Evidence for a unique DNA-dependent RNA polymerase in cereal crops

Trujillo, Joshua T.; Seetharam, Arun S.; Hufford, Matthew B.; Beilstein, Mark A.; Mosher, Rebecca A.

doi:10.1101/272708

Cited by 8 publications

(16 citation statements)

References 41 publications

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“…Poaceae-specific duplication of putative Pol V largest (NRPE1) and second-largest (NRPD2) subunits raises interesting questions about the assembly of multiple non-canonical polymerases in rice (Trujillo et al 2018). Zheng and colleagues recently demonstrated that NRPF1 is not redundant with NRPE1, and not required for RdDM in seedlings (Zheng et al 2021), suggesting that each paralogous largest subunit has unique function.…”

Section: Discussionmentioning

confidence: 99%

“…Together, these two largest subunits form the catalytic center of the polymerase. In the grass family, NRPE1 and NRPD2 duplicated, giving rise to NRPF1 and NRPF2, respectively (Trujillo et al 2018). Phylogenetic analysis suggests that these paralogs have new functions, however their functions are not clear.…”

Section: Introductionmentioning

confidence: 99%

“…Like mutations of the largest subunits, nrpd2 plants do not exhibit developmental phenotypes in Arabidopsis. In maize, there are three second subunit paralogs (two copies of NRPD2 and one copy of NRPF2) and phylogenetic analysis suggests these paralogs are functionally distinct (Haag et al 2014;Trujillo et al 2018). Mutants of NRPD2a show disrupted 24-nt siRNA production and defective paramutation, suggesting that there is little redundancy between paralogs (Sidorenko et al 2009;Stonaker et al 2009), while immunoprecipitation of polymerase complexes also hints that the duplicated NRPD2 subunits in grasses are not functionally redundant (Haag et al 2014;Trujillo et al 2018).…”

Section: Introductionmentioning

confidence: 99%

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A Null Allele of the Pol IV Second Subunit is Viable in Oryza sativa

Chakraborty

Trujillo

Kendall

et al. 2021

Preprint

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All eukaryotes possess three DNA-dependent RNA polymerases, Pols I-III, while land plants possess two additional polymerases, Pol IV and Pol V. Derived through duplication of Pol II subunits, Pol IV produces 24-nt siRNAs that interact with Pol V transcripts to target de novo DNA methylation and silence transcription of transposons. Members of the grass family encode additional duplicated subunits of Pol IV and V, raising questions regarding the function of each paralog. In this study, we identify a null allele of the putative Pol IV second subunit, NRPD2, and demonstrate that NRPD2 is the sole subunit functioning with NRPD1 in small RNA production and CHH methylation in leaves. Homozygous nrpd2 mutants have neither gametophytic defects, nor embryo lethality, although adult plants are dwarf and sterile.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A Null Allele of the Pol IV Second Subunit is Viable in Oryza sativa

Chakraborty

Trujillo

Kendall

et al. 2021

Preprint

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“…Future genetic analyses and artificial co-targeting strategies [60] will help dissect the complex interplay between the multiple layers of chromatin modification and non-coding RNA regulation in plants. eudicot plants [62,191]. Although the molecular and biological functions of these extra RNA polymerase subunits remain unknown, they might reinforce or even extend the RdDM machinery in species like rice, barley and maize.…”

Section: Discussionmentioning

confidence: 99%

Non-coding RNA polymerases that silence transposable elements and reprogram gene expression in plants

2020

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Multisubunit RNA polymerase (Pol) complexes are the core machinery for gene expression in eukaryotes. The enzymes Pol I, Pol II and Pol III transcribe distinct subsets of nuclear genes. This family of nuclear RNA polymerases expanded in terrestrial plants by the duplication of Pol II subunit genes. Two Pol II-related enzymes, Pol IV and Pol V, are highly specialized in the production of regulatory, non-coding RNAs. Pol IV and Pol V are the central players of RNA-directed DNA methylation (RdDM), an RNA interference pathway that represses transposable elements (TEs) and selected genes. Genetic and biochemical analyses of Pol IV/V subunits are now revealing how these enzymes evolved from ancestral Pol II to sustain non-coding RNA biogenesis in silent chromatin. Intriguingly, Pol IV-RdDM regulates genes that influence flowering time, reproductive development, stress responses and plant–pathogen interactions. Pol IV target genes vary among closely related taxa, indicating that these regulatory circuits are often species-specific. Data from crops like maize, rice, tomato and Brassica rapa suggest that dynamic repositioning of TEs, accompanied by Pol IV targeting to TE-proximal genes, leads to the reprogramming of plant gene expression over short evolutionary timescales.

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“…Functional information residing in the sequence motif (H) adjacent to the C can influence both the frequency of methylation and the recruitment of specific methyltransferases acting upon the trinucleotide (Law & Jacobsen, ; Gouil & Baulcombe, ). The RNA‐directed DNA methylation (RdDM) pathway employs specialized plant‐specific RNA polymerases to establish DNA methylation: NRPD or POLIV, NRPE or POLV and the recently described grass‐ (Poacea) specific NRPF or POLVI (Box ) (Haag & Pikaard, ; Zhou & Law, ; Trujillo et al ., ). RNA POLYMERASE IV (POLIV) transcribes short (26–45 nucleotides) single‐stranded RNA (ssRNA) from the template/target loci.…”

Section: Establishing Dna Methylation Through the Rna‐directed Dna Mementioning

confidence: 97%

DNA methylation in Marchantia polymorpha

et al. 2019

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Summary Methylation of DNA is an epigenetic mechanism for the control of gene expression. Alterations in the regulatory pathways involved in the establishment, perpetuation and removal of DNA methylation can lead to severe developmental alterations. Our understanding of the mechanistic aspects and relevance of DNA methylation comes from remarkable studies in well‐established angiosperm plant models including maize and Arabidopsis. The study of plant models positioned at basal lineages opens exciting opportunities to expand our knowledge on the function and evolution of the components of DNA methylation. In this Tansley Insight, we summarize current progress in our understanding of the molecular basis and relevance of DNA methylation in the liverwort Marchantia polymorpha.

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Evidence for a unique DNA-dependent RNA polymerase in cereal crops

Abstract: 38. CC-BY-NC-ND 4.0 International license It is made available under a (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.

Cited by 8 publications

References 41 publications

A Null Allele of the Pol IV Second Subunit is Viable in Oryza sativa

A Null Allele of the Pol IV Second Subunit is Viable in Oryza sativa

Non-coding RNA polymerases that silence transposable elements and reprogram gene expression in plants

DNA methylation in Marchantia polymorpha

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