Sequence, Structure and Context Preferences of Human RNA
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Effects of Chromosome Specific Introgression in Upland Cotton on Fiber and Agronomic Traits
Genetics: Published Articles Ahead of Print, published on December 30, 2005 as 10.1534/genetics.105.053371 1 Effects of Chromosome Specific Introgression in Upland Cotton on Fiber and Agronomic Traits * 1 * † * Sukumar Saha, Johnie N. Jenkins, Jixiang Wu, Jack C. McCarty, * ‡ § †† Osman A. Gutiérrez, Richard G. Percy, Roy G. Cantrell, and David M. Stelly *United States Department of Agriculture-Agriculture Research Service, Crop Science Research † Laboratory, Mississippi State, Mississippi 39762, Department of Plant and Soil Sciences, ‡ Mississippi State University, Mississippi State, Mississippi 39762, United States Department of Agriculture-Agriculture Research Service, Maricopa Agricultural Center, Maricopa, Arizona § †† 85239, Cotton Incorporated, Raleigh, North Carolina 27513, and Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas 77843 Disclaimer: Mention of trademark or proprietary product does not constitute a guarantee or warranty of the product by the United States Department of Agriculture and does not imply its approval to the exclusion of other products that may also be suitable. 2 Running head: Evaluation of fiber and agronomic traits using chromosome substitution lines Key words: Chromosome substitution, Cotton, QTL, Germplasm, Mapping 1 Corresponding author: United States Department of Agriculture-Agriculture Research Service, Crop Science Research Laboratory, 810 Highway 12 East, Mississippi State, Mississippi 39762- 5367. E-mail: [email protected] 3 ABSTRACT Interspecific chromosome substitution is among the most powerful means of introgression and steps toward quantitative trait locus (QTL) identification. By reducing the genetic “noise” from other chromosomes, it greatly empowers the detection of genetic effects by specific chromosomes on quantitative traits. Here, we report on such results for 14 cotton lines (CS-B) with specific chromosomes or chromosome arms from G. -
DNA Damage Activates a Spatially Distinct Late Cytoplasmic Cell-Cycle Checkpoint Network Controlled by MK2-Mediated RNA Stabilization
DNA Damage Activates a Spatially Distinct Late Cytoplasmic Cell-Cycle Checkpoint Network Controlled by MK2-Mediated RNA Stabilization The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Reinhardt, H. Christian, Pia Hasskamp, Ingolf Schmedding, Sandra Morandell, Marcel A.T.M. van Vugt, XiaoZhe Wang, Rune Linding, et al. “DNA Damage Activates a Spatially Distinct Late Cytoplasmic Cell-Cycle Checkpoint Network Controlled by MK2-Mediated RNA Stabilization.” Molecular Cell 40, no. 1 (October 2010): 34–49.© 2010 Elsevier Inc. As Published http://dx.doi.org/10.1016/j.molcel.2010.09.018 Publisher Elsevier B.V. Version Final published version Citable link http://hdl.handle.net/1721.1/85107 Terms of Use Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. Molecular Cell Article DNA Damage Activates a Spatially Distinct Late Cytoplasmic Cell-Cycle Checkpoint Network Controlled by MK2-Mediated RNA Stabilization H. Christian Reinhardt,1,6,7,8 Pia Hasskamp,1,10,11 Ingolf Schmedding,1,10,11 Sandra Morandell,1 Marcel A.T.M. van Vugt,5 XiaoZhe Wang,9 Rune Linding,4 Shao-En Ong,2 David Weaver,9 Steven A. Carr,2 and Michael B. Yaffe1,2,3,* 1David H. Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02132, USA 2Broad Institute of MIT and Harvard, Cambridge, MA 02132, USA 3Center for Cell Decision Processes, -
RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases
G C A T T A C G G C A T genes Review RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases Amber Willbanks, Shaun Wood and Jason X. Cheng * Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL 60637, USA; [email protected] (A.W.); [email protected] (S.W.) * Correspondence: [email protected] Abstract: Chromatin structure plays an essential role in eukaryotic gene expression and cell identity. Traditionally, DNA and histone modifications have been the focus of chromatin regulation; however, recent molecular and imaging studies have revealed an intimate connection between RNA epigenetics and chromatin structure. Accumulating evidence suggests that RNA serves as the interplay between chromatin and the transcription and splicing machineries within the cell. Additionally, epigenetic modifications of nascent RNAs fine-tune these interactions to regulate gene expression at the co- and post-transcriptional levels in normal cell development and human diseases. This review will provide an overview of recent advances in the emerging field of RNA epigenetics, specifically the role of RNA modifications and RNA modifying proteins in chromatin remodeling, transcription activation and RNA processing, as well as translational implications in human diseases. Keywords: 5’ cap (5’ cap); 7-methylguanosine (m7G); R-loops; N6-methyladenosine (m6A); RNA editing; A-to-I; C-to-U; 2’-O-methylation (Nm); 5-methylcytosine (m5C); NOL1/NOP2/sun domain Citation: Willbanks, A.; Wood, S.; (NSUN); MYC Cheng, J.X. RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases. Genes 2021, 12, 627. -
