Non-coding variants impact cis-regulatory coordination in a cell type-specific manner
Abstract Background Interactions among cis-regulatory elements (CREs) play a crucial role in gene regulation. Various approaches have been developed to map these interactions genome-wide, including those relying on interindividual epigenomic variation to identify groups of covariable regulatory elem...
| Published in: | Genome Biology |
|---|---|
| Main Authors: | Olga Pushkarev, Guido van Mierlo, Judith Franziska Kribelbauer, Wouter Saelens, Vincent Gardeux, Bart Deplancke |
| Format: | Article |
| Language: | English |
| Published: |
BMC
2024-07-01
|
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13059-024-03333-4 |
Similar Items
Cis-meQTL for cocaine use-associated DNA methylation in an HIV-positive cohort show pleiotropic effects on multiple traits
by: Youshu Cheng, et al.
Published: (2023-09-01)
by: Youshu Cheng, et al.
Published: (2023-09-01)
Epigenome profiling reveals distinctive regulatory features and cis-regulatory elements in pepper
by: Hongji Yang, et al.
Published: (2025-05-01)
by: Hongji Yang, et al.
Published: (2025-05-01)
Immune disease variants modulate gene expression in regulatory CD4+ T cells
by: Lara Bossini-Castillo, et al.
Published: (2022-04-01)
by: Lara Bossini-Castillo, et al.
Published: (2022-04-01)
Inferring cell-type-specific causal gene regulatory networks during human neurogenesis
by: Nil Aygün, et al.
Published: (2023-05-01)
by: Nil Aygün, et al.
Published: (2023-05-01)
Architecture and evolution of the cis-regulatory system of the echinoderm kirrelL gene
by: Jian Ming Khor, et al.
Published: (2022-02-01)
by: Jian Ming Khor, et al.
Published: (2022-02-01)
Epigenomic identification of vernalization cis-regulatory elements in winter wheat
by: Yanhong Liu, et al.
Published: (2024-07-01)
by: Yanhong Liu, et al.
Published: (2024-07-01)
Integration of functional genomics and statistical fine-mapping systematically characterizes adult-onset and childhood-onset asthma genetic associations
by: Xiaoyuan Zhong, et al.
Published: (2025-04-01)
by: Xiaoyuan Zhong, et al.
Published: (2025-04-01)
Cis-regulatory atlas of primary human CD4+ T cells
by: Kurtis Stefan, et al.
Published: (2023-05-01)
by: Kurtis Stefan, et al.
Published: (2023-05-01)
A combination of transcriptomics and epigenomics identifies genes and regulatory elements involved in embryonic tail development in the mouse
by: Yong-Xuan Chen, et al.
Published: (2025-03-01)
by: Yong-Xuan Chen, et al.
Published: (2025-03-01)
Changes in Cis-regulatory Elements during Morphological Evolution
by: Yu-Lee Paul, et al.
Published: (2012-10-01)
by: Yu-Lee Paul, et al.
Published: (2012-10-01)
A map of cis-regulatory modules and constituent transcription factor binding sites in 80% of the mouse genome
by: Pengyu Ni, et al.
Published: (2022-10-01)
by: Pengyu Ni, et al.
Published: (2022-10-01)
A novel cis-regulatory element regulates αD and αA-globin gene expression in chicken erythroid cells
by: Josué Cortés-Fernández de Lara, et al.
Published: (2024-04-01)
by: Josué Cortés-Fernández de Lara, et al.
Published: (2024-04-01)
Enhancing Ebony? Common Associations With a cis-Regulatory Haplotype for Drosophila melanogaster Thoracic Pigmentation in a Japanese Population and Australian Populations
by: Marina Telonis-Scott, et al.
Published: (2018-07-01)
by: Marina Telonis-Scott, et al.
Published: (2018-07-01)
Cis-regulatory evolution integrated the Bric-à-brac transcription factors into a novel fruit fly gene regulatory network
by: Maxwell J Roeske, et al.
Published: (2018-01-01)
by: Maxwell J Roeske, et al.
Published: (2018-01-01)
Analysis of cis-regulatory changes underlying phenotype divergence shaped by domestication in pigs
by: Chunpeng Liu, et al.
Published: (2024-11-01)
by: Chunpeng Liu, et al.
Published: (2024-11-01)
Genome-wide analysis of histone modifications can contribute to the identification of candidate cis-regulatory regions in the threespine stickleback fish
by: Genta Okude, et al.
Published: (2024-07-01)
by: Genta Okude, et al.
Published: (2024-07-01)
Accurate prediction of functional states of cis-regulatory modules reveals common epigenetic rules in humans and mice
by: Pengyu Ni, et al.
Published: (2022-10-01)
by: Pengyu Ni, et al.
Published: (2022-10-01)
CREaTor: zero-shot cis-regulatory pattern modeling with attention mechanisms
by: Yongge Li, et al.
Published: (2023-11-01)
by: Yongge Li, et al.
Published: (2023-11-01)
Cis-regulatory basis of sister cell type divergence in the vertebrate retina
by: Daniel P Murphy, et al.
Published: (2019-10-01)
by: Daniel P Murphy, et al.
Published: (2019-10-01)
Prediction of target genes and functional types of cis-regulatory modules in the human genome reveals their distinct properties
by: Sisi Yuan, et al.
Published: (2025-07-01)
by: Sisi Yuan, et al.
Published: (2025-07-01)
Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG
by: Zhana Duren, et al.
Published: (2022-05-01)
by: Zhana Duren, et al.
