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Genome-Wide Profiling of Transcription Initiation with STRIPE-seq

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Yeast Functional Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2477))

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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Authors and Affiliations

  1. Department of Biology, Indiana University, Bloomington, IN, USA

    Robert A. Policastro & Gabriel E. Zentner

  2. Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN, USA

    Gabriel E. Zentner

  3. eGenesis, Inc., Cambridge, MA, USA

    Gabriel E. Zentner

Authors
  1. Robert A. Policastro
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  2. Gabriel E. Zentner
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Correspondence to Gabriel E. Zentner .

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Editors and Affiliations

  1. Institut de Biologie Paris Seine, Sorbonne Université, Paris, France

    Frédéric Devaux

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Policastro, R.A., Zentner, G.E. (2022). Genome-Wide Profiling of Transcription Initiation with STRIPE-seq. In: Devaux, F. (eds) Yeast Functional Genomics. Methods in Molecular Biology, vol 2477. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2257-5_2

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  • DOI: https://doi.org/10.1007/978-1-0716-2257-5_2

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