Predicting enhancer-promoter interaction from genomic sequence with deep neural networks.

Quantitative Biology
Shashank SinghJian Ma

Abstract

In the human genome, distal enhancers are involved in regulating target genes through proximal promoters by forming enhancer-promoter interactions. Although recently developed high-throughput experimental approaches have allowed us to recognize potential enhancer-promoter interactions genome-wide, it is still largely unclear to what extent the sequence-level information encoded in our genome help guide such interactions. Here we report a new computational method (named "SPEID") using deep learning models to predict enhancer-promoter interactions based on sequence-based features only, when the locations of putative enhancers and promoters in a particular cell type are given. Our results across six different cell types demonstrate that SPEID is effective in predicting enhancer-promoter interactions as compared to state-of-the-art methods that only use information from a single cell type. As a proof-of-principle, we also applied SPEID to identify somatic non-coding mutations in melanoma samples that may have reduced enhancer-promoter interactions in tumor genomes. This work demonstrates that deep learning models can help reveal that sequence-based features alone are sufficient to reliably predict enhancer-promoter interactions gen...Continue Reading

References

Oct 23, 1997·Neural Computation·S Hochreiter, J Schmidhuber
Feb 28, 2007·Genome Biology·Shobhit GuptaWilliam Stafford Noble
Feb 28, 2009·Journal of Cellular Biochemistry·Melissa J Fullwood, Yijun Ruan
Feb 19, 2011·Bioinformatics·Charles E GrantWilliam Stafford Noble
Jul 24, 2012·Cell·Eran HodisLynda Chin
Sep 8, 2012·Nature·UNKNOWN ENCODE Project Consortium
Sep 8, 2012·Nature·Amartya SanyalJob Dekker
Sep 11, 2014·Biological Chemistry·Boet van Riel, Frank Rosenbauer
Nov 18, 2014·Nature Cell Biology·Christopher John BowmanBrian David Dynlacht
Feb 20, 2015·Nature·UNKNOWN Roadmap Epigenomics ConsortiumManolis Kellis
Mar 15, 2015·Cell·Tom Sexton, Giacomo Cavalli
Apr 8, 2015·Nature Neuroscience·Christopher L FrankAnne E West
May 29, 2015·Nature·Yann LeCunGeoffrey Hinton
Jul 28, 2015·Nature Biotechnology·Babak AlipanahiBrendan J Frey
Aug 8, 2015·Nature Biotechnology·Yongjin Park, Manolis Kellis
Aug 25, 2015·Nature Methods·Jian Zhou, Olga G Troyanskaya
Sep 5, 2015·Nucleic Acids Research·Sushmita RoyRupa Sridharan
Nov 21, 2015·Nucleic Acids Research·Ivan V KulakovskiyVsevolod J Makeev
Jan 23, 2016·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Yifeng LiWyeth W Wasserman
Mar 11, 2016·Nature Communications·Yun ZhuWei Wang
Jul 31, 2016·Molecular Systems Biology·Christof AngermuellerOliver Stegle
Jan 6, 2017·PLoS Computational Biology·Sheng WangJinbo Xu
May 19, 2017·Nucleic Acids Research·Ivan Krivega, Ann Dean
Sep 9, 2017·Bioinformatics·Sai ZhangJianyang Zeng
Apr 6, 2018·Journal of the Royal Society, Interface·Travers ChingCasey S Greene
Jun 2, 2018·BMC Bioinformatics·Yifeng LiWyeth W Wasserman

❮ Previous
Next ❯

Citations

Oct 24, 2020·Briefings in Bioinformatics·Xiaoping MinXiangxiang Zeng
Jul 11, 2020·Nature Communications·Tarik J SalamehFeng Yue
Feb 23, 2021·Biosemiotics·Mykola Husev, Andrij Rovenchak
Feb 27, 2021·Briefings in Bioinformatics·Hao LvHao Lin
Jul 25, 2019·Nature Genetics·Fan Cao, Melissa J Fullwood
Mar 1, 2020·Quantitative Biology·Jie RenFengzhu Sun
May 23, 2021·Briefings in Bioinformatics·Amlan TalukderHaiyan Hu
Apr 6, 2021·PeerJ. Computer Science·Michal B RozenwaldMikhail S Gelfand
Apr 30, 2021·Frontiers in Genetics·Sijie YangPeiyao Zhao
Oct 15, 2020·Science China. Life Sciences·Jianxiao LiuJianbing Yan
Dec 7, 2020·Briefings in Bioinformatics·Fu-Ying DaoHao Lin
Jun 29, 2021·Frontiers in Molecular Biosciences·Jan ZrimecAleksej Zelezniak
Jul 27, 2021·The Plant Genome·Osval Antonio Montesinos-LópezJosé Crossa
Aug 8, 2021·International Journal of Molecular Sciences·Kinga SzymanMichał Dąbrowski

❮ 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.