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Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation | Nature Structural & Molecular Biology
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RNA 3′-end formation is thought to be crucial in controlling gene expression. Direct RNA sequencing was used to analyze the 3′ ends of Arabidopsis thaliana RNA in unprecedented detail, revealing extreme heterogeneity of RNA 3′ ends, patterns of cleavage and polyadenylation, and previously unrecognized noncoding RNAs. It has recently been shown that RNA 3′-end formation plays a more widespread role in controlling gene expression than previously thought. To examine the impact of regulated 3′-end formation genome-wide, we applied direct RNA sequencing to A. thaliana. Here we show the authentic transcriptome in unprecedented detail and describe the effects of 3′-end formation on genome organization. We reveal extreme heterogeneity in RNA 3′ ends, discover previously unrecognized noncoding RNAs and propose widespread reannotation of the genome. We explain the origin of most poly(A)+ antisense RNAs and identify cis elements that control 3′-end formation in different registers. These findings are essential to understanding what the genome actually encodes, how it is organized and how regulated 3′-end formation affects these processes.
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headline:Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation
description:RNA 3â²-end formation is thought to be crucial in controlling gene expression. Direct RNA sequencing was used to analyze the 3â² ends of Arabidopsis thaliana RNA in unprecedented detail, revealing extreme heterogeneity of RNA 3â² ends, patterns of cleavage and polyadenylation, and previously unrecognized noncoding RNAs. It has recently been shown that RNA 3â²-end formation plays a more widespread role in controlling gene expression than previously thought. To examine the impact of regulated 3â²-end formation genome-wide, we applied direct RNA sequencing to A. thaliana. Here we show the authentic transcriptome in unprecedented detail and describe the effects of 3â²-end formation on genome organization. We reveal extreme heterogeneity in RNA 3â² ends, discover previously unrecognized noncoding RNAs and propose widespread reannotation of the genome. We explain the origin of most poly(A)+ antisense RNAs and identify cis elements that control 3â²-end formation in different registers. These findings are essential to understanding what the genome actually encodes, how it is organized and how regulated 3â²-end formation affects these processes.
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Protein Structure
Membrane Biology
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headline:Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation
description:RNA 3â²-end formation is thought to be crucial in controlling gene expression. Direct RNA sequencing was used to analyze the 3â² ends of Arabidopsis thaliana RNA in unprecedented detail, revealing extreme heterogeneity of RNA 3â² ends, patterns of cleavage and polyadenylation, and previously unrecognized noncoding RNAs. It has recently been shown that RNA 3â²-end formation plays a more widespread role in controlling gene expression than previously thought. To examine the impact of regulated 3â²-end formation genome-wide, we applied direct RNA sequencing to A. thaliana. Here we show the authentic transcriptome in unprecedented detail and describe the effects of 3â²-end formation on genome organization. We reveal extreme heterogeneity in RNA 3â² ends, discover previously unrecognized noncoding RNAs and propose widespread reannotation of the genome. We explain the origin of most poly(A)+ antisense RNAs and identify cis elements that control 3â²-end formation in different registers. These findings are essential to understanding what the genome actually encodes, how it is organized and how regulated 3â²-end formation affects these processes.
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