KH domain protein RCF3 is a tissue-biased regulator of the plant miRNA biogenesis cofactor HYL1

Karlsson, Patricia; Christie, Michael; Seymour, Danelle K.; Wang, Huan; Wang, Xi; Hagmann, Jörg; Kulcheski, Franceli Rodrigues; Manavella, Pablo Andrés

doi:10.1073/pnas.1512865112

Cited by 64 publications

(59 citation statements)

References 38 publications

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“…These PCR products were mixed and assembled by overlapping PCR and amplified with primers 5 ′ -GTTCGTTAGACTGGTTTAGGT-3 ′ and 5 ′ -TTTGGAGAAGAAGGCTTCTCT-3 ′ . The final PCR product, in which GFP was fused with NUP1, was cloned into a Gatewaycompatible pGREEN-IIS binary destination vector (Karlsson et al 2015). Similarly, to make the mCherry:CENH3 fusion protein, mCherry was amplified with primers 5 ′ -GTAAAAATCAATGG CCATCATCAAGGAGTT-3 ′ and 5 ′ -ACGCGATGCTTGGTTCTCGC ACCGCCACCCTTGTACAGCTCGTCCATGC-3 ′ , cenH3 (AT1G 01370) was amplified with primers 5 ′ -GCGAGAACCAAGCATCG CGT-3 ′ and 5 ′ -TCACCATGGTCTGCCTTTTC-3 ′ , these PCR products were assembled by overlapping PCR and amplified with primers 5 ′ -GTAAAAATCAATGGCCATCATCAAGGAGTT-3 ′ and 5 ′ -TC ACCATGGTCTGCCTTTTC-3 ′ .…”

Section: Plasmid Constructionmentioning

confidence: 99%

“…Similarly, to make the mCherry:CENH3 fusion protein, mCherry was amplified with primers 5 ′ -GTAAAAATCAATGG CCATCATCAAGGAGTT-3 ′ and 5 ′ -ACGCGATGCTTGGTTCTCGC ACCGCCACCCTTGTACAGCTCGTCCATGC-3 ′ , cenH3 (AT1G 01370) was amplified with primers 5 ′ -GCGAGAACCAAGCATCG CGT-3 ′ and 5 ′ -TCACCATGGTCTGCCTTTTC-3 ′ , these PCR products were assembled by overlapping PCR and amplified with primers 5 ′ -GTAAAAATCAATGGCCATCATCAAGGAGTT-3 ′ and 5 ′ -TC ACCATGGTCTGCCTTTTC-3 ′ . The PCR product was cloned into a Gateway-compatible pGREEN-IIS binary destination vector containing a 35S promoter (Karlsson et al 2015).…”

Section: Plasmid Constructionmentioning

confidence: 99%

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Nonrandom domain organization of the Arabidopsis genome at the nuclear periphery

Cheng

et al. 2017

Genome Res.

106

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The nuclear space is not a homogeneous biochemical environment. Many studies have demonstrated that the transcriptional activity of a gene is linked to its positioning within the nuclear space. Following the discovery of lamin-associated domains (LADs), which are transcriptionally repressed chromatin regions, the nonrandom positioning of chromatin at the nuclear periphery and its biological relevance have been studied extensively in animals. However, it remains unknown whether comparable chromatin organizations exist in plants. Here, using a strategy using restriction enzyme-mediated chromatin immunoprecipitation, we present genome-wide identification of nonrandom domain organization of chromatin at the peripheral zone of Arabidopsis thaliana nuclei. We show that in various tissues, 10%-20% of the regions on the chromosome arms are anchored at the nuclear periphery, and these regions largely overlap between different tissues. Unlike LADs in animals, the identified domains in plants are not gene-poor or A/T-rich. These domains are enriched with silenced protein-coding genes, transposable element genes, and heterochromatic marks, which collectively define a repressed environment. In addition, these domains strongly correlate with our genome-wide chromatin interaction data set (Hi-C) by largely explaining the patterns of chromatin compartments, revealed on Hi-C maps. Moreover, our results reveal a spatial compartment of different DNA methylation pathways that regulate silencing of transposable elements, where the CHH methylation of transposable elements located at the nuclear periphery and in the interior are preferentially mediated by CMT2 and DRM methyltransferases, respectively. Taken together, the results demonstrate functional partitioning of the Arabidopsis genome in the nuclear space.

