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Across eukaryotes, gene regulation is manifested via chromatin states roughly distinguished as heterochromatin and euchromatin. The establishment, maintenance, and modulation of the chromatin states is mediated using several factors including chromatin modifiers. However, factors that avoid the intrusion of silencing signals into protein-coding genes are poorly understood. Here we show that a plant specific paralog of RNA polymerase (Pol) II, named Pol IV, is involved in avoidance of facultative heterochromatic marks in protein-coding genes, in addition to its well-established functions in silencing repeats and transposons. In its absence, H3K27 trimethylation (me3) mark intruded the protein-coding genes, more profoundly in genes embedded with repeats. In a subset of genes, spurious transcriptional activity resulted in small(s) RNA production, leading to post-transcriptional gene silencing. We show that such effects are significantly pronounced in rice, a plant with a larger genome with distributed heterochromatin compared withArabidopsis. Our results indicate the division of labor among plant-specific polymerases, not just in establishing effective silencing via sRNAs and DNA methylation but also in influencing chromatin boundaries.

 

We present a fully-coupled, implicit-in-time framework for solving a thermodynamically-consistent Cahn-Hilliard Navier-Stokes system that models two-phase flows. In this work, we extend the block iterative method presented in Khanwale et al. [Simulating two-phase flows with thermodynamically consistent energy stable Cahn-Hilliard Navier-Stokes equations on parallel adaptive octree based meshes, J. Comput. Phys. (2020)], to a fully-coupled, provably second-order accurate scheme in time, while maintaining energy-stability. The new method requires fewer matrix assemblies in each Newton iteration resulting in faster solution time. The method is based on a fully-implicit Crank-Nicolson scheme in time and a pressure stabilization for an equal order Galerkin formulation. That is, we use a conforming continuous Galerkin (cG) finite element method in space equipped with a residual-based variational multiscale (RBVMS) procedure to stabilize the pressure. We deploy this approach on a massively parallel numerical implementation using parallel octree-based adaptive meshes. We present comprehensive numerical experiments showing detailed comparisons with results from the literature for canonical cases, including the single bubble rise, Rayleigh-Taylor instability, and lid-driven cavity flow problems. We analyze in detail the scaling of our numerical implementation.