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Computational Analysis of Maize Enhancer Regulatory Elements Using ATAC-STARR-seq.
Marand, Alexandre P.
Afiliación
  • Marand AP; Department of Genetics, University of Georgia, Athens, USA.
bioRxiv ; 2023 Jan 21.
Article en En | MEDLINE | ID: mdl-36711646
The blueprints to development, response to the environment, and cellular function are largely the manifestation of distinct gene expression programs controlled by the spatiotemporal activity of cis-regulatory elements. Although biochemical methods for identifying accessible chromatin - a hallmark of active cis-regulatory elements - have been developed, approaches capable of measuring and quantifying cis-regulatory activity are only beginning to be realized. Massively Parallel Reporter Assays coupled to chromatin accessibility profiling present a high-throughput solution for testing the transcription-activating capacity of millions of putatively regulatory DNA sequences in parallel. However, clear computational pipelines for analyzing these high-throughput sequencing-based reporter assays are lacking. In this protocol, I layout and rationalize a computational framework for the processing and analysis of Assay for Transposase Accessible Chromatin profiling followed by Self-Transcribed Active Regulatory Region sequencing (ATAC-STARR-seq) data from a recent study in Zea mays. The approach described herein can be adapted to other sequencing-based reporter assays and is largely agnostic to the model organism with the appropriate input substitutions.
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Texto completo: 1 Banco de datos: MEDLINE Idioma: En Revista: BioRxiv Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos

Texto completo: 1 Banco de datos: MEDLINE Idioma: En Revista: BioRxiv Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos