1
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Chowdhury R, Wang Y, Campbell M, Goderie SK, Doyle F, Tenenbaum SA, Kusek G, Kiehl TR, Ansari SA, Boles NC, Temple S. STAU2 binds a complex RNA cargo that changes temporally with production of diverse intermediate progenitor cells during mouse corticogenesis. Development 2021; 148:271165. [PMID: 34345913 DOI: 10.1242/dev.199376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 07/05/2021] [Indexed: 12/18/2022]
Abstract
STAU2 is a double-stranded RNA-binding protein enriched in the nervous system. During asymmetric divisions in the developing mouse cortex, STAU2 preferentially distributes into the intermediate progenitor cell (IPC), delivering RNA molecules that can impact IPC behavior. Corticogenesis occurs on a precise time schedule, raising the hypothesis that the cargo STAU2 delivers into IPCs changes over time. To test this, we combine RNA-immunoprecipitation with sequencing (RIP-seq) over four stages of mouse cortical development, generating a comprehensive cargo profile for STAU2. A subset of the cargo was 'stable', present at all stages, and involved in chromosome organization, macromolecule localization, translation and DNA repair. Another subset was 'dynamic', changing with cortical stage, and involved in neurogenesis, cell projection organization, neurite outgrowth, and included cortical layer markers. Notably, the dynamic STAU2 cargo included determinants of IPC versus neuronal fates and genes contributing to abnormal corticogenesis. Knockdown of one STAU2 target, Taf13, previously linked to microcephaly and impaired myelination, reduced oligodendrogenesis in vitro. We conclude that STAU2 contributes to the timing of corticogenesis by binding and delivering complex and temporally regulated RNA cargo into IPCs.
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Affiliation(s)
- Rebecca Chowdhury
- Neural Stem Cell Institute, Regenerative Research Foundation, Rensselaer, NY 12144, USA
| | - Yue Wang
- Neural Stem Cell Institute, Regenerative Research Foundation, Rensselaer, NY 12144, USA
| | - Melissa Campbell
- Neural Stem Cell Institute, Regenerative Research Foundation, Rensselaer, NY 12144, USA
| | - Susan K Goderie
- Neural Stem Cell Institute, Regenerative Research Foundation, Rensselaer, NY 12144, USA
| | - Francis Doyle
- Nanobioscience Constellation, College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY 12203, USA
| | - Scott A Tenenbaum
- Nanobioscience Constellation, College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY 12203, USA
| | - Gretchen Kusek
- Neural Stem Cell Institute, Regenerative Research Foundation, Rensselaer, NY 12144, USA
| | - Thomas R Kiehl
- Neural Stem Cell Institute, Regenerative Research Foundation, Rensselaer, NY 12144, USA
| | - Suraiya A Ansari
- Department of Biochemistry and Molecular Biology, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 17666, Al Ain, United Arab Emirates
| | - Nathan C Boles
- Neural Stem Cell Institute, Regenerative Research Foundation, Rensselaer, NY 12144, USA
| | - Sally Temple
- Neural Stem Cell Institute, Regenerative Research Foundation, Rensselaer, NY 12144, USA
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2
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Chandrasekaran A, Lee MY, Zhang X, Hasan S, Desta H, Tenenbaum SA, Melendez JA. Redox and mTOR-dependent regulation of plasma lamellar calcium influx controls the senescence-associated secretory phenotype. Exp Biol Med (Maywood) 2020; 245:1560-1570. [PMID: 32686475 PMCID: PMC7787549 DOI: 10.1177/1535370220943122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 06/27/2020] [Indexed: 12/18/2022] Open
Abstract
IMPACT STATEMENT Through its ability to evoke responses from cells in a paracrine fashion, the senescence-associated secretory phenotype (SASP) has been linked to numerous age-associated disease pathologies including tumor invasion, cardiovascular dysfunction, neuroinflammation, osteoarthritis, and renal disease. Strategies which limit the amplitude and duration of SASP serve to delay age-related degenerative decline. Here we demonstrate that the SASP regulation is linked to shifts in intracellular Ca2+ homeostasis and strategies which rescue redox-dependent calcium entry including enzymatic H2O2 scavenging, TRP modulation, or mTOR inhibition block SASP and TRPC6 gene expression. As Ca2+ is indispensable for secretion from both secretory and non-secretory cells, it is exciting to speculate that the expression of plasma lamellar TRP channels critical for the maintenance of intracellular Ca2+ homeostasis may be coordinately regulated with the SASP.
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Affiliation(s)
- Akshaya Chandrasekaran
- SUNY Polytechnic Institute, Colleges of Nanoscale Science and Engineering, Albany, NY 12203, USA
| | - May Y Lee
- SUNY Polytechnic Institute, Colleges of Nanoscale Science and Engineering, Albany, NY 12203, USA
| | - Xuexin Zhang
- College of Medicine, Penn State University, Hershey, PA 17033, USA
| | - Shaheen Hasan
- SUNY Polytechnic Institute, Colleges of Nanoscale Science and Engineering, Albany, NY 12203, USA
| | - Habben Desta
- SUNY Polytechnic Institute, Colleges of Nanoscale Science and Engineering, Albany, NY 12203, USA
| | - Scott A Tenenbaum
- SUNY Polytechnic Institute, Colleges of Nanoscale Science and Engineering, Albany, NY 12203, USA
| | - J Andrés Melendez
- SUNY Polytechnic Institute, Colleges of Nanoscale Science and Engineering, Albany, NY 12203, USA
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3
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Muralidharan-Chari V, Wurz Z, Doyle F, Henry M, Diendorfer A, Tenenbaum SA, Borth N, Eveleth E, Sharfstein ST. PTSelect™: A post-transcriptional technology that enables rapid establishment of stable CHO cell lines and surveillance of clonal variation. J Biotechnol 2020; 325:360-371. [PMID: 33115662 DOI: 10.1016/j.jbiotec.2020.09.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/07/2020] [Accepted: 09/27/2020] [Indexed: 10/23/2022]
Abstract
Currently, stable Chinese hamster ovary cell lines producing therapeutic, recombinant proteins are established either by antibiotic and/or metabolic selection. Here, we report a novel technology, PTSelect™ that utilizes an siRNA cloned upstream of the gene of interest (GOI) that is processed to produce functional PTSelect™-siRNAs, which enable cell enrichment. Cells with stably integrated GOI are selected and separated from cells without GOI by transfecting CD4/siRNA mRNA regulated by PTSelect™-siRNAs and exploiting the variable expression of CD4 on the cell surface. This study describes the PTSelect™ principle and compares the productivity, doubling time and stability of clones developed by PTSelect™ with conventionally developed clones. PTSelect™ rapidly established a pool population with comparable stability and productivity to pools generated by traditional methods and can further be used to easily monitor productivity changes due to clonal drift, identifying individual cells with reduced productivity.
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Affiliation(s)
| | - Zachary Wurz
- HocusLocus, LLC, 253 Fuller Road, Albany NY 12203, USA
| | - Francis Doyle
- College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY, New York 12203, USA
| | - Matthew Henry
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Andreas Diendorfer
- Austrian Centre of Industrial Biotechnology, Graz, Austria, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Scott A Tenenbaum
- College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY, New York 12203, USA
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology, Graz, Austria, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Susan T Sharfstein
- College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY, New York 12203, USA.
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4
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Mubaid S, Ma JF, Omer A, Ashour K, Lian XJ, Sanchez BJ, Robinson S, Cammas A, Dormoy-Raclet V, Di Marco S, Chittur SV, Tenenbaum SA, Gallouzi IE. HuR counteracts miR-330 to promote STAT3 translation during inflammation-induced muscle wasting. Proc Natl Acad Sci U S A 2019; 116:17261-17270. [PMID: 31405989 PMCID: PMC6717253 DOI: 10.1073/pnas.1905172116] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Debilitating cancer-induced muscle wasting, a syndrome known as cachexia, is lethal. Here we report a posttranscriptional pathway involving the RNA-binding protein HuR as a key player in the onset of this syndrome. Under these conditions, HuR switches its function from a promoter of muscle fiber formation to become an inducer of muscle loss. HuR binds to the STAT3 (signal transducer and activator of transcription 3) mRNA, which encodes one of the main effectors of this condition, promoting its expression both in vitro and in vivo. While HuR does not affect the stability and the cellular movement of this transcript, HuR promotes the translation of the STAT3 mRNA by preventing miR-330 (microRNA 330)-mediated translation inhibition. To achieve this effect, HuR directly binds to a U-rich element in the STAT3 mRNA-3'untranslated region (UTR) located within the vicinity of the miR-330 seed element. Even though the binding sites of HuR and miR-330 do not overlap, the recruitment of either one of them to the STAT3-3'UTR negatively impacts the binding and the function of the other factor. Therefore, together, our data establish the competitive interplay between HuR and miR-330 as a mechanism via which muscle fibers modulate, in part, STAT3 expression to determine their fate in response to promoters of muscle wasting.
