@article {129504, title = {Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains.}, journal = {Genome Res}, year = {2023}, month = {2023 Jun 05}, abstract = {

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 with 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.

}, issn = {1549-5469}, doi = {10.1101/gr.277353.122}, author = {Vivek Hari Sundar G and Swetha, Chenna and Basu, Debjani and Pachamuthu, Kannan and Raju, Steffi and Chakraborty, Tania and Mosher, Rebecca A and Shivaprasad, P V} } @article {99103, title = {Essential role of γ-clade RNA-dependent RNA polymerases in rice development and yield-related traits is linked to their atypical polymerase activities regulating specific genomic regions.}, journal = {New Phytol}, year = {2021}, month = {2021 Aug 27}, abstract = {

RNA-dependent RNA polymerases (RDR) generate double-stranded (ds)RNA triggers for RNA silencing across eukaryotes. Among the three clades, α- and β-clade members are key components of RNA silencing and mediators of stress responses across eukaryotes. However, γ-clade members are unusual in that they are represented in phylogenetically distant plants and fungi, and their functions are unknown. Using genetic, bioinformatic and biochemical methods, we show that γ-clade RDRs from Oryza sativa L. are involved in plant development as well as regulation of expression of coding and non-coding RNAs. Overexpression of γ-clade RDRs in transgenic rice and tobacco plants resulted in robust growth phenotype, whereas their silencing in rice displayed strong inhibition of growth. Small (s)RNA and RNA-seq analysis of OsRDR3 mis-expression lines suggested that it is specifically involved in the regulation of repeat-rich regions in the genome. Biochemical analysis confirmed that OsRDR3 has robust polymerase activities on both single stranded (ss)RNA and ssDNA templates similar to the activities reported for α-clade RDRs such as AtRDR6. Our results provide the first evidence of the importance of γ-clade RDRs in plant development, their atypical biochemical activities, and their contribution to the regulation of gene expression.

}, issn = {1469-8137}, doi = {10.1111/nph.17700}, author = {Jha, Vikram and Narjala, Anushree and Basu, Debjani and Sujith, T N and Pachamuthu, Kannan and Chenna, Swetha and Nair, Ashwin and Shivaprasad, Padubidri V} } @article {82950, title = {Rice-specific Argonaute 17 controls reproductive growth and yield-associated phenotypes.}, journal = {Plant Mol Biol}, volume = {105}, year = {2021}, month = {2020 Sep 22}, pages = {99-114}, abstract = {

KEY MESSAGE: This manuscript describes the functions of an Argonaute protein named AGO17 in rice. AGO17 is required for the development of rice reproductive tissues. Argonaute (AGO) proteins are a well-conserved multigene family of regulators mediating gene silencing across eukaryotes. Monocot plants have additional members of AGO, the functions of which are poorly understood. Among the non-dicot AGO1 clade members in monocots, AGO17 expresses highly in reproductive tissues. Here we show that overexpression of Oryza sativa indica AGO17 in rice resulted in robust growth and increased yield, whereas its silencing resulted in reduced panicle length, less fertility, and poor growth. Small (s)RNA transcriptome analysis revealed misregulation of several miRNAs and other categories of sRNAs in silenced and overexpression lines, in agreement with its likely competition with other AGO1 clade members. Targets of differentially expressed miRNAs included previously unreported target RNAs coding for proteins involved in development, phase transition, and transport. Our results indicate a distinctive role for OsAGO17 in rice reproductive development that could be harnessed to improve yield.

}, issn = {1573-5028}, doi = {10.1007/s11103-020-01071-2}, author = {Pachamuthu, Kannan and Swetha, Chenna and Basu, Debjani and Das, Soumita and Singh, Indira and Sundar, Vivek Hari and Sujith, T N and Shivaprasad, Padubidri V} } @article {45303, title = {Major domestication-related phenotypes in indica rice are due to loss of miRNA-mediated laccase silencing.}, journal = {Plant Cell}, year = {2018}, month = {2018 Oct 19}, abstract = {

Domestication of rice included conversion of perennial wild species with few seeds to short plants that produced abundant seeds. Most domestication-associated changes were due to variations in transcription factors and other key genes such as enzymes. Here, we show that multiple yield-related traits associated with indica rice domestication are linked to micro (mi) RNA mediated regulation. Analysis of small (s) RNA datasets from cultivated indica rice lines, a few landraces and two wild relatives of rice revealed the presence of abundant 22-nucleotide (nt) reads in wild relatives that mapped to miR397 precursors. miR397 expressed at very high levels in wild relatives and at negligible levels in high-yielding cultivated lines. In its genera-specific form of 22-nt, miR397 targeted mRNAs coding for laccases to decay and induce robust secondary cascade silencing in wild species that required RNA-dependent RNA polymerase 6. In wild species of rice, reduced expression of laccases resulted in low lignification. As expected, over-expression of miR397 induced de-domestication phenotypes. Interestingly, nearly 26 unknown QTLs previously implicated for rice yield overlapped with laccases and miR397 genes. These results suggest the involvement of miRNAs in rice domestication-associated phenotypes.

}, issn = {1532-298X}, doi = {10.1105/tpc.18.00472}, author = {Swetha, Chenna and Basu, Debjani and Pachamuthu, Kannan and Tirumalai, Varsha and Nair, Ashwin and Prasad, Melvin and Shivaprasad, Padubidri V} }