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Pelisek J, Yundung Y, Reutersberg B, Meuli L, Rössler F, Rabin L, Kopp R, Zimmermann A. Swiss Vascular Biobank: Evaluation of Optimal Extraction Method and Admission Solution for Preserving RNA from Human Vascular Tissue. J Clin Med 2023; 12:5109. [PMID: 37568514 PMCID: PMC10420000 DOI: 10.3390/jcm12155109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023] Open
Abstract
Proper biobanking is essential for obtaining reliable data, particularly for next-generation sequencing approaches. Diseased vascular tissues, having extended atherosclerotic pathologies, represent a particular challenge due to low RNA quality. In order to address this issue, we isolated RNA from vascular samples collected in our Swiss Vascular Biobank (SVB); these included abdominal aortic aneurysm (AAA), peripheral arterial disease (PAD), healthy aorta (HA), and muscle samples. We used different methods, investigated various admission solutions, determined RNA integrity numbers (RINs), and performed expression analyses of housekeeping genes (ACTB, GAPDH), ribosomal genes (18S, 28S), and long non-coding RNAs (MALAT1, H19). Our results show that RINs from diseased vascular tissue are low (2-4). If the isolation of primary cells is intended, as in our SVB, a cryoprotective solution is a better option for tissue preservation than RNAlater. Because RNA degradation proceeds randomly, controls with similar RINs are recommended. Otherwise, the data might convey differences in RNA degradation rather than the expressions of the corresponding genes. Moreover, since the 18S and 28S genes in the diseased vascular samples were degraded and corresponded with the low RINs, we believe that DV200, which represents the total RNA's disintegration state, is a better decision-making aid in choosing samples for omics analyses.
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Affiliation(s)
- Jaroslav Pelisek
- Department of Vascular Surgery, University Hospital Zurich, 8091 Zurich, Switzerland; (Y.Y.); (L.R.); (R.K.); (A.Z.)
| | - Yankey Yundung
- Department of Vascular Surgery, University Hospital Zurich, 8091 Zurich, Switzerland; (Y.Y.); (L.R.); (R.K.); (A.Z.)
| | - Benedikt Reutersberg
- Department of Vascular Surgery, University Hospital Zurich, 8091 Zurich, Switzerland; (Y.Y.); (L.R.); (R.K.); (A.Z.)
| | - Lorenz Meuli
- Department of Vascular Surgery, University Hospital Zurich, 8091 Zurich, Switzerland; (Y.Y.); (L.R.); (R.K.); (A.Z.)
| | - Fabian Rössler
- Department of Surgery and Transplantation, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Laetitia Rabin
- Department of Vascular Surgery, University Hospital Zurich, 8091 Zurich, Switzerland; (Y.Y.); (L.R.); (R.K.); (A.Z.)
| | - Reinhard Kopp
- Department of Vascular Surgery, University Hospital Zurich, 8091 Zurich, Switzerland; (Y.Y.); (L.R.); (R.K.); (A.Z.)
| | - Alexander Zimmermann
- Department of Vascular Surgery, University Hospital Zurich, 8091 Zurich, Switzerland; (Y.Y.); (L.R.); (R.K.); (A.Z.)
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2
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Costa SM, Saramago M, Matos RG, Arraiano CM, Viegas SC. How hydrolytic exoribonucleases impact human disease: Two sides of the same story. FEBS Open Bio 2022. [PMID: 35247037 DOI: 10.1002/2211-5463.13392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/16/2022] [Accepted: 03/03/2022] [Indexed: 11/05/2022] Open
Abstract
RNAs are extremely important molecules inside the cell which perform many different functions. For example, messenger RNAs, transfer RNAs, and ribosomal RNAs are involved in protein synthesis, whereas non-coding RNAs have numerous regulatory roles. Ribonucleases are the enzymes responsible for the processing and degradation of all types of RNAs, having multiple roles in every aspect of RNA metabolism. However, the involvement of RNases in disease is still not well understood. This review focuses on the involvement of the RNase II/RNB family of 3'-5' exoribonucleases in human disease. This can be attributed to direct effects, whereby mutations in the eukaryotic enzymes of this family (Dis3 (or Rrp44), Dis3L1 (or Dis3L), and Dis3L2) are associated with a disease, or indirect effects, whereby mutations in the prokaryotic counterparts of RNase II/RNB family (RNase II and/or RNase R) affect the physiology and virulence of several human pathogens. In this review, we will compare the structural and biochemical characteristics of the members of the RNase II/RNB family of enzymes. The outcomes of mutations impacting enzymatic function will be revisited, in terms of both the direct and indirect effects on disease. Furthermore, we also describe the SARS-CoV-2 viral exoribonuclease and its importance to combat COVID-19 pandemic. As a result, RNases may be a good therapeutic target to reduce bacterial and viral pathogenicity. These are the two perspectives on RNase II/RNB family enzymes that will be presented in this review.
