; WDM; TIA-1; RNA-binding protein TIA-1; p40-TIA-1; Nucleolysin TIA-1 isoform p40 Application Instructions Application table Application Dilution IHC-P 1:50 - 1:200 WB 1:500 - 1:2000 Application Note IHC-P: Antigen Retrieval: Heat mediated. * The dilutions indicate recommended starting dilutions and the optimal dilutions or concentrations should be determined by the scientist. Calculated Mw 43 kDa Observed Size ~ 45 kDa Properties Form Liquid Purification Affinity purified. Buffer PBS (pH 7.4), 150mM NaCl, 0.02% Sodium azide and 50% Glycerol. Preservative 0.02% Sodium azide Stabilizer 50% Glycerol Storage instruction For continuous use, store undiluted antibody at 2-8°C for up to a week. For long-term storage, aliquot and store at -20°C. Storage in frost free freezers is not recommended. Avoid repeated freeze/thaw cycles. Suggest spin the vial prior to opening. The antibody solution should be gently mixed before use. www.arigobio.com 1/2 Note For laboratory research only, not for drug, diagnostic or other use. Bioinformation Gene Symbol TIA1 Gene Full Name TIA1 cytotoxic granule-associated RNA binding protein Background The product encoded by this gene is a member of a RNA-binding protein family and possesses nucleolytic activity against cytotoxic lymphocyte (CTL) target cells. -
MOCHI Enables Discovery of Heterogeneous Interactome Modules in 3D Nucleome
Downloaded from genome.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome Dechao Tian1,# , Ruochi Zhang1,# , Yang Zhang1, Xiaopeng Zhu1, and Jian Ma1,* 1Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA #These two authors contributed equally *Correspondence: [email protected] Contact To whom correspondence should be addressed: Jian Ma School of Computer Science Carnegie Mellon University 7705 Gates-Hillman Complex 5000 Forbes Avenue Pittsburgh, PA 15213 Phone: +1 (412) 268-2776 Email: [email protected] 1 Downloaded from genome.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press Abstract The composition of the cell nucleus is highly heterogeneous, with different constituents forming complex interactomes. However, the global patterns of these interwoven heterogeneous interactomes remain poorly understood. Here we focus on two different interactomes, chromatin interaction network and gene regulatory network, as a proof-of-principle, to identify heterogeneous interactome modules (HIMs), each of which represents a cluster of gene loci that are in spatial contact more frequently than expected and that are regulated by the same group of transcription factors. HIM integrates transcription factor binding and 3D genome structure to reflect “transcriptional niche” in the nucleus. We develop a new algorithm MOCHI to facilitate the discovery of HIMs based on network motif clustering in heterogeneous interactomes. By applying MOCHI to five different cell types, we found that HIMs have strong spatial preference within the nucleus and exhibit distinct functional properties. Through integrative analysis, this work demonstrates the utility of MOCHI to identify HIMs, which may provide new perspectives on the interplay between transcriptional regulation and 3D genome organization. -
U1 Snrnp Regulates Chromatin Retention of Noncoding Rnas
Article U1 snRNP regulates chromatin retention of noncoding RNAs https://doi.org/10.1038/s41586-020-2105-3 Yafei Yin1 ✉, J. Yuyang Lu1, Xuechun Zhang1, Wen Shao1, Yanhui Xu1, Pan Li1,2, Yantao Hong1, Li Cui1, Ge Shan3, Bin Tian4, Qiangfeng Cliff Zhang1,2 & Xiaohua Shen1 ✉ Received: 26 November 2018 Accepted: 9 January 2020 Long noncoding RNAs (lncRNAs) and promoter- or enhancer-associated unstable Published online: xx xx xxxx transcripts locate preferentially to chromatin, where some regulate chromatin structure, Check for updates transcription and RNA processing1–13. Although several RNA sequences responsible for nuclear localization have been identifed—such as repeats in the lncRNA Xist and Alu-like elements in long RNAs14–16—how lncRNAs as a class are enriched at chromatin remains unknown. Here we describe a random, mutagenesis-coupled, high-throughput method that we name ‘RNA elements for subcellular localization by sequencing’ (mutREL-seq). Using this method, we discovered an RNA motif that recognizes the U1 small nuclear ribonucleoprotein (snRNP) and is essential for the localization of reporter RNAs to chromatin. Across the genome, chromatin-bound lncRNAs are enriched with 5′ splice sites and depleted of 3′ splice sites, and exhibit high levels of U1 snRNA binding compared with cytoplasm-localized messenger RNAs. Acute depletion of U1 snRNA or of the U1 snRNP protein component SNRNP70 markedly reduces the chromatin association of hundreds of lncRNAs and unstable transcripts, without altering the overall transcription rate in cells. In addition, rapid degradation of SNRNP70 reduces the localization of both nascent and polyadenylated lncRNA transcripts to chromatin, and disrupts the nuclear and genome-wide localization of the lncRNA Malat1. -