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Affiliation(s)
- Souad Mubaid
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Jennifer F Ma
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Amr Omer
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Kholoud Ashour
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Xian J Lian
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Brenda J Sanchez
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Samantha Robinson
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Anne Cammas
- Cancer Research Centre of Toulouse, INSERM UMR 1037, 31037 Toulouse, France
- Université Toulouse III Paul Sabatier, 31330 Toulouse, France
- Laboratoire d'Excellence "TOUCAN," 31037 Toulouse, France
| | - Virginie Dormoy-Raclet
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire de Bordeaux, 33076 Bordeaux Cedex, France
| | - Sergio Di Marco
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Sridar V Chittur
- College of Nanoscale Sciences, State University of New York (SUNY) Polytechnic Institute, Albany, NY 12203
- College of Engineering, SUNY Polytechnic Institute, Albany, NY 12203
| | - Scott A Tenenbaum
- College of Nanoscale Sciences, State University of New York (SUNY) Polytechnic Institute, Albany, NY 12203
- College of Engineering, SUNY Polytechnic Institute, Albany, NY 12203
| | - Imed-Eddine Gallouzi
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada;
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5
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Huang K, Doyle F, Wurz ZE, Tenenbaum SA, Hammond RK, Caplan JL, Meyers BC. FASTmiR: an RNA-based sensor for in vitro quantification and live-cell localization of small RNAs. Nucleic Acids Res 2017; 45:e130. [PMID: 28586459 PMCID: PMC5737440 DOI: 10.1093/nar/gkx504] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 05/27/2017] [Indexed: 01/19/2023] Open
Abstract
Small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), play a variety of important regulatory roles in many eukaryotes. Their small size has made it challenging to study them directly in live cells. Here we describe an RNA-based fluorescent sensor for small RNA detection both in vitro and in vivo, adaptable for any small RNA. It utilizes an sxRNA switch for detection of miRNA–mRNA interactions combined with a fluorophore-binding sequence ‘Spinach’, a GFP-like RNA aptamer for which the RNA–fluorophore complex exhibits strong and consistent fluorescence under an excitation wavelength. Two example sensors, FASTmiR171 and FASTmiR122, can rapidly detect and quantify the levels of miR171 and miR122 in vitro. The sensors can determine relative levels of miRNAs in total RNA extracts with sensitivity similar to small RNA sequencing and northern blots. FASTmiR sensors were also used to estimate the copy number range of miRNAs in total RNA extracts. To localize and analyze the spatial distribution of small RNAs in live, single cells, tandem copies of FASTmiR122 were expressed in different cell lines. FASTmiR122 was able to quantitatively detect the differences in miR122 levels in Huh7 and HEK293T cells demonstrating its potential for tracking miRNA expression and localization in vivo.
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Affiliation(s)
- Kun Huang
- Bio-Imaging Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA.,Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
| | - Francis Doyle
- Nanobioscience Constellation, State University of New York- Polytechnic Institute, College of Nanoscale Science and Engineering, Albany, NY 12203, USA
| | - Zachary E Wurz
- Nanobioscience Constellation, State University of New York- Polytechnic Institute, College of Nanoscale Science and Engineering, Albany, NY 12203, USA
| | - Scott A Tenenbaum
- Nanobioscience Constellation, State University of New York- Polytechnic Institute, College of Nanoscale Science and Engineering, Albany, NY 12203, USA
| | - Reza K Hammond
- Bio-Imaging Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA.,Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA
| | - Jeffrey L Caplan
- Bio-Imaging Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA.,Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
| | - Blake C Meyers
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA.,Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO 63132, USA.,University of Missouri-Columbia, Division of Plant Sciences, 52 Agriculture Lab, Columbia, MO 65211, USA
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6
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Doyle F, Lapsia S, Spadaro S, Wurz ZE, Bhaduri-McIntosh S, Tenenbaum SA. Engineering Structurally Interacting RNA (sxRNA). Sci Rep 2017; 7:45393. [PMID: 28350000 PMCID: PMC5368982 DOI: 10.1038/srep45393] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 02/22/2017] [Indexed: 01/01/2023] Open
Abstract
RNA-based three-way junctions (3WJs) are naturally occurring structures found in many functional RNA molecules including rRNA, tRNA, snRNA and ribozymes. 3WJs are typically characterized as resulting from an RNA molecule folding back on itself in cis but could also form in trans when one RNA, for instance a microRNA binds to a second structured RNA, such as a mRNA. Trans-3WJs can influence the final shape of one or both of the RNA molecules and can thus provide a means for modulating the availability of regulatory motifs including potential protein or microRNA binding sites. Regulatory 3WJs generated in trans represent a newly identified regulatory category that we call structurally interacting RNA or sxRNA for convenience. Here we show that they can be rationally designed using familiar cis-3WJ examples as a guide. We demonstrate that an sxRNA “bait” sequence can be designed to interact with a specific microRNA “trigger” sequence, creating a regulatable RNA-binding protein motif that retains its functional activity. Further, we show that when placed downstream of a coding sequence, sxRNA can be used to switch “ON” translation of that sequence in the presence of the trigger microRNA and the amount of translation corresponded with the amount of microRNA present.
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Affiliation(s)
- Francis Doyle
- Nanobioscience Constellation, College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY New York 12203, USA
| | - Sameer Lapsia
- Department of Pediatrics, Stony Brook University School of Medicine, Stony Brook, NY 11794, USA
| | - Salvatore Spadaro
- Department of Pediatrics, Stony Brook University School of Medicine, Stony Brook, NY 11794, USA
| | - Zachary E Wurz
- HocusLocus, LLC, 253 Fuller Road, Nanofab North, Albany NY 12203, USA
| | - Sumita Bhaduri-McIntosh
- Pediatric Infectious Diseases, Departments of Pediatrics and Molecular Genetics and Microbiology, Stony Brook University School of Medicine, Stony Brook, NY 11794, USA
| | - Scott A Tenenbaum
- Nanobioscience Constellation, College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY New York 12203, USA
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7
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Doyle F, Leonardi A, Endres L, Tenenbaum SA, Dedon PC, Begley TJ. Gene- and genome-based analysis of significant codon patterns in yeast, rat and mice genomes with the CUT Codon UTilization tool. Methods 2016; 107:98-109. [PMID: 27245397 PMCID: PMC5014648 DOI: 10.1016/j.ymeth.2016.05.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/16/2016] [Accepted: 05/17/2016] [Indexed: 01/09/2023] Open
Abstract
The translation of mRNA in all forms of life uses a three-nucleotide codon and aminoacyl-tRNAs to synthesize a protein. There are 64 possible codons in the genetic code, with codons for the ∼20 amino acids and 3 stop codons having 1- to 6-fold degeneracy. Recent studies have shown that families of stress response transcripts, termed modification tunable transcripts (MoTTs), use distinct codon biases that match specifically modified tRNAs to regulate their translation during a stress. Similarly, translational reprogramming of the UGA stop codon to generate selenoproteins or to perform programmed translational read-through (PTR) that results in a longer protein, requires distinct codon bias (i.e., more than one stop codon) and, in the case of selenoproteins, a specifically modified tRNA. In an effort to identify transcripts that have codon usage patterns that could be subject to translational control mechanisms, we have used existing genome and transcript data to develop the gene-specific Codon UTilization (CUT) tool and database, which details all 1-, 2-, 3-, 4- and 5-codon combinations for all genes or transcripts in yeast (Saccharomyces cerevisiae), mice (Mus musculus) and rats (Rattus norvegicus). Here, we describe the use of the CUT tool and database to characterize significant codon usage patterns in specific genes and groups of genes. In yeast, we demonstrate how the CUT database can be used to identify genes that have runs of specific codons (e.g., AGA, GAA, AAG) linked to translational regulation by tRNA methyltransferase 9 (Trm9). We further demonstrate how groups of genes can be analyzed to find significant dicodon patterns, with the 80 Gcn4-regulated transcripts significantly (P<0.00001) over-represented with the AGA-GAA dicodon. We have also used the CUT database to identify mouse and rat transcripts with internal UGA codons, with the surprising finding of 45 and 120 such transcripts, respectively, which is much larger than expected. The UGA data suggest that there could be many more translationally reprogrammed transcripts than currently reported. CUT thus represents a multi-species codon-counting database that can be used with mRNA-, translation- and proteomics-based results to better understand and model translational control mechanisms.
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Affiliation(s)
- Frank Doyle
- State University of New York – SUNY Polytechnic Institute, College of Nanoscale Science and Engineering, Albany, NY
| | - Andrea Leonardi
- State University of New York – SUNY Polytechnic Institute, College of Nanoscale Science and Engineering, Albany, NY
| | - Lauren Endres
- State University of New York – SUNY Polytechnic Institute, College of Arts and Sciences, Utica, NY
| | - Scott A. Tenenbaum
- State University of New York – SUNY Polytechnic Institute, College of Nanoscale Science and Engineering, Albany, NY
| | - Peter C. Dedon
- Department of Biological Engineering and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA
- Singapore-MIT Alliance for Research and Technology, Singapore
| | - Thomas J. Begley
- State University of New York – SUNY Polytechnic Institute, College of Nanoscale Science and Engineering, Albany, NY
- RNA Institute, University at Albany, State University of New York
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8
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Cassar PA, Carpenedo RL, Samavarchi-Tehrani P, Olsen JB, Park CJ, Chang WY, Chen Z, Choey C, Delaney S, Guo H, Guo H, Tanner RM, Perkins TJ, Tenenbaum SA, Emili A, Wrana JL, Gibbings D, Stanford WL. Integrative genomics positions MKRN1 as a novel ribonucleoprotein within the embryonic stem cell gene regulatory network. EMBO Rep 2015; 16:1334-57. [PMID: 26265008 PMCID: PMC4670460 DOI: 10.15252/embr.201540974] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 07/15/2015] [Indexed: 02/04/2023] Open
Abstract
In embryonic stem cells (ESCs), gene regulatory networks (GRNs) coordinate gene expression to maintain ESC identity; however, the complete repertoire of factors regulating the ESC state is not fully understood. Our previous temporal microarray analysis of ESC commitment identified the E3 ubiquitin ligase protein Makorin‐1 (MKRN1) as a potential novel component of the ESC GRN. Here, using multilayered systems‐level analyses, we compiled a MKRN1‐centered interactome in undifferentiated ESCs at the proteomic and ribonomic level. Proteomic analyses in undifferentiated ESCs revealed that MKRN1 associates with RNA‐binding proteins, and ensuing RIP‐chip analysis determined that MKRN1 associates with mRNAs encoding functionally related proteins including proteins that function during cellular stress. Subsequent biological validation identified MKRN1 as a novel stress granule‐resident protein, although MKRN1 is not required for stress granule formation, or survival of unstressed ESCs. Thus, our unbiased systems‐level analyses support a role for the E3 ligase MKRN1 as a ribonucleoprotein within the ESC GRN.
