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CRUP: a comprehensive framework to predict condition-specific regulatory units

by Hengstler, Jan , Manke, Thomas , Longinotto, John , Kiemer, Alexandra K. , Gasparoni, Nina , Czepukojc, Beate , Yang, Xinyi , Ramisch, Anna , Pospisilik, John A. , Heyne, Steffen , Vingron, Martin , Walter, Jörn , Li, Na , Arrigoni, Laura , Kinkley, Sarah , Pap, Thomas , Meijsing, Sebastiaan H. , Glaser, Laura V. , Cadenas, Cristina , Chung, Ho-Ryun , Römer-Hillmann, Anja , Benner, Philipp , Kessler, Sonja M. , Schöpflin, Robert , Heinrich, Verena , Fuchs, Alisa

in Animal Genetics and Genomics / Animals / Arthritis, Experimental - genetics / Arthritis, Rheumatoid - genetics / Bioinformatics / Biomedical and Life Sciences / chromatin immunoprecipitation / Chromatin Immunoprecipitation Sequencing / Classification / computer software / Differential analysis / Enhancer dynamics / Enhancer Elements, Genetic / Enhancer prediction / Enhancers / Epigenetics / Evolutionary Biology / Gene expression / Gene regulation / genome / Genomes / Histone Code / Histones / Human Genetics / Life Sciences / Method / Mice / Microbial Genetics and Genomics / Plant Genetics and Genomics / prediction / Random forest / Rheumatoid arthritis / Software / species / Stem cells

2019

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2019

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2019

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Journal Article

CRUP: a comprehensive framework to predict condition-specific regulatory units

Hengstler, Jan,

Manke, Thomas,

Longinotto, John,

Kiemer, Alexandra K.,

Gasparoni, Nina,

Czepukojc, Beate,

Yang, Xinyi,

Ramisch, Anna,

Pospisilik, John A.,

Heyne, Steffen,

Vingron, Martin,

Walter, Jörn,

Li, Na,

Arrigoni, Laura,

Kinkley, Sarah,

Pap, Thomas,

Meijsing, Sebastiaan H.,

Glaser, Laura V.,

Cadenas, Cristina,

Chung, Ho-Ryun,

Römer-Hillmann, Anja,

Benner, Philipp,

Kessler, Sonja M.,

Schöpflin, Robert,

Heinrich, Verena,

Fuchs, Alisa

2019

Overview

We present the software Condition-specific Regulatory Units Prediction (CRUP) to infer from epigenetic marks a list of regulatory units consisting of dynamically changing enhancers with their target genes. The workflow consists of a novel pre-trained enhancer predictor that can be reliably applied across cell types and species, solely based on histone modification ChIP-seq data. Enhancers are subsequently assigned to different conditions and correlated with gene expression to derive regulatory units. We thoroughly test and then apply CRUP to a rheumatoid arthritis model, identifying enhancer-gene pairs comprising known disease genes as well as new candidate genes.

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Publisher

BioMed Central,Springer Nature B.V,BMC

Subject

Animal Genetics and Genomics

/ Animals

/ Arthritis, Experimental - genetics

/ Arthritis, Rheumatoid - genetics

/ Bioinformatics

/ Biomedical and Life Sciences

/ chromatin immunoprecipitation