scholarly journals Rice MEL2 regulates the timing of meiotic transition as a component of cytoplasmic RNA granules

2021 ◽  
Author(s):  
Manaki Mimura ◽  
Seijiro Ono ◽  
Ken-Ichi Nonomura
Keyword(s):  
Rna Binding ◽  
Land Plant ◽  
Land Plants ◽  
Transcriptional Level ◽  
Functional Conservation ◽  
Rna Granules ◽  
Intrinsically Disordered ◽  
Domain Structures ◽  
Cytoplasmic Rna ◽  
Mother Cells

Cytoplasmic RNA granules play important roles in gene expression at the post-transcriptional level. In this study, we found that the rice RNA-binding protein MEIOSIS ARRESTED AT LEPTOTENE2 (MEL2), which contributes to the control of meiotic entry timing, was a constituent of RNA granules, frequently associating with processing bodies and stress granules in the cytoplasm of premeiotic spore mother cells. MEL2 has four conserved domains and a large intrinsically disordered region, which is often responsible for formation and maintenance of granular structures. MEL2-like proteins with diverse domain structures are widely conserved in land plants and charophyte algae. In basal land plants, MEL2-like proteins are exclusively expressed in the sporophyte, which expresses meiotic genes, suggesting the functional conservation of MEL2 among land plant species. We propose here that MEL2 participates in post-transcriptional regulation of meiotic genes as a component of RNA granules to ensure proper timing of the meiotic transition.

At the Interface of Three Nucleic Acids: The Role of RNA-Binding Proteins and Poly(ADP-ribose) in DNA Repair

Acta Naturae ◽  
2017 ◽  
Vol 9 (2) ◽  
pp. 4-16 ◽  
Author(s):  
E. E. Alemasova ◽  
O. I. Lavrik
Keyword(s):  
Dna Damage ◽  
Dna Repair ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Protein ◽  
Regulation Of Gene Expression ◽  
Rna Granules ◽  
Dna And Rna ◽  
Cytoplasmic Rna

RNA-binding proteins (RBPs) regulate RNA metabolism, from synthesis to decay. When bound to RNA, RBPs act as guardians of the genome integrity at different levels, from DNA damage prevention to the post-transcriptional regulation of gene expression. Recently, RBPs have been shown to participate in DNA repair. This fact is of special interest as DNA repair pathways do not generally involve RNA. DNA damage in higher organisms triggers the formation of the RNA-like polymer - poly(ADP-ribose) (PAR). Nucleic acid-like properties allow PAR to recruit DNA- and RNA-binding proteins to the site of DNA damage. It is suggested that poly(ADP-ribose) and RBPs not only modulate the activities of DNA repair factors, but that they also play an important role in the formation of transient repairosome complexes in the nucleus. Cytoplasmic biomolecules are subjected to similar sorting during the formation of RNA assemblages by functionally related mRNAs and promiscuous RBPs. The Y-box-binding protein 1 (YB-1) is the major component of cytoplasmic RNA granules. Although YB-1 is a classic RNA-binding protein, it is now regarded as a non-canonical factor of DNA repair.

scholarly journals Proteome-wide quantitative RNA interactome capture (qRIC) identifies phosphorylation sites with regulatory potential in RBM20

2021 ◽  
Author(s):  
Carlos Henrique Vieira-Vieira ◽  
Vita Dauksaite ◽  
Michael Gotthardt ◽  
Matthias Selbach
Keyword(s):  
Posttranslational Modification ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Transcriptional Level ◽  
Phosphorylation Sites ◽  
Rna Granules ◽  
Regulatory Phosphorylation ◽  
Splicing Regulator ◽  
Regulatory Potential

RNA-binding proteins (RBPs) are major regulators of gene expression at the post- transcriptional level. While many posttranslational modification sites in RBPs have been identified, little is known about how these modifications regulate RBP function. Here, we developed quantitative RNA-interactome capture (qRIC) to quantify the fraction of cellular RBPs pulled down with polyadenylated mRNAs. Applying qRIC to HEK293T cells quantified pull-down efficiencies of over 300 RBPs. Combining qRIC with phosphoproteomics allowed us to systematically compare pull-down efficiencies of phosphorylated and non-phosphorylated forms of RBPs. Over hundred phosphorylation events increased or decreased pull-down efficiency compared to the unmodified RBPs and thus have regulatory potential. Our data captures known regulatory phosphorylation sites in ELAVL1, SF3B1 and UPF1 and identifies new potentially regulatory sites. Follow-up experiments on the cardiac splicing regulator RBM20 revealed that multiple phosphorylation sites in the C-terminal disordered region affect nucleo-cytoplasmic localization, association with cytosolic RNA granules and alternative splicing. Together, we show that qRIC is a scalable method to identify functional posttranslational modification sites in RBPs.