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Affiliation(s)
- Paul A Cassar
- Institute of Medical Science University of Toronto, Toronto, ON, Canada Collaborative Program in Genome Biology and Bioinformatics, University of Toronto, Toronto, ON, Canada
| | - Richard L Carpenedo
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | | | - Jonathan B Olsen
- Collaborative Program in Genome Biology and Bioinformatics, University of Toronto, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Chang Jun Park
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada
| | - Wing Y Chang
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Zhaoyi Chen
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Chandarong Choey
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Sean Delaney
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Huishan Guo
- Department of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Hongbo Guo
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - R Matthew Tanner
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Theodore J Perkins
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada Department of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Scott A Tenenbaum
- Colleges of Nanoscale Science & Engineering SUNY Polytechnic Institute, Albany, NY, USA
| | - Andrew Emili
- Collaborative Program in Genome Biology and Bioinformatics, University of Toronto, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Jeffrey L Wrana
- Collaborative Program in Genome Biology and Bioinformatics, University of Toronto, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Derrick Gibbings
- Department of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, ON, Canada
| | - William L Stanford
- Institute of Medical Science University of Toronto, Toronto, ON, Canada Collaborative Program in Genome Biology and Bioinformatics, University of Toronto, Toronto, ON, Canada Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada Department of Biochemistry, Microbiology & Immunology, University of Ottawa, Ottawa, ON, Canada Ottawa Institute of Systems Biology, Ottawa, ON, Canada
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9
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Iuliano JN, Kutscha PD, Biderman NJ, Subbaram S, Groves TR, Tenenbaum SA, Hempel N. Metastatic bladder cancer cells distinctively sense and respond to physical cues of collagen fibril-mimetic nanotopography. Exp Biol Med (Maywood) 2014; 240:601-10. [PMID: 25465204 DOI: 10.1177/1535370214560973] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 10/08/2014] [Indexed: 01/17/2023] Open
Abstract
Tumor metastasis is characterized by enhanced invasiveness and migration of tumor cells through the extracellular matrix (ECM), resulting in extravasation into the blood and lymph and colonization at secondary sites. The ECM provides a physical scaffold consisting of components such as collagen fibrils, which have distinct dimensions at the nanoscale. In addition to the interaction of peptide moieties with tumor cell integrin clusters, the ECM provides a physical guide for tumor cell migration. Using nanolithography we set out to mimic the physical dimensions of collagen fibrils using lined nanotopographical silicon surfaces and to explore whether metastatic tumor cells are uniquely able to respond to these physical dimensions. Etched silicon surfaces containing nanoscale lined patterns with varying trench and ridge sizes (65-500 nm) were evaluated for their ability to distinguish between a non-metastatic (253 J) and a highly metastatic (253 J-BV) derivative bladder cancer cell line. Enhanced alignment was distinctively observed for the metastatic cell lines on feature sizes that mimic the dimensions of collagen fibrils (65-100 nm lines, 1:1-1:1.5 pitch). Further, these sub-100 nm lines acted as guides for migration of metastatic cancer cells. Interestingly, even at this subcellular scale, metastatic cell migration was abrogated when cells were forced to move perpendicular to these lines. Compared to flat surfaces, 65 nm lines enhanced the formation of actin stress fibers and filopodia of metastatic cells. This was accompanied by increased formation of focal contacts, visualized by immunofluorescent staining of phospho-focal adhesion kinase along the protruding lamellipodia. Simple lined nanotopography appears to be an informative platform for studying the physical cues of the ECM in a pseudo-3D format and likely mimics physical aspects of collagen fibrils. Metastatic cancer cells appear distinctively well adapted to sense these features using filopodia protrusions to enhance their alignment and migration.
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Affiliation(s)
- James N Iuliano
- Nanobioscience Constellation, College of Nanoscale Science, SUNY Polytechnic Institute, State University of New York, Albany, NY 12203, USA University at Albany, State University of New York, Albany, NY 12203, USA
| | - Paul D Kutscha
- Nanobioscience Constellation, College of Nanoscale Science, SUNY Polytechnic Institute, State University of New York, Albany, NY 12203, USA University at Albany, State University of New York, Albany, NY 12203, USA
| | - N J Biderman
- Nanoengineering Constellation, College of Nanoscale Engineering, SUNY Polytechnic Institute, State University of New York, Albany, NY 12203, USA University at Albany, State University of New York, Albany, NY 12203, USA
| | - Sita Subbaram
- Center for Cell Biology and Cancer Research, Albany Medical College, Albany, NY 12209, USA
| | - Timothy R Groves
- Nanoengineering Constellation, College of Nanoscale Engineering, SUNY Polytechnic Institute, State University of New York, Albany, NY 12203, USA
| | - Scott A Tenenbaum
- Nanobioscience Constellation, College of Nanoscale Science, SUNY Polytechnic Institute, State University of New York, Albany, NY 12203, USA
| | - Nadine Hempel
- Nanobioscience Constellation, College of Nanoscale Science, SUNY Polytechnic Institute, State University of New York, Albany, NY 12203, USA
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Schmidt SA, Foley PL, Jeong DH, Rymarquis LA, Doyle F, Tenenbaum SA, Belasco JG, Green PJ. Identification of SMG6 cleavage sites and a preferred RNA cleavage motif by global analysis of endogenous NMD targets in human cells. Nucleic Acids Res 2014; 43:309-23. [PMID: 25429978 PMCID: PMC4288159 DOI: 10.1093/nar/gku1258] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
In metazoans, cleavage by the endoribonuclease SMG6 is often the first degradative event in non-sense-mediated mRNA decay (NMD). However, the exact sites of SMG6 cleavage have yet to be determined for any endogenous targets, and most evidence as to the identity of SMG6 substrates is indirect. Here, we use Parallel Analysis of RNA Ends to specifically identify the 5′ termini of decay intermediates whose production is dependent on SMG6 and the universal NMD factor UPF1. In this manner, the SMG6 cleavage sites in hundreds of endogenous NMD targets in human cells have been mapped at high resolution. In addition, a preferred sequence motif spanning most SMG6 cleavage sites has been discovered and validated by mutational analysis. For many SMG6 substrates, depletion of SMG6 resulted in the accumulation of decapped transcripts, an effect indicative of competition between SMG6-dependent and SMG6-independent NMD pathways. These findings provide key insights into the mechanisms by which mRNAs targeted by NMD are degraded.
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Affiliation(s)
- Skye A Schmidt
- Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
| | - Patricia L Foley
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | - Dong-Hoon Jeong
- Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
| | - Linda A Rymarquis
- Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
| | - Francis Doyle
- Department of Life Science, Hallym University, Chuncheon, Gangwon, Republic of Korea
| | - Scott A Tenenbaum
- Department of Life Science, Hallym University, Chuncheon, Gangwon, Republic of Korea
| | - Joel G Belasco
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | - Pamela J Green
- Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
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11
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Abstract
A large portion of the human genome is transcribed but not translated. In this post genomic era, regulatory functions of RNA have been shown to be increasingly important. As RNA function often depends on its ability to adopt alternative structures, it is difficult to predict RNA three-dimensional structures directly from sequence. Single-molecule approaches show potentials to solve the problem of RNA structural polymorphism by monitoring molecular structures one molecule at a time. This work presents a method to precisely manipulate the folding and structure of single RNA molecules using optical tweezers. First, methods to synthesize molecules suitable for single-molecule mechanical work are described. Next, various calibration procedures to ensure the proper operations of the optical tweezers are discussed. Next, various experiments are explained. To demonstrate the utility of the technique, results of mechanically unfolding RNA hairpins and a single RNA kissing complex are used as evidence. In these examples, the nanomanipulation technique was used to study folding of each structural domain, including secondary and tertiary, independently. Lastly, the limitations and future applications of the method are discussed.
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Affiliation(s)
- William Stephenson
- Nanoscale Engineering Graduate Program, College of Nanoscale Science and Engineering, University at Albany, State University of New York
| | - Gorby Wan
- Nanoscale Science Undergraduate Program, College of Nanoscale Science and Engineering, University at Albany, State University of New York
| | - Scott A Tenenbaum
- Nanobioscience Constellation, College of Nanoscale Science and Engineering, University at Albany, State University of New York; The RNA Institute, University at Albany, State University of New York
| | - Pan T X Li
- The RNA Institute, University at Albany, State University of New York; Department of Biological Sciences, University at Albany, State University of New York;
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12
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Abstract
The wide array of vital functions that RNA performs is dependent on its ability to dynamically fold into different structures in response to intracellular and extracellular changes. RNA-binding proteins regulate much of this activity by targeting specific RNA structures or motifs. One of these structures, the 3-way RNA junction, is characteristically found in ribosomal RNA and results from the RNA folding in cis, to produce three separate helices that meet around a central unpaired region. Here we demonstrate that 3-way junctions can also form in trans as a result of the binding of microRNAs in an unconventional manner with mRNA by splinting two non-contiguous regions together. This may be used to reinforce the base of a stem-loop motif being targeted by an RNA-binding protein. Trans interactions between non-coding RNA and mRNA may be used to control the post-transcriptional regulatory code and suggests a possible role for some of the recently described transcripts of unknown function expressed from the human genome.
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Affiliation(s)
- Francis Doyle
- Nanobioscience Constellation, College of Nanoscale Science and Engineering, State University of New York Albany, NY, USA
| | - Scott A Tenenbaum
- Nanobioscience Constellation, College of Nanoscale Science and Engineering, State University of New York Albany, NY, USA
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13
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Stephenson W, Keller S, Santiago R, Albrecht JE, Asare-Okai PN, Tenenbaum SA, Zuker M, Li PTX. Combining temperature and force to study folding of an RNA hairpin. Phys Chem Chem Phys 2014; 16:906-17. [DOI: 10.1039/c3cp52042k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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14
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Stephenson WT, Keller S, Tenenbaum SA, Zuker M, Li PT. Structural Polymorphism of (Cag)N Repeat RNA Elucidated using Single Molecule Nanomanipulation. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.1653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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15
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Jayaseelan S, Doyle F, Tenenbaum SA. Profiling post-transcriptionally networked mRNA subsets using RIP-Chip and RIP-Seq. Methods 2013; 67:13-9. [PMID: 24257445 DOI: 10.1016/j.ymeth.2013.11.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 11/06/2013] [Accepted: 11/07/2013] [Indexed: 11/26/2022] Open
Abstract
Post-transcriptional regulation of messenger RNA contributes to numerous aspects of gene expression. The key component to this level of regulation is the interaction of RNA-binding proteins (RBPs) and their associated target mRNA. Splicing, stability, localization, translational efficiency, and alternate codon use are just some of the post-transcriptional processes regulated by RBPs. Central to our understanding of these processes is the need to characterize the network of RBP-mRNA associations and create a map of this functional post-transcriptional regulatory system. Here we provide a detailed methodology for mRNA isolation using RBP immunoprecipitation (RIP) as a primary partitioning approach followed by microarray (Chip) or next generation sequencing (NGS) analysis. We do this by using specific antibodies to target RBPs for the capture of associated RNA cargo. RIP-Chip/Seq has proven to be is a versatile, genomic technique that has been widely used to study endogenous RBP-RNA associations.
