Identification of putative reader proteins of 5-methylcytosine and its derivatives in Caenorhabditis elegans RNA

Isabela Cunha Navarro; Kin  Man Suen; Dalila Bensaddek; Arun Tanpure; Angus Lamond; Shankar Balasubramanian; Eric Alexander  Miska

doi:10.1101/2022.01.24.477592

Identification of putative reader proteins of 5-methylcytosine and its derivatives in Caenorhabditis elegans RNA

Isabela Cunha Navarro, Kin Man Suen, Dalila Bensaddek, Arun Tanpure, Angus Lamond, Shankar Balasubramanian, Eric Alexander Miska (Lead / Corresponding author)

Research output: Working paper/Preprint › Preprint

Abstract

Methylation of carbon-5 of cytosines (m5C) is a post-transcriptional nucleotide modification of RNA with widespread distribution across organisms. m5C has been shown to participate in mRNA transport and maintain mRNA stability through its recognition by the reader proteins ALYREF and YBX1, respectively. We recently showed that m5C is required for Caenorhabditis elegans development and fertility under heat stress. To contribute to the understanding of how m5C and its oxidative derivatives mediate their functions, we developed RNA baits bearing modified cytosines in diverse structural contexts to pulldown potential readers in C. elegans. Our mass spectrometry analyses reveal unique binding proteins for each of the modifications. We validate our dataset by demonstrating that the nematode ALYREF homologues ALY-1 and ALY-2 preferentially bind m5C in vitro. The dataset presented here serves as an important scientific resource that will support the discovery of new functions of m5C and its derivatives.

Original language	English
Publisher	BioRxiv
Pages	1-23
Number of pages	23
DOIs	https://doi.org/10.1101/2022.01.24.477592
Publication status	Submitted - 25 Jan 2022

Keywords

RNA
5-methylcytosine
Caenorhabditis elegans
epitranscriptomics
readers

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10.1101/2022.01.24.477592Licence: CC BY-NC-ND

1 Article

Identification of putative reader proteins of 5-methylcytosine and its derivatives in Caenorhabditis elegans RNA [version 1; peer review: 1 approved, 2 approved with reservations]
Navarro, I. C., Suen, K. M., Bensaddek, D., Tanpure, A., Lamond, A., Balasubramanian, S. & Miska, E. A., 17 Nov 2022, In: Wellcome Open Research. 7, 19 p., 282.
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title = "Identification of putative reader proteins of 5-methylcytosine and its derivatives in Caenorhabditis elegans RNA",

abstract = "Methylation of carbon-5 of cytosines (m5C) is a post-transcriptional nucleotide modification of RNA with widespread distribution across organisms. m5C has been shown to participate in mRNA transport and maintain mRNA stability through its recognition by the reader proteins ALYREF and YBX1, respectively. We recently showed that m5C is required for Caenorhabditis elegans development and fertility under heat stress. To contribute to the understanding of how m5C and its oxidative derivatives mediate their functions, we developed RNA baits bearing modified cytosines in diverse structural contexts to pulldown potential readers in C. elegans. Our mass spectrometry analyses reveal unique binding proteins for each of the modifications. We validate our dataset by demonstrating that the nematode ALYREF homologues ALY-1 and ALY-2 preferentially bind m5C in vitro. The dataset presented here serves as an important scientific resource that will support the discovery of new functions of m5C and its derivatives.",

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AU - Tanpure, Arun

AU - Lamond, Angus

AU - Balasubramanian, Shankar

AU - Miska, Eric Alexander

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AB - Methylation of carbon-5 of cytosines (m5C) is a post-transcriptional nucleotide modification of RNA with widespread distribution across organisms. m5C has been shown to participate in mRNA transport and maintain mRNA stability through its recognition by the reader proteins ALYREF and YBX1, respectively. We recently showed that m5C is required for Caenorhabditis elegans development and fertility under heat stress. To contribute to the understanding of how m5C and its oxidative derivatives mediate their functions, we developed RNA baits bearing modified cytosines in diverse structural contexts to pulldown potential readers in C. elegans. Our mass spectrometry analyses reveal unique binding proteins for each of the modifications. We validate our dataset by demonstrating that the nematode ALYREF homologues ALY-1 and ALY-2 preferentially bind m5C in vitro. The dataset presented here serves as an important scientific resource that will support the discovery of new functions of m5C and its derivatives.

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KW - 5-methylcytosine

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KW - epitranscriptomics

KW - readers

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BT - Identification of putative reader proteins of 5-methylcytosine and its derivatives in Caenorhabditis elegans RNA

PB - BioRxiv

ER -

Identification of putative reader proteins of 5-methylcytosine and its derivatives in Caenorhabditis elegans RNA

Abstract

Keywords

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Research output

Identification of putative reader proteins of 5-methylcytosine and its derivatives in Caenorhabditis elegans RNA [version 1; peer review: 1 approved, 2 approved with reservations]

Cite this