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Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria

ABSTRACT: Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria

PROVIDER: PRJNA483041 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7609040_1.fastq.gz	Fastqsanger.gz
	SRR7609040_2.fastq.gz	Fastqsanger.gz
	SRR7609050_1.fastq.gz	Fastqsanger.gz
	SRR7609050_2.fastq.gz	Fastqsanger.gz
	SRR7609041_1.fastq.gz	Fastqsanger.gz

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Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria

Project description:The complexity and intricacy of prokaryotic transcriptomes—once deemed well understood and simple—are increasingly being discovered and appreciated. The ability to determine full-length sequences of all transcripts in the cell is essential for understanding the gene regulatory repertoire of a species. Standard RNA-seq requires fragmentation of RNA for short-read sequencing, which automatically decouples the 5' sequence of a RNA molecule from its 3' sequence. Intramolecular ligation of 5' and 3' ends represents a potential strategy for simultaneously capturing the sequences of both termini. However, counterintuitively, it is more challenging to circularize prokaryotic transcripts than eukaryotic ones due to a lack of poly(A) tails. Consequently, a method capable of comprehensively profiling full-length transcripts in prokaryotes is still urgently needed. In this work, we developed a workflow, termed SEnd-seq, that simultaneously reads both ends of all bacterial RNAs—including small non-coding RNAs—with single-nucleotide resolution. This method enabled us for the first time to determine the correlated occurrence of transcription start sites (TSS) and termination sites (TTS) across the whole transcriptome, and achieve an unprecedented map of its operon architecture. Using E. coli as a model system, we identified thousands of new TSS and TTS, many of which were found to be condition dependent. These results significantly expand our knowledge of the regulatory elements existing in the E. coli genome and improve our understanding of many aspects of bacterial RNA metabolism.

2019-05-19 | GSE117737 | GEO

Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria.

Project description:The ability to determine full-length nucleotide composition of individual RNA molecules is essential for understanding the architecture and function of a transcriptome. However, experimental approaches capable of capturing the sequences of both 5' and 3' termini of the same transcript remain scarce. In the present study, simultaneous 5' and 3' end sequencing (SEnd-seq)-a high-throughput and unbiased method that simultaneously maps transcription start and termination sites with single-nucleotide resolution-is presented. Using this method, a comprehensive view of the Escherichia coli transcriptome was obtained, which displays an unexpected level of complexity. SEnd-seq notably expands the catalogue of transcription start sites and termination sites, defines unique transcription units and detects prevalent antisense RNA. Strikingly, the results of the present study unveil widespread overlapping bidirectional terminators located between opposing gene pairs. Furthermore, it has been shown that convergent transcription is a major contributor to highly efficient bidirectional termination both in vitro and in vivo. This finding highlights an underappreciated role of RNA polymerase conflicts in shaping transcript boundaries and suggests an evolutionary strategy for modulating transcriptional output by arranging gene orientation.

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