Abundance and distribution of RNA polymerase II in Arabidopsis interphase nuclei

Schubert, Veit; Weißhart, Klaus

doi:10.1093/jxb/erv091

Cited by 48 publications

(50 citation statements)

References 90 publications

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“…We used antibodies specific for the elongating form (phosphorylated at Ser2 of the CTD repeats) and specific for the nonphosphorylated form of RNAPII. In Arabidopsis interphase nuclei, the majority of RNAPII is globally dispersed in the euchromatic part of the nucleoplasm (Schubert and Weisshart, 2015). Consistently, our SIM analyses revealed that ELF7/SPT6L and both forms of RNAPII comprised separate, dispersed, reticulate structures within the euchromatin, but they were absent from the nucleolus and heterochromatin ( Figure 3).…”

Section: Elf7 and Spt6l Colocalize With Rnapii In Euchromatinsupporting

confidence: 76%

The Composition of the Arabidopsis RNA Polymerase II Transcript Elongation Complex Reveals the Interplay between Elongation and mRNA Processing Factors

et al. 2017

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Transcript elongation factors (TEFs) are a heterogeneous group of proteins that control the efficiency of transcript elongation of subsets of genes by RNA polymerase II (RNAPII) in the chromatin context. Using reciprocal tagging in combination with affinity purification and mass spectrometry, we demonstrate that in Arabidopsis thaliana, the TEFs SPT4/SPT5, SPT6, FACT, PAF1-C, and TFIIS copurified with each other and with elongating RNAPII, while P-TEFb was not among the interactors. Additionally, NAP1 histone chaperones, ATP-dependent chromatin remodeling factors, and some histone-modifying enzymes including Elongator were repeatedly found associated with TEFs. Analysis of double mutant plants defective in different combinations of TEFs revealed genetic interactions between genes encoding subunits of PAF1-C, FACT, and TFIIS, resulting in synergistic/epistatic effects on plant growth/development. Analysis of subnuclear localization, gene expression, and chromatin association did not provide evidence for an involvement of the TEFs in transcription by RNAPI (or RNAPIII). Proteomics analyses also revealed multiple interactions between the transcript elongation complex and factors involved in mRNA splicing and polyadenylation, including an association of PAF1-C with the polyadenylation factor CstF. Therefore, the RNAPII transcript elongation complex represents a platform for interactions among different TEFs, as well as for coordinating ongoing transcription with mRNA processing.

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Section: Elf7 and Spt6l Colocalize With Rnapii In Euchromatinsupporting

confidence: 76%

The Composition of the Arabidopsis RNA Polymerase II Transcript Elongation Complex Reveals the Interplay between Elongation and mRNA Processing Factors

et al. 2017

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“…Highly transcribed genes showed a tendency to couple in our data, suggesting that there is "AB" On the other hand, when we examined chromatin loops smaller than 6 kb, we found that a subset of them had strong Pol II binding on both interacting partners (Fig. 4D, highlighted with an arrow), perhaps reflecting active RNA polymerases aggregated within short distances (Schubert and Weisshart 2015). To address whether this pattern arises from interactions between highly expressed genes located close to each other in the genome and/or interactions within the same gene body, we focused on Pol II ChIPseq peaks in small chromatin loops.…”

Section: Transcribed Genes Do Not Show Strong Preference To Couplementioning

confidence: 66%

“…This model has been refined using advanced microscopy techniques. While the majority of active RNA Pol II molecules are globally dispersed in both animal and plant nuclei, a small subset forms clusters (Schubert 2014;Zhao et al 2014;Schubert and Weisshart 2015). To ask whether highly expressed genes that are at least 6 kb apart are more likely to interact with each other than less highly expressed genes, we selected genes based on their transcript levels, which correlated with Pol II binding (Fig.…”

Section: Transcribed Genes Do Not Show Strong Preference To Couplementioning

confidence: 99%

Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution

et al. 2016

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The three-dimensional packing of the genome plays an important role in regulating gene expression. We have used Hi-C, a genome-wide chromatin conformation capture (3C) method, to analyze Arabidopsis thaliana chromosomes dissected into subkilobase segments, which is required for gene-level resolution in this species with a gene-dense genome. We found that the repressive H3K27me3 histone mark is overrepresented in the promoter regions of genes that are in conformational linkage over long distances. In line with the globally dispersed distribution of RNA polymerase II in A. thaliana nuclear space, actively transcribed genes do not show a strong tendency to associate with each other. In general, there are often contacts between 5 ′ and 3 ′ ends of genes, forming local chromatin loops. Such self-loop structures of genes are more likely to occur in more highly expressed genes, although they can also be found in silent genes. Silent genes with local chromatin loops are highly enriched for the histone variant H3.3 at their 5 ′ and 3 ′ ends but depleted of repressive marks such as heterochromatic histone modifications and DNA methylation in flanking regions. Our results suggest that, different from animals, a major theme of genome folding in A. thaliana is the formation of structural units that correspond to gene bodies.

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“…Such studies include the mapping of RNA polymerase II in interphase nuclei of Arabidopsis in fixed samples with Cy and AlexaFluor fluorophores (Schubert and Weisshart, 2015) and the visualization of cortical microtubules in fixed root cells immunolabeled with antibodies conjugated to the photoswitchable fluorophore AlexaFluor 647 at a resolution of approximately 50 nm (Dong et al, 2015).…”

Section: Single-molecule Localization Microscopymentioning

confidence: 99%

Advances in Imaging Plant Cell Dynamics

et al. 2017

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Abundance and distribution of RNA polymerase II in Arabidopsis interphase nuclei

Abstract: HighlightSuper-resolution microscopy reveals the number of RNA polymerase II molecules in plant interphase nuclei. Both active and inactive polymerase variants aggregate in a range known from mammalian transcription factories.

Cited by 48 publications

References 90 publications

The Composition of the Arabidopsis RNA Polymerase II Transcript Elongation Complex Reveals the Interplay between Elongation and mRNA Processing Factors

The Composition of the Arabidopsis RNA Polymerase II Transcript Elongation Complex Reveals the Interplay between Elongation and mRNA Processing Factors

Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution

Advances in Imaging Plant Cell Dynamics

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