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Affiliation(s)
- Susana M Costa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Margarida Saramago
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Rute G Matos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Cecília M Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
| | - Sandra C Viegas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157, Oeiras, Portugal
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3
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Pashler AL, Towler BP, Jones CI, Haime HJ, Burgess T, Newbury SF. Genome-wide analyses of XRN1-sensitive targets in osteosarcoma cells identify disease-relevant transcripts containing G-rich motifs. RNA (NEW YORK, N.Y.) 2021; 27:1265-1280. [PMID: 34266995 PMCID: PMC8457002 DOI: 10.1261/rna.078872.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
XRN1 is a highly conserved exoribonuclease which degrades uncapped RNAs in a 5'-3' direction. Degradation of RNAs by XRN1 is important in many cellular and developmental processes and is relevant to human disease. Studies in D. melanogaster demonstrate that XRN1 can target specific RNAs, which have important consequences for developmental pathways. Osteosarcoma is a malignancy of the bone and accounts for 2% of all pediatric cancers worldwide. Five-year survival of patients has remained static since the 1970s and therefore furthering our molecular understanding of this disease is crucial. Previous work has shown a down-regulation of XRN1 in osteosarcoma cells; however, the transcripts regulated by XRN1 which might promote osteosarcoma remain elusive. Here, we confirm reduced levels of XRN1 in osteosarcoma cell lines and patient samples and identify XRN1-sensitive transcripts in human osteosarcoma cells. Using RNA-seq in XRN1-knockdown SAOS-2 cells, we show that 1178 genes are differentially regulated. Using a novel bioinformatic approach, we demonstrate that 134 transcripts show characteristics of direct post-transcriptional regulation by XRN1. Long noncoding RNAs (lncRNAs) are enriched in this group, suggesting that XRN1 normally plays an important role in controlling lncRNA expression in these cells. Among potential lncRNAs targeted by XRN1 is HOTAIR, which is known to be up-regulated in osteosarcoma and contributes to disease progression. We have also identified G-rich and GU motifs in post-transcriptionally regulated transcripts which appear to sensitize them to XRN1 degradation. Our results therefore provide significant insights into the specificity of XRN1 in human cells which are relevant to disease.
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Affiliation(s)
- Amy L Pashler
- Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PS, United Kingdom
| | - Benjamin P Towler
- Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PS, United Kingdom
| | - Christopher I Jones
- Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PS, United Kingdom
| | - Hope J Haime
- Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PS, United Kingdom
| | - Tom Burgess
- Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PS, United Kingdom
| | - Sarah F Newbury
- Brighton and Sussex Medical School, University of Sussex, Brighton, BN1 9PS, United Kingdom
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4
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Coelho VL, de Brito TF, de Abreu Brito IA, Cardoso MA, Berni MA, Araujo HMM, Sammeth M, Pane A. Analysis of ovarian transcriptomes reveals thousands of novel genes in the insect vector Rhodnius prolixus. Sci Rep 2021; 11:1918. [PMID: 33479356 PMCID: PMC7820597 DOI: 10.1038/s41598-021-81387-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 12/30/2020] [Indexed: 01/29/2023] Open
Abstract
Rhodnius prolixus is a Triatominae insect species and a primary vector of Chagas disease. The genome of R. prolixus has been recently sequenced and partially assembled, but few transcriptome analyses have been performed to date. In this study, we describe the stage-specific transcriptomes obtained from previtellogenic stages of oogenesis and from mature eggs. By analyzing ~ 228 million paired-end RNA-Seq reads, we significantly improved the current genome annotations for 9206 genes. We provide extended 5' and 3' UTRs, complete Open Reading Frames, and alternative transcript variants. Strikingly, using a combination of genome-guided and de novo transcriptome assembly we found more than two thousand novel genes, thus increasing the number of genes in R. prolixus from 15,738 to 17,864. We used the improved transcriptome to investigate stage-specific gene expression profiles during R. prolixus oogenesis. Our data reveal that 11,127 genes are expressed in the early previtellogenic stage of oogenesis and their transcripts are deposited in the developing egg including key factors regulating germline development, genome integrity, and the maternal-zygotic transition. In addition, GO term analyses show that transcripts encoding components of the steroid hormone receptor pathway, cytoskeleton, and intracellular signaling are abundant in the mature eggs, where they likely control early embryonic development upon fertilization. Our results significantly improve the R. prolixus genome and transcriptome and provide novel insight into oogenesis and early embryogenesis in this medically relevant insect.