Large-Scale Analysis of Genome and Transcriptome Alterations in Multiple Tumors Unveils Novel Cancer-Relevant Splicing Networks
Downloaded from genome.cshlp.org on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press Large-scale analysis of genome and transcriptome alterations in multiple tumors unveils novel cancer-relevant splicing networks Endre Sebestyén1,*, Babita Singh1,*, Belén Miñana1,2, Amadís Pagès1, Francesca Mateo3, Miguel Angel Pujana3, Juan Valcárcel1,2,4, Eduardo Eyras1,4,5 1Universitat Pompeu Fabra, Dr. Aiguader 88, E08003 Barcelona, Spain 2Centre for Genomic Regulation, Dr. Aiguader 88, E08003 Barcelona, Spain 3Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), E08908 L’Hospitalet del Llobregat, Spain. 4Catalan Institution for Research and Advanced Studies, Passeig Lluís Companys 23, E08010 Barcelona, Spain *Equal contribution 5Correspondence to: [email protected] Keywords: alternative splicing, RNA binding proteins, splicing networks, cancer 1 Downloaded from genome.cshlp.org on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press Abstract Alternative splicing is regulated by multiple RNA-binding proteins and influences the expression of most eukaryotic genes. However, the role of this process in human disease, and particularly in cancer, is only starting to be unveiled. We systematically analyzed mutation, copy number and gene expression patterns of 1348 RNA-binding protein (RBP) genes in 11 solid tumor types, together with alternative splicing changes in these tumors and the enrichment of binding motifs in the alternatively spliced sequences. Our comprehensive study reveals widespread alterations in the expression of RBP genes, as well as novel mutations and copy number variations in association with multiple alternative splicing changes in cancer drivers and oncogenic pathways. Remarkably, the altered splicing patterns in several tumor types recapitulate those of undifferentiated cells. -
Ribosome Profiling Reveals an Important Role for Translational Control in Circadian Gene Expression
Downloaded from genome.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Research Ribosome profiling reveals an important role for translational control in circadian gene expression Christopher Jang,1,4 Nicholas F. Lahens,2,4 John B. Hogenesch,2 and Amita Sehgal1,3 1Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA; 2Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA; 3Howard Hughes Medical Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA Physiological and behavioral circadian rhythms are driven by a conserved transcriptional/translational negative feedback loop in mammals. Although most core clock factors are transcription factors, post-transcriptional control introduces delays that are critical for circadian oscillations. Little work has been done on circadian regulation of translation, so to address this deficit we conducted ribosome profiling experiments in a human cell model for an autonomous clock. We found that most rhythmic gene expression occurs with little delay between transcription and translation, suggesting that the lag in the ac- cumulation of some clock proteins relative to their mRNAs does not arise from regulated translation. Nevertheless, we found that translation occurs in a circadian fashion for many genes, sometimes imposing an additional level of control on rhythmically expressed mRNAs and, in other cases, conferring rhythms on noncycling mRNAs. Most cyclically tran- scribed RNAs are translated at one of two major times in a 24-h day, while rhythmic translation of most noncyclic RNAs is phased to a single time of day. -
RNA-Binding Proteins and the Complex Pathophysiology of ALS
International Journal of Molecular Sciences Review RNA-Binding Proteins and the Complex Pathophysiology of ALS Wanil Kim 1,†, Do-Yeon Kim 2,* and Kyung-Ha Lee 1,* 1 Division of Cosmetic Science and Technology, Daegu Haany University, Hanuidae-ro 1, Gyeongsan, Gyeongbuk 38610, Korea; [email protected] 2 Department of Pharmacology, School of Dentistry, Kyungpook National University, Daegu 41940, Korea * Correspondence: [email protected] (D.-Y.K.); [email protected] (K.-H.L.); Tel.: +82-53-660-6880 (D.-Y.K.); +82-53-819-7743 (K.