Marand, A. P. — Page 2 | Search bioRxiv

bioRxiv2020

A cis-regulatory atlas in maize at single-cell resolution

Cis-regulatory elements (CREs) encode the genomic blueprints of spatiotemporal gene expression programs enabling highly specialized cell functions. To identify CREs at cell-type resolution in Zea mays, we implemented single-cell sequencing of Assay for Transposase Accessible Chromatin (scATAC-seq) in seedlings, embryonic roots, crown roots, axillary buds, and pistillate and staminate inflorescence. We describe 92 states of chromatin accessibility across 165,913 putative CREs and 52 known cell types. Patterns of transcription factor (TF) motif accessibility predicted cell identity with high accuracy, uncovered putative non-cell autonomous TFs, and revealed TF motifs underlying higher-order chromatin interactions. Comparison of maize and Arabidopsis thaliana developmental trajectories identified TF motifs with conserved patterns of accessibility. Cell type-specific CREs were enriched with enhancer activity, phenotype-associated genetic variants, and signatures of breeding-era selection. These data, along with companion software, Socrates, afford a comprehensive framework for understanding cellular heterogeneity, evolution, and cis-regulatory grammar of cell-type specification in a major crop.

genetics↗

bioRxiv2020

Cis-regulatory elements within TEs can influence expression of nearby maize genes

Transposable elements (TEs) have the potential to create regulatory variation both through disruption of existing DNA regulatory elements and through creation of novel DNA regulatory elements. In a species with a large genome, such as maize, the many TEs interspersed with genes creates opportunities for significant allelic variation due to TE presence/absence polymorphisms among individuals. We used information on putative regulatory elements in combination with knowledge about TE polymorphisms in maize to identify TE insertions that interrupt existing accessible chromatin regions (ACRs) in B73 as well as examples of polymorphic TEs that contain ACRs among four inbred lines of maize including B73, Mo17, W22, and PH207. The TE insertions in three other assembled maize genomes (Mo17, W22 or PH207) that interrupt ACRs that are present in the B73 genome can trigger changes to the chromatin suggesting the potential for both genetic and epigenetic influences of these insertions. Nearly 20% of the ACRs located over 2kb from the nearest gene are located within an annotated TE. These are regions of unmethylated DNA that show evidence for functional importance similar to ACRs that are not present within TEs. Using a large panel of maize genotypes we tested if there is an association between the presence of TE insertions that interrupt, or carry, an ACR and the expression of nearby genes. TEs that carry ACRs exhibit an enrichment for being associated with higher expression of nearby genes, suggesting that these TEs may create novel regulatory elements. These analyses highlight the potential for TEs to rewire transcriptional responses in eukaryotic genomes. Data AvailabilityIn this study we utilize previously published datasets that are available through the following accessions: SRX4727413, SRR8738272, and SRR8740852.

plant biology↗