Exonuclease combinations reduce noises in 3D genomics technologies

Nucleic Acids Research
Siyuan KongYubo Zhang

Abstract

Chromosome conformation-capture technologies are widely used in 3D genomics; however, experimentally, such methods have high-noise limitations and, therefore, require significant bioinformatics efforts to extract reliable distal interactions. Miscellaneous undesired linear DNAs, present during proximity-ligation, represent a main noise source, which needs to be minimized or eliminated. In this study, different exonuclease combinations were tested to remove linear DNA fragments from a circularized DNA preparation. This method efficiently removed linear DNAs, raised the proportion of annulation and increased the valid-pairs ratio from ∼40% to ∼80% for enhanced interaction detection in standard Hi-C. This strategy is applicable for development of various 3D genomics technologies, or optimization of Hi-C sequencing efficiency.

References

Apr 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·S T Lovett, R D Kolodner
May 29, 2002·Proceedings of the National Academy of Sciences of the United States of America·Laura A LetticeSumihare Noji
Mar 11, 2003·Nucleic Acids Research·Krithika SubramanianRichard S Myers
May 24, 2008·Nature·Qi-Long YingAustin Smith
Jul 22, 2008·Analytical Biochemistry·Pichumani BalagurumoorthyAmin I Kassis
Jan 5, 2012·Genes & Development·Elzo de Wit, Wouter de Laat
Mar 8, 2013·Current Opinion in Cell Biology·Andrea Smallwood, Bing Ren
Apr 5, 2013·PloS One·Alexey A GavrilovSergey V Razin
May 28, 2013·Molecular Cell·Jennifer E Phillips-Cremins, Victor G Corces
Feb 7, 2014·Genome Research·Ferhat AyWilliam Stafford Noble
Aug 8, 2015·Genome Biology·Xinxian DengChristine M Disteche
Aug 27, 2015·Genome Biology·Takashi NaganoPeter Fraser
Sep 4, 2015·Genome Biology·Ferhat Ay, William S Noble
Dec 2, 2015·Genome Biology·Nicolas ServantEmmanuel Barillot
Feb 3, 2016·F1000Research·Steven WingettSimon Andrews
Jun 25, 2016·Genes & Development·Annette Denker, Wouter de Laat
Jul 29, 2016·Cell Systems·Neva C DurandErez Lieberman Aiden
Jul 29, 2016·Cell Systems·Neva C DurandErez Lieberman Aiden
Nov 4, 2016·Nature Reviews. Molecular Cell Biology·Anthony D SchmittBing Ren
Aug 9, 2017·Annual Review of Cell and Developmental Biology·Miao Yu, Bing Ren
Sep 15, 2017·Nature·Job DekkerUNKNOWN 4D Nucleome Network
Oct 21, 2017·Methods in Molecular Biology·Stefan Grob, Giacomo Cavalli
Dec 1, 2017·Nucleic Acids Research·A Marieke OudelaarJim R Hughes
Jan 6, 2019·Cell Biology and Toxicology·Siyuan Kong, Yubo Zhang
Mar 21, 2019·Genome Biology·Galip Gürkan YardımcıWilliam S Noble

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSM1718027
GSM862720
GSM1689796
GSM1689797
SRR1658722
SRR1658724
GSE125656

Methods Mentioned

BETA
Hi-C
PCR
proximity-ligation
electrophoresis
scraping
exo-Hi-C
HiC-Pro
ChIP

Software Mentioned

APA
Hi
Juicebox Browser
HiC
QuASAR
HiCCUPS
Exo
HOMER
FitHiC
GenomeDISCO

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.