scholarly journals RNA granules

2006 ◽  
Vol 172 (6) ◽  
pp. 803-808 ◽  
Author(s):  
Paul Anderson ◽  
Nancy Kedersha
Keyword(s):  
Messenger Rna ◽  
Posttranscriptional Regulation ◽  
Spatial Organization ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Regulation Of Gene Expression ◽  
Processing Bodies ◽  
Rna Granules ◽  
Cytoplasmic Rna ◽  
Messenger Rna Translation

Cytoplasmic RNA granules in germ cells (polar and germinal granules), somatic cells (stress granules and processing bodies), and neurons (neuronal granules) have emerged as important players in the posttranscriptional regulation of gene expression. RNA granules contain various ribosomal subunits, translation factors, decay enzymes, helicases, scaffold proteins, and RNA-binding proteins, and they control the localization, stability, and translation of their RNA cargo. We review the relationship between different classes of these granules and discuss how spatial organization regulates messenger RNA translation/decay.

scholarly journals RNA-binding proteins with mixed charge domains self-assemble and aggregate in Alzheimer’s Disease

2018 ◽  
Author(s):  
Isaac Bishof ◽  
Eric B. Dammer ◽  
Duc M. Duong ◽  
Marla Gearing ◽  
James J. Lah ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Significant Proportion ◽  
Mass Spectrometry Analysis ◽  
Rna Granules ◽  
Intrinsically Disordered ◽  
Small Nuclear Ribonucleoprotein

ABSTRACTU1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and other RNA binding proteins (RBPs) are mislocalized to cytoplasmic neurofibrillary Tau aggregates in Alzheimer’s disease (AD), yet understanding of the mechanisms that cause their aggregation is limited. Many RBPs that aggregate in neurodegenerative diseases self-assemble into RNA granules through intrinsically disordered low complexity (LC) domains. We report here that a LC domain within U1-70K of mixed charge, containing highly repetitive complementary repeats of basic (R/K) and acidic (D/E) residues, shares many of the same properties of the Q/N-rich LC domains found in the RBPs TDP-43 and FUS. These properties include the ability to self-assemble into oligomers, and to form nuclear granules. To analyze the functional roles of the U1-70K LC domains, we performed co-immunoprecipitation and quantitative mass spectrometry analysis of recombinant U1-70K and deletions lacking the C-terminal LC domain(s). A network-driven approach resolved functional classes of U1-70K interacting proteins that showed dependency on the U1-70K LC domain(s) for their interaction. This included structurally similar RBPs, such as LUC7L3 and RBM25, which require their respective mixed charge domains for reciprocal interactions with U1-70K and for participation in nuclear RNA granules. Strikingly, a significant proportion of RBPs with mixed charge domains have elevated insolubility in AD brain proteome compared to controls. Furthermore, we show that the mixed charge LC domain of U1-70K can interact with Tau from AD brain. These findings highlight mechanisms for mixed charge domains in stabilizing RBP interactions and in potentially mediating co-aggregation with pathological Tau isoforms in AD.

scholarly journals Recruitment of mRNAs to P granules by gelation with intrinsically-disordered proteins

2019 ◽  
Author(s):  
Chih-Yung S. Lee ◽  
Andrea Putnam ◽  
Tu Lu ◽  
Shuaixin He ◽  
John Paul T. Ouyang ◽  
...  
Keyword(s):  
Cell Fate ◽  
Intrinsically Disordered Proteins ◽  
Intrinsically Disordered Protein ◽  
Disordered Proteins ◽  
P Granules ◽  
C Elegans ◽  
Rna Granules ◽  
Intrinsically Disordered ◽  
Cytoplasmic Rna ◽  
Germ Granules

AbstractAnimals with germ plasm assemble cytoplasmic RNA granules (germ granules) that segregate with the embryonic germ lineage. How germ granules assemble and recruit RNA is not well understood. Here we characterize the assembly and RNA composition of the germ (P) granules of C. elegans. ∼500 maternal mRNAs are recruited into P granules by a sequence independent mechanism that favors mRNAs with low ribosome coverage. Translational activation correlates temporally with P granule exit for two mRNAs that code for germ cell fate regulators. mRNAs are recruited into the granules by MEG-3, an intrinsically disordered protein that condenses with RNA to form nanoscale gels. Our observations reveal parallels between germ granules and stress granules and suggest that cytoplasmic RNA granules are reversible super-assemblies of nanoscale RNA-protein gel condensates.

scholarly journals RNA-binding proteins, RNA granules, and gametes: is unity strength?