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Affiliation(s)
- Sabarinath Jayaseelan
- SUNY-College of Nanoscale Science and Engineering, Nanobioscience Constellation, State University of New York, Albany, NY 12203, USA
| | - Francis Doyle
- SUNY-College of Nanoscale Science and Engineering, Nanobioscience Constellation, State University of New York, Albany, NY 12203, USA
| | - Scott A Tenenbaum
- SUNY-College of Nanoscale Science and Engineering, Nanobioscience Constellation, State University of New York, Albany, NY 12203, USA.
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16
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Stephenson W, Asare-Okai PN, Chen AA, Keller S, Santiago R, Tenenbaum SA, Garcia AE, Fabris D, Li PTX. The essential role of stacking adenines in a two-base-pair RNA kissing complex. J Am Chem Soc 2013; 135:5602-11. [PMID: 23517345 DOI: 10.1021/ja310820h] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In minimal RNA kissing complexes formed between hairpins with cognate GACG tetraloops, the two tertiary GC pairs are likely stabilized by the stacking of 5'-unpaired adenines at each end of the short helix. To test this hypothesis, we mutated the flanking adenines to various nucleosides and examined their effects on the kissing interaction. Electrospray ionization mass spectrometry was used to detect kissing dimers in a multiequilibria mixture, whereas optical tweezers were applied to monitor the (un)folding trajectories of single RNA molecules. The experimental findings were rationalized by molecular dynamics simulations. Together, the results showed that the stacked adenines are indispensable for the tertiary interaction. By shielding the tertiary base pairs from solvent and reducing their fraying, the stacked adenines made terminal pairs act more like interior base pairs. The purine double-ring of adenine was essential for effective stacking, whereas additional functional groups modulated the stabilizing effects through varying hydrophobic and electrostatic forces. Furthermore, formation of the kissing complex was dominated by base pairing, whereas its dissociation was significantly influenced by the flanking bases. Together, these findings indicate that unpaired flanking nucleotides play essential roles in the formation of otherwise unstable two-base-pair RNA tertiary interactions.
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Affiliation(s)
- William Stephenson
- Nanoscale Engineering Graduate Program, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, USA
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17
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Lin Y, Li Z, Ozsolak F, Kim SW, Arango-Argoty G, Liu TT, Tenenbaum SA, Bailey T, Monaghan AP, Milos PM, John B. An in-depth map of polyadenylation sites in cancer. Nucleic Acids Res 2012; 40:8460-71. [PMID: 22753024 PMCID: PMC3458571 DOI: 10.1093/nar/gks637] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 05/16/2012] [Accepted: 06/06/2012] [Indexed: 12/22/2022] Open
Abstract
We present a comprehensive map of over 1 million polyadenylation sites and quantify their usage in major cancers and tumor cell lines using direct RNA sequencing. We built the Expression and Polyadenylation Database to enable the visualization of the polyadenylation maps in various cancers and to facilitate the discovery of novel genes and gene isoforms that are potentially important to tumorigenesis. Analyses of polyadenylation sites indicate that a large fraction (∼30%) of mRNAs contain alternative polyadenylation sites in their 3' untranslated regions, independent of the cell type. The shortest 3' untranslated region isoforms are preferentially upregulated in cancer tissues, genome-wide. Candidate targets of alternative polyadenylation-mediated upregulation of short isoforms include POLR2K, and signaling cascades of cell-cell and cell-extracellular matrix contact, particularly involving regulators of Rho GTPases. Polyadenylation maps also helped to improve 3' untranslated region annotations and identify candidate regulatory marks such as sequence motifs, H3K36Me3 and Pabpc1 that are isoform dependent and occur in a position-specific manner. In summary, these results highlight the need to go beyond monitoring only the cumulative transcript levels for a gene, to separately analysing the expression of its RNA isoforms.
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Affiliation(s)
- Yuefeng Lin
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA 02139, College of Nanoscale Science and Engineering, University at Albany-Suny, Albany, NY, USA, Institute for Molecular Bioscience, the University of Queensland, Queensland, Australia and Department of Neurobiology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Zhihua Li
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA 02139, College of Nanoscale Science and Engineering, University at Albany-Suny, Albany, NY, USA, Institute for Molecular Bioscience, the University of Queensland, Queensland, Australia and Department of Neurobiology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Fatih Ozsolak
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA 02139, College of Nanoscale Science and Engineering, University at Albany-Suny, Albany, NY, USA, Institute for Molecular Bioscience, the University of Queensland, Queensland, Australia and Department of Neurobiology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Sang Woo Kim
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA 02139, College of Nanoscale Science and Engineering, University at Albany-Suny, Albany, NY, USA, Institute for Molecular Bioscience, the University of Queensland, Queensland, Australia and Department of Neurobiology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Gustavo Arango-Argoty
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA 02139, College of Nanoscale Science and Engineering, University at Albany-Suny, Albany, NY, USA, Institute for Molecular Bioscience, the University of Queensland, Queensland, Australia and Department of Neurobiology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Teresa T. Liu
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA 02139, College of Nanoscale Science and Engineering, University at Albany-Suny, Albany, NY, USA, Institute for Molecular Bioscience, the University of Queensland, Queensland, Australia and Department of Neurobiology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Scott A. Tenenbaum
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA 02139, College of Nanoscale Science and Engineering, University at Albany-Suny, Albany, NY, USA, Institute for Molecular Bioscience, the University of Queensland, Queensland, Australia and Department of Neurobiology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Timothy Bailey
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA 02139, College of Nanoscale Science and Engineering, University at Albany-Suny, Albany, NY, USA, Institute for Molecular Bioscience, the University of Queensland, Queensland, Australia and Department of Neurobiology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - A. Paula Monaghan
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA 02139, College of Nanoscale Science and Engineering, University at Albany-Suny, Albany, NY, USA, Institute for Molecular Bioscience, the University of Queensland, Queensland, Australia and Department of Neurobiology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Patrice M. Milos
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA 02139, College of Nanoscale Science and Engineering, University at Albany-Suny, Albany, NY, USA, Institute for Molecular Bioscience, the University of Queensland, Queensland, Australia and Department of Neurobiology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Bino John
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA 02139, College of Nanoscale Science and Engineering, University at Albany-Suny, Albany, NY, USA, Institute for Molecular Bioscience, the University of Queensland, Queensland, Australia and Department of Neurobiology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
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Lapidus KAB, Nwokafor C, Scott D, Baroni TE, Tenenbaum SA, Hiroi N, Singer RH, Czaplinski K. Transgenic expression of ZBP1 in neurons suppresses cocaine-associated conditioning. Learn Mem 2012; 19:35-42. [PMID: 22240322 DOI: 10.1101/lm.024471.111] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
To directly address whether regulating mRNA localization can influence animal behavior, we created transgenic mice that conditionally express Zipcode Binding Protein 1 (ZBP1) in a subset of neurons in the brain. ZBP1 is an RNA-binding protein that regulates the localization, as well as translation and stability of target mRNAs in the cytoplasm. We took advantage of the absence of ZBP1 expression in the mature brain to examine the effect of expressing ZBP1 on animal behavior. We constructed a transgene conditionally expressing a GFP-ZBP1 fusion protein in a subset of forebrain neurons and compared cocaine-cued place conditioning in these mice versus noninduced littermates. Transgenic ZBP1 expression resulted in impaired place conditioning relative to nonexpressing littermates, and acutely repressing expression of the transgene restored normal cocaine conditioning. To gain insight into the molecular changes that accounted for this change in behavior, we identified mRNAs that specifically immunoprecipitated with transgenic ZBP1 protein from the brains of these mice. These data suggest that RNA-binding proteins can be used as a tool to identify the post-transcriptional regulation of gene expression in the establishment and function of neural circuits involved in addiction behaviors.
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Affiliation(s)
- Kyle A B Lapidus
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461-1975, USA
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Shukla GC, Haque F, Tor Y, Wilhelmsson LM, Toulmé JJ, Isambert H, Guo P, Rossi JJ, Tenenbaum SA, Shapiro BA. A boost for the emerging field of RNA nanotechnology. ACS Nano 2011; 5:3405-18. [PMID: 21604810 PMCID: PMC3102291 DOI: 10.1021/nn200989r] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
This Nano Focus article highlights recent advances in RNA nanotechnology as presented at the First International Conference of RNA Nanotechnology and Therapeutics, which took place in Cleveland, OH, USA (October 23-25, 2010) ( http://www.eng.uc.edu/nanomedicine/RNA2010/ ), chaired by Peixuan Guo and co-chaired by David Rueda and Scott Tenenbaum. The conference was the first of its kind to bring together more than 30 invited speakers in the frontier of RNA nanotechnology from France, Sweden, South Korea, China, and throughout the United States to discuss RNA nanotechnology and its applications. It provided a platform for researchers from academia, government, and the pharmaceutical industry to share existing knowledge, vision, technology, and challenges in the field and promoted collaborations among researchers interested in advancing this emerging scientific discipline. The meeting covered a range of topics, including biophysical and single-molecule approaches for characterization of RNA nanostructures; structure studies on RNA nanoparticles by chemical or biochemical approaches, computation, prediction, and modeling of RNA nanoparticle structures; methods for the assembly of RNA nanoparticles; chemistry for RNA synthesis, conjugation, and labeling; and application of RNA nanoparticles in therapeutics. A special invited talk on the well-established principles of DNA nanotechnology was arranged to provide models for RNA nanotechnology. An Administrator from National Institutes of Health (NIH) National Cancer Institute (NCI) Alliance for Nanotechnology in Cancer discussed the current nanocancer research directions and future funding opportunities at NCI. As indicated by the feedback received from the invited speakers and the meeting participants, this meeting was extremely successful, exciting, and informative, covering many groundbreaking findings, pioneering ideas, and novel discoveries.
