A low-complexity region in human XRN1 directly recruits deadenylation and decapping factors in 5'-3' messenger RNA decay.

Chung-Te Chang,Lara Wohlbold,Dipankar Bhandari,Ramona Weber,Yevgen Levdansky,Ying Chen,Sowndarya Muthukumar,Catia Igreja,Elisa Izaurralde,Eugene Valkov

doi:10.1093/nar/gkz633

Chung-Te Chang, Lara Wohlbold + Show 8 more

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https://doi.org/10.1093/nar/gkz633

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Abstract

XRN1 is the major cytoplasmic exoribonuclease in eukaryotes, which degrades deadenylated and decapped mRNAs in the last step of the 5′–3′ mRNA decay pathway. Metazoan XRN1 interacts with decapping factors coupling the final stages of decay. Here, we reveal a direct interaction between XRN1 and the CCR4–NOT deadenylase complex mediated by a low-complexity region in XRN1, which we term the ‘C-terminal interacting region’ or CIR. The CIR represses reporter mRNA deadenylation in human cells when overexpressed and inhibits CCR4–NOT and isolated CAF1 deadenylase activity in vitro. Through complementation studies in an XRN1-null cell line, we dissect the specific contributions of XRN1 domains and regions toward decay of an mRNA reporter. We observe that XRN1 binding to the decapping activator EDC4 counteracts the dominant negative effect of CIR overexpression on decay. Another decapping activator PatL1 directly interacts with CIR and alleviates the CIR-mediated inhibition of CCR4–NOT activity in vitro. Ribosome profiling revealed that XRN1 loss impacts not only on mRNA levels but also on the translational efficiency of many cellular transcripts likely as a consequence of incomplete decay. Our findings reveal an additional layer of direct interactions in a tightly integrated network of factors mediating deadenylation, decapping and 5′–3′ exonucleolytic decay.

Highlights

The spatial and temporal control of gene expression is crucial for many biological processes such as embryonic development, cell proliferation and immune response
Expressed GFP-XRN1 immunoprecipitated all tested endogenous subunits of the CCR4– NOT including NOT1, NOT2, NOT3 and CAF1 in the presence of RNase A suggesting that these interactions were not bridged by RNA (Figure 1A)
We show that human XRN1 interacts with the CCR4–NOT deadenylation complex as well as a decapping factor PatL1, extending the repertoire of XRN1 interactors beyond the previously reported association with the decapping factor EDC4

Summary

Introduction

The spatial and temporal control of gene expression is crucial for many biological processes such as embryonic development, cell proliferation and immune response. One means to regulate gene expression is via control of mRNA levels through targeted mRNA decay. Cytoplasmic mRNA decay is usually initiated by shortening of the poly(A) tail, a process termed deadenylation [1,2,3,4], which is mediated by PAN2/PAN3 and CCR4–NOT deadenylase complexes [5,6,7]. The CCR4–NOT is conserved in all eukaryotes and is principally responsible for the poly(A) tail shortening of the bulk transcriptome [4,8]. The CCR4–NOT is recruited to transcripts by RNA-binding factors such as tristetraprolin (TTP), Nanos or Roquin, which bind specific sequences in the 3 UTR of target mRNAs [10,11,12,13,14,15,16,17,18]

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