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Section: Plasmid Constructionmentioning

confidence: 99%

Section: Plasmid Constructionmentioning

confidence: 99%

Nonrandom domain organization of the Arabidopsis genome at the nuclear periphery

Cheng

et al. 2017

Genome Res.

106

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“…How this protein might affect nodulation is not clear, although recent work has identified roles for members of this gene family in the regulation of miRNAs (Karlsson et al, 2015), suggesting that Medtr5g088410 could affect the expression of genes involved in nodulation. It is expressed at a comparatively low level in both nodules and roots with no distinct peak in time of expression (Supplemental Fig.…”

Section: Genetics Of Nodulationmentioning

confidence: 99%

Validating Genome-Wide Association Candidates Controlling Quantitative Variation in Nodulation

Curtin

Tiffin²,

Guhlin³

et al. 2017

Plant Physiol.

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“…Several protein factors, including DDL, CDC5, PRL1, and CBP20/80 (two cap-binding proteins), associate with the DCL1 complex to promote pri-miRNA processing (14,17,(20)(21)(22), whereas the elongator complex, NOT2 and MODIFIER OF SNC1, 2 (MOS2, an RNA-binding protein), are required for the correct assembly of the DCL1 complex (16,23). Proteins including SICKLE (SIC, a proline-rich protein), RECEPTOR FOR ACTIVATED C KINASE 1 (RACK1), STABILIZED1 (STA1, a pre-mRNA processing factor 6 homolog), HOS5 and GRP7 (a glycine-rich RNA-binding protein), act outside of the DCL1 complex to participate in pri-miRNA processing (24)(25)(26)(27)(28)(29). Protein modifications also regulate the activity of the DCL1 complex.…”

mentioning

confidence: 99%

STV1, a ribosomal protein, binds primary microRNA transcripts to promote their interaction with the processing complex in Arabidopsis

Liu

Zhang

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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MicroRNAs (miRNAs) are key regulators of gene expression. They are processed from primary miRNA transcripts (pri-miRNAs), most of which are transcribed by DNA-dependent polymerase II (Pol II). miRNA levels are precisely controlled to maintain various biological processes. Here, we report that SHORT VALVE 1 (STV1), a conserved ribosomal protein, acts in miRNA biogenesis in Arabidopsis. A portion of STV1 localizes in the nucleus and binds pri-miRNAs. Using primiR172b as a reporter, we show that STV1 binds the stem-loop flanked by a short 5′ arm within pri-miRNAs. Lack of STV1 reduces the association of pri-miRNAs with their processing complex. These data suggest that STV1 promotes miRNA biogenesis through facilitating the recruitment of pri-miRNAs to their processing complex. Furthermore, we show that STV1 indirectly involves in the occupancy of Pol II at the promoters of miRNA coding genes (MIR) and influences MIR promoter activities. Based on these results, we propose that STV1 refines the accumulation of miRNAs through its combined effects on pri-miRNA processing and transcription. This study uncovers an extraribosomal function of STV1.

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KH domain protein RCF3 is a tissue-biased regulator of the plant miRNA biogenesis cofactor HYL1

Cited by 64 publications

References 38 publications

Nonrandom domain organization of the Arabidopsis genome at the nuclear periphery

Nonrandom domain organization of the Arabidopsis genome at the nuclear periphery

Validating Genome-Wide Association Candidates Controlling Quantitative Variation in Nodulation

STV1, a ribosomal protein, binds primary microRNA transcripts to promote their interaction with the processing complex in Arabidopsis

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