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Affiliation(s)
- Girish C. Shukla
- Center for Gene Regulation in Health and Disease, Department of Biological Sciences, Cleveland State University, Cleveland, Ohio 44115, United States
| | - Farzin Haque
- Nanobiomedical Center, College of Engineering and Applied Science, and College of Medicine, University of Cincinnati, Cincinnati, Ohio 45267, United States
| | - Yitzhak Tor
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - L. Marcus Wilhelmsson
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, Kemivägen 10, SE-412 96 Göteborg, Sweden
| | - Jean-Jacques Toulmé
- Université Bordeaux Segalen, INSERM U869, Bâtiment 3A 1er étage, 33076 Bordeaux Cedex, France
| | - Hervé Isambert
- Institut Curie, Research Division, CNRS UMR 168, 11 rue P. & M. Curie, 75005 Paris, France
| | - Peixuan Guo
- Nanobiomedical Center, College of Engineering and Applied Science, and College of Medicine, University of Cincinnati, Cincinnati, Ohio 45267, United States
| | - John J. Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California 91010, United States
| | - Scott A. Tenenbaum
- College of Nanoscale Science & Engineering, University at Albany-SUNY, Albany, New York 12203, United States
| | - Bruce A. Shapiro
- Center for Cancer Research Nanobiology Program, National Cancer Institute at Frederick, Frederick, Maryland 21702, United States
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Abstract
A detailed understanding of post-transcriptional gene expression is necessary to correlate the different elements involved in the many levels of RNA-protein interactions that are needed to coordinate the cellular biomolecular machinery. The profile of mRNA, a major component of this machinery, can be examined after isolation from specific RNA-binding proteins (RBPs). RIP-Chip or ribonomic profiling is a versatilein vivo technique that has been widely used to study post-transcriptional gene regulation and the localization of mRNA. Here we elaborately detail the methodology for mRNA isolation using RBP immunoprecipitation (RIP) as a primary approach. Specific antibodies are used to target RBPs, which are then used to capture the associated mRNA.
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Abstract
A post-transcriptional operon is a set of monocistronic mRNAs encoding functionally related proteins that are co-regulated by a group of RNA-binding proteins and/or small non-coding RNAs so that protein expression is coordinated at the post-transcriptional level. The post-transcriptional operon model (PTO) is used to describe data from an assortment of methods (e.g. RIP-Chip, CLIP-Chip, miRNA profiling, ribosome profiling) that globally address the functionality of mRNA. Several examples of post-transcriptional operons have been documented in the literature and demonstrate the usefulness of the model in identifying new participants in cellular pathways as well as in deepening our understanding of cellular responses.
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Affiliation(s)
- Scott A Tenenbaum
- College of Nanoscale Science and Engineering, Nanoscale Constellation, University at Albany-SUNY, Rensselaer, NY, USA.
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22
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Abstract
Like protein coding sequences, functional motifs in RNA elements are frequently conserved, but this conservation is most often at the structure level rather than sequence based. Proper characterization of these structural RNA motifs is both the key and the limiting step to understanding the nature of RNA-protein interactions. The discovery of elements targeted by RNA-binding proteins and how they function remains one of the most active, yet elusive areas of RNA biology. Only a limited number of these elements have been well characterized with many of the fundamental rules yet to be discovered. Here we present a comprehensive list of web based resources that can be used in the study and identification of RNA-based structural and regulatory motifs and provide a survey of the informatic resources that can have been developed to facilitate this research.
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Affiliation(s)
- Ajish D George
- Department of Biomedical Sciences, School of Public Health, Gen∗NY∗Sis Center for Excellence in Cancer Genomics, University at Albany-SUNY, Rensselaer, NY, USA.
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Perrotti M, Jain R, Abriel LM, Baroni TE, Corbett AB, Tenenbaum SA. Dutasteride monotherapy in men with serologic relapse following radical therapy for adenocarcinoma of the prostate: a pilot study. Urol Oncol 2010; 30:133-8. [PMID: 20800512 DOI: 10.1016/j.urolonc.2010.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Revised: 01/16/2010] [Accepted: 01/17/2010] [Indexed: 01/22/2023]
Abstract
OBJECTIVE The objective of this study was to assess the effect of dutasteride on serum prostate specific antigen (PSA) levels in men with serologic relapse following radical prostatectomy and/or radiation therapy for clinically localized adenocarcinoma of the prostate. METHODS A prospective, single institution, IRB approved trial was conducted. Entry criteria required that all participants have serologic disease relapse only with serum PSA levels between 0.4 and 10.0 ng/ml. Enrolled participants were treated with 0.5 mg dutasteride daily. The primary endpoints were serum PSA level and clinical recurrence. The rate of durable decline in PSA was assessed according to the recommendations of the Prostate-Specific Antigen Working Group. RESULTS Thirty-five patients provided informed consent and participated in the present study. At a median follow-up duration of 27 months (range, 4-42 months), 46% of enrolled men had a serum PSA decrease of greater than 10%, and 25% had a serum PSA decrease of greater than 50% (P < 0.001). Pre-study PSA doubling time (PSADT) (≥12 months vs. <12 months), and Gleason score (≤6 vs. ≥7) were associated with a better response to dutasteride, but only PSADT was statistically significant (P < 0.001). Thirty percent of patients experienced PSA progression (increase in serum PSA of greater than 50%). Two (6%) patients developed bone metastasis. No patient was removed from the study for drug-related toxicity. CONCLUSIONS In the present pilot study, treatment with dutasteride resulted in a significant decrease in serum PSA in men with serologic relapse following radical treatment for adenocarcinoma of the prostate. These data appear to suggest that dutasteride may delay or prevent progression of prostate cancer in some men with biochemical relapse after radical therapy. These findings require confirmation in the setting of a larger, longer trial.
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Affiliation(s)
- Michael Perrotti
- Urologic Oncology Service, St. Peter's Cancer Care Center, Albany, NY 12208, USA.
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Stoecklin G, Tenenbaum SA, Mayo T, Chittur SV, George AD, Baroni TE, Blackshear PJ, Anderson P. Genome-wide analysis identifies interleukin-10 mRNA as target of tristetraprolin. J Biol Chem 2008; 283:11689-99. [PMID: 18256032 PMCID: PMC2431067 DOI: 10.1074/jbc.m709657200] [Citation(s) in RCA: 201] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Revised: 02/04/2008] [Indexed: 01/22/2023] Open
Abstract
Tristetraprolin (TTP) is an RNA-binding protein required for the rapid degradation of mRNAs containing AU-rich elements. Targets regulated by TTP include the mRNAs encoding tumor necrosis factor-alpha, granulocyte-macrophage colony-stimulating factor, interleukin-2 (IL-2), and immediate early response 3. To identify novel target mRNAs of TTP in macrophages, we used a genome-wide approach that combines RNA immunoprecipitation and microarray analysis. A list was compiled of 137 mRNAs that are associated with TTP with an estimated accuracy on the order of 90%. Sequence analysis revealed a highly significant enrichment of AU-rich element motifs, with AUUUA pentamers present in 96% and UUAUUUAUU nonamers present in 44% of TTP-associated mRNAs. We further show that IL-10 is a novel target regulated by TTP. IL-10 mRNA levels were found to be elevated because of a reduced decay rate in primary macrophages from TTP(-/-) mice. Our study demonstrates the importance of experimental approaches for identifying targets of RNA-binding proteins.
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Affiliation(s)
- Georg Stoecklin
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.
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Perrotti M, Baroni TE, Abraham C, Moran ME, Tenenbaum SA. EFFICACY OF DUTASTERIDE IN MEN WITH PSA RELAPSE FOLLOWING PRIMARY LOCAL THERAPY FOR ADENOCARCINOMA OF THE PROSTATE. J Urol 2008. [DOI: 10.1016/s0022-5347(08)60522-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Mazroui R, Di Marco S, Clair E, von Roretz C, Tenenbaum SA, Keene JD, Saleh M, Gallouzi IE. Caspase-mediated cleavage of HuR in the cytoplasm contributes to pp32/PHAP-I regulation of apoptosis. ACTA ACUST UNITED AC 2008; 180:113-27. [PMID: 18180367 PMCID: PMC2213623 DOI: 10.1083/jcb.200709030] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The RNA-binding protein HuR affects cell fate by regulating the stability and/or the translation of messenger RNAs that encode cell stress response proteins. In this study, we delineate a novel regulatory mechanism by which HuR contributes to stress-induced cell death. Upon lethal stress, HuR translocates into the cytoplasm by a mechanism involving its association with the apoptosome activator pp32/PHAP-I. Depleting the expression of pp32/PHAP-I by RNA interference reduces both HuR cytoplasmic accumulation and the efficiency of caspase activation. In the cytoplasm, HuR undergoes caspase-mediated cleavage at aspartate 226. This cleavage activity is significantly reduced in the absence of pp32/PHAP-I. Substituting aspartate 226 with an alanine creates a noncleavable isoform of HuR that, when overexpressed, maintains its association with pp32/PHAP-I and delays the apoptotic response. Thus, we propose a model in which HuR association with pp32/PHAP-I and its caspase-mediated cleavage constitutes a regulatory step that contributes to an amplified apoptotic response.
