Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli.

Skalenko, Kyle S, Li, Lingting, Zhang, Yuanchao, Vvedenskaya, Irina O, Winkelman, Jared T, Cope, Alexander L, Taylor, Deanne M, Shah, Premal, Ebright, Richard H, Kinney, Justin B, Zhang, Yu, Nickels, Bryce E (July 2021) Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli. Proceedings of the National Academy of Sciences of USA, 118 (27). e2106388118-e2106388118. ISSN 0027-8424

URL: https://www.ncbi.nlm.nih.gov/pubmed/34187896
DOI: 10.1073/pnas.2106388118

Abstract

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.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transcription
organism description > bacteria > escherichia coli
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA expression > primer
CSHL Authors:
Communities: CSHL labs > Kinney lab
SWORD Depositor: CSHL Elements
Depositing User: CSHL Elements
Date: 6 July 2021
Date Deposited: 01 Jul 2021 18:13
Last Modified: 19 Jul 2021 13:08
PMCID: PMC8271711
URI: https://repository.cshl.edu/id/eprint/40239

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