Detecting Differential Transcription Factor Activity from ATAC-Seq Data

Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry
Ignacio J TripodiRobin D Dowell

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.

References

Jan 4, 1996·The New England Journal of Medicine·D S Latchman
Jul 3, 1999·Nature Genetics·S TavazoieG M Church
Jun 14, 2000·Journal of Medical Genetics·S D SmithD Hoover
Dec 31, 2005·Nucleic Acids Research·V MatysE Wingender
Mar 24, 2009·Nature Methods·Jay R HesselberthJohn A Stamatoyannopoulos
Aug 12, 2009·Nature Reviews. Genetics·Peggy J Farnham
Nov 13, 2009·Nucleic Acids Research·Elodie Portales-CasamarAlbin Sandelin
Dec 26, 2009·Reproductive Biology and Endocrinology : RB&E·Karin TammMadis Metsis
Apr 16, 2010·Nature·Tae-Kyung KimMichael E Greenberg
Jun 10, 2010·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Monica MariniRoberto Ravazzolo
Nov 25, 2011·Methods in Molecular Biology·Padmaja Gade, Dhan V Kalvakolanu
Aug 8, 2012·Nature Reviews. Genetics·François Spitz, Eileen E M Furlong
Sep 7, 2012·Genome Biology·Troy W WhitfieldZhiping Weng
Sep 8, 2012·Nature·UNKNOWN ENCODE Project Consortium
Sep 8, 2012·Nature·Shane NephJohn A Stamatoyannopoulos
Sep 8, 2012·Science·Matthew T MauranoJohn A Stamatoyannopoulos
Nov 24, 2012·Nucleic Acids Research·Ivan V KulakovskiyVsevolod J Makeev
Dec 25, 2012·Nature Cell Biology·Patricia A J Muller, Karen H Vousden
Mar 19, 2013·Cell·Tong Ihn Lee, Richard A Young
May 3, 2013·Genome Research·Nasun HahW Lee Kraus
Aug 22, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Steven N HartJean-Pierre Kocher
Feb 12, 2014·Genome Research·Piotr J BalwierzErik van Nimwegen
Mar 8, 2014·PLoS Genetics·Darren A CusanovichYoav Gilad
Mar 13, 2014·Nature Reviews. Genetics·Daria ShlyuevaAlexander Stark
Mar 29, 2014·Trends in Biochemical Sciences·Michael T Y LamChristopher K Glass
Jun 4, 2014·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Mikhail Spivakov
Nov 5, 2014·Nature·Kyle Kai-How FarhBradley E Bernstein
Dec 5, 2014·Genome Medicine·Olivia Corradin, Peter C Scacheri
Feb 20, 2015·Nature·UNKNOWN Roadmap Epigenomics ConsortiumManolis Kellis
Mar 24, 2015·Nature Methods·Charles G DankoAdam Siepel
May 6, 2015·Nature Genetics·Borbala MifsudCameron S Osborne

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Citations

Jul 28, 2019·Immunology·Candace C LiuAaron M Newman
Apr 28, 2020·Journal of Bioinformatics and Computational Biology·Nazmus SalehinPierre Osteil
Feb 6, 2020·Genome Biology·Feng YanNicholas C Wong
Jun 17, 2020·Current Protocols in Human Genetics·Jason P Smith, Nathan C Sheffield
Aug 12, 2020·The Journal of Clinical Investigation·Sanjay RajagopalanShyam Biswal
Apr 2, 2020·Molecular Cell·Charli B FantDylan J Taatjes
Nov 18, 2021·The EMBO Journal·Ann K HoganDaniel R Foltz

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Datasets Mentioned

BETA
GSE58740
SRR1448795
SRR3493635
GSE87822
SRR4413811
and
GSE104720
SRR6148319

Methods Mentioned

BETA
immunoprecipitation
ChIP-seq
ChIP
footprinting
RNA-seq
PRO-seq
Assay
ATAC-seq

Software Mentioned

HaploReg
DAStk
bedtools
trimmomatic
Differential ATAC - seq toolkit ( DAStk )
Bowtie
samtools
FastQC
FIMO
fastq

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