scholarly journals AGO4 is specifically required for heterochromatic siRNA accumulation at Pol V-dependent loci in Arabidopsis thaliana

2016 ◽  
Author(s):  
Feng Wang ◽  
Michael J. Axtell
Keyword(s):  
Arabidopsis Thaliana ◽  
Rna Polymerase ◽  
Critical Role ◽  
Small Subset ◽  
Data Sets ◽  
Pol V ◽  
Genome Wide ◽  
Secondary Sirnas ◽  
Rna Polymerase Iv ◽  
Heterochromatic Sirna

Significance statementGenome-wide characterization of AGO4-dependent siRNAs revealed that AGO4 is required for the accumulation of a small subset of heterochromatic siRNAs in Arabidopsis thaliana. These AGO4-depdenent siRNAs are likely secondary het-siRNAs produced by a self-reinforcing loop of RdDM. Slicing-defective AGO4 is unable to fully complement het-siRNA accumulation from an ago4 mutant, demonstrating the critical role of AGO4 catalytic ability in het-siRNA accumulation.Summary: 152; Introduction: 618; Results: 1291; Discussion: 1013; Experimental procedures: 881; Acknowledgements: 24; Figure legends: 568; Author contribution: 25; Conflict of interest: 13; Funding: 34; References: 1289SummaryIn plants, 24 nucleotide long heterochromatic siRNAs (het-siRNAs) transcriptionally regulate gene expression by RNA-directed DNA methylation (RdDM). The biogenesis of most het-siRNAs depends on the plant-specific RNA polymerase IV (Pol IV), and ARGONAUTE4 (AGO4) is a major het-siRNA effector protein. Through genome-wide analysis of sRNA-seq data sets, we found that AGO4 is required for the accumulation of a small subset of het-siRNAs. The accumulation of AGO4-dependent het-siRNAs also requires several factors known to participate in the effector portion of the RdDM pathway, including RNA POLYMERASE V (POL V), DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) and SAWADEE HOMEODOMAIN HOMOLOG 1 (SHH1). Like many AGO proteins, AGO4 is an endonuclease that can ‘slice’ RNAs. We found that a slicing-defective AGO4 was unable to fully recover AGO4-dependent het-siRNA accumulation from ago4 mutant plants. Collectively, our data suggest that AGO4-dependent siRNAs are secondary siRNAs dependent on the prior activity of the RdDM pathway at certain loci.

scholarly journals Genome-wide co-expression distributions as a metric to prioritize genes of functional importance

2020 ◽  
Author(s):  
Pâmela A. Alexandre ◽  
Nicholas J. Hudson ◽  
Sigrid A. Lehnert ◽  
Marina R.S. Fortes ◽  
Marina Naval-Sánchez ◽  
...  
Keyword(s):  
Network Connectivity ◽  
Wide Distribution ◽  
Small Subset ◽  
Data Sets ◽  
Biological Signal ◽  
Genome Wide ◽  
Gene Level ◽  
Complementary Strategy ◽  
Enrichment Process ◽  
Genome Wide Gene Expression

AbstractGenome-wide gene expression is routinely used as a tool to gain a systems-level understanding of complex, biological processes. Numerical approaches that have been used to highlight influential genes include abundance, differential expression, differential variation, network connectivity and differential connectivity. Network connectivity tends to be built on a small subset of extremely high co-expression signals that are deemed significant, but this overlooks the vast majority of pairwise signals. Here, we aimed to assess a complementary strategy, namely whether the entire shape of the distribution of genome-wide co-expression values contains a meaningful biological signal that has hitherto remained hidden from view. We have developed a computational pipeline to assign one of 8 distributions (including normal, skewed, bimodal, kurtotic, inverted) to every gene. We then used a hypergeometric enrichment process to determine if particular genes (regulators versus non-regulators) and properties (differentially expressed or not) tend to be associated with particular distributions greater than would be expected by chance. Examination of several distinct data sets spanning 4 species indicates that there is indeed an additional biological signal present in the genome-wide distribution of co-expression values which would be overlooked by currently adopted approaches.Author summaryHigh-throughput technologies, such as RNA-Seq, enables access to a vast amount of data. Here, we describe a new approach to interrogate these data and extract further information to help researchers to understand complex phenotypes. Our method is based on gene-level co-expression distributions which were compared to eight possible template shapes to group genes with similar behaviours. The method was tested using five different datasets and the consistency of the results indicate it can be used as a complementary strategy to analyse transcriptomic data.

scholarly journals Single nucleosome imaging reveals loose genome chromatin networks via active RNA polymerase II

2019 ◽  
Vol 218 (5) ◽  
pp. 1511-1530 ◽  
Author(s):  
Ryosuke Nagashima ◽  
Kayo Hibino ◽  
S.S. Ashwin ◽  
Michael Babokhov ◽  
Shin Fujishiro ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Computational Modeling ◽  
Rna Polymerase Ii ◽  
Gene Transcription ◽  
Liquid Droplet ◽  
Critical Role ◽  
Chromatin Domain ◽  
Related Factors ◽  
Chromatin Dynamics ◽  
Genome Wide

Although chromatin organization and dynamics play a critical role in gene transcription, how they interplay remains unclear. To approach this issue, we investigated genome-wide chromatin behavior under various transcriptional conditions in living human cells using single-nucleosome imaging. While transcription by RNA polymerase II (RNAPII) is generally thought to need more open and dynamic chromatin, surprisingly, we found that active RNAPII globally constrains chromatin movements. RNAPII inhibition or its rapid depletion released the chromatin constraints and increased chromatin dynamics. Perturbation experiments of P-TEFb clusters, which are associated with active RNAPII, had similar results. Furthermore, chromatin mobility also increased in resting G0 cells and UV-irradiated cells, which are transcriptionally less active. Our results demonstrated that chromatin is globally stabilized by loose connections through active RNAPII, which is compatible with models of classical transcription factories or liquid droplet formation of transcription-related factors. Together with our computational modeling, we propose the existence of loose chromatin domain networks for various intra-/interchromosomal contacts via active RNAPII clusters/droplets.

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