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Long noncoding RNAs are substrates for cytoplasmic capping enzyme
Avik Mukherjee
Institute of Health Sciences, Presidency University, Kolkata, India
Search for more papers by this authorSafirul Islam
Institute of Health Sciences, Presidency University, Kolkata, India
Search for more papers by this authorRachel E. Kieser
Center for RNA Therapeutics, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
Search for more papers by this authorDaniel L. Kiss
Center for RNA Therapeutics, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
Weill Cornell Medical College, New York, NY, USA
Houston Methodist Cancer Center, Houston, TX, USA
Houston Methodist Academic Institute, Houston, TX, USA
Search for more papers by this authorCorresponding Author
Chandrama Mukherjee
Institute of Health Sciences, Presidency University, Kolkata, India
Correspondence
C. Mukherjee, Institute of Health Sciences, Presidency University, Plot No. DG/02/02, Premises No. 14-0358, Action Area 1D, Kolkata 700156, India
Tel: +919903950076
E-mail: [email protected]
Search for more papers by this authorAvik Mukherjee
Institute of Health Sciences, Presidency University, Kolkata, India
Search for more papers by this authorSafirul Islam
Institute of Health Sciences, Presidency University, Kolkata, India
Search for more papers by this authorRachel E. Kieser
Center for RNA Therapeutics, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
Search for more papers by this authorDaniel L. Kiss
Center for RNA Therapeutics, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
Weill Cornell Medical College, New York, NY, USA
Houston Methodist Cancer Center, Houston, TX, USA
Houston Methodist Academic Institute, Houston, TX, USA
Search for more papers by this authorCorresponding Author
Chandrama Mukherjee
Institute of Health Sciences, Presidency University, Kolkata, India
Correspondence
C. Mukherjee, Institute of Health Sciences, Presidency University, Plot No. DG/02/02, Premises No. 14-0358, Action Area 1D, Kolkata 700156, India
Tel: +919903950076
E-mail: [email protected]
Search for more papers by this authorAbstract
Cytoplasmic capping returns a cap to specific mRNAs, thus protecting uncapped RNAs from decay. Prior to the identification of cytoplasmic capping, uncapped mRNAs were thought to be degraded. Here, we test whether long noncoding RNAs (lncRNAs) are substrates of the cytoplasmic capping enzyme (cCE). The subcellular localisation of 14 lncRNAs associated with sarcomas were examined in U2OS osteosarcoma cells. We used 5′ rapid amplification of cDNA ends (RACE) to assay uncapped forms of these lncRNAs. Inhibiting cytoplasmic capping elevated uncapped forms of selected lncRNAs indicating a plausible role of cCE in targeting them. Analysis of published cap analysis of gene expression (CAGE) data shows increased prevalence of certain 5’-RACE cloned sequences, suggesting that these uncapped lncRNAs are targets of cytoplasmic capping.
Open Research
Data accessibility
The CAGE data that support the findings of this study were mined from and are available in the ZENBU Genome Browser at ZENBU—genome browser (riken.jp). Summaries of, and links to the data sets used to gather all the CAGE data have been posted to Figshare and are available in the public domain at this link: https://doi.org/10.6084/m9.figshare.22080956.v1. Two tables at that link include the exact coordinates and links to obtain the data for each lncRNA presented in this manuscript and all the numerical data used to generate the CAGE graphs in the paper.
Supporting Information
| Filename | Description |
|---|---|
| feb214603-sup-0001-Supinfo.docxWord 2007 document , 1.5 MB |
Fig. S1. Expanded plot of the data shown in Fig. 1B. Fig. S2. Expanded plot of the data shown in Fig 3C. Fig. S3. 5’ RACE to detect uncapped lncRNAs in cells expressing NCK1-M3. Fig. S4. CAGE tags near the 5′-RACE ends from the parental U2OS cells. Fig. S5. CAGE tags near the 5′-RACE ends from U2OS cells transiently transfected to block the cytoplasmic capping enzyme complex. Fig. S6. CAGE results for full-length lncRNA transcripts. Table S1. Sequences of primers and oligos used in this study. Table S2. Selected lncRNAs for this study with additional identification terms for confirmation of target transcripts. |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
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