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CapZyme-Seq Comprehensively Defines Promoter-Sequence Determinants for RNA 5' Capping with NAD

IO. Vvedenskaya, JG. Bird, Y. Zhang, Y. Zhang, X. Jiao, I. Barvík, L. Krásný, M. Kiledjian, DM. Taylor, RH. Ebright, BE. Nickels,

. 2018 ; 70 (3) : 553-564.e9. [pub] 20180419

Jazyk angličtina Země Spojené státy americké

Typ dokumentu časopisecké články, Research Support, N.I.H., Extramural, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/bmc19012709
E-zdroje Online Plný text

NLK Cell Press Free Archives od 1997-12-01 do Před 1 rokem
Free Medical Journals od 1997 do Před 1 rokem
Free Medical Journals od 1997 do Před 1 rokem
Open Access Digital Library od 1997-12-01
Elsevier Open Access Journals od 1997-12-01 do 2023-06-15
Elsevier Open Archive Journals od 1997-12-01 do Před 1 rokem

Odkazy

PubMed 29681497
DOI 10.1016/j.molcel.2018.03.014
Knihovny.cz E-zdroje

Nucleoside-containing metabolites such as NAD+ can be incorporated as 5' caps on RNA by serving as non-canonical initiating nucleotides (NCINs) for transcription initiation by RNA polymerase (RNAP). Here, we report CapZyme-seq, a high-throughput-sequencing method that employs NCIN-decapping enzymes NudC and Rai1 to detect and quantify NCIN-capped RNA. By combining CapZyme-seq with multiplexed transcriptomics, we determine efficiencies of NAD+ capping by Escherichia coli RNAP for ∼16,000 promoter sequences. The results define preferred transcription start site (TSS) positions for NAD+ capping and define a consensus promoter sequence for NAD+ capping: HRRASWW (TSS underlined). By applying CapZyme-seq to E. coli total cellular RNA, we establish that sequence determinants for NCIN capping in vivo match the NAD+-capping consensus defined in vitro, and we identify and quantify NCIN-capped small RNAs (sRNAs). Our findings define the promoter-sequence determinants for NCIN capping with NAD+ and provide a general method for analysis of NCIN capping in vitro and in vivo.

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