Literature DB >> 19802594

Analysis of miRNA Modifications.

Bin Yu1, Xuemei Chen.   

Abstract

After transcription, a large number of cellular RNAs employ modifications to increase their diversity and functional potential. Modifications can occur on the base, ribose, or both, and are important steps in the maturation of many RNAs. Our lab recently showed that plant microRNAs (miRNAs) possess a 2'-O-methyl group on the ribose of the 3' terminal nucleotide, and that this methyl group is added after miRNA/miRNA* formation. One function of this modification is to protect miRNAs from 3' terminal uridylation by an unknown enzymatic activity. It is possible that uridylation of miRNAs triggers their degradation. Here we describe a protocol to purify a specific miRNA in order to determine its molecular mass so that the presence of a modification can be inferred, an in vivo method to detect 3' terminal modification of miRNAs, and an (alpha-32P) dATP incorporation assay to study 3' terminal uridylation of miRNAs.

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Year:  2010        PMID: 19802594      PMCID: PMC5134323          DOI: 10.1007/978-1-60327-005-2_10

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  18 in total

1.  MicroRNAs in plants.

Authors:  Brenda J Reinhart; Earl G Weinstein; Matthew W Rhoades; Bonnie Bartel; David P Bartel
Journal:  Genes Dev       Date:  2002-07-01       Impact factor: 11.361

2.  Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing.

Authors:  A Grishok; A E Pasquinelli; D Conte; N Li; S Parrish; I Ha; D L Baillie; A Fire; G Ruvkun; C C Mello
Journal:  Cell       Date:  2001-07-13       Impact factor: 41.582

3.  SERRATE is a novel nuclear regulator in primary microRNA processing in Arabidopsis.

Authors:  Li Yang; Ziqiang Liu; Feng Lu; Aiwu Dong; Hai Huang
Journal:  Plant J       Date:  2006-08-02       Impact factor: 6.417

4.  Human let-7 stem-loop precursors harbor features of RNase III cleavage products.

Authors:  Eugenia Basyuk; Florence Suavet; Alain Doglio; Rémy Bordonné; Edouard Bertrand
Journal:  Nucleic Acids Res       Date:  2003-11-15       Impact factor: 16.971

5.  Incorporation of terminal phosphorothioates into oligonucleotides.

Authors:  S Alefelder; B K Patel; F Eckstein
Journal:  Nucleic Acids Res       Date:  1998-11-01       Impact factor: 16.971

6.  Identification of nuclear dicing bodies containing proteins for microRNA biogenesis in living Arabidopsis plants.

Authors:  Yuda Fang; David L Spector
Journal:  Curr Biol       Date:  2007-04-19       Impact factor: 10.834

7.  HEN1 functions pleiotropically in Arabidopsis development and acts in C function in the flower.

Authors:  Xuemei Chen; Jun Liu; Yulan Cheng; Dongxuan Jia
Journal:  Development       Date:  2002-03       Impact factor: 6.868

8.  Methylation protects miRNAs and siRNAs from a 3'-end uridylation activity in Arabidopsis.

Authors:  Junjie Li; Zhiyong Yang; Bin Yu; Jun Liu; Xuemei Chen
Journal:  Curr Biol       Date:  2005-08-23       Impact factor: 10.834

9.  Methylation as a crucial step in plant microRNA biogenesis.

Authors:  Bin Yu; Zhiyong Yang; Junjie Li; Svetlana Minakhina; Maocheng Yang; Richard W Padgett; Ruth Steward; Xuemei Chen
Journal:  Science       Date:  2005-02-11       Impact factor: 47.728

10.  Arabidopsis HEN1: a genetic link between endogenous miRNA controlling development and siRNA controlling transgene silencing and virus resistance.

Authors:  Stéphanie Boutet; Franck Vazquez; Jun Liu; Christophe Béclin; Mathilde Fagard; Ariane Gratias; Jean Benoit Morel; Patrice Crété; Xuemei Chen; Hervé Vaucheret
Journal:  Curr Biol       Date:  2003-05-13       Impact factor: 10.834

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  11 in total

1.  Intact microRNA analysis using high resolution mass spectrometry.

Authors:  Majlinda Kullolli; Emily Knouf; Maria Arampatzidou; Muneesh Tewari; Sharon J Pitteri
Journal:  J Am Soc Mass Spectrom       Date:  2013-10-31       Impact factor: 3.109

Review 2.  Novel RNA modifications in the nervous system: form and function.

Authors:  John S Satterlee; Maria Basanta-Sanchez; Sandra Blanco; Jin Billy Li; Kate Meyer; Jonathan Pollock; Ghazaleh Sadri-Vakili; Agnieszka Rybak-Wolf
Journal:  J Neurosci       Date:  2014-11-12       Impact factor: 6.167

Review 3.  Functions of Kaposi's sarcoma-associated herpesvirus microRNAs.

Authors:  Joseph M Ziegelbauer
Journal:  Biochim Biophys Acta       Date:  2011-05-18

4.  A TRIzol-based method for high recovery of plasma sncRNAs approximately 30 to 60 nucleotides.

Authors:  Kristen P Rodgers; Alicia Hulbert; Hamza Khan; Maria Shishikura; Shun Ishiyama; Malcolm V Brock; Yuping Mei
Journal:  Sci Rep       Date:  2022-04-26       Impact factor: 4.996

5.  PIWI associated siRNAs and piRNAs specifically require the Caenorhabditis elegans HEN1 ortholog henn-1.

Authors:  Taiowa A Montgomery; Young-Soo Rim; Chi Zhang; Robert H Dowen; Carolyn M Phillips; Sylvia E J Fischer; Gary Ruvkun
Journal:  PLoS Genet       Date:  2012-04-19       Impact factor: 5.917

6.  Chimira: analysis of small RNA sequencing data and microRNA modifications.

Authors:  Dimitrios M Vitsios; Anton J Enright
Journal:  Bioinformatics       Date:  2015-06-20       Impact factor: 6.937

7.  An improved method to quantitate mature plant microRNA in biological matrices using modified periodate treatment and inclusion of internal controls.

Authors:  Haiqiu Huang; Jamin Roh; Cindy D Davis; Thomas T Y Wang
Journal:  PLoS One       Date:  2017-04-11       Impact factor: 3.240

8.  A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry.

Authors:  Samuel Wein; Byron Andrews; Timo Sachsenberg; Helena Santos-Rosa; Oliver Kohlbacher; Tony Kouzarides; Benjamin A Garcia; Hendrik Weisser
Journal:  Nat Commun       Date:  2020-02-17       Impact factor: 14.919

9.  henn-1/HEN1 Promotes Germline Immortality in Caenorhabditis elegans.

Authors:  Joshua M Svendsen; Kailee J Reed; Tarah Vijayasarathy; Brooke E Montgomery; Rachel M Tucci; Kristen C Brown; Taylor N Marks; Dieu An H Nguyen; Carolyn M Phillips; Taiowa A Montgomery
Journal:  Cell Rep       Date:  2019-12-03       Impact factor: 9.423

Review 10.  RNA Modification and Its Implication in Plant Pathogenic Fungi.

Authors:  Junhyun Jeon; Song Hee Lee
Journal:  Plant Pathol J       Date:  2021-12-01       Impact factor: 1.795

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