Reproduction ◽  
2011 ◽  
Vol 142 (6) ◽  
pp. 803-817 ◽  
Author(s):  
Mai Nguyen-Chi ◽  
Dominique Morello
Keyword(s):  
Germ Cells ◽  
Small Rna ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Mrna Translation ◽  
Rna Granules ◽  
Ribonucleoprotein Complexes ◽  
Cytoplasmic Rna

Changes in mRNA translation and degradation represent post-transcriptional processes operating during gametogenesis and early embryogenesis to ensure regulated protein synthesis. Numerous mRNA-binding proteins (RBPs) have been described in multiple animal models that contribute to the control of mRNA translation and decay during oogenesis and spermatogenesis. An emerging view from studies performed in germ cells and somatic cells is that RBPs associate with their target mRNAs in RNA–protein (or ribonucleoprotein) complexes (mRNPs) that assemble in various cytoplasmic RNA granules that communicate with the translation machinery and control mRNA storage, triage, and degradation. In comparison withXenopus, Caenorhabditis elegans, orDrosophila, the composition and role of cytoplasmic RNA-containing granules in mammalian germ cells are still poorly understood. However, regained interest for these structures has emerged with the recent discovery of their role in small RNA synthesis and transposon silencing through DNA methylation. In this review, we will briefly summarize our current knowledge on cytoplasmic RNA granules in murine germ cells and describe the role of some of the RBPs they contain in regulating mRNA metabolism and small RNA processing during gametogenesis.

scholarly journals Spatial patterning of P granules by RNA-induced phase separation of the intrinsically-disordered protein MEG-3

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Jarrett Smith ◽  
Deepika Calidas ◽  
Helen Schmidt ◽  
Tu Lu ◽  
Dominique Rasoloson ◽  
...  
Keyword(s):  
Phase Separation ◽  
Rna Binding ◽  
Intrinsically Disordered Protein ◽  
General Mechanism ◽  
P Granules ◽  
Rna Granules ◽  
Intrinsically Disordered ◽  
Disordered Protein

RNA granules are non-membrane bound cellular compartments that contain RNA and RNA binding proteins. The molecular mechanisms that regulate the spatial distribution of RNA granules in cells are poorly understood. During polarization of the C. elegans zygote, germline RNA granules, called P granules, assemble preferentially in the posterior cytoplasm. We present evidence that P granule asymmetry depends on RNA-induced phase separation of the granule scaffold MEG-3. MEG-3 is an intrinsically disordered protein that binds and phase separates with RNA in vitro. In vivo, MEG-3 forms a posterior-rich concentration gradient that is anti-correlated with a gradient in the RNA-binding protein MEX-5. MEX-5 is necessary and sufficient to suppress MEG-3 granule formation in vivo, and suppresses RNA-induced MEG-3 phase separation in vitro. Our findings suggest that MEX-5 interferes with MEG-3’s access to RNA, thus locally suppressing MEG-3 phase separation to drive P granule asymmetry. Regulated access to RNA, combined with RNA-induced phase separation of key scaffolding proteins, may be a general mechanism for controlling the formation of RNA granules in space and time.

scholarly journals Evolution of RGF/GLV/CLEL Peptide Hormones and Their Roles in Land Plant Growth and Regulation

2021 ◽  
Vol 22 (24) ◽  
pp. 13372
Author(s):  
Yitian Fang ◽  
Jinke Chang ◽  
Tao Shi ◽  
Wenchun Luo ◽  
Yang Ou ◽  
...  
Keyword(s):  
Root Development ◽  
Plant Root ◽  
Purifying Selection ◽  
Land Plant ◽  
Land Plants ◽  
Functional Conservation ◽  
Key Innovation ◽  
Peptide Family ◽  
Duplication Events ◽  
Cell Niche