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Affiliation(s)
- Vitor Lima Coelho
- Institute of Biomedical Sciences (ICB), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Maira Arruda Cardoso
- Institute of Biomedical Sciences (ICB), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mateus Antonio Berni
- Institute of Biomedical Sciences (ICB), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Helena Maria Marcolla Araujo
- Institute of Biomedical Sciences (ICB), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Rio de Janeiro, Brazil
| | - Michael Sammeth
- Institute of Biophysics Carlos Chagas Filho (IBCCF), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Department of Applied Sciences, Institute of Bioanalysis, Coburg University, Coburg, Germany
| | - Attilio Pane
- Institute of Biomedical Sciences (ICB), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
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5
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Zhang L, Xu W, Gao X, Li W, Qi S, Guo D, Ajayi OE, Ding SW, Wu Q. lncRNA Sensing of a Viral Suppressor of RNAi Activates Non-canonical Innate Immune Signaling in Drosophila. Cell Host Microbe 2020; 27:115-128.e8. [PMID: 31917956 DOI: 10.1016/j.chom.2019.12.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 10/10/2019] [Accepted: 11/18/2019] [Indexed: 12/30/2022]
Abstract
Antiviral immunity in insects is mediated by the RNA interference (RNAi) pathway. Viruses evade antiviral RNAi by expressing virulence factors known as viral suppressors of RNAi (VSR). Here, we report the identification of VINR, a Drosophila VSR-interacting long non-coding (lnc) RNA that activates non-canonical innate immune signaling upon detection of the dsRNA-binding VSR of Drosophila C virus (DCV). VINR is required for the induction of antimicrobial peptide (AMP) genes but dispensable for antiviral RNAi. VINR functions by preventing the ubiquitin proteasome-dependent degradation of Cactin, a coiled-coil and arginine-serine-rich domain-containing protein that regulates a non-cannonical antimicrobial pathway for AMP induction. CRISPR-Cas9 knockout of VINR in Drosophila cells enhances DCV replication independently of antiviral RNAi, and VINR-knockout adult flies exhibit enhanced disease susceptibility to DCV and bacteria. Our findings reveal a counter counter-defense strategy activated by a lncRNA in response to the viral suppression of the primary antiviral RNAi immunity.
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Affiliation(s)
- Liqin Zhang
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Wen Xu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Xinlei Gao
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Wenjie Li
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Shuishui Qi
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Dongyang Guo
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Olugbenga Emmanuel Ajayi
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Shou-Wei Ding
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside CA, USA
| | - Qingfa Wu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China.
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6
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Chang CT, Muthukumar S, Weber R, Levdansky Y, Chen Y, Bhandari D, Igreja C, Wohlbold L, Valkov E, Izaurralde E. A low-complexity region in human XRN1 directly recruits deadenylation and decapping factors in 5'-3' messenger RNA decay. Nucleic Acids Res 2019; 47:9282-9295. [PMID: 31340047 PMCID: PMC6753473 DOI: 10.1093/nar/gkz633] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 07/08/2019] [Accepted: 07/15/2019] [Indexed: 12/27/2022] Open
Abstract
XRN1 is the major cytoplasmic exoribonuclease in eukaryotes, which degrades deadenylated and decapped mRNAs in the last step of the 5'-3' mRNA decay pathway. Metazoan XRN1 interacts with decapping factors coupling the final stages of decay. Here, we reveal a direct interaction between XRN1 and the CCR4-NOT deadenylase complex mediated by a low-complexity region in XRN1, which we term the 'C-terminal interacting region' or CIR. The CIR represses reporter mRNA deadenylation in human cells when overexpressed and inhibits CCR4-NOT and isolated CAF1 deadenylase activity in vitro. Through complementation studies in an XRN1-null cell line, we dissect the specific contributions of XRN1 domains and regions toward decay of an mRNA reporter. We observe that XRN1 binding to the decapping activator EDC4 counteracts the dominant negative effect of CIR overexpression on decay. Another decapping activator PatL1 directly interacts with CIR and alleviates the CIR-mediated inhibition of CCR4-NOT activity in vitro. Ribosome profiling revealed that XRN1 loss impacts not only on mRNA levels but also on the translational efficiency of many cellular transcripts likely as a consequence of incomplete decay. Our findings reveal an additional layer of direct interactions in a tightly integrated network of factors mediating deadenylation, decapping and 5'-3' exonucleolytic decay.
