Journal Article

The Tudor SND1 protein is an m6A RNA reader essential for replication of Kaposi’s sarcoma-associated herpesvirus

Wilson, Stuart A, Whitehouse, Adrian, Baquero-Perez, Belinda, Carr, Ian M, Yonchev, Ivaylo D, Antanaviciute, Agne

2019

Overview

N6-methyladenosine (m6A) is the most abundant internal RNA modification of cellular mRNAs. m6A is recognised by YTH domain-containing proteins, which selectively bind to m6A-decorated RNAs regulating their turnover and translation. Using an m6A-modified hairpin present in the Kaposi’s sarcoma associated herpesvirus (KSHV) ORF50 RNA, we identified seven members from the ‘Royal family’ as putative m6A readers, including SND1. RIP-seq and eCLIP analysis characterised the SND1 binding profile transcriptome-wide, revealing SND1 as an m6A reader. We further demonstrate that the m6A modification of the ORF50 RNA is critical for SND1 binding, which in turn stabilises the ORF50 transcript. Importantly, SND1 depletion leads to inhibition of KSHV early gene expression showing that SND1 is essential for KSHV lytic replication. This work demonstrates that members of the ‘Royal family’ have m6A-reading ability, greatly increasing their epigenetic functions beyond protein methylation. When a cell needs to make a protein, it reads from the master copy of the gene in the DNA and prints out temporary duplicates called mRNA. These duplicates then act as templates for protein production. Both DNA and mRNA can be further modified by adding on chemical tags that recruit specific proteins. While chemical modifications in DNA are known to control the activity of genes, their role in mRNA is only just being uncovered. One of the most common chemical modifications in mRNA is the addition of a methyl group called m6A. This methyl group has also been found in the mRNA of certain viruses, including the Kaposi’s sarcoma-associated herpesvirus (KSHV) which causes cancer. Recent work has shown that a family of proteins, known as the YTH family, can recognise and bind to this specific methyl group and regulate the rate at which mRNA degrades. To investigate whether other proteins can recognise m6A, Baquero-Pérez et al. mapped the m6A residues of mRNAs encoded by KSHV genes and looked at which proteins the methyl mark interacts with. The experiments revealed that a family of proteins – nicknamed the ‘Royal family’ – that recognise methyl groups in proteins, can also bind to mRNA that contains m6A. Baquero-Pérez et al. showed that a member of this family, SND1, can read the m6A methyl mark on mRNAs from both the virus and the host cell. Further experiments showed that SND1 binds to and stabilises a viral mRNA which provides the template for a protein that the virus needs to replicate. When SND1 was removed from human immune cells infected with KSHV, this caused the virus to replicate less efficiently. The discovery that the Royal family of proteins can recognise methylated mRNA as well as methylated proteins suggests that there may be a common feature that allows proteins to read methylation. Understanding the shape of this feature could lead to new treatments that block viruses from making the proteins they need to replicate.

• Publisher: eLife Sciences Publications Ltd,eLife Sciences Publications, Ltd
• Subject: Deoxyribonucleic acid / DNA / DNA methylation / Gene expression / Kaposis sarcoma / m6A / Microbiology and Infectious Disease / Molecular biology / N6-methyladenosine / Proteins / Replication / RNA modification / Sarcoma / Transcription / virus infection