Emerging roles for RNA polymerase II CTD in Arabidopsis

•We examine regulation of transcription and RNA processing through CTD modifications. •We highlight elements regulating post-translational modification of the CTD. •Plants lack key regulatory components involved in promoter-proximal pausing. •Plants lack key components of the Nrd1-dependent transcription termination pathway. •RNAPII CTD phosphorylation is required for miRNA biogenesis. Post-translational modifications of the carboxy-terminal domain of the largest subunit of RNA polymerase II (RNAPII CTD) provide recognition marks to coordinate recruitment of numerous nuclear factors controlling transcription, cotranscriptional RNA processing, chromatin remodeling, and RNA export. Compared with the progress in yeast and mammals, deciphering the regulatory roles of position-specific combinatorial CTD modifications, the so-called CTD code, is still at an early stage in plants. In this review, we discuss some of the recent advances in understanding of the molecular mechanisms controlling the deposition and recognition of RNAPII CTD marks in plants during the transcriptional cycle and highlight some intriguing differences between regulatory components characterized in yeast, mammals, and plants. Post-translational modifications of the carboxy-terminal domain of the largest subunit of RNA polymerase II (RNAPII CTD) provide recognition marks to coordinate recruitment of numerous nuclear factors controlling transcription, cotranscriptional RNA processing, chromatin remodeling, and RNA export. Compared with the progress in yeast and mammals, deciphering the regulatory roles of position-specific combinatorial CTD modifications, the so-called CTD code, is still at an early stage in plants. In this review, we discuss some of the recent advances in understanding of the molecular mechanisms controlling the deposition and recognition of RNAPII CTD marks in plants during the transcriptional cycle and highlight some intriguing differences between regulatory components characterized in yeast, mammals, and plants. argonautes are main components of the silencing effector complexes that are involved in small RNA-directed silencing. after the C-terminal domain of a breast cancer susceptibility domain is an evolutionarily conserved phosphopeptide-binding domain. cyclin-dependent kinase (CDK)-activating kinase 1 is a CTD Ser7-kinase. an evolutionarily conserved nuclear protein complex formed from CBP20 and CBP80/ABH1. COMPASS and COMPASS-like complexes are conserved complexes that catalyze methylation of histone H3K4 at the early body of a transcribed gene. CPLs catalyze dephosphorylation of the RNAPII CTD in Arabidopsis. CDKs control RNA metabolism and checkpoint transitions of the cell cycle. a heterodimer of Spt4 and Spt5. prolyl isomerase catalyzes isomerization of the RNAPII CTD in yeast. a chromatin-specific histone chaperone formed from Spt16 and Pob3. a plant-specific protein containing two RNA-recognition motifs and one WW domain that is required for early transcription termination genome wide. a catalytic domain containing the DXDXT/V catalytic motif that is found in many CTD phosphatases. a spen family protein that controls early 3′ end formation. a plant homolog of yeast Pfs2p and mammalian WDR33, which are conserved RNA 3′ end processing factors. dimethylated lysine 4 of histone H3. trimethylated lysine 4 of histone H3. a small, non-coding RNA molecule that is processed from stem–loop precursors transcribed by RNAPII. an RNA molecule containing genetic information from the DNA of a gene, which is translated to protein by ribosomes. a bifunctional capping enzyme in mammals. a complex formed from four proteins (NELF-A, NELF-B, NELF-C or NELF-D, and NELFE). RNAPII-associated complex is a highly conserved protein complex that regulates histone modifications throughout the transcription cycle. catalyzes isomerization of the carboxy-terminal domain of the RNAPII CTD in mammals. an RNA-binding protein involved in transcription-coupled splicing. a heterodimer complex comprising a catalytic subunit, CDK9, and a coregulatory cyclin partner. an immature single strand of mRNA that contains both exons and introns. the initial transcript of a miRNA gene before processing to pre-miRNA. synthesizes mRNAs and many small RNAs using DNA as template. a zinc-finger protein that is essential for proper trimming and maturation of miRNAs. a histone deacetyltransferase complex that prevents the initiation of transcription of cryptic transcripts. dephosphorylates Ser5P marks of the carboxy-terminal domain of the RNAPII CTD. small, double-stranded RNA (dsRNA) molecules that control the level of target transcripts via target cleavage, DNA methylation, or translational inhibition. RNA–protein complexes that are components of the spliceosome. RNA molecules (approximately 70–500 nt) that form snRNPs with proteins and are involved in RNA processing and telomere maintenance. guides the processing of precursors of rRNA (pre-rRNAs) and post-transcriptional modifications of rRNA, tRNA, and snRNA. a multifunctional complex involved in chromatin modifications at gene promoter regions, chromatin remodeling, transcription pre-initiation complex assembly, and transcription elongation. a multifunctional CTD phosphatase. a subgroup of the AMP superfamily. a basal transcription factor that is a member of the transcription pre-initiation complex. a multisubunit basal transcription factor that has important roles in transcription and the DNA repair system. a protein–protein-interacting domain that binds to proline-rich motifs and phosphorylated serine/threonine–proline sites.