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Affiliation(s)
- Rachid Mazroui
- Department of Biochemistry, McGill University Health Center, McGill University, Montreal, Quebec H3G 146, Canada
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Baroni TE, Chittur SV, George AD, Tenenbaum SA. Advances in RIP-chip analysis : RNA-binding protein immunoprecipitation-microarray profiling. Methods Mol Biol 2008; 419:93-108. [PMID: 18369977 DOI: 10.1007/978-1-59745-033-1_6] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In eukaryotic organisms, gene regulatory networks require an additional level of coordination that links transcriptional and post-transcriptional processes. Messenger RNAs have traditionally been viewed as passive molecules in the pathway from transcription to translation. However, it is now clear that RNA-binding proteins (RBPs) play a major role in regulating multiple mRNAs to facilitate gene expression patterns. On this basis, post-transcriptional and transcriptional gene expression networks appear to be very analogous. Our previous research focused on targeting RBPs to develop a better understanding of post-transcriptional gene-expression processing and the regulation of mRNA networks. We developed technologies for purifying endogenously formed RBP-mRNA complexes from cellular extracts and identifying the associated messages using genome-scale, microarray technology, a method called ribonomics or RNA-binding protein immunoprecipitation-microarray (Chip) profiling or RIP-Chip. The use of the RIP-Chip methods has provided great insight into the infrastructure of coordinated eukaryotic post-transcriptional gene expression, insights which could not have been obtained using traditional RNA expression profiling approaches (1). This chapter describes the most current RIP-Chip techniques as we presently practice them. We also discuss some of the informatic aspects that are unique to analyzing RIP-Chip data.
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Affiliation(s)
- Timothy E Baroni
- Department of Biomedical Sciences, University at Albany-SUNY, School of Public Health, Rensselaer, NY, USA
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Doyle F, Zaleski C, George AD, Stenson EK, Ricciardi A, Tenenbaum SA. Bioinformatic tools for studying post-transcriptional gene regulation : The UAlbany TUTR collection and other informatic resources. Methods Mol Biol 2008; 419:39-52. [PMID: 18369974 DOI: 10.1007/978-1-59745-033-1_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The untranslated regions (UTRs) of many mRNAs contain sequence and structural motifs that are used to regulate the stability, localization, and translatability of the mRNA. It should be possible to discover previously unidentified RNA regulatory motifs by examining many related nucleotide sequences, which are assumed to contain a common motif. This is a general practice for discovery of DNA-based sequence-based patterns, in which alignment tools are heavily exploited. However, because of the complexity of sequential and structural components of RNA-based motifs, simple-alignment tools are frequently inadequate. The consensus sequences they find frequently have the potential for significant variability at any given position and are only loosely characterized. The development of RNA-motif discovery tools that infer and integrate structural information into motif discovery is both necessary and expedient. Here, we provide a selected list of existing web-accessible algorithms for the discovery of RNA motifs, which, although not exhaustive, represents the current state of the art. To facilitate the development, evaluation, and training of new software programs that identify RNA motifs, we created the UAlbany training UTR (TUTR) database, which is a collection of validated sets of sequences containing experimentally defined regulatory motifs. Presently, eleven training sets have been generated with associated indexes and "answer sets" provided that identify where the previously characterized RNA motif [the iron responsive element (IRE), AU-rich class-2 element (ARE), selenocysteine insertion sequence (SECIS), etc.] resides in each sequence. The UAlbany TUTR collection is a shared resource that is available to researchers for software development and as a research aid.
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Affiliation(s)
- Francis Doyle
- Department of Biomedical Sciences, University at Albany-SUNY, School of Public Health, Rensselaer, NY, USA
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Abstract
We propose that microRNAs could modulate RNA-binding protein binding sites in a dynamic manner. We suggest that the cis-regulatory code targeted by microRNAs is, at least in part, the same as that read by mRNA-binding proteins. Our hypothesis predicts that microRNAs indirectly or directly bind to RNA-binding protein binding sites. Alternatively, the microRNA-mRNA interactions can themselves be the target of an mRNA-binding protein. Lastly, we envision examples where multiple mRNA regulatory elements are simultaneously influenced by microRNA-mRNA interactions such that the binding of one or more microRNA results in conformational changes in the structure of the mRNA, thereby, either revealing or masking a second regulatory element.
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Affiliation(s)
- Ajish D George
- University at Albany-SUNY, Gen*NY*Sis Center for Excellence in Cancer Genomics, Department of Biomedical Sciences, School of Public Health, Rensselaer, New York 12144, USA
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Abstract
To address the role of the RS domain in shuttling and how it is differentially required for constitutive and alternative splicing, Lin et al. (2005 [in the November 11 issue of Molecular Cell]) employ an elegant somatic complementation system to reveal a novel phosphorylation-dependent mechanism regulating distinct recycling pathways for SR proteins during mRNP maturation.
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Affiliation(s)
- Scott A Tenenbaum
- Molecular Genetics, Department of Biomedical Sciences, School of Public Health, Ge*NY*Sis Center for Excellence in Cancer Genomics, 1 Discovery Drive, Room 220, Rensselaer, New York 12144, USA
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Di Marco S, Mazroui R, Dallaire P, Chittur S, Tenenbaum SA, Radzioch D, Marette A, Gallouzi IE. NF-kappa B-mediated MyoD decay during muscle wasting requires nitric oxide synthase mRNA stabilization, HuR protein, and nitric oxide release. Mol Cell Biol 2005; 25:6533-45. [PMID: 16024790 PMCID: PMC1190341 DOI: 10.1128/mcb.25.15.6533-6545.2005] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Muscle wasting (cachexia) is a consequence of chronic diseases, such as cancer, and is associated with degradation of muscle proteins such as MyoD. The cytokines tumor necrosis factor alpha and gamma interferon induce muscle degeneration by activating the transcription factor NF-kappaB and its target genes. Here, we show that a downstream target of NF-kappaB is the nitric oxide (NO) synthase gene (iNos) and suggest that NO production stimulates MyoD mRNA loss. In fact, although cytokine treatment of iNos(-/-) mice activated NF-kappaB, it did not trigger MyoD mRNA degeneration, demonstrating that NF-kappaB-mediated muscle wasting requires an active iNOS-NO pathway. The induced expression of iNOS by cytokines relies on both transcriptional activation via NF-kappaB and increased mRNA stability via the RNA-binding protein HuR. Moreover, we show that HuR regulates iNOS expression in an AMP-activated protein kinase (AMPK)-dependent manner. Furthermore, AMPK activation results in HuR nuclear sequestration, inhibition of iNOS synthesis, and reduction in cytokine-induced MyoD loss. These results define iNOS and HuR as critical players in cytokine-induced cachexia, establishing them as potential therapeutic targets.
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Affiliation(s)
- Sergio Di Marco
- Department of Biochemistry, McGill University, McIntyre Building, room 904, 3655 Promenade Sir William Osler, Montreal, Quebec H3G 1Y6, Canada
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Tenenbaum SA, Morris CA, Alexander SS, McFerrin HE, Garry RF, Leissinger CA. Evidence of HIV exposure and transient seroreactivity in archived HIV-negative severe hemophiliac sera. Virol J 2005; 2:65. [PMID: 16107217 PMCID: PMC1232868 DOI: 10.1186/1743-422x-2-65] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2005] [Accepted: 08/17/2005] [Indexed: 11/21/2022] Open
Abstract
Background Approximately 25% of hemophiliacs that were frequently exposed to blood clotting factor concentrates (CFCs) contaminated with human immunodeficiency virus (HIV) are presently HIV seronegative. In this study, we sought to determine if some of these individuals were at any time transiently HIV seropositive. In the early to mid-1980s the majority of severe hemophilia patients were exposed to CFCs contaminated with HIV. Although many of these hemophiliacs became HIV-positive, a small percentage did not become infected. To determine if some of these individuals successfully resisted viral infection, we attempted to document the presence of transient HIV reactive antibodies in archived plasma samples (1980–1992) from currently HIV-negative severe hemophiliacs who had a high probability of repeated exposure to HIV contaminated CFC. Archived plasma samples were retrospectively tested using an FDA approved HIV-1Ab HIV-1/HIV-2 (rDNA) enzyme immunoassay (EIA) and a HIV-1 Western blot assay (Wb), neither of which were commercially available until the late 1980s, which was after many of these samples had been drawn. Results We found that during the high risk years of exposure to HIV contaminated CFC (1980–1987), low levels of plasma antibodies reactive with HIV proteins were detectable in 87% (13/15) of the haemophiliacs tested. None of these individuals are presently positive for HIV proviral DNA as assessed by polymerase chain reaction (PCR). Conclusion Our data suggest that some severe hemophiliacs with heavy exposure to infectious HIV contaminated CFC had only transient low-level humoral immune responses reactive with HIV antigens yet remained HIV-negative and apparently uninfected. Our data supports the possibility of HIV exposure without sustained infection and the existence of HIV-natural resistance in some individuals.
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Affiliation(s)
- Scott A Tenenbaum
- Department of Biomedical Sciences, Ge*NY*Sis Center for Excellence in Cancer Genomics, University at Albany-SUNY, Albany, NY, USA
| | - Cindy A Morris
- Microbiology and Immunology, Tulane University School of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Steve S Alexander
- Ortho Diagnostic Systems, HlV and Hepatitis Research and Development, Raritan, NJ, USA
| | - Harris E McFerrin
- Microbiology and Immunology, Tulane University School of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Robert F Garry
- Microbiology and Immunology, Tulane University School of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Cindy A Leissinger
- Department of Medicine, Section of Hematology and Medical Oncology, Tulane University School of Medicine, New Orleans, LA, USA
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Sander DM, Szabo S, Gallaher WR, Deas JE, Thompson JJ, Cao Y, Luo-Zhang H, Liu LG, Colmegna I, Koehler J, Espinoza LR, Alexander SS, Hart DJ, Tom DM, Fermin CD, Jaspan JJ, Kulakosky PC, Tenenbaum SA, Wilson RB, Garry RF. Involvement of human intracisternal A-type retroviral particles in autoimmunity. Microsc Res Tech 2005; 68:222-34. [PMID: 16276517 DOI: 10.1002/jemt.20234] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Prior studies have linked retroviruses to various arthropathies and autoimmune diseases. Sjögren's syndrome (SS), a systemic autoimmune disease, is characterized by aggressive infiltration of lymphocytes into the salivary and lacrimal glands, resulting in destruction of the glands and dry mouth and eyes (sicca syndrome). The infiltrating lymphocytes in SS may become overtly malignant, and thus, the incidence of lymphoma is greatly increased in SS patients. A human intracisternal A-type retroviral particle type I (HIAP-I) has been isolated from persons with SS. HIAP-I shares a limited number of antigenic epitopes with human immunodeficiency virus (HIV), but is distinguishable from HIV by morphological, physical, and biochemical criteria. A substantial majority of patients with SS or systemic lupus erythematosus (SLE) have serum antibodies to the proteins of this human retrovirus. Fewer than 3% of the normal blood donor population have antibodies to any HIAP-associated proteins. A second type of a human intracisternal A-type retrovirus, HIAP-II, was detected in a subset of patients with idiopathic CD4 lymphocytopenia (ICL), an AIDS-like immunodeficiency disease. Most HIAP-II positive ICL patients were also antinuclear antibody positive. Reviewed here are additional studies from several laboratories suggesting that HIAP or related viruses may be involved in SLE and other autoimmune conditions. Additionally, results of comprehensive surveys of autoimmune patients to determine seroreactivity to HIAP, and other human retroviruses, including HIV and human T-lymphotropic virus type I, are reported.
