Genome-Wide Profiling of Transcription Initiation with STRIPE-seq

Overview

Journal Methods Mol Biol

Specialty Molecular Biology

Date 2022 May 6

PMID 35524109

Authors

Robert A Policastro

Gabriel E Zentner

Affiliations

Soon will be listed here.

Abstract

Transcription start site (TSS) usage is a critical factor in the regulation of gene expression. A number of methods for global TSS mapping have been developed, but barriers of expense, technical difficulty, time, and/or cost have limited their broader adoption. To address these issues, we developed Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq). Requiring only three enzymatic steps with intervening bead cleanups, a STRIPE-seq library can be prepared from as little as 50 ng total RNA in ~5 h at a cost of ~$12 (US). In addition to profiling TSS usage, STRIPE-seq provides information on transcript levels that can be used for differential expression analysis. Thanks to its simplicity and low cost, we envision that STRIPE-seq could be employed by any molecular biology laboratory interested in profiling transcription initiation.

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References

Calvo S, Pagliarini D, Mootha V . Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans. Proc Natl Acad Sci U S A. 2009; 106(18):7507-12. PMC: 2669787. DOI: 10.1073/pnas.0810916106. View

Malabat C, Feuerbach F, Ma L, Saveanu C, Jacquier A . Quality control of transcription start site selection by nonsense-mediated-mRNA decay. Elife. 2015; 4. PMC: 4434318. DOI: 10.7554/eLife.06722. View

Kurihara Y, Makita Y, Kawashima M, Fujita T, Iwasaki S, Matsui M . Transcripts from downstream alternative transcription start sites evade uORF-mediated inhibition of gene expression in . Proc Natl Acad Sci U S A. 2018; 115(30):7831-7836. PMC: 6064979. DOI: 10.1073/pnas.1804971115. View

Mejia-Guerra M, Li W, Galeano N, Vidal M, Gray J, Doseff A . Core Promoter Plasticity Between Maize Tissues and Genotypes Contrasts with Predominance of Sharp Transcription Initiation Sites. Plant Cell. 2015; 27(12):3309-20. PMC: 4707454. DOI: 10.1105/tpc.15.00630. View

Ushijima T, Hanada K, Gotoh E, Yamori W, Kodama Y, Tanaka H . Light Controls Protein Localization through Phytochrome-Mediated Alternative Promoter Selection. Cell. 2017; 171(6):1316-1325.e12. DOI: 10.1016/j.cell.2017.10.018. View

Reyes A, Huber W . Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues. Nucleic Acids Res. 2017; 46(2):582-592. PMC: 5778607. DOI: 10.1093/nar/gkx1165. View

Pal S, Gupta R, Kim H, Wickramasinghe P, Baubet V, Showe L . Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development. Genome Res. 2011; 21(8):1260-72. PMC: 3149493. DOI: 10.1101/gr.120535.111. View

Haberle V, Li N, Hadzhiev Y, Plessy C, Previti C, Nepal C . Two independent transcription initiation codes overlap on vertebrate core promoters. Nature. 2014; 507(7492):381-385. PMC: 4820030. DOI: 10.1038/nature12974. View

Boyd M, Thodberg M, Vitezic M, Bornholdt J, Vitting-Seerup K, Chen Y . Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies. Nat Commun. 2018; 9(1):1661. PMC: 5916929. DOI: 10.1038/s41467-018-03766-z. View

10.

Demircioglu D, Cukuroglu E, Kindermans M, Nandi T, Calabrese C, Fonseca N . A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters. Cell. 2019; 178(6):1465-1477.e17. DOI: 10.1016/j.cell.2019.08.018. View

11.

Bhardwaj V, Semplicio G, Erdogdu N, Manke T, Akhtar A . MAPCap allows high-resolution detection and differential expression analysis of transcription start sites. Nat Commun. 2019; 10(1):3219. PMC: 6667505. DOI: 10.1038/s41467-019-11115-x. View

12.

Wakaguri H, Yamashita R, Suzuki Y, Sugano S, Nakai K . DBTSS: database of transcription start sites, progress report 2008. Nucleic Acids Res. 2007; 36(Database issue):D97-101. PMC: 2238895. DOI: 10.1093/nar/gkm901. View

13.

Ni T, Corcoran D, Rach E, Song S, Spana E, Gao Y . A paired-end sequencing strategy to map the complex landscape of transcription initiation. Nat Methods. 2010; 7(7):521-7. PMC: 3197272. DOI: 10.1038/nmeth.1464. View

14.

Arribere J, Gilbert W . Roles for transcript leaders in translation and mRNA decay revealed by transcript leader sequencing. Genome Res. 2013; 23(6):977-87. PMC: 3668365. DOI: 10.1101/gr.150342.112. View

15.

Pelechano V, Wei W, Steinmetz L . Extensive transcriptional heterogeneity revealed by isoform profiling. Nature. 2013; 497(7447):127-31. PMC: 3705217. DOI: 10.1038/nature12121. View

16.

Gu W, Lee H, Chaves D, Youngman E, Pazour G, Conte Jr D . CapSeq and CIP-TAP identify Pol II start sites and reveal capped small RNAs as C. elegans piRNA precursors. Cell. 2012; 151(7):1488-500. PMC: 3581324. DOI: 10.1016/j.cell.2012.11.023. View

17.

Park D, Morris A, Battenhouse A, Iyer V . Simultaneous mapping of transcript ends at single-nucleotide resolution and identification of widespread promoter-associated non-coding RNA governed by TATA elements. Nucleic Acids Res. 2014; 42(6):3736-49. PMC: 3973313. DOI: 10.1093/nar/gkt1366. View

18.

Core L, Martins A, Danko C, Waters C, Siepel A, Lis J . Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nat Genet. 2014; 46(12):1311-20. PMC: 4254663. DOI: 10.1038/ng.3142. View

19.

Negroni M, Buc H . Retroviral recombination: what drives the switch?. Nat Rev Mol Cell Biol. 2001; 2(2):151-5. DOI: 10.1038/35052098. View

20.

Zhu Y, Machleder E, Chenchik A, Li R, Siebert P . Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction. Biotechniques. 2001; 30(4):892-7. DOI: 10.2144/01304pf02. View