Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing

Abstract Background The dynamic process of transcription termination produces transient RNA intermediates that are difficult to distinguish from each other via short-read sequencing methods. Results Here, we use single-molecule nascent RNA sequencing to characterize the various forms of transient RN...

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Autores principales:	Weipeng Mo, Bo Liu, Hong Zhang, Xianhao Jin, Dongdong Lu, Yiming Yu, Yuelin Liu, Jinbu Jia, Yanping Long, Xian Deng, Xiaofeng Cao, Hongwei Guo, Jixian Zhai
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Transcription termination Nascent RNA Nanopore sequencing Arabidopsis Biology (General) QH301-705.5 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/81b9f74ccc1949c2a14114ff7a68c238
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spelling	oai:doaj.org-article:81b9f74ccc1949c2a14114ff7a68c2382021-11-28T12:40:52ZLandscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing10.1186/s13059-021-02543-41474-760Xhttps://doaj.org/article/81b9f74ccc1949c2a14114ff7a68c2382021-11-01T00:00:00Zhttps://doi.org/10.1186/s13059-021-02543-4https://doaj.org/toc/1474-760XAbstract Background The dynamic process of transcription termination produces transient RNA intermediates that are difficult to distinguish from each other via short-read sequencing methods. Results Here, we use single-molecule nascent RNA sequencing to characterize the various forms of transient RNAs during termination at genome-wide scale in wildtype Arabidopsis and in atxrn3, fpa, and met1 mutants. Our data reveal a wide range of termination windows among genes, ranging from ~ 50 nt to over 1000 nt. We also observe efficient termination before downstream tRNA genes, suggesting that chromatin structure around the promoter region of tRNA genes may block pol II elongation. 5′ Cleaved readthrough transcription in atxrn3 with delayed termination can run into downstream genes to produce normally spliced and polyadenylated mRNAs in the absence of their own transcription initiation. Consistent with previous reports, we also observe long chimeric transcripts with cryptic splicing in fpa mutant; but loss of CG DNA methylation has no obvious impact on termination in the met1 mutant. Conclusions Our method is applicable to establish a comprehensive termination landscape in a broad range of species.Weipeng MoBo LiuHong ZhangXianhao JinDongdong LuYiming YuYuelin LiuJinbu JiaYanping LongXian DengXiaofeng CaoHongwei GuoJixian ZhaiBMCarticleTranscription terminationNascent RNANanopore sequencingArabidopsisBiology (General)QH301-705.5GeneticsQH426-470ENGenome Biology, Vol 22, Iss 1, Pp 1-21 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Transcription termination Nascent RNA Nanopore sequencing Arabidopsis Biology (General) QH301-705.5 Genetics QH426-470
spellingShingle	Transcription termination Nascent RNA Nanopore sequencing Arabidopsis Biology (General) QH301-705.5 Genetics QH426-470 Weipeng Mo Bo Liu Hong Zhang Xianhao Jin Dongdong Lu Yiming Yu Yuelin Liu Jinbu Jia Yanping Long Xian Deng Xiaofeng Cao Hongwei Guo Jixian Zhai Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing
description	Abstract Background The dynamic process of transcription termination produces transient RNA intermediates that are difficult to distinguish from each other via short-read sequencing methods. Results Here, we use single-molecule nascent RNA sequencing to characterize the various forms of transient RNAs during termination at genome-wide scale in wildtype Arabidopsis and in atxrn3, fpa, and met1 mutants. Our data reveal a wide range of termination windows among genes, ranging from ~ 50 nt to over 1000 nt. We also observe efficient termination before downstream tRNA genes, suggesting that chromatin structure around the promoter region of tRNA genes may block pol II elongation. 5′ Cleaved readthrough transcription in atxrn3 with delayed termination can run into downstream genes to produce normally spliced and polyadenylated mRNAs in the absence of their own transcription initiation. Consistent with previous reports, we also observe long chimeric transcripts with cryptic splicing in fpa mutant; but loss of CG DNA methylation has no obvious impact on termination in the met1 mutant. Conclusions Our method is applicable to establish a comprehensive termination landscape in a broad range of species.
format	article
author	Weipeng Mo Bo Liu Hong Zhang Xianhao Jin Dongdong Lu Yiming Yu Yuelin Liu Jinbu Jia Yanping Long Xian Deng Xiaofeng Cao Hongwei Guo Jixian Zhai
author_facet	Weipeng Mo Bo Liu Hong Zhang Xianhao Jin Dongdong Lu Yiming Yu Yuelin Liu Jinbu Jia Yanping Long Xian Deng Xiaofeng Cao Hongwei Guo Jixian Zhai
author_sort	Weipeng Mo
title	Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing
title_short	Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing
title_full	Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing
title_fullStr	Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing
title_full_unstemmed	Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing
title_sort	landscape of transcription termination in arabidopsis revealed by single-molecule nascent rna sequencing
publisher	BMC
publishDate	2021
url	https://doaj.org/article/81b9f74ccc1949c2a14114ff7a68c238
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Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing

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