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Literature DB >> 25541487

Uncapped 5' ends of mRNAs targeted by cytoplasmic capping map to the vicinity of downstream CAGE tags.

Daniel L Kiss¹, Kenji Oman², Ralf Bundschuh³, Daniel R Schoenberg⁴.

Abstract

In mammalian transcriptomes approximately 25% of 5' ends determined by Capped Analysis of Gene Expression (CAGE) map to locations within spliced exons. The current study sought to determine if the cytoplasmic capping complex participates in generating these downstream CAGE tags. 5'-RACE was used to amplify the uncapped ends of target transcripts that accumulate when cytoplasmic capping is blocked. Sequencing of these RACE products mapped the positions of uncapped ends either exactly to or just downstream of archived CAGE tags. These findings support a role for cytoplasmic capping in generating the downstream capped ends identified by CAGE.

Entities: CellLine Chemical Disease Gene Mutation Species

Keywords: CAGE; Cytoplasm; Cytoplasmic capping; Mammalian cell; Uncapped 5′ end; mRNA capping

Mesh：

Substances：

Year: 2014 PMID： 25541487 PMCID： PMC4306605 DOI： 10.1016/j.febslet.2014.12.009

Source DB: PubMed Journal: FEBS Lett ISSN： 0014-5793 Impact factor: 4.124

14 in total

1. BLAT--the BLAST-like alignment tool.

Authors: W James Kent
Journal: Genome Res Date: 2002-04 Impact factor: 9.043

2. The UCSC Table Browser data retrieval tool.

Authors: Donna Karolchik; Angela S Hinrichs; Terrence S Furey; Krishna M Roskin; Charles W Sugnet; David Haussler; W James Kent
Journal: Nucleic Acids Res Date: 2004-01-01 Impact factor: 16.971

3. Identification of a cytoplasmic complex that adds a cap onto 5'-monophosphate RNA.

Authors: Yuichi Otsuka; Nancy L Kedersha; Daniel R Schoenberg
Journal: Mol Cell Biol Date: 2009-02-17 Impact factor: 4.272

Review 4. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Authors: S F Altschul; T L Madden; A A Schäffer; J Zhang; Z Zhang; W Miller; D J Lipman
Journal: Nucleic Acids Res Date: 1997-09-01 Impact factor: 16.971

5. Beta -Globin mRNA decay in erythroid cells: UG site-preferred endonucleolytic cleavage that is augmented by a premature termination codon.

Authors: Audrey Stevens; Yang Wang; Kirsten Bremer; Jing Zhang; Robert Hoepfner; Michael Antoniou; Daniel R Schoenberg; Lynne E Maquat
Journal: Proc Natl Acad Sci U S A Date: 2002-09-19 Impact factor: 11.205

6. Identification of cytoplasmic capping targets reveals a role for cap homeostasis in translation and mRNA stability.

Authors: Chandrama Mukherjee; Deepak P Patil; Brian A Kennedy; Baskar Bakthavachalu; Ralf Bundschuh; Daniel R Schoenberg
Journal: Cell Rep Date: 2012-08-23 Impact factor: 9.423

7. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression.

Authors: Philippe Batut; Alexander Dobin; Charles Plessy; Piero Carninci; Thomas R Gingeras
Journal: Genome Res Date: 2012-08-30 Impact factor: 9.043

8. Human beta-globin mRNAs that harbor a nonsense codon are degraded in murine erythroid tissues to intermediates lacking regions of exon I or exons I and II that have a cap-like structure at the 5' termini.

Authors: S K Lim; L E Maquat
Journal: EMBO J Date: 1992-09 Impact factor: 11.598

9. SMG6 cleavage generates metastable decay intermediates from nonsense-containing β-globin mRNA.

Authors: Roshan Mascarenhas; Julie A Dougherty; Daniel R Schoenberg
Journal: PLoS One Date: 2013-09-25 Impact factor: 3.240

10. The UCSC Genome Browser database: 2014 update.

Authors: Donna Karolchik; Galt P Barber; Jonathan Casper; Hiram Clawson; Melissa S Cline; Mark Diekhans; Timothy R Dreszer; Pauline A Fujita; Luvina Guruvadoo; Maximilian Haeussler; Rachel A Harte; Steve Heitner; Angie S Hinrichs; Katrina Learned; Brian T Lee; Chin H Li; Brian J Raney; Brooke Rhead; Kate R Rosenbloom; Cricket A Sloan; Matthew L Speir; Ann S Zweig; David Haussler; Robert M Kuhn; W James Kent
Journal: Nucleic Acids Res Date: 2013-11-21 Impact factor: 16.971

14 in total

1. mRNA 5' ends targeted by cytoplasmic recapping cluster at CAGE tags and select transcripts are alternatively spliced.

Authors: Mikaela R Berger; Rolando Alvarado; Daniel L Kiss
Journal: FEBS Lett Date: 2019-03-09 Impact factor: 4.124

2. African Swine Fever Virus NP868R Capping Enzyme Promotes Reovirus Rescue during Reverse Genetics by Promoting Reovirus Protein Expression, Virion Assembly, and RNA Incorporation into Infectious Virions.

Authors: Heather E Eaton; Takeshi Kobayashi; Terence S Dermody; Randal N Johnston; Philippe H Jais; Maya Shmulevitz
Journal: J Virol Date: 2017-05-12 Impact factor: 5.103

Review 3. A recap of RNA recapping.

Authors: Jackson B Trotman; Daniel R Schoenberg
Journal: Wiley Interdiscip Rev RNA Date: 2018-09-05 Impact factor: 9.957

Uncapped 5' ends of mRNAs targeted by cytoplasmic capping map to the vicinity of downstream CAGE tags.

1. BLAT--the BLAST-like alignment tool.

2. The UCSC Table Browser data retrieval tool.

3. Identification of a cytoplasmic complex that adds a cap onto 5'-monophosphate RNA.

Review 4. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

5. Beta -Globin mRNA decay in erythroid cells: UG site-preferred endonucleolytic cleavage that is augmented by a premature termination codon.

6. Identification of cytoplasmic capping targets reveals a role for cap homeostasis in translation and mRNA stability.

7. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression.

8. Human beta-globin mRNAs that harbor a nonsense codon are degraded in murine erythroid tissues to intermediates lacking regions of exon I or exons I and II that have a cap-like structure at the 5' termini.

9. SMG6 cleavage generates metastable decay intermediates from nonsense-containing β-globin mRNA.

10. The UCSC Genome Browser database: 2014 update.

1. mRNA 5' ends targeted by cytoplasmic recapping cluster at CAGE tags and select transcripts are alternatively spliced.

2. African Swine Fever Virus NP868R Capping Enzyme Promotes Reovirus Rescue during Reverse Genetics by Promoting Reovirus Protein Expression, Virion Assembly, and RNA Incorporation into Infectious Virions.

Review 3. A recap of RNA recapping.

4. RNA-binding proteins and heat-shock protein 90 are constituents of the cytoplasmic capping enzyme interactome.

Review 5. Regulation of mRNA capping in the cell cycle.

6. Analyzing (Re)Capping of mRNA Using Transcript Specific 5' End Sequencing.

7. Identifying transcription start sites and active enhancer elements using BruUV-seq.

8. Cap homeostasis is independent of poly(A) tail length.

Review 9. mRNA capping: biological functions and applications.

10. RNA guanine-7 methyltransferase catalyzes the methylation of cytoplasmically recapped RNAs.