Pre-mRNA processing factors differentially impact coordination between co-transcriptional cleavage and transcription termination
Abstract Co-transcriptional cleavage and transcription termination are closely related processes during mRNA maturation, yet their coordination remains poorly understood due to difficulties in detecting these transient events. Here, we applied single-molecule nascent RNA sequencing to simultaneously...
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Nature Portfolio
2025-08-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-62555-7 |
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| author | Xianhao Jin Juzuo Li Wenqin Lu Xian Deng Yanping Wei Yi Shu Bo Liu Zhijian Liu Yanping Long Xinlong Zhu Qili Fei Yiji Xia Qingshun Q. Li Scott D. Michaels Xiaofeng Cao Michael Lenhard Jixian Zhai |
| author_facet | Xianhao Jin Juzuo Li Wenqin Lu Xian Deng Yanping Wei Yi Shu Bo Liu Zhijian Liu Yanping Long Xinlong Zhu Qili Fei Yiji Xia Qingshun Q. Li Scott D. Michaels Xiaofeng Cao Michael Lenhard Jixian Zhai |
| author_sort | Xianhao Jin |
| collection | DOAJ |
| description | Abstract Co-transcriptional cleavage and transcription termination are closely related processes during mRNA maturation, yet their coordination remains poorly understood due to difficulties in detecting these transient events. Here, we applied single-molecule nascent RNA sequencing to simultaneously capture the cleavage status and readthrough distance on the same nascent RNA molecules and characterize 14 mutants of various pre-mRNA processing factors in Arabidopsis. Our results reveal diverse roles for these processing factors in coordinating cleavage and termination: core components of CPSF and CstF complex stimulate both cleavage and termination, facilitating access to exoribonuclease AtXRN3; mutations in nuclear poly(A) polymerase PAPS1 and AtXRN3 caused delayed termination with minimal effects on cleavage, suggesting their roles are further downstream; BORDER proteins facilitate termination while simultaneously inhibiting cleavage, suggesting a complex interplay between these two actions; the phosphatase SSU72 specifically promotes efficient termination without affecting cleavage. Our method also enables us to distinguish cleaved readthrough transcripts from full-length readthrough, and we found termination factor FPA specifically promotes termination of cleaved readthrough, suggesting FPA facilitates access of AtXRN3 to the 3’ cleavage product. Our comprehensive datasets reveal cleavage and termination are highly coordinated during pre-mRNA processing. |
| format | Article |
| id | doaj-art-45e73ea75a384294b977773f71791a8a |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-45e73ea75a384294b977773f71791a8a2025-08-20T04:03:00ZengNature PortfolioNature Communications2041-17232025-08-0116111310.1038/s41467-025-62555-7Pre-mRNA processing factors differentially impact coordination between co-transcriptional cleavage and transcription terminationXianhao Jin0Juzuo Li1Wenqin Lu2Xian Deng3Yanping Wei4Yi Shu5Bo Liu6Zhijian Liu7Yanping Long8Xinlong Zhu9Qili Fei10Yiji Xia11Qingshun Q. Li12Scott D. Michaels13Xiaofeng Cao14Michael Lenhard15Jixian Zhai16Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and TechnologyShenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and TechnologyShenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and TechnologyState Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and TechnologyShenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and TechnologyKey Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal UniversityShenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and TechnologyShenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and TechnologyAgricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesDepartment of Biology, Hong Kong Baptist UniversityBiomedical Sciences, College of Dental Medicine, Western University of Health SciencesDepartment of Biology, Indiana UniversityState Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesInstitute of Biochemistry and Biology, University of PotsdamShenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and TechnologyAbstract Co-transcriptional cleavage and transcription termination are closely related processes during mRNA maturation, yet their coordination remains poorly understood due to difficulties in detecting these transient events. Here, we applied single-molecule nascent RNA sequencing to simultaneously capture the cleavage status and readthrough distance on the same nascent RNA molecules and characterize 14 mutants of various pre-mRNA processing factors in Arabidopsis. Our results reveal diverse roles for these processing factors in coordinating cleavage and termination: core components of CPSF and CstF complex stimulate both cleavage and termination, facilitating access to exoribonuclease AtXRN3; mutations in nuclear poly(A) polymerase PAPS1 and AtXRN3 caused delayed termination with minimal effects on cleavage, suggesting their roles are further downstream; BORDER proteins facilitate termination while simultaneously inhibiting cleavage, suggesting a complex interplay between these two actions; the phosphatase SSU72 specifically promotes efficient termination without affecting cleavage. Our method also enables us to distinguish cleaved readthrough transcripts from full-length readthrough, and we found termination factor FPA specifically promotes termination of cleaved readthrough, suggesting FPA facilitates access of AtXRN3 to the 3’ cleavage product. Our comprehensive datasets reveal cleavage and termination are highly coordinated during pre-mRNA processing.https://doi.org/10.1038/s41467-025-62555-7 |
| spellingShingle | Xianhao Jin Juzuo Li Wenqin Lu Xian Deng Yanping Wei Yi Shu Bo Liu Zhijian Liu Yanping Long Xinlong Zhu Qili Fei Yiji Xia Qingshun Q. Li Scott D. Michaels Xiaofeng Cao Michael Lenhard Jixian Zhai Pre-mRNA processing factors differentially impact coordination between co-transcriptional cleavage and transcription termination Nature Communications |
| title | Pre-mRNA processing factors differentially impact coordination between co-transcriptional cleavage and transcription termination |
| title_full | Pre-mRNA processing factors differentially impact coordination between co-transcriptional cleavage and transcription termination |
| title_fullStr | Pre-mRNA processing factors differentially impact coordination between co-transcriptional cleavage and transcription termination |
| title_full_unstemmed | Pre-mRNA processing factors differentially impact coordination between co-transcriptional cleavage and transcription termination |
| title_short | Pre-mRNA processing factors differentially impact coordination between co-transcriptional cleavage and transcription termination |
| title_sort | pre mrna processing factors differentially impact coordination between co transcriptional cleavage and transcription termination |
| url | https://doi.org/10.1038/s41467-025-62555-7 |
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