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Author(s): Gurol M. Suel [1]; Jordi Garcia-Ojalvo [2]; Louisa M. Liberman [1]; Michael B. Elowitz (corresponding author) [1] Certain types of cellular differentiation are probabilistic and transient [1, 2, 3]. [...]

Root branching in plants relies on the de novo formation of lateral roots. These are initiated from founder cells, triggering new formative divisions that generate lateral root primordia (LRP). The LRP size and shape depends on the balance between positive and negative signals that control cell proliferation., The mechanisms controlling proliferation potential of LRP cells remains poorly understood. We found that Arabidopsis thaliana MYB36, which have been previously shown to regulate genes required for Casparian strip formation and the transition from proliferation to differentiation in the primary root, plays a new role in controlling LRP development at later stages., We found that MYB36 is a novel component of LR development at later stages. MYB36 was expressed in the cells surrounding LRP where it controls a set of peroxidase genes, which maintain reactive oxygen species (ROS) balance. This was required to define the transition between proliferating and arrested cells inside the LRP, coinciding with the change from flat to dome-shaped primordia. Reducing the levels of hydrogen peroxide (H2O2) in myb36-5 significantly rescues the mutant phenotype., Our results uncover a role for MYB36 outside the endodermis during LRP development through a mechanism analogous to regulating the proliferation/differentiation transition in the root meristem. [ABSTRACT FROM AUTHOR]

Pairs of RNA molecules transcribed from partially or entirely complementary loci are called cis-natural antisense transcripts (cis-NATs), and they play key roles in the regulation of gene expression in many organisms. A promising experimental tool for profiling sense and antisense transcription is strand-specific RNA sequencing (ssRNA-seq). To identify cis-NATs using ssRNA-seq, we developed a new computational method based on a model comparison framework that incorporates the inherent variable efficiency of generating perfectly strand-specific libraries. Applying the method to new ssRNA-seq data from whole-root and cell-type"specific Arabidopsis libraries confirmed most of the known cis-NAT pairs and identified 918 additional cis-NAT pairs. Newly identified cis-NAT pairs are supported by polyadenylation data, alternative splicing patterns, and RT-PCR validation. We found 209 cis-NAT pairs that have opposite expression levels in neighboring cell types, implying cell-type"specific roles for cis-NATs. By integrating a genome-wide epigenetic profile of Arabidopsis, we identified a unique chromatin signature of cis-NATs, suggesting a connection between cis-NAT transcription and chromatin modification in plants. An analysis of small-RNA sequencing data showed that 1/44% of cis-NAT pairs produce putative cis-NAT"induced siRNAs. Taken together, our data and analyses illustrate the potential for multifaceted regulatory roles of plant cis-NATs. [ABSTRACT FROM AUTHOR]