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. -
Dramatic Nucleolar Dispersion in the Salivary Gland of Schwenkfeldina Sp
www.nature.com/scientificreports OPEN Dramatic nucleolar dispersion in the salivary gland of Schwenkfeldina sp. (Diptera: Sciaridae) José Mariano Amabis & Eduardo Gorab * Micronucleoli are among the structures composing the peculiar scenario of the nucleolus in salivary gland nuclei of dipterans representative of Sciaridae. Micronucleolar bodies contain ribosomal DNA and RNA, are transcriptionally active and may appear free in the nucleoplasm or associated with specifc chromosome regions in salivary gland nuclei. This report deals with an extreme case of nucleolar fragmentation/dispersion detected in the salivary gland of Schwenkfeldina sp. Such a phenomenon in this species was found to be restricted to cell types undergoing polyteny and seems to be diferentially controlled according to the cell type. Furthermore, transcriptional activity was detected in virtually all the micronucleolar bodies generated in the salivary gland. The relative proportion of the rDNA in polytene and diploid tissues showed that rDNA under-replication did not occur in polytene nuclei suggesting that the nucleolar and concomitant rDNA dispersion in Schwenkfeldina sp. may refect a previously hypothesised process in order to counterbalance the rDNA loss due to the under-replication. The chromosomal distribution of epigenetic markers for the heterochromatin agreed with early cytological observations in this species suggesting that heterochromatin is spread throughout the chromosome length of Schwenkfeldina sp. A comparison made with results from another sciarid species argues for a role played by the heterochromatin in the establishment of the rDNA topology in polytene nuclei of Sciaridae. Transcriptional activity of ribosomal RNA (rRNA) genes in specifc chromosome regions is the primary event for the local assembly of the nucleolus, the starting site of ribosome biogenesis. -
Prevalence and Significance of Nonsense-‐Mediated Mrna Decay
Prevalence and Significance of Nonsense-Mediated mRNA Decay Coupled with Alternative Splicing in Diverse Eukaryotic Organisms By Courtney Elizabeth French A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Molecular and Cell Biology in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Steven E. Brenner, Co-Chair Professor Donald C. Rio, Co-Chair Professor Britt A. Glaunsinger Professor Sandrine Dudoit Spring 2016 Prevalence and Significance of Nonsense-Mediated mRNA Decay Coupled with Alternative Splicing in Diverse Eukaryotic Organisms Copyright 2016 by Courtney Elizabeth French Abstract Prevalence and Significance of Nonsense-Mediated mRNA Decay Coupled with Alternative Splicing in Diverse Eukaryotic Organisms by Courtney Elizabeth French Doctor of Philosophy in Molecular and Cell Biology University of California, Berkeley Professor Steven E. Brenner, Co-Chair Professor Donald C. Rio, Co-Chair Alternative splicing plays a crucial role in increasing the amount of protein diversity and in regulating gene expression at the post-transcriptional level. In humans, almost all genes produce more than one mRNA isoform and, while the fraction varies, many other species also have a substantial number of alternatively spliced genes. Alternative splicing is regulated by splicing factors, often in a developmental time- or tissue-specific manner. Mis- regulation of alternative splicing, via mutations in splice sites, splicing regulatory elements, or splicing factors, can lead to disease states, including cancers. Thus, characterizing how alternative splicing shapes the transcriptome will lead to greater insights into the regulation of numerous cellular pathways and many aspects of human health. A critical tool for investigating alternative splicing is high-throughput mRNA sequencing (RNA-seq). -
MCG10 (PCBP4) (NM 033008) Human Recombinant Protein Product Data