Rooting is a key innovation during plant terrestrialization. RGFs/GLVs/CLELs are a family of secreted peptides, playing key roles in root stem cell niche maintenance and pattern formation. The origin of this peptide family is not well characterized. RGFs and their receptor genes, RGIs, were investigated comprehensively using phylogenetic and genetic analyses. We identified 203 RGF genes from 24 plant species, representing a variety of land plant lineages. We found that the RGF genes originate from land plants and expand via multiple duplication events. The lineage-specific RGF duplicates are retained due to their regulatory divergence, while a majority of RGFs experienced strong purifying selection in most land plants. Functional analysis indicated that RGFs and their receptor genes, RGIs, isolated from liverwort, tomato, and maize possess similar biological functions with their counterparts from Arabidopsis in root development. RGFs and RGIs are likely coevolved in land plants. Our studies shed light on the origin and functional conservation of this important peptide family in plant root development.

scholarly journals Spatial patterning of P granules by RNA-induced phase separation of the intrinsically-disordered protein MEG-3

2016 ◽  
Author(s):  
Jarrett Smith ◽  
Deepika Calidas ◽  
Helen Schmidt ◽  
Tu Lu ◽  
Dominique Rasoloson ◽  
...  
Keyword(s):  
Phase Separation ◽  
Rna Binding ◽  
Intrinsically Disordered Protein ◽  
P Granules ◽  
C Elegans ◽  
Rna Granules ◽  
Intrinsically Disordered ◽  
Disordered Protein

ABSTRACTRNA granules are non-membrane bound cellular compartments that contain RNA and RNA binding proteins. The molecular mechanisms that regulate the spatial distribution of RNA granules in cells are poorly understood. During polarization of the C. elegans zygote, germline RNA granules, called P granules, assemble preferentially in the posterior cytoplasm. We present evidence that P granule asymmetry depends on RNA-induced phase separation of the granule scaffold MEG-3. MEG-3 is an intrinsically disordered protein that binds and phase separates with RNA in vitro. In vivo, MEG-3 forms a posterior-rich concentration gradient that is anti-correlated with a gradient in the RNA-binding protein MEX-5. MEX-5 is necessary and sufficient to suppress MEG-3 granule formation in vivo, and suppresses RNA-induced MEG-3 phase separation in vitro. Our findings support a model whereby MEX-5 functions as an mRNA sink to locally suppress MEG-3 phase separation and drive P granule asymmetry.HIGHLIGHTS- The intrinsically-disordered protein MEG-3 is essential for localized assembly of P granules in C. elegans zygotes.- MEG-3 binds RNA and RNA stimulates MEG-3 phase separation.- The RNA-binding protein MEX-5 inhibits MEG-3 granule assembly in the anterior cytoplasm by sequestering RNA.

Dri1 mediates heterochromatin assembly via RNAi and histone deacetylation

Genetics ◽  
2021 ◽  
Author(s):  
Hyoju Ban ◽  
Wenqi Sun ◽  
Yu-hang Chen ◽  
Yong Chen ◽  
Fei Li
Keyword(s):  
Histone Deacetylases ◽  
Genome Stability ◽  
Rna Binding ◽  
Histone Deacetylation ◽  
Rnai Pathway ◽  
Chromatin Domain ◽  
Heterochromatin Protein 1 ◽  
Intrinsically Disordered ◽  
C Terminus ◽  
Heterochromatin Assembly

Abstract Heterochromatin, a transcriptionally silenced chromatin domain, is important for genome stability and gene expression. Histone 3 lysine 9 methylation (H3K9me) and histone hypoacetylation are conserved epigenetic hallmarks of heterochromatin. In fission yeast, RNA interference (RNAi) plays a key role in H3K9 methylation and heterochromatin silencing. However, how RNAi machinery and histone deacetylases (HDACs) are coordinated to ensure proper heterochromatin assembly is still unclear. Previously, we showed that Dpb4, a conserved DNA polymerase epsilon subunit, plays a key role in the recruitment of HDACs to heterochromatin during S phase. Here, we identified a novel RNA-binding protein Dri1 that interacts with Dpb4. GFP-tagged Dri1 forms distinct foci mostly in the nucleus, showing a high degree of colocalization with Swi6/Heterochromatin Protein 1. Deletion of dri1+ leads to defects in silencing, H3K9me, and heterochromatic siRNA generation. We also showed that Dri1 physically associates with heterochromatic transcripts, and is required for the recruitment of the RNA-induced transcriptional silencing (RITS) complex via interacting with the complex. Furthermore, loss of Dri1 decreases the association of the Sir2 HDAC with heterochromatin. We further demonstrated that the C-terminus of Dri1 that includes an intrinsically disordered (IDR) region and three zinc fingers is crucial for its role in silencing. Together, our evidences suggest that Dri1 facilitates heterochromatin assembly via the RNAi pathway and HDAC.

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