Genome wide approaches to identify protein-DNA interactions

Current Medicinal Chemistry
Tao MaLiguo Wang

Abstract

Transcription factors are DNA-binding proteins that play key roles in many fundamental biological processes. Unraveling their interactions with DNA is essential to identify their target genes and understand the regulatory network. Genome-wide identification of their binding sites became feasible thanks to recent progress in experimental and computational approaches. ChIP-chip, ChIP-seq, and ChIP-exo are three widely used techniques to demarcate genome-wide transcription factor binding sites. This review aims to provide an overview of these three techniques including their experiment procedures, computational approaches, and popular analytic tools. ChIP-chip, ChIP-seq, and ChIP-exo have been the major techniques to study genome-wide in vivo protein-DNA interaction. Due to the rapid development of next-generation sequencing technology, array-based ChIP-chip is deprecated and ChIP-seq has become the most widely used technique to identify transcription factor binding sites in genome-wide. The newly developed ChIP-exo further improves the spatial resolution to single nucleotide. Numerous tools have been developed to analyze ChIP-chip, ChIP-seq and ChIP-exo data. However, different programs may employ different mechanisms or underlyi...Continue Reading

References

Jul 28, 2005·Bioinformatics·Hongkai Ji, Wing Hung Wong
Aug 10, 2006·Proceedings of the National Academy of Sciences of the United States of America·W Evan JohnsonX Shirley Liu
Mar 3, 2007·Bioinformatics·Jun S SongX Shirley Liu
Apr 5, 2007·Nature Protocols·Joel D NelsonKarol Bomsztyk
Jun 2, 2007·Science·David S JohnsonBarbara Wold
Oct 31, 2007·PLoS Computational Biology·X Shirley Liu
Sep 19, 2008·Genome Biology·Yong ZhangX Shirley Liu
Nov 4, 2008·Nature Biotechnology·Hongkai JiWing H Wong
Nov 26, 2008·Nature Biotechnology·Peter V KharchenkoPeter J Park
Jan 6, 2009·Nature Biotechnology·Joel RozowskyMark B Gerstein
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jun 19, 2009·Nature·Susan E CelnikerUNKNOWN modENCODE Consortium
Sep 9, 2009·Nature Reviews. Genetics·Peter J Park
Nov 3, 2009·Nature Methods·Shirley PepkeAli Mortazavi
May 13, 2010·Briefings in Bioinformatics·Heng Li, Nils Homer
Oct 5, 2010·Combinatorial Chemistry & High Throughput Screening·Yi-Zeng LiangKelvin Chan
Oct 15, 2010·Nature Biotechnology·Bradley E BernsteinJames A Thomson
Oct 1, 2011·Nature Protocols·Mazhar Adli, Bradley E Bernstein
Nov 30, 2011·Nature Reviews. Genetics·Todd J Treangen, Steven L Salzberg
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Sep 8, 2012·Nature·UNKNOWN ENCODE Project Consortium
Sep 8, 2012·Genome Research·Stephen G LandtMichael Snyder
Nov 19, 2013·PLoS Computational Biology·Timothy BaileyJie Zhang
Jan 1, 2014·PloS One·Cristian Del FabbroFederico M Giorgi
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Sep 25, 2014·Nucleic Acids Research·Liguo WangWei Li
Oct 14, 2017·Genome Research·Mingxiang Teng, Rafael A Irizarry

❮ Previous
Next ❯

Citations

Jan 17, 2020·Current Medicinal Chemistry·Zunnan Huang, Ruo-Xu Gu
May 1, 2021·International Journal of Molecular Sciences·Chia-Chun TsengShun-Jen Chang
Aug 21, 2021·Briefings in Bioinformatics·Jian ZhangLukasz Kurgan

❮ Previous
Next ❯

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.