-H.L.) † Current Address: Department of Biochemistry, College of Medicine, Gyeongsang National University, Jinju 52828, Korea. Abstract: Genetic analyses of patients with amyotrophic lateral sclerosis (ALS) have identified disease- causing mutations and accelerated the unveiling of complex molecular pathogenic mechanisms, which may be important for understanding the disease and developing therapeutic strategies. Many disease-related genes encode RNA-binding proteins, and most of the disease-causing RNA or proteins encoded by these genes form aggregates and disrupt cellular function related to RNA metabolism. Disease-related RNA or proteins interact or sequester other RNA-binding proteins. Eventually, many disease-causing mutations lead to the dysregulation of nucleocytoplasmic shuttling, the dysfunction of stress granules, and the altered dynamic function of the nucleolus as well as other membrane- less organelles. As RNA-binding proteins are usually components of several RNA-binding protein complexes that have other roles, the dysregulation of RNA-binding proteins tends to cause diverse forms of cellular dysfunction. Therefore, understanding the role of RNA-binding proteins will help elucidate the complex pathophysiology of ALS. -
Inhibiting PARP1 Splicing Along with Inducing DNA Damage As Potential Breast Cancer Therapy
Reem Alsayed 3/26/21 03-545, S21 Professor Ihab Younis Inhibiting PARP1 Splicing along with Inducing DNA Damage as Potential Breast Cancer Therapy Student: Reem Alsayed Spring 2021 Professor: Ihab Younis 1 Reem Alsayed 3/26/21 03-545, S21 Professor Ihab Younis Abstract: Triple negative breast cancer is a deadly cancer and once it has metastasized it is deemed incurable. The need for an effective therapy is rising, and recent therapies include targeting the DNA damage response pathway. PARP1 is one of the first responders to DNA damage, and has been targeted for inhibition along with the stimulation of DNA damage as a treatment for breast cancer. However, such treatments lack in specificity, and only target one or two domains of the PARP1 protein, whereas PARP1 has other functions pertaining to multiple cancer hallmarks such as promoting angiogenesis, metastasis, inflammation, life cycle regulation, and regulation of tumorigenic genes. In this project, we hypothesize that by inhibiting the PARP1 protein production, we will be able to effectively inhibit all cancer hallmarks that are facilitated by PARP1, and we achieve this by inhibiting the splicing of PARP1. Splicing is the removal of intervening sequences (introns) in the pre-mRNA and the joining of the expressed sequences (exons). For PARP1, we blocked intron 22 splicing by introducing an Antisense Morpholino Oligonucleotide (AMO) that blocks the binding of the spliceosome. The results obtained demonstrate that 50uM PARP1 AMO inhibits PARP1 splicing >88%, as well as inhibits protein production. Additionally, the combination of PARP1 AMO and Doxorubicin lead to a loss in cell proliferation. -
In Silico Identification of EP400 and TIA1 As Critical Transcription Factors Involved in Human Hepatocellular Carcinoma Relapse
952 ONCOLOGY LETTERS 19: 952-964, 2020 In silico identification of EP400 and TIA1 as critical transcription factors involved in human hepatocellular carcinoma relapse WEIGUO HONG1, YAN HU1, ZHENPING FAN2, RONG GAO1, RUICHUANG YANG1, JINGFENG BI1 and JUN HOU1 1Clinical Research and Management Center, and 2Liver Disease Center for Cadre Medical Care, Fifth Medical Center, Chinese PLA General Hospital, Beijing 100039, P.R. China Received May 15, 2019; Accepted October 22, 2019 DOI: 10.3892/ol.2019.11171 Abstract. Hepatocellular carcinoma (HCC) is the second TIA1 may therefore serve as potential prognostic and thera- leading cause of cancer-associated mortality worldwide. peutic biomarkers. Transcription factors (TFs) are crucial proteins that regulate gene expression during cancer progression; however, the roles Introduction of TFs in HCC relapse remain unclear. To identify the TFs that drive HCC relapse, the present study constructed co-expres- Hepatocellular carcinoma (HCC) is one of the most common sion network and identified the Tan module the most relevant types of cancer and the second leading cause of cancer-asso- to HCC relapse. Numerous hub TFs (highly connected) were ciated mortality worldwide (1). Its incidence is increasing in subsequently obtained from the Tan module according to the numerous countries (2). Progression of HCC is characterized intra-module connectivity and the protein-protein interac- by abnormal cell differentiation, fast infiltrating growth, early tion network connectivity. Next, E1A-binding protein p400 metastasis, high‑grade malignancy and poor prognosis (3). (EP400) and TIA1 cytotoxic granule associated RNA binding Liver transplantation (LT) is considered to be one of the protein (TIA1) were identified as hub TFs differentially major treatment options for HCC (4), as not only it eliminates connected between the relapsed and non-relapsed subnet- the tumor but could also cure the underlying liver disease.