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Affiliation(s)
- David M Sander
- Graduate Program in Molecular and Cellular Biology and Department of Microbiology and Immunology, Tulane University Health Sciences Center, New Orleans, Louisiana, USA.
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Abstract
RNA-binding proteins can organize messenger RNAs (mRNAs) into structurally and functionally related subsets, thus facilitating the coordinate production of gene classes necessary for complex cellular processes. Historically, in vitro methods primarily have been used to identify individual targets of mRNA-binding proteins. However, more direct methods are required for the identification of endogenously associated RNAs and their cognate proteins. To better understand posttranscriptional mRNA organization within the cell, we developed a systems biology approach to identify multiple-endogenous mRNA transcripts associated with RNA-binding proteins. This approach, termed ribonomics, takes advantage of high-throughput genomic array technologies that have greatly advanced the study of global gene expression changes. This chapter describes techniques for purifying mRNA-protein complexes (mRNPs) and identifying the associated mRNAs
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Affiliation(s)
- Luiz O F Penalva
- The Center For RNA Biology, Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
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Intine RV, Tenenbaum SA, Sakulich AL, Keene JD, Maraia RJ. Differential phosphorylation and subcellular localization of La RNPs associated with precursor tRNAs and translation-related mRNAs. Mol Cell 2003; 12:1301-7. [PMID: 14636586 DOI: 10.1016/s1097-2765(03)00429-5] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The La protein facilitates the production of tRNAs in the nucleus and the translation of specific mRNAs in the cytoplasm. We report that human La that is phosphorylated on serine 366 (pLa) is nucleoplasmic and associated with precursor tRNAs and other nascent RNA polymerase III transcripts while nonphosphorylated (np)La is cytoplasmic and associated with a subset of mRNAs that contain 5'-terminal oligopyrimidine (5'TOP) motifs known to control protein synthesis. Thus, La ribonucleoproteins (RNP) exist in distinct states that differ in subcellular localization, serine 366 phosphorylation, and associated RNAs. These results are consistent with a model in which the relative concentrations of the La S366 isoforms in different subcellular compartments in conjunction with the relative concentrations of specific RNA ligands in these compartments determine the differential association of npLa and pLa with their respective classes of associated RNAs.
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Affiliation(s)
- Robert V Intine
- Laboratory of Molecular Growth Regulation, National Institute of Child Health and Development, Bethesda, MD 20892, USA
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Abstract
Coordinated gene expression is influenced by transcriptional and posttranscriptional events and is necessary for efficient cell growth and differentiation. Genomic array technologies have afforded great advances in identifying global changes of gene expression in response to a variety of environmental stimuli. However, it has been a challenge to assess whether a concomitant effect on protein expression reflects the coordinated regulation of distinct subsets of mRNAs detected by cDNA arrays [Proc. Natl. Acad. Sci. U. S. A. 98 (2001) 7018]. We have expanded the utility of cDNA arrays by using them to assist in elucidating combinatorial posttranscriptional eukaryotic operons [Mol. Cell 9 (2002) 1161]. In this study, we have used two mRNA partitioning methods in which: (1) subsets of mRNAs are isolated as endogenous mRNP complexes using autoimmune patient sera, and (2) transcriptional contributions to gene expression are assessed using cDNA array analysis of an en masse nuclear run-on assay (emRUN). The combination of these methods can provide an additional 'systems biology' discovery approach to gene expression analysis based upon the physical partitioning of mRNA subsets, as well as a functional partitioning of transcriptional and posttranscriptional processes. We demonstrate how these approaches can reduce transcriptomic complexity by partitioning mRNAs into biologically relevant subsets in order to derive information about the expression of multiple, but functionally linked, genes.
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Affiliation(s)
- Scott A Tenenbaum
- Center for RNA Biology, Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
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37
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Abstract
Genomic array analysis of endogenous mammalian ribonucleoproteins has recently revealed three novel findings: (1) mRNA binding proteins are associated with unique subpopulations of messages, (2) the compositions of these mRNA subsets can vary with growth conditions, and (3) the same mRNA species can be found in multiple mRNP complexes. Based on these and other findings, we propose a model of posttranscriptional gene expression in which mRNA binding proteins regulate mRNAs as subpopulations during cell growth and development. This model predicts that functionally related genes are regulated posttranscriptionally as groups by specific mRNA binding proteins that recognize sequence elements in common among the mRNAs.
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Affiliation(s)
- Jack D Keene
- Center for RNA Biology, Department of Microbiology, Duke University Medical Center, Durham, NC 27710, USA.
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Eystathioy T, Chan EKL, Tenenbaum SA, Keene JD, Griffith K, Fritzler MJ. A phosphorylated cytoplasmic autoantigen, GW182, associates with a unique population of human mRNAs within novel cytoplasmic speckles. Mol Biol Cell 2002; 13:1338-51. [PMID: 11950943 PMCID: PMC102273 DOI: 10.1091/mbc.01-11-0544] [Citation(s) in RCA: 286] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
A novel human cellular structure has been identified that contains a unique autoimmune antigen and multiple messenger RNAs. This complex was discovered using an autoimmune serum from a patient with motor and sensory neuropathy and contains a protein of 182 kDa. The gene and cDNA encoding the protein indicated an open reading frame with glycine-tryptophan (GW) repeats and a single RNA recognition motif. Both the patient's serum and a rabbit serum raised against the recombinant GW protein costained discrete cytoplasmic speckles designated as GW bodies (GWBs) that do not overlap with the Golgi complex, endosomes, lysosomes, or peroxisomes. The mRNAs associated with GW182 represent a clustered set of transcripts that are presumed to reside within the GW complexes. We propose that the GW ribonucleoprotein complex is involved in the posttranscriptional regulation of gene expression by sequestering a specific subset of gene transcripts involved in cell growth and homeostasis.
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Tenenbaum SA, Lager PJ, Carson CC, Keene JD. Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays. Methods 2002; 26:191-8. [PMID: 12054896 DOI: 10.1016/s1046-2023(02)00022-1] [Citation(s) in RCA: 233] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Although in vitro methods have been used to identify putative targets of mRNA-binding proteins, direct in vivo methods are needed to identify endogenously associated mRNAs and their cognate proteins. Therefore, we have developed high-throughput methods to identify structurally and/or functionally related mRNA transcripts through their endogenous association with RNA-binding proteins. We have termed the identification and analysis of mRNA subsets using RNA-associated proteins ribonomics, and have established four primary steps for the method: (1) isolation of endogenous mRNA-protein complexes (mRNPs) under optimized conditions, (2) the en masse characterization of the protein and mRNA components associated with the targeted mRNP complexes, (3) identification of sequences or structural similarities among members of the mRNA subset, and (4) determination of functional relationships among the protein products coded for by members of the mRNA subset. We have hypothesized that mRNAs are organized into structurally and functionally linked groups to better affect information transfer through coordinate gene expression. The functional consequences of such organization would be to facilitate the production of proteins that regulate processes necessary for growth and differentiation. This article describes a series of biochemical techniques that deal with the first two steps of ribonomic profiling: purifying endogenous mRNP complexes and identifying multiple mRNA targets using microarray analysis.
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Affiliation(s)
- Scott A Tenenbaum
- Department of Microbiology, Duke University Medical Center, Durham, NC 27710, USA
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Brown V, Jin P, Ceman S, Darnell JC, O'Donnell WT, Tenenbaum SA, Jin X, Feng Y, Wilkinson KD, Keene JD, Darnell RB, Warren ST. Microarray identification of FMRP-associated brain mRNAs and altered mRNA translational profiles in fragile X syndrome. Cell 2001; 107:477-87. [PMID: 11719188 DOI: 10.1016/s0092-8674(01)00568-2] [Citation(s) in RCA: 847] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fragile X syndrome results from the absence of the RNA binding FMR protein. Here, mRNA was coimmunoprecipitated with the FMRP ribonucleoprotein complex and used to interrogate microarrays. We identified 432 associated mRNAs from mouse brain. Quantitative RT-PCR confirmed some to be >60-fold enriched in the immunoprecipitant. In parallel studies, mRNAs from polyribosomes of fragile X cells were used to probe microarrays. Despite equivalent cytoplasmic abundance, 251 mRNAs had an abnormal polyribosome profile in the absence of FMRP. Although this represents <2% of the total messages, 50% of the coimmunoprecipitated mRNAs with expressed human orthologs were found in this group. Nearly 70% of those transcripts found in both studies contain a G quartet structure, demonstrated as an in vitro FMRP target. We conclude that translational dysregulation of mRNAs normally associated with FMRP may be the proximal cause of fragile X syndrome, and we identify candidate genes relevant to this phenotype.
