Survival in Quiescence Requires the Euchromatic Deployment of Clr4/SUV39H by Argonaute-Associated Small RNAs

Joh, Richard I.; Khanduja, Jasbeer Singh; Calvo, Isabel A.; Mistry, Meeta; Palmieri, Christina M.; Savol, Andrej J.; Sui, Shannan Ho; Sadreyev, Ruslan I.; Aryee, Martin J.; Motamedi, Massoud

doi:10.1016/j.molcel.2016.11.020

Cited by 33 publications

(41 citation statements)

References 71 publications

(111 reference statements)

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“…Whereas RNAi machinery is required for establishing H3K9me at repetitive DNA elements and certain regulated genes 26,31 , RNAi-independent mechanisms involving MTREC and its associated factors assemble facultative heterochromatin at meiotic genes 14,17,25 . Our ChIP-chip and ChIP analyses showed that loss of the RNAi component Ago1 did not affect H3K9me peaks that are detected in cells grown at 18°C (Supplementary Fig.…”

Section: Resultsmentioning

confidence: 99%

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Iron homeostasis regulates facultative heterochromatin assembly in adaptive genome control

Larkin

Thillainadesan

Dhakshnamoorthy

et al. 2018

Nat Struct Mol Biol

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Iron metabolism is critical for sustaining life and maintaining human health. Here, we find that iron homeostasis is linked to facultative heterochromatin assembly and regulation of gene expression during adaptive genome control. We show that the fission yeast Clr4/Suv39h histone methyltransferase is part of a rheostat-like mechanism, in which transcriptional up-regulation of mRNAs in response to environmental change provides feedback to prevent their uncontrolled expression through heterochromatin assembly. Interestingly, proper iron homeostasis is required, as depletion of iron or down-regulation of iron transporters caused defects in heterochromatin assembly and unrestrained upregulation of gene expression. Remarkably, an unbiased genetic screen revealed that restoration of iron homeostasis is sufficient to re-establish facultative heterochromatin and proper gene control genome-wide. These results establish a role for iron homeostasis in facultative heterochromatin assembly and reveal a dynamic mechanism for reprogramming the genome in response to environmental changes.

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Section: Resultsmentioning

confidence: 99%

“…The RNA interference (RNAi) machinery targets facultative heterochromatin assembly at regulated genes 17,26,29,31 , in addition to constitutive heterochromatin assembly at centromeric repeats 27,32 . In another pathway, MTREC associated proteins recruit Clr4 to assemble facultative heterochromatin islands at meiotic genes 14,17,25,33 .…”

mentioning

confidence: 99%

Iron homeostasis regulates facultative heterochromatin assembly in adaptive genome control

Larkin

Thillainadesan

Dhakshnamoorthy

et al. 2018

Nat Struct Mol Biol

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“…We processed the data as mentioned in the corresponding download pages, before subjecting them to RAPID. We restricted our analysis to the sRNA-enriched genes available from their supplement [15] which can be accessed from https://bit.ly/2GSLcks. After pre-processing we subjected each GSM dataset to rapidStats, and compared them using rapidNorm.…”

Section: Schizosaccharomyces Pombementioning

confidence: 99%

“…The fission yeast, or Schizosaccharomyces pombe, is another widely studied unicellular eukaryotic model organism, where RNAi pathways are prevalent. We explored the time point datasets of WT, and three different knockdowns of S.pombe from the study by [15]. In this study, the authors investigated quiescence associated changes in small RNA transcriptomes and epigenetic modifications to identify the key players involved in quiescence.…”

Section: Analysis Of Schizosaccharomyces Pombe Knockdownsmentioning

confidence: 99%

“…They also examined the role of RNAi proteins, by knocking down three of them, namely, Ago1, Clr4, and Dcr1. One of the key findings was that during quiescence in S.pombe, a set of sRNAenriched genes were identified as crucial elements for the survival of the organism [15]. We explored these sRNA-enriched genes using RAPID, to demonstrate the discovering potential of RAPID.…”

Section: Analysis Of Schizosaccharomyces Pombe Knockdownsmentioning

confidence: 99%

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Automated analysis of small RNA datasets with RAPID

Karunanithi

Simón

Schulz

2018

Preprint

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Understanding the role of short-interfering RNA (siRNA) in diverse biological processes is of current interest and often approached through small RNA sequencing. However, analysis of these datasets is difficult due to the complexity of biological RNA processing pathways, which differ between species. Several properties like strand specificity, length distribution, and distribution of soft-clipped bases are few parameters known to guide researchers in understanding the role of siRNAs. We present RAPID, a generic eukaryotic siRNA analysis pipeline, which captures information inherent in the datasets and automatically produces numerous visualizations as user-friendly HTML reports, covering multiple categories required for siRNA analysis. RAPID also facilitates an automated comparison of multiple datasets, with one of the normalization techniques dedicated for siRNA knockdown analysis, and integrates differential expression analysis using DESeq2. RAPID is available under MIT license at https://github.com/SchulzLab/RAPID.We recommend using it as a conda environment available from https://anaconda.org/bioconda/rapid.

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Shaping the chromatin landscape at rRNA and tRNA genes, an emerging new role for RNA polymerase II transcription?

Yague‐Sanz

2023

Yeast

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Eukaryotic genes must be condensed into chromatin while remaining accessible to the transcriptional machinery to support gene expression. Among the three eukaryotic RNA polymerases (RNAP), RNAPII is unique, partly because of the C‐terminal domain (CTD) of its largest subunit, Rpb1. Rpb1 CTD can be extensively modified during the transcription cycle, allowing for the co‐transcriptional recruitment of specific interacting proteins. These include chromatin remodeling factors that control the opening or closing of chromatin. How the CTD‐less RNAPI and RNAPIII deal with chromatin at rRNA and tRNA genes is less understood. Here, we review recent advances in our understanding of how the chromatin at tRNA genes and rRNA genes can be remodeled in response to environmental cues in yeast, with a particular focus on the role of local RNAPII transcription in recruiting chromatin remodelers at these loci. In fission yeast, RNAPII transcription at tRNA genes is important to re‐establish a chromatin environment permissive to tRNA transcription, which supports growth from stationary phase. In contrast, local RNAPII transcription at rRNA genes correlates with the closing of the chromatin in starvation in budding and fission yeast, suggesting a role in establishing silent chromatin. These opposite roles might support a general model where RNAPII transcription recruits chromatin remodelers to tRNA and rRNA genes to promote the closing and reopening of chromatin in response to the environment.

show abstract

Survival in Quiescence Requires the Euchromatic Deployment of Clr4/SUV39H by Argonaute-Associated Small RNAs

Cited by 33 publications

References 71 publications

Iron homeostasis regulates facultative heterochromatin assembly in adaptive genome control

Iron homeostasis regulates facultative heterochromatin assembly in adaptive genome control

Automated analysis of small RNA datasets with RAPID

Shaping the chromatin landscape at rRNA and tRNA genes, an emerging new role for RNA polymerase II transcription?

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