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DOI	10.1073/pnas.2106388118
	Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli
	Skalenko K.S.; Li L.; Zhang Y.; Vvedenskaya I.O.; Winkelman J.T.; Cope A.L.; Taylor D.M.; Shah P.; Ebright R.H.; Kinney J.B.; Zhang Y.; Nickels B.E.
发表日期	2021
ISSN	0027-8424
卷号	118 期号:27
英文摘要	Chemical modifications of RNA 5′-ends enable “epitranscriptomic” regulation, influencing multiple aspects of RNA fate. In transcription initiation, a large inventory of substrates compete with nucleoside triphosphates for use as initiating entities, providing an ab initio mechanism for altering the RNA 5′-end. In Escherichia coli cells, RNAs with a 5′-end hydroxyl are generated by use of dinucleotide RNAs as primers for transcription initiation, “primer-dependent initiation.” Here, we use massively systematic transcript end readout (MASTER) to detect and quantify RNA 5′-ends generated by primer-dependent initiation for ∼410 (∼1,000,000) promoter sequences in E. coli. The results show primer-dependent initiation in E. coli involves any of the 16 possible dinucleotide primers and depends on promoter sequences in, upstream, and downstream of the primer binding site. The results yield a consensus sequence for primer-dependent initiation, YTSS−2NTSS−1NTSSWTSS+1, where TSS is the transcription start site, NTSS−1NTSS is the primer binding site, Y is pyrimidine, and W is A or T. Biochemical and structure-determination studies show that the base pair (nontemplate-strand base:template-strand base) immediately upstream of the primer binding site (Y:RTSS−2, where R is purine) exerts its effect through the base on the DNA template strand (RTSS−2) through interchain base stacking with the RNA primer. Results from analysis of a large set of natural, chromosomally encoded E. coli promoters support the conclusions from MASTER. Our findings provide a mechanistic and structural description of how TSS-region sequence hard-codes not only the TSS position but also the potential for epitranscriptomic regulation through primer-dependent transcription initiation. © 2021 National Academy of Sciences. All rights reserved.
英文关键词	NanoRNA; Primer; Promoter; RNA modification; RNA polymerase
语种	英语
scopus关键词	complementary DNA; dinucleotide; nucleoside triphosphate; oligonucleotide; primer DNA; primer RNA; RNA polymerase; messenger RNA; primer DNA; affinity chromatography; anion exchange chromatography; Article; cell growth; chromosomal localization; complementarity determining region; Escherichia coli; gene amplification; gene sequence; high throughput sequencing; in vitro study; in vivo study; ligation; nonhuman; plasmid; polymerase chain reaction; promoter region; RNA isolation; site directed mutagenesis; Thermus thermophilus; transcription initiation; bacterial chromosome; binding site; Escherichia coli; gene expression regulation; genetics; metabolism; nucleotide sequence; transcription initiation site; Base Sequence; Binding Sites; Chromosomes, Bacterial; DNA Primers; Escherichia coli; Gene Expression Regulation, Bacterial; Promoter Regions, Genetic; RNA, Messenger; Transcription Initiation Site; Transcription Initiation, Genetic
来源期刊	Proceedings of the National Academy of Sciences of the United States of America
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/251136
作者单位	Department of Genetics, Rutgers University, Piscataway, NJ 08854, United States; Waksman Institute, Rutgers University, Piscataway, NJ 08854, United States; Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China; Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19041, United States; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States; Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, United States; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, United States
推荐引用方式 GB/T 7714	Skalenko K.S.,Li L.,Zhang Y.,et al. Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli[J],2021,118(27).
APA	Skalenko K.S..,Li L..,Zhang Y..,Vvedenskaya I.O..,Winkelman J.T..,...&Nickels B.E..(2021).Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli.Proceedings of the National Academy of Sciences of the United States of America,118(27).
MLA	Skalenko K.S.,et al."Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli".Proceedings of the National Academy of Sciences of the United States of America 118.27(2021).