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for TP300749 MCG10 (PCBP4) (NM_033008) Human Recombinant Protein Product data: Product Type: Recombinant Proteins Description: Recombinant protein of human poly(rC) binding protein 4 (PCBP4), transcript variant 3 Species: Human Expression Host: HEK293T Tag: C-Myc/DDK Predicted MW: 41.3 kDa Concentration: >50 ug/mL as determined by microplate BCA method Purity: > 80% as determined by SDS-PAGE and Coomassie blue staining Buffer: 25 mM Tris.HCl, pH 7.3, 100 mM glycine, 10% glycerol Preparation: Recombinant protein was captured through anti-DDK affinity column followed by conventional chromatography steps. Storage: Store at -80°C. Stability: Stable for 12 months from the date of receipt of the product under proper storage and handling conditions. Avoid repeated freeze-thaw cycles. RefSeq: NP_127501 Locus ID: 57060 UniProt ID: P57723, A0A024R2Y0 RefSeq Size: 2040 Cytogenetics: 3p21.2 RefSeq ORF: 1209 Synonyms: CBP; LIP4; MCG10 This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 2 MCG10 (PCBP4) (NM_033008) Human Recombinant Protein – TP300749 Summary: This gene encodes a member of the KH-domain protein subfamily. Proteins of this subfamily, also referred to as alpha-CPs, bind to RNA with a specificity for C-rich pyrimidine regions. Alpha-CPs play important roles in post-transcriptional activities and have different cellular distributions. -
An Adipocyte-Specific Lncrap2 - Igf2bp2 Complex Enhances Adipogenesis and Energy Expenditure by Stabilizing Target Mrnas
bioRxiv preprint doi: https://doi.org/10.1101/2020.09.29.318980; this version posted September 29, 2020. 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. An adipocyte-specific lncRAP2 - Igf2bp2 complex enhances adipogenesis and energy expenditure by stabilizing target mRNAs Juan R. Alvarez-Dominguez1,4, Sally Winther2, Jacob B. Hansen2, Harvey F. Lodish1,3,* and Marko Knoll1,5,* 1 Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA 2 Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100 Copenhagen, Denmark 3 Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, 21 Ames Street, Cambridge, MA, 02142, USA 4 Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA 5 Institute for Diabetes Research, Helmholtz Zentrum München, Heidemannstrasse 1, 80939 München, Germany *correspondence: [email protected], [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.09.29.318980; this version posted September 29, 2020. 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. Abstract lncRAP2 is a conserved cytoplasmic adipocyte-specific lncRNA required for adipogenesis. Using hybridization-based purification combined with in vivo interactome analyses, we show that lncRAP2 forms ribonucleoprotein complexes with several mRNA stability and translation modulators, among them Igf2bp2. -
APOBEC1 Complementation Factor (A1CF) and RBM47 Interact in Tissue-Specific Regulation of C to U RNA Editing in Mouse Intestine and Liver
Downloaded from rnajournal.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press APOBEC1 complementation factor (A1CF) and RBM47 interact in tissue-specific regulation of C to U RNA editing in mouse intestine and liver Valerie Blanc1, Yan Xie1, Susan Kennedy1, Jesse D. Riordan2, Deborah C. Rubin1, Blair B. Madison1, Jason C. Mills1, Joseph H. Nadeau2, Nicholas O. Davidson1,3 1Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63105, 2Pacific Northwest Research Institute, Seattle, WA 98122 3To whom communication should be addressed: Email: [email protected] Running title: A1CF and RBM47 interactively regulate C to U RNA editing Keywords: APOBEC1; A1CF; RBM47; ApoB; Intestine; Liver Downloaded from rnajournal.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press ABSTRACT (246 words) Mammalian C to U RNA is mediated by APOBEC1, the catalytic deaminase, together with RNA binding cofactors (including A1CF and RBM47) whose relative physiological requirements are unresolved. Although A1CF complements APOBEC1 for in-vitro RNA editing, A1cf–/– mice exhibited no change in apolipoproteinB (apoB) RNA editing, while Rbm47 mutant mice exhibited impaired intestinal RNA editing of apoB as well as other targets. Here we examined the role of A1CF and RBM47 in adult mouse liver and intestine, following deletion of either one or both gene products and also following forced (liver or intestinal) transgenic A1CF expression. There were minimal changes in hepatic and intestinal apoB RNA editing in A1cf–/– mice and no changes in either liver- or intestine-specific A1CF transgenic mice. Rbm47 liver-specific knockout (Rbm47LKO) mice demonstrated reduced editing in a subset (11 of 20) RNA targets, including apoB. -
Genes with 5' Terminal Oligopyrimidine Tracts Preferentially Escape Global Suppression of Translation by the SARS-Cov-2 NSP1 Protein