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MESH Headings
- Amino Acid Sequence
- Animals
- Brain Chemistry
- Centrifugation, Density Gradient
- Disease Models, Animal
- Fragile X Mental Retardation Protein
- Fragile X Syndrome/genetics
- Humans
- Ligands
- Macromolecular Substances
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Models, Genetic
- Molecular Sequence Data
- Nerve Tissue Proteins/deficiency
- Nerve Tissue Proteins/genetics
- Nerve Tissue Proteins/physiology
- Oligonucleotide Array Sequence Analysis
- Polymerase Chain Reaction
- Precipitin Tests
- Protein Binding
- Protein Biosynthesis
- RNA, Messenger/chemistry
- RNA, Messenger/isolation & purification
- RNA, Messenger/metabolism
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/physiology
- Regulatory Sequences, Nucleic Acid
- Ribosomes/metabolism
- Sequence Alignment
- Sequence Homology, Amino Acid
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Affiliation(s)
- V Brown
- Howard Hughes Medical Institute, Department of Human Genetics, Department of Pediatrics, Atlanta, GA 30322, USA
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Abstract
Genomic array technologies provide a means for profiling global changes in gene expression under a variety of conditions. However, it has been difficult to assess whether transcriptional or posttranscriptional regulation is responsible for these changes. Additionally, fluctuations in gene expression in a single cell type within a complex tissue like a tumor may be masked by overlapping profiles of all cell types in the population. In this paper, we describe the use of cDNA arrays to identify subsets of mRNAs contained in endogenous messenger ribonucleoprotein complexes (mRNPs) that are cell type specific. We identified mRNA subsets from P19 embryonal carcinoma stem cells by using mRNA-binding proteins HuB, eIF-4E, and PABP that are known to play a role in translation. The mRNA profiles associated with each of these mRNPs were unique and represented gene clusters that differed from total cellular RNA. Additionally, the composition of mRNAs detected in HuB-mRNP complexes changed dramatically after induction of neuronal differentiation with retinoic acid. We suggest that the association of structurally related mRNAs into mRNP complexes is dynamic and may help regulate posttranscriptional events such as mRNA turnover and translation. Recovering proteins specifically associated with mRNP complexes to identify and profile endogenously clustered mRNAs should provide insight into structural and functional relationships among gene transcripts and/or their protein products. We have termed this approach to functional genomics ribonomics and suggest that it will provide a useful paradigm for organizing genomic information in a biologically relevant manner.
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Affiliation(s)
- S A Tenenbaum
- Department of Microbiology, Duke University Medical Center, Durham, NC 27710, USA
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Tenenbaum SA, Rice JC, Espinoza LR, Cuéllar ML, Plymale DR, Sander DM, Williamson LL, Haislip AM, Gluck OS, Tesser JR. Use of antipolymer antibody assay in recipients of silicone breast implants. Lancet 1997; 349:449-54. [PMID: 9040573 DOI: 10.1016/s0140-6736(96)07131-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
BACKGROUND Local complications (encapsulation, rashes, rupture, and leakage) can occur after placement of silicone gel-containing breast implants (SBI). Whether SBI exposure results in systemic manifestations in some recipients is controversial. We have carried out a blinded study to assess whether there is any difference between SBI recipients and non-exposed controls in the proportions positive for serum antibodies directed against polymeric substances. METHODS We recruited female SBI recipients (including those without symptoms) who presented to a single rheumatology clinic. A physician global assessment was used to classify SBI recipients who did not meet criteria for specific autoimmune diseases according to the severity of local and systemic signs and symptoms. Controls were recruited from among clinic staff and their acquaintances. Results of the antipolymer antibody (APA) assay were compared with those of an assay for antinuclear antibodies (ANA) and with the severity of the signs and symptoms. FINDINGS Positive APA results were found in one (3%) of 34 SBI recipients with limited symptoms, two (8%) of 26 with mild symptoms, seven (44%) of 16 with moderate symptoms, and 13 (68%) of 19 with advanced symptoms. Four (17%) of 23 healthy non-SBI-exposed controls and two (10%) of 20 non-exposed women with classic autoimmune diseases were positive for APA. Thus, women with moderate or advanced symptoms were significantly more likely than those with limited or mild symptoms, or non-exposed controls to have APA (p < 0.001). The proportion with positive ANA results was higher for women with classic autoimmune diseases 14 (70%) of 20 than for any SBI-exposed subgroup (0-33%). INTERPRETATION The APA assay can objectively contribute to distinguishing between SBI recipients with limited or mild signs and symptoms. SBI recipients with more severe manifestations, and patients with specific autoimmune diseases. Further studies will be needed to define the signs and symptoms associated with exposure to SBI.
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Affiliation(s)
- S A Tenenbaum
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
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43
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Scandurro AB, Rondon IJ, Wilson RB, Tenenbaum SA, Garry RF, Beckman BS. Interaction of erythropoietin RNA binding protein with erythropoietin RNA requires an association with heat shock protein 70. Kidney Int 1997; 51:579-84. [PMID: 9027743 DOI: 10.1038/ki.1997.83] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Synthesis of erythropoietin (Epo), the glycoprotein hormone that regulates red blood cell formation, is induced in response to low oxygen stress (hypoxia), and is regulated at both transcriptional and post-transcriptional levels. We have previously described an Epo RNA binding protein (ERBP) which specifically binds to the 3'-untranslated region of Epo mRNA and is likely involved in the regulation of Epo mRNA stability. Since heat shock proteins (hsps) are induced in response to a variety of stresses, including hypoxia, we tested the possibility that hsps are involved in ERBP-Epo RNA complex formation. When human anti-hsp70 antibody was added to ERBP-containing human hepatoma cell (Hep3B) lysates, the ERBP-Epo RNA complex was inhibited in an electrophoretic mobility band shift assay. In addition, the anti-hsp70 antibody-inhibited complex could be rescued if lysates were pretreated with purified inducible hsp70, but not with bovine serum albumin (BSA). In vivo studies using quercetin to inhibit hsp70 induction support the notion that hsp70 is involved in ERBP-Epo RNA complex formation. Taken together, these findings suggest involvement of hsp70 in ERBP-Epo mRNA complex formation, and our model suggests a novel role for hsps in the regulation of EPO mRNA stability.
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Affiliation(s)
- A B Scandurro
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, Louisiana, USA
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Chiang CF, Tenenbaum SA, Verret CR, Leissinger CA, Garry RF. Activity of granzyme A, a serine protease in the killing granules of cytotoxic T lymphocytes, is reduced in cells from HIV-infected hemophiliacs. AIDS Res Hum Retroviruses 1996; 12:235-9. [PMID: 8835202 DOI: 10.1089/aid.1996.12.235] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Cytotoxic CD8+ lymphocytes (CTLs) kill virally infected target cells by releasing cytotoxic granules. The primary objective of this study was to determine whether the activity of granzyme A, a serine protease in the killing granules of CTLs is altered in HIV-infected hemophiliacs. A sensitive colorimetric assay that measures cleavage of a synthetic substrate, N alpha-benzyloxycarbonyl-L-lysine thiobenzyl ester (BLT), was used to quantitate granzyme A activity. Granzyme A activities from hemophiliacs were normalized to to granzyme A activities of healthy donors run concurrently. Granzyme A activity in CD8+ T cells from HIV-seropositive hemophiliacs was significantly lower than granzyme A activity in cells from HIV-seronegative hemophiliacs (0.48 units +/- 0.086/CD8+ T cell and 1.573 +/- 0.434 units/CD8+ T cell, respectively; p < 0.005). These results indicate that cytotoxic cells in HIV-infected hemophiliacs have reduced granzyme A activity, which may result in a defect in CTL-mediated cell killing in these patients.
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Affiliation(s)
- C F Chiang
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, USA
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Cuéllar ML, Scopelitis E, Tenenbaum SA, Garry RF, Silveira LH, Cabrera G, Espinoza LR. Serum antinuclear antibodies in women with silicone breast implants. J Rheumatol 1995; 22:236-40. [PMID: 7738944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
OBJECTIVE Recent evidence suggests that immunologic abnormalities are not uncommon in individuals with silicone breast implants. The purpose of our study was to evaluate in a consecutive manner, the prevalence of autoimmunity as assessed by the presence of antinuclear antibodies in a larger number of patients with silicone breast implants. METHODS Antinuclear antibody (ANA) testing using an indirect immunofluorescence technique was performed on 813 individuals with silicone breast implants. All subjects except for 3 transsexual males, were female. The overwhelming majority, over 99%, were white. The average age of the subjects was 46.2, with a range of 17 to 72 years. RESULTS ANA positivity was found in 244 of 813 individuals (30%) using a mouse kidney substrate; and in 470 of 813 (57.8%) using a HEp-2 cell line. The most common immunofluorescent pattern found using HEp-2 was speckled, present in 341 (72.5%) individuals, followed by homogeneous pattern in 113 (24%), nucleolar in 63 (13.4%), and 5 (1.06%) were anticentromere. Anti-dsDNA antibodies measured by an ELISA assay were found in 6 of 71 patients (8%). Rheumatoid factor and C-reactive protein were found above healthy controls in less than 10% of cases studied. The high prevalence of ANA found in patients with silicone breast implants agrees with similar observations by others. The finding of anticentromere and nucleolar patterns has great interest and relevance. These fairly distinct ANA patterns are most commonly seen in the idiopathic form of scleroderma and related conditions. CONCLUSION These findings suggest that ANA positivity is relatively common in individuals with silicone breast implants, and may support the existence of autoimmune mechanisms in the pathogenesis of the clinical manifestations seen in this population.
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Affiliation(s)
- M L Cuéllar
- Department of Medicine, LSU Medical Center at New Orleans, USA
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Tenenbaum SA, Voss TG, Garry RF, Gallaher WR. Sequence similarities between retroviral proteins and components of the spliceosome. AIDS Res Hum Retroviruses 1994; 10:521-2. [PMID: 7917513 DOI: 10.1089/aid.1994.10.521] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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Garry RF, Hart DJ, Tenenbaum SA, Luo-Zhang H, Breeding SA, Alexander SS. Sjögren's syndrome and assays for retroviral proteins: reply. Arthritis Rheum 1992; 35:1405. [PMID: 1445467 DOI: 10.1002/art.1780351134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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