生物
计算生物学
抄写(语言学)
核糖核酸
微生物群
遗传学
RNA聚合酶
RNA序列
转录组
基因
基因表达
哲学
语言学
作者
Albert C. Vill,Edward J. Rice,Iwijn De Vlaminck,Charles G. Danko,Ilana Brito
出处
期刊:Nature microbiology
日期:2024-01-03
卷期号:9 (1): 241-250
标识
DOI:10.1038/s41564-023-01558-w
摘要
Bacteria respond to environmental stimuli through precise regulation of transcription initiation and elongation. Bulk RNA sequencing primarily characterizes mature transcripts, so to identify actively transcribed loci we need to capture RNA polymerase (RNAP) complexed with nascent RNA. However, such capture methods have only previously been applied to culturable, genetically tractable organisms such as E. coli and B. subtilis. Here we apply precision run-on sequencing (PRO-seq) to profile nascent transcription in cultured E. coli and diverse uncultured bacteria. We demonstrate that PRO-seq can characterize the transcription of small, structured, or post-transcriptionally modified RNAs, which are often absent from bulk RNA-seq libraries. Applying PRO-seq to the human microbiome highlights taxon-specific RNAP pause motifs and pause-site distributions across non-coding RNA loci that reflect structure-coincident pausing. We also uncover concurrent transcription and cleavage of CRISPR guide RNAs and transfer RNAs. We demonstrate the utility of PRO-seq for exploring transcriptional dynamics in diverse microbial communities. PRO-seq, which does not need antibodies or epitope tags on RNAP, is adapted to report nascent transcription in bacteria including human gut microbiome samples.
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