Downloaded from rnajournal.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Genes with 5′ terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 Nsp1 protein Shilpa Raoa, Ian Hoskinsa, Tori Tonna, P. Daniela Garciaa, Hakan Ozadama, Elif Sarinay Cenika, Can Cenika,1 a Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA 1Corresponding author: [email protected] Key words: SARS-CoV-2, Nsp1, MeTAFlow, translation, ribosome profiling, RNA-Seq, 5′ TOP, Ribo-Seq, gene expression 1 Downloaded from rnajournal.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Abstract Viruses rely on the host translation machinery to synthesize their own proteins. Consequently, they have evolved varied mechanisms to co-opt host translation for their survival. SARS-CoV-2 relies on a non-structural protein, Nsp1, for shutting down host translation. However, it is currently unknown how viral proteins and host factors critical for viral replication can escape a global shutdown of host translation. Here, using a novel FACS-based assay called MeTAFlow, we report a dose-dependent reduction in both nascent protein synthesis and mRNA abundance in cells expressing Nsp1. We perform RNA-Seq and matched ribosome profiling experiments to identify gene-specific changes both at the mRNA expression and translation level. We discover that a functionally-coherent subset of human genes are preferentially translated in the context of Nsp1 expression. These genes include the translation machinery components, RNA binding proteins, and others important for viral pathogenicity. Importantly, we uncovered a remarkable enrichment of 5′ terminal oligo-pyrimidine (TOP) tracts among preferentially translated genes. -
Investigation of the Underlying Hub Genes and Molexular Pathogensis in Gastric Cancer by Integrated Bioinformatic Analyses
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 2020. 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. Investigation of the underlying hub genes and molexular pathogensis in gastric cancer by integrated bioinformatic analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 2020. 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 The high mortality rate of gastric cancer (GC) is in part due to the absence of initial disclosure of its biomarkers. The recognition of important genes associated in GC is therefore recommended to advance clinical prognosis, diagnosis and and treatment outcomes. The current investigation used the microarray dataset GSE113255 RNA seq data from the Gene Expression Omnibus database to diagnose differentially expressed genes (DEGs). Pathway and gene ontology enrichment analyses were performed, and a proteinprotein interaction network, modules, target genes - miRNA regulatory network and target genes - TF regulatory network were constructed and analyzed. Finally, validation of hub genes was performed. The 1008 DEGs identified consisted of 505 up regulated genes and 503 down regulated genes. -
RNA Dynamics in Alzheimer's Disease
molecules Review RNA Dynamics in Alzheimer’s Disease Agnieszka Rybak-Wolf 1,* and Mireya Plass 2,3,4,* 1 Max Delbrück Center for Molecular Medicine (MDC), Berlin Institute for Medical Systems Biology (BIMSB), 10115 Berlin, Germany 2 Gene Regulation of Cell Identity, Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, 08908 Barcelona, Spain 3 Program for Advancing Clinical Translation of Regenerative Medicine of Catalonia, P-CMR[C], L’Hospitalet del Llobregat, 08908 Barcelona, Spain 4 Center for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain * Correspondence: [email protected] (A.R.-W.); [email protected] (M.P.) Abstract: Alzheimer’s disease (AD) is the most common age-related neurodegenerative disorder that heavily burdens healthcare systems worldwide. There is a significant requirement to understand the still unknown molecular mechanisms underlying AD. Current evidence shows that two of the major features of AD are transcriptome dysregulation and altered function of RNA binding proteins (RBPs), both of which lead to changes in the expression of different RNA species, including microRNAs (miRNAs), circular RNAs (circRNAs), long non-coding RNAs (lncRNAs), and messenger RNAs (mRNAs). In this review, we will conduct a comprehensive overview of how RNA dynamics are altered in AD and how this leads to the differential expression of both short and long RNA species. We will describe how RBP expression and function are altered in AD and how this impacts the expression of different RNA species. Furthermore, we will also show how changes in the abundance Citation: Rybak-Wolf, A.; Plass, M.