Arabidopsis mRNA decay landscape shaped by XRN 5′‐3′ exoribonucleases

Abstract

5 0 -3 0 exoribonucleases (XRNs) play crucial roles in the control of RNA processing, quality, and quantity in eukaryotes. Although genome-wide profiling of RNA decay fragments is now feasible, how XRNs shape the plant mRNA degradome remains elusive. Here, we profiled and analyzed the RNA degradomes of Arabidopsis wild-type and mutant plants with defects in XRN activity. Deficiency of nuclear XRN3 or cytoplasmic XRN4 activity but not nuclear XRN2 activity greatly altered Arabidopsis mRNA decay profiles. Short excised linear introns and cleaved pre-mRNA fragments downstream of polyadenylation sites were polyadenylated and stabilized in the xrn3 mutant, demonstrating the unique function of XRN3 in the removal of cleavage remnants from pre-mRNA processing. Further analysis of stabilized XRN3 substrates confirmed that pre-mRNA 3 0 end cleavage frequently occurs after adenosine. The most abundant decay intermediates in wildtype plants include not only the primary substrates of XRN4 but also the products of XRN4-mediated cytoplasmic decay. An increase in decay intermediates with 5 0 ends upstream of a consensus motif in the xrn4 mutant suggests that there is an endonucleolytic cleavage mechanism targeting the 3 0 untranslated regions of many Arabidopsis mRNAs. However, analysis of decay fragments in the xrn4 mutant indicated that, except for microRNA-directed slicing, endonucleolytic cleavage events in the coding sequence rarely result in major decay intermediates. Together, these findings reveal the major substrates and products of nuclear and cytoplasmic XRNs along Arabidopsis transcripts and provide a basis for precise interpretation of RNA degradome data.

Genome-wide analysis of mRNA decay in Arabidopsis shoot and root reveals the importance of co-translational mRNA decay in the general mRNA turnover

“…However, transcripts from other subgroups present also RNA decay feedback. We and others proposed that XRN4 is not the only exoribonuclease involved in CTRD ( 16 , 53 ). Interestingly, in fry1 mutant, 5′-3′ mRNA decay seems more repressed than in xrn4 ( 53 ).…”

“…We and others proposed that XRN4 is not the only exoribonuclease involved in CTRD ( 16 , 53 ). Interestingly, in fry1 mutant, 5′-3′ mRNA decay seems more repressed than in xrn4 ( 53 ). In fry1 mutant, a constitutive accumulation of 3′-phosphoadenpsione 5′-phosphate (PAP) is observed resulting in inhibition of XRN activity ( 54 ).…”

Comparison of Xrn1 and Rat1 5′ → 3′ exoribonucleases in budding yeast supports the specific role of Xrn1 in cotranslational mRNA decay

“…Rat1 performs important nuclear activities related to RNA metabolism, including rRNA and small nucleolar RNA processing, as well as poly-A +dependent and -independent mRNA transcription termination (Kim et al, 2004). The existence of both nuclear (Rat1/Xrn2 family) and cytoplasmic (Xrn1 family) 5′ → 3′ XRNs is common in a variety of studied eukaryotes (Chang et al, 2011;Han et al, 2023), and suggests that their functional interchangeability extends across species (reviewed in Nagarajan et al, 2013).…”

Comparison of Xrn1 and Rat1 5′→3′ exoribonucleases in budding yeast supports the unique role of Xrn1 in co-translational mRNA decay

“…Rat1 performs important nuclear activities related to RNA metabolism, including rRNA and snoRNA processing, as well as poly-A + dependent and independent mRNA transcription termination (Kim et al, 2004). The existence of both nuclear (Rat1/Xrn2 family) and cytoplasmic (Xrn1 family) 5'-3' exoribonucleases is common in a variety of studied eukaryotes (Chang et al, 2011;Han et al, 2023) and suggests that functional interchangeability extends across species (reviewed in Nagarajan et al, 2013).…”