Identification of transcription factor binding sites using ATAC-seq

Genome Biology
Zhijian LiIvan G Costa

Abstract

Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) is a simple protocol for detection of open chromatin. Computational footprinting, the search for regions with depletion of cleavage events due to transcription factor binding, is poorly understood for ATAC-seq. We propose the first footprinting method considering ATAC-seq protocol artifacts. HINT-ATAC uses a position dependency model to learn the cleavage preferences of the transposase. We observe strand-specific cleavage patterns around transcription factor binding sites, which are determined by local nucleosome architecture. By incorporating all these biases, HINT-ATAC is able to significantly outperform competing methods in the prediction of transcription factor binding sites with footprints.

References

May 17, 2000·Bioinformatics·G D Stormo
Apr 9, 2004·Proceedings of the National Academy of Sciences of the United States of America·Peter J SaboJohn A Stamatoyannopoulos
Dec 31, 2005·Nucleic Acids Research·V MatysE Wingender
Aug 6, 2008·Annual Review of Genetics·William S Reznikoff
Sep 19, 2008·Genome Biology·Yong ZhangX Shirley Liu
Dec 27, 2008·IEEE Transactions on Pattern Analysis and Machine Intelligence·Shihao JiLawrence Carin
Mar 17, 2009·BMC Bioinformatics·Bartek WilczynskiJerzy Tiuryn
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Sep 24, 2009·Bioinformatics·Janne KorhonenEsko Ukkonen
Oct 1, 2010·The Journal of Immunology : Official Journal of the American Association of Immunologists·Piritta FelkerMartin Zenke
Nov 11, 2011·Bioinformatics·Gabriel Cuellar-PartidaTimothy L Bailey
Mar 1, 2012·Nature Methods·Jason Ernst, Manolis Kellis
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Sep 8, 2012·Nature·UNKNOWN ENCODE Project Consortium
Sep 8, 2012·Nature·Robert E ThurmanJohn A Stamatoyannopoulos
Sep 8, 2012·Nature·Shane NephJohn A Stamatoyannopoulos
Sep 11, 2012·Cell·Shane NephJohn A Stamatoyannopoulos
Apr 12, 2013·Proceedings of the National Academy of Sciences of the United States of America·Allan LazaroviciHarmen J Bussemaker
Aug 12, 2014·Science·David Lara-AstiasoIdo Amit
Sep 23, 2014·Molecular Cell·Myong-Hee SungGordon L Hager
Oct 9, 2014·Nucleic Acids Research·Galip Gürkan YardımcıUwe Ohler
Dec 18, 2014·Genome Biology·Michael I LoveSimon Anders
Mar 10, 2015·Nature Biotechnology·Qiye HeJulia Zeitlinger
Jun 18, 2015·Nature·Jason D BuenrostroWilliam J Greenleaf
Jun 28, 2015·Nucleic Acids Research·Jens Keilwagen, Jan Grau
Aug 19, 2015·Nature Methods·Christian SchmidlChristoph Bock
Oct 18, 2015·Nucleic Acids Research·Qiong LinMartin Zenke
Feb 24, 2016·Nature Methods·Eduardo G GusmaoIvan G Costa
Feb 26, 2016·Nature Methods·Jeff Vierstra, John A Stamatoyannopoulos

❮ Previous
Next ❯

Citations

Oct 5, 2019·Nucleic Acids Research·Karl J V NordströmJörn Walter
Feb 28, 2019·Genome Biology·Zhijian LiIvan G Costa
Jan 10, 2020·Development·Carlos Perez-CervantesIvan P Moskowitz
Feb 12, 2020·Neuropsychopharmacology : Official Publication of the American College of Neuropsychopharmacology·Kathleen E MorrisonTracy L Bale
Oct 8, 2019·PLoS Biology·Krithika RamachandranGrant D Barish
Aug 6, 2020·EMBO Molecular Medicine·Büşra Erarslan-UysalAndreas E Kulozik
Aug 15, 2020·Human Molecular Genetics·George Andrew S InglisAndrew Escayg
Oct 23, 2019·Proceedings of the National Academy of Sciences of the United States of America·Min ZhangJames F Martin
May 20, 2020·Genome Research·Luca MarianiMartha L Bulyk
Jun 17, 2020·Current Protocols in Human Genetics·Jason P Smith, Nathan C Sheffield
Feb 23, 2020·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Judit Salces-OrtizJosefa González
Jul 17, 2020·Frontiers in Cellular Neuroscience·Xue-Qi PengChang-Mei Liu
Jun 6, 2019·Epigenetics & Chromatin·Kyu-Seon OhMyong-Hee Sung
Jul 2, 2020·Biology·Stephanie StranskySimone Sidoli
Apr 6, 2020·Journal of Neural Transmission·Jochen OhnmachtRejko Krüger
Apr 28, 2020·Journal of Bioinformatics and Computational Biology·Nazmus SalehinPierre Osteil
Feb 6, 2020·Genome Biology·Feng YanNicholas C Wong
Sep 27, 2020·Proceedings of the National Academy of Sciences of the United States of America·Alexandra MaslovaUNKNOWN Immunological Genome Project
Oct 10, 2020·Nature Communications·Kristin E MurphyPatrick J Murphy
Oct 31, 2020·Nucleic Acids Research·Fan WangChunquan Li
Sep 23, 2020·Genome Génome / Conseil National De Recherches Canada·Ian C TobiasJennifer A Mitchell
Jan 8, 2021·Neuron·Ethan J ArmandEran A Mukamel
Jan 10, 2021·Scientific Reports·Billie G C GriffithMargaret C Frame
Jul 3, 2020·Computational and Structural Biotechnology Journal·Barbara HöllbacherN Henriette Uhlenhaut
Jan 10, 2021·Journal of Dental Research·Y XiaoZ Chen
Nov 18, 2020·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Diana C DeLuciaJohn K Lee
May 27, 2020·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Jordan L SmithWen Xue
Dec 29, 2020·Frontiers in Genetics·Óscar M LezcanoElena Gómez-Díaz
Oct 17, 2020·Molecular & Cellular Proteomics : MCP·Guido van Mierlo, Michiel Vermeulen
Nov 15, 2020·Science Advances·Andrew B CaldwellShankar Subramaniam
Feb 20, 2021·Briefings in Functional Genomics·Veronica Bergo, Eirini Trompouki
Sep 24, 2020·Cell Reports·Rebecca LeylekJuliana Idoyaga
Feb 28, 2021·Nature Communications·Ricardo D'Oliveira AlbanusStephen C J Parker

❮ Previous
Next ❯

Datasets Mentioned

BETA
GM12878
GM12787
cells

Methods Mentioned

BETA
footprinting
ChIP-seq
ATAC-seq
FACS
PCR

Software Mentioned

chromHMM
MACS2
HINT
samtools
Jaspar
Bowtie2
Trim Galore
DeFCoM
MOODS C + +
Transfac

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.