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Affiliation(s)
- Chung-Te Chang
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Sowndarya Muthukumar
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Ramona Weber
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Yevgen Levdansky
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Ying Chen
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Dipankar Bhandari
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Catia Igreja
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Lara Wohlbold
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Eugene Valkov
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Elisa Izaurralde
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
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7
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Hughes SC, Simmonds AJ. Drosophila mRNA Localization During Later Development: Past, Present, and Future. Front Genet 2019; 10:135. [PMID: 30899273 PMCID: PMC6416162 DOI: 10.3389/fgene.2019.00135] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 02/11/2019] [Indexed: 12/12/2022] Open
Abstract
Multiple mechanisms tightly regulate mRNAs during their transcription, translation, and degradation. Of these, the physical localization of mRNAs to specific cytoplasmic regions is relatively easy to detect; however, linking localization to functional regulatory roles has been more difficult to establish. Historically, Drosophila melanogaster is a highly effective model to identify localized mRNAs and has helped identify roles for this process by regulating various cell activities. The majority of the well-characterized functional roles for localizing mRNAs to sub-regions of the cytoplasm have come from the Drosophila oocyte and early syncytial embryo. At present, relatively few functional roles have been established for mRNA localization within the relatively smaller, differentiated somatic cell lineages characteristic of later development, beginning with the cellular blastoderm, and the multiple cell lineages that make up the gastrulating embryo, larva, and adult. This review is divided into three parts—the first outlines past evidence for cytoplasmic mRNA localization affecting aspects of cellular activity post-blastoderm development in Drosophila. The majority of these known examples come from highly polarized cell lineages such as differentiating neurons. The second part considers the present state of affairs where we now know that many, if not most mRNAs are localized to discrete cytoplasmic regions in one or more somatic cell lineages of cellularized embryos, larvae or adults. Assuming that the phenomenon of cytoplasmic mRNA localization represents an underlying functional activity, and correlation with the encoded proteins suggests that mRNA localization is involved in far more than neuronal differentiation. Thus, it seems highly likely that past-identified examples represent only a small fraction of localization-based mRNA regulation in somatic cells. The last part highlights recent technological advances that now provide an opportunity for probing the role of mRNA localization in Drosophila, moving beyond cataloging the diversity of localized mRNAs to a similar understanding of how localization affects mRNA activity.
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Affiliation(s)
- Sarah C Hughes
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.,Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Andrew J Simmonds
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
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8
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Pirouz M, Ebrahimi AG, Gregory RI. Unraveling 3'-end RNA uridylation at nucleotide resolution. Methods 2019; 155:10-19. [PMID: 30395968 PMCID: PMC6387850 DOI: 10.1016/j.ymeth.2018.10.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/29/2018] [Accepted: 10/30/2018] [Indexed: 12/26/2022] Open
Abstract
Post-transcriptional modification of RNA, the so-called 'Epitranscriptome', can regulate RNA structure, stability, localization, and function. Numerous modifications have been identified in virtually all classes of RNAs, including messenger RNAs (mRNAs), transfer RNAs (tRNAs), ribosomal RNAs (rRNAs), microRNAs (miRNAs), and other noncoding RNAs (ncRNAs). These modifications may occur internally (by base or sugar modifications) and include RNA methylation at different nucleotide positions, or by the addition of various nucleotides at the 3'-end of certain transcripts by a family of terminal nucleotidylyl transferases. Developing methods to specifically and accurately detect and map these modifications is essential for understanding the molecular function(s) of individual RNA modifications and also for identifying and characterizing the proteins that may read, write, or erase them. Here, we focus on the characterization of RNA species targeted by 3' terminal uridylyl transferases (TUTases) (TUT4/7, also known as Zcchc11/6) and a 3'-5' exoribonuclease, Dis3l2, in the recently identified Dis3l2-mediated decay (DMD) pathway - a dedicated quality control pathway for a subset of ncRNAs. We describe the detailed methods used to precisely identify 3'-end modifications at nucleotide level resolution with a particular focus on the U1 and U2 small nuclear RNA (snRNA) components of the Spliceosome. These tools can be applied to investigate any RNA of interest and should facilitate studies aimed at elucidating the functional relevance of 3'-end modifications.
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Affiliation(s)
- Mehdi Pirouz
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Aref G Ebrahimi
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02115, USA
| | - Richard I Gregory
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Harvard Initiative for RNA Medicine, Boston, MA 02115, USA.
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