Article

Abstract

• Transcription factors are managers of the cellular factory, and key components to many diseases. Many non-coding single nucleotide polymorphisms affect transcription factors, either by directly altering the protein or its functional activity at individual binding sites. Here we first briefly summarize high-throughput approaches to studying transcription factor activity. We then demonstrate, using published chromatin accessibility data (specifically ATAC-seq), that the genome-wide profile of TF recognition motifs relative to regions of open chromatin can determine the key transcription factor altered by a perturbation. Our method of determining which TFs are altered by a perturbation is simple, is quick to implement, and can be used when biological samples are limited. In the future, we envision that this method could be applied to determine which TFs show altered activity in response to a wide variety of drugs and diseases.

Creator

• Tripodi, Ignacio J
• Allen, Mary Ann
• Dowell, Robin D

Date Issued

• 2018-05-10

Academic Affiliation

• Molecular, Cellular & Developmental Biology (MCDB)

Journal Title

• Molecules

Journal Issue/Number

• 5

Journal Volume

• 23

Subject

• DNA
• Sequence Analysis
• Nucleotide Motifs
• Humans
• Transcription Factors
• Mutation
• Cell Line
• Disease
• Tumor

Dernière modification

• 2022-10-03

Identifier

• PubMed ID: 29748466

Resource Type

• Article

Déclaration de droits

• In Copyright

DOI

•  https://doi.org/10.3390/molecules23051136

ISSN

• 1420-3049

Language

• English [eng]

License

• Creative Commons BY Attribution 4.0 International

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La vignette	Titre	Date de téléchargement	Visibilité	actes
	detectingDifferentialTranscriptionFactorActivityFromAtacSe.pdf	2019-12-05	Public	Télécharger