scholarly journals SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA

2018 ◽  
Vol 28 (12) ◽  
pp. 1943-1956 ◽  
Author(s):  
Nevena Cvetesic ◽  
Harry G. Leitch ◽  
Malgorzata Borkowska ◽  
Ferenc Müller ◽  
Piero Carninci ◽  
...  
Keyword(s):  
High Resolution ◽  
Transcription Start Site ◽  
Start Site ◽  
Transcription Start ◽  
Total Rna ◽  
Site Mapping

scholarly journals MAPCap: A fast and quantitative transcription start site profiling protocol

2019 ◽  
Author(s):  
Vivek Bhardwaj ◽  
Giuseppe Semplicio ◽  
Niyazi Umut Erdogdu ◽  
Asifa Akhtar
Keyword(s):  
High Resolution ◽  
Differential Expression ◽  
Transcription Start Site ◽  
Expression Analysis ◽  
Differential Expression Analysis ◽  
Start Site ◽  
Transcription Start ◽  
Transcription Start Sites

Abstract Below we present a simple and quick TSS quantification protocol, MAPCap (Multiplexed Affinity Purification of Capped RNA) that enables users to combine high-resolution detection of transcription start-sites and differential expression analysis. MAPCap can be used to profile TSS from dozens of samples in a multiplexed way, in 16-18 hours. MAPCap data can be analyzed using our easy-to-use software icetea (https://bioconductor.org/packages/icetea), which allows users to detect robust TSS using replicates, and perform differential TSS analysis.

scholarly journals Application of a Schizosaccharomyces pombe Edc1-fused Dcp1–Dcp2 decapping enzyme for transcription start site mapping

RNA ◽  
2017 ◽  
Vol 24 (2) ◽  
pp. 251-257 ◽  
Author(s):  
David R. Paquette ◽  
Jeffrey S. Mugridge ◽  
David E. Weinberg ◽  
John D. Gross
Keyword(s):  
Schizosaccharomyces Pombe ◽  
Transcription Start Site ◽  
Start Site ◽  
Transcription Start ◽  
Site Mapping ◽  
Decapping Enzyme

Transcription Start-Site Mapping

2003 ◽  
pp. 105-124 ◽  
Author(s):  
Farahnaz Movahedzadeh ◽  
Jorge A. Gonzalez-Y-Merchand ◽  
Robert A Cox
Keyword(s):  
Transcription Start Site ◽  
Start Site ◽  
Transcription Start ◽  
Site Mapping

The Role of XPB/Ssl2 dsDNA Translocase Processivity in Transcription Start-site Scanning

2021 ◽  
pp. 166813
Author(s):  
Eric J. Tomko ◽  
Olivia Luyties ◽  
Jenna K. Rimel ◽  
Chi-Lin Tsai ◽  
Jill O. Fuss ◽  
...  
Keyword(s):  
Transcription Start Site ◽  
Start Site ◽  
Transcription Start

scholarly journals Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection

2016 ◽  
Vol 113 (21) ◽  
pp. E2899-E2905 ◽  
Author(s):  
Irina O. Vvedenskaya ◽  
Hanif Vahedian-Movahed ◽  
Yuanchao Zhang ◽  
Deanne M. Taylor ◽  
Richard H. Ebright ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Transcription Start Site ◽  
Transcription Initiation ◽  
Specific Protein ◽  
Start Site ◽  
Transcription Start ◽  
Transcription Bubble ◽  
Recognition Element

During transcription initiation, RNA polymerase (RNAP) holoenzyme unwinds ∼13 bp of promoter DNA, forming an RNAP-promoter open complex (RPo) containing a single-stranded transcription bubble, and selects a template-strand nucleotide to serve as the transcription start site (TSS). In RPo, RNAP core enzyme makes sequence-specific protein–DNA interactions with the downstream part of the nontemplate strand of the transcription bubble (“core recognition element,” CRE). Here, we investigated whether sequence-specific RNAP–CRE interactions affect TSS selection. To do this, we used two next-generation sequencing-based approaches to compare the TSS profile of WT RNAP to that of an RNAP derivative defective in sequence-specific RNAP–CRE interactions. First, using massively systematic transcript end readout, MASTER, we assessed effects of RNAP–CRE interactions on TSS selection in vitro and in vivo for a library of 47 (∼16,000) consensus promoters containing different TSS region sequences, and we observed that the TSS profile of the RNAP derivative defective in RNAP–CRE interactions differed from that of WT RNAP, in a manner that correlated with the presence of consensus CRE sequences in the TSS region. Second, using 5′ merodiploid native-elongating-transcript sequencing, 5′ mNET-seq, we assessed effects of RNAP–CRE interactions at natural promoters in Escherichia coli, and we identified 39 promoters at which RNAP–CRE interactions determine TSS selection. Our findings establish RNAP–CRE interactions are a functional determinant of TSS selection. We propose that RNAP–CRE interactions modulate the position of the downstream end of the transcription bubble in RPo, and thereby modulate TSS selection, which involves transcription bubble expansion or transcription bubble contraction (scrunching or antiscrunching).

Sign in / Sign up

Export Citation Format

Share Document