Published: (2022-05-01)
Improving Chromatin-Interaction Prediction Using Single-Cell Open-Chromatin Profiles and Making Insight Into the Cis-Regulatory Landscape of the Human Brain
by: Neetesh Pandey, et al.
Published: (2021-10-01)
by: Neetesh Pandey, et al.
Published: (2021-10-01)
ATAC-Seq Reveals the Landscape of Open Chromatin and cis-Regulatory Elements in the Phytophthora sojae Genome
by: Zhichao Zhang, et al.
Published: (2022-04-01)
by: Zhichao Zhang, et al.
Published: (2022-04-01)
G-quadruplexes as pivotal components of cis-regulatory elements in the human genome
by: Rongxin Zhang, et al.
Published: (2024-08-01)
by: Rongxin Zhang, et al.
Published: (2024-08-01)
PeakMatcher facilitates updated Aedes aegypti embryonic cis-regulatory element map
by: Ronald J. Nowling, et al.
Published: (2021-01-01)
by: Ronald J. Nowling, et al.
Published: (2021-01-01)
A new suite of reporter vectors and a novel landing site survey system to study cis-regulatory elements in diverse insect species
by: Kevin D. Deem, et al.
Published: (2024-05-01)
by: Kevin D. Deem, et al.
Published: (2024-05-01)
Prediction and Experimental Validation of a New Salinity-Responsive Cis-Regulatory Element (CRE) in a Tilapia Cell Line
by: Chanhee Kim, et al.
Published: (2022-05-01)
by: Chanhee Kim, et al.
Published: (2022-05-01)
Conservation of <i>cis</i>-Regulatory Syntax Underlying Deuterostome Gastrulation
by: Lorena Buono, et al.
Published: (2024-06-01)
by: Lorena Buono, et al.
Published: (2024-06-01)
Decoding the chromatin accessibility in Andrographis paniculata genome, a case study of genome-wide investigation of the cis-regulatory elements in medicinal plants
by: Mingkun Huang, et al.
Published: (2024-09-01)
by: Mingkun Huang, et al.
Published: (2024-09-01)
Uncovering the multi-layer cis-regulatory landscape of rice via integrative nascent RNA analysis
by: Marina Goliasse, et al.
Published: (2025-08-01)
by: Marina Goliasse, et al.
Published: (2025-08-01)
Quantitative analysis of the ThrbCRM1-centered gene regulatory network
by: Benjamin Souferi, et al.
Published: (2019-04-01)
by: Benjamin Souferi, et al.
Published: (2019-04-01)
Whole-Genome Sequencing Reveals the Role of Cis-Regulatory Elements and eQTL/sQTL in the Adaptive Selection of Hubei Indigenous Cattle
by: Liangyu Shi, et al.
Published: (2025-04-01)
by: Liangyu Shi, et al.
Published: (2025-04-01)
Functional genomic analysis delineates regulatory mechanisms of GWAS-identified bipolar disorder risk variants
by: Rui Chen, et al.
Published: (2022-05-01)
by: Rui Chen, et al.
Published: (2022-05-01)
Predominant contribution of cis‐regulatory divergence in the evolution of mouse alternative splicing
by: Qingsong Gao, et al.
Published: (2015-07-01)
by: Qingsong Gao, et al.
Published: (2015-07-01)
Genetic Architecture of Transcription and Chromatin Regulation
by: Kwoneel Kim, et al.
Published: (2015-06-01)
by: Kwoneel Kim, et al.
Published: (2015-06-01)
A role for heritable transcriptomic variation in maize adaptation to temperate environments
by: Guangchao Sun, et al.
Published: (2023-03-01)
by: Guangchao Sun, et al.
Published: (2023-03-01)
MicroSalmon: A Comprehensive, Searchable Resource of Predicted MicroRNA Targets and 3′UTR Cis-Regulatory Elements in the Full-Length Sequenced Atlantic Salmon Transcriptome
by: Sigmund Ramberg, et al.
Published: (2021-09-01)
by: Sigmund Ramberg, et al.
Published: (2021-09-01)
Identification of Cis-Regulatory Sequences Controlling Pollen-Specific Expression of Hydroxyproline-Rich Glycoprotein Genes in <i>Arabidopsis thaliana</i>
by: Yichao Li, et al.
Published: (2020-12-01)
by: Yichao Li, et al.
Published: (2020-12-01)
Understanding Disease Susceptibility through Population Genomics
by: Seonggyun Han, et al.
Published: (2012-12-01)
by: Seonggyun Han, et al.
Published: (2012-12-01)
Understanding the Dynamics of Gene Regulatory Systems; Characterisation and Clinical Relevance of cis-Regulatory Polymorphisms
by: Philip Cowie, et al.
Published: (2013-01-01)
by: Philip Cowie, et al.
Published: (2013-01-01)
Similar Items
-
Cis-meQTL for cocaine use-associated DNA methylation in an HIV-positive cohort show pleiotropic effects on multiple traits
by: Youshu Cheng, et al.
Published: (2023-09-01) -
Epigenome profiling reveals distinctive regulatory features and cis-regulatory elements in pepper
by: Hongji Yang, et al.
Published: (2025-05-01) -
Immune disease variants modulate gene expression in regulatory CD4+ T cells
by: Lara Bossini-Castillo, et al.
Published: (2022-04-01) -
Inferring cell-type-specific causal gene regulatory networks during human neurogenesis
by: Nil Aygün, et al.
Published: (2023-05-01) -
Architecture and evolution of the cis-regulatory system of the echinoderm kirrelL gene
by: Jian Ming Khor, et al.
Published: (2022-02-01)
