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Arabidopsis mRNA decay landscape shaped by XRN 5'-3' exoribonucleases.
Han, Wan-Yin; Hou, Bo-Han; Lee, Wen-Chi; Chan, Tze-Ching; Lin, Tzu-Hsiang; Chen, Ho-Ming.
Afiliación
  • Han WY; Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan.
  • Hou BH; Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University, Taichung 40227, Taiwan, and Academia Sinica, Taipei, 11529, Taiwan.
  • Lee WC; Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, 40227, Taiwan.
  • Chan TC; Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan.
  • Lin TH; Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan.
  • Chen HM; Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan.
Plant J ; 114(4): 895-913, 2023 05.
Article en En | MEDLINE | ID: mdl-36987558
5'-3' 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' end cleavage frequently occurs after adenosine. The most abundant decay intermediates in wild-type 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' ends upstream of a consensus motif in the xrn4 mutant suggests that there is an endonucleolytic cleavage mechanism targeting the 3' 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.
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Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Arabidopsis / Proteínas de Arabidopsis Idioma: En Revista: Plant J Asunto de la revista: BIOLOGIA MOLECULAR / BOTANICA Año: 2023 Tipo del documento: Article País de afiliación: Taiwán

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Arabidopsis / Proteínas de Arabidopsis Idioma: En Revista: Plant J Asunto de la revista: BIOLOGIA MOLECULAR / BOTANICA Año: 2023 Tipo del documento: Article País de afiliación: Taiwán