Document Type
Article
Publication Date
9-2-2024
Original Citation
Poirion O,
Zuo W,
Spruce C,
Baker C,
Daigle S,
Olson A,
Skelly D,
Chesler E,
Baker CL,
White B.
Enhlink infers distal and context-specific enhancer-promoter linkages. JGM, JMG
Keywords
Enhancer Elements, Genetic, Promoter Regions, Genetic, Animals, Mice, Software, Quantitative Trait Loci, Corpus Striatum, Single-Cell Analysis
JAX Source
JGM, JMG
ISSN
1474-760X
PMID
39223609
DOI
https://doi.org/10.1186/s13059-024-03374-9
Grant
Research reported in this publication was supported by The Jackson Laboratory Cube Initiative and the Jackson Labora- tory Scientific Support Internal Fund (SSIF) mechanism with the project id: 19005–21-05. Further funding was provided, in part, by the National Institute of General Medical Sciences grant R35GM133724 to CLB and the Jackson Laboratory Director’s Innovation Fund to CLB and EJC. P50 DA039841 supports the Center for Systems Neurogenetics of Addiction o EJC. Data generation through the Single Cell Biology service was supported in part by the JAX Cancer Center (P30 CA034196). Additional support was also provided by The Jackson Laboratory Cube Initiative.
Abstract
Enhlink is a computational tool for scATAC-seq data analysis, facilitating precise interrogation of enhancer function at the single-cell level. It employs an ensemble approach incorporating technical and biological covariates to infer condition-specific regulatory DNA linkages. Enhlink can integrate multi-omic data for enhanced specificity, when available. Evaluation with simulated and real data, including multi-omic datasets from the mouse striatum and novel promoter capture Hi-C data, demonstrate that Enhlink outperfoms alternative methods. Coupled with eQTL analysis, it identified a putative super-enhancer in striatal neurons. Overall, Enhlink offers accuracy, power, and potential for revealing novel biological insights in gene regulation.
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.