ArticleGenome biology2023
Inferring cell-type-specific causal gene regulatory networks during human neurogenesis.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 17 citations in OpenAlex.
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- A deep generative model for deciphering cellular dynamics and in silico drug discovery in complex diseases.Nature biomedical engineering · 2025Article
- Hybrids reveal accessible chromatinbioRxiv : the preprint server for biology · 2025Article
- Probabilistic classification of gene-by-treatment interactions on molecular count phenotypes.PLoS genetics · 2025Article
- Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation.bioRxiv : the preprint server for biology · 2024Article
- Regulatory networks of coresident subgenomes during rapid fiber cell elongation in upland cotton.Plant communications · 2024Article
- Genes with differential expression across ancestries are enriched in ancestry-specific disease effects likely due to gene-by-environment interactions.American journal of human genetics · 2024Article
- Genetics of cell-type-specific post-transcriptional gene regulation during human neurogenesis.American journal of human genetics · 2024Article
- Gene regulatory networks in disease and ageing.Nature reviews. Nephrology · 2024Review
- A single-cell multimodal view on gene regulatory network inference from transcriptomics and chromatin accessibility data.Briefings in bioinformatics · 2024Review
- Article
- COLOCdb: a comprehensive resource for multi-model colocalization of complex traits.Nucleic acids research · 2024Article
- Genetics of cell-type-specific post-transcriptional gene regulation during human neurogenesis.bioRxiv : the preprint server for biology · 2023Article
- Inferring cell-type-specific causal gene regulatory networks during human neurogenesis.Genome biology · 2023Article
- The trouble with triples: Examining the impact of measurement error in mediation analysis.Genetics · 2023Article
- Article
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundGenetic variation influences both chromatin accessibility, assessed in chromatin accessibility quantitative trait loci (caQTL) studies, and gene expression, assessed in expression QTL (eQTL) studies. Genetic variants can impact either nearby genes (cis-eQTLs) or distal genes (trans-eQTLs). Colocalization between caQTL and eQTL, or cis- and trans-eQTLs suggests that they share causal variants. However, pairwise colocalization between these molecular QTLs does not guarantee a causal relationship. Mediation analysis can be applied to assess the evidence supporting causality versus independence between molecular QTLs. Given that the function of QTLs can be cell-type-specific, we performed mediation analyses to find epigenetic and distal regulatory causal pathways for genes within two major cell types of the developing human cortex, progenitors and neurons.
resultsWe find that the expression of 168 and 38 genes is mediated by chromatin accessibility in progenitors and neurons, respectively. We also find that the expression of 11 and 12 downstream genes is mediated by upstream genes in progenitors and neurons. Moreover, we discover that a genetic locus associated with inter-individual differences in brain structure shows evidence for mediation of SLC26A7 through chromatin accessibility, identifying molecular mechanisms of a common variant association to a brain trait.
conclusionsIn this study, we identify cell-type-specific causal gene regulatory networks whereby the impacts of variants on gene expression were mediated by chromatin accessibility or distal gene expression. Identification of these causal paths will enable identifying and prioritizing actionable regulatory targets perturbing these key processes during neurodevelopment.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.