Biology subjects

Engelhorn, J.

Publications and source records attributed to Engelhorn, J..

3 recordsLinked to original sources

bioRxiv2023

Phenotypic variation in maize can be largely explained by genetic variation at transcription factor binding sites

Comprehensive maps of functional variation at transcription factor (TF) binding sites (cis-elements) are crucial for elucidating how genotype shapes phenotype. Here we report the construction of a pan-cistrome of the maize leaf under well-watered and drought conditions. We quantified haplotype-specific TF footprints across a pan-genome of 25 maize hybrids and mapped over two-hundred thousand genetic variants (termed binding-QTL) linked to cis-element occupancy. Three lines of evidence support the functional significance of binding-QTL: i) they coincide with numerous known causative loci that regulate traits, including VGT1, Trehalase1, and the MITE transposon near ZmNAC111 under drought; ii) their footprint bias is mirrored between inbred parents and by ChIP-seq; iii) partitioning genetic variation across genomic regions demonstrates that binding-QTL capture the majority of heritable trait variation across [~]70% of 143 phenotypes. Our study provides a promising approach to make previously hidden cis-variation more accessible for genetic studies and multi-target engineering of complex traits.

genomics↗

bioRxiv2023

MINI-AC: Inference of plant gene regulatory networks using bulk or single-cell accessible chromatin profiles

Gene regulatory networks (GRNs) represent the interactions between transcription factors (TF) and their target genes. GRNs control transcriptional programs involved in growth, development and stress responses, ultimately affecting diverse agricultural traits. While recent developments in accessible chromatin (AC) profiling technologies make it possible to identify context-specific regulatory DNA, learning the underlying GRNs remains a major challenge. We developed MINI-AC (Motif-Informed Network Inference based on Accessible Chromatin), a method that combines AC data from bulk or single-cell experiments with TF binding site information to learn GRNs in plants. We benchmarked MINI-AC using bulk AC datasets from different Arabidopsis thaliana tissues and showed that it outperforms other methods to identify correct TFs binding sites. In maize, a crop with a complex genome and abundant distal AC regions, MINI-AC successfully inferred leaf GRNs with experimentally confirmed, both proximal and distal, TF-target gene interactions. Furthermore, we showed that both AC regions and footprints are valid alternatives to infer AC-based GRNs with MINI-AC. Finally, we combined MINI-AC predictions from bulk and single-cell AC datasets to identify general and cell-type specific maize leaf regulators. Focusing on C4 metabolism, we identified diverse regulatory interactions in specialized cell types for this photosynthetic pathway. MINI-AC represents a powerful tool for inferring accurate AC-derived GRNs in plants and identifying known and novel candidate regulators, improving our understanding of gene regulation in plants.

bioinformatics↗

bioRxiv2022

Mapping Responsive Genomic Elements to Heat Stress in a Maize Diversity Panel

Many plant species exhibit genetic variation for tolerating environmental stress. A transcriptome investigation of over 100 maize inbreds revealed many cis- and trans-acting eQTLs that influence the expression response to heat stress. The cis-acting eQTL in response to heat stress are identified in genes with differential responses to heat stress between genotypes as well as genes that are only expressed under heat stress. The cis-acting variants for heat stress responsive expression likely result from distinct promoter activities and the differential heat responses of the alleles were confirmed for selected genes using transient expression assays. Global foot-printing of transcription factor binding was performed in control and heat stress conditions to document regions with heat-enriched transcription factor binding occupancies. Footprints enriched near proximal regions of characterized heat-responsive genes in a large association panel can be utilized for prioritizing functional genomic regions that regulate genotype-specific responses under heat stress.

plant biology↗