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.

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 Proximity RNA labeling by APEX-Seq Reveals the Organization of Translation Initiation Complexes and Repressive RNA Granules

2018 ◽  
Author(s):  
Alejandro Padròn ◽  
Shintaro Iwasaki ◽  
Nicholas T. Ingolia
Keyword(s):  
Translation Initiation ◽  
Messenger Rna ◽  
Spatial Organization ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Rna Granules ◽  
Ribonucleoprotein Complexes ◽  
Spatial Environment ◽  
Dynamic Structures ◽  
As Stress

AbstractDiverse ribonucleoprotein complexes control messenger RNA processing, translation, and decay. Transcripts in these complexes localize to specific regions of the cell and can condense into non-membrane-bound structures such as stress granules. It has proven challenging to map the RNA composition of these large and dynamic structures, however. We therefore developed an RNA proximity labeling technique, APEX-Seq, which uses the ascorbate peroxidase APEX2 to probe the spatial organization of the transcriptome. We show that APEX-Seq can resolve the localization of RNAs within the cell and determine their enrichment or depletion near key RNA-binding proteins. Matching the spatial transcriptome, as revealed by APEX-Seq, with the spatial proteome determined by APEX-mass spectrometry (APEX-MS) provides new insights into the organization of translation initiation complexes on active mRNAs, as well as exposing unanticipated complexity in stress granule composition, and provides a powerful and general approach to explore the spatial environment of macromolecules.

scholarly journals Core spliceosomal Sm proteins as constituents of cytoplasmic mRNPs in plants

2019 ◽  
Author(s):  
Malwina Hyjek-Składanowska ◽  
Mateusz Bajczyk ◽  
Marcin Gołębiewski ◽  
Przemysław Nuc ◽  
Agnieszka Kołowerzo-Lubnau ◽  
...  
Keyword(s):  
Posttranscriptional Regulation ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Regulation Of Gene Expression ◽  
Mrna Translation ◽  
Mrna Splicing ◽  
Sm Proteins ◽  
Cytoplasmic Bodies ◽  
Evolutionarily Conserved ◽  
Processing Steps

ABSTRACTIn light of recent studies, many of the cytoplasmic posttranscriptional mRNA processing steps take place in highly specialized microdomains referred to as cytoplasmic bodies. These evolutionarily conserved microdomains are sites of regulation for both mRNA translation and degradation. It has been shown that in the larch microsporocyte cytoplasm, there is a significant pool of Sm proteins not related to snRNP complexes. These Sm proteins accumulate within distinct cytoplasmic bodies (S-bodies) that also contain mRNA. Sm proteins constitute an evolutionarily ancient family of small RNA-binding proteins. In eukaryotic cells, these molecules are involved in pre-mRNA splicing. The latest research indicates that in addition to this well-known function, Sm proteins could also have an impact on mRNA at subsequent stages of its life cycle. The aim of this work was to verify the hypothesis that canonical Sm proteins are part of the cytoplasmic mRNP complex and thus function in the posttranscriptional regulation of gene expression in plants.

scholarly journals Identification of hemicatenane-specific binding proteins by fractionation of HeLa nuclei extracts

2020 ◽  
Vol 477 (2) ◽  
pp. 509-524
Author(s):  
Oumayma Rouis ◽  
Cédric Broussard ◽  
François Guillonneau ◽  
Jean-Baptiste Boulé ◽  
Emmanuelle Delagoutte
Keyword(s):  
Spatial Organization ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Specific Binding ◽  
Regulation Of Gene Expression ◽  
Double Stranded Dna ◽  
Nuclear Extracts ◽  
Interesting Possibility

DNA hemicatenanes (HCs) are four-way junctions in which one strand of a double-stranded helix is catenated with one strand of another double-stranded DNA. Frequently mentioned as DNA replication, recombination and repair intermediates, they have been proposed to participate in the spatial organization of chromosomes and in the regulation of gene expression. To explore potential roles of HCs in genome metabolism, we sought to purify proteins capable of binding specifically HCs by fractionating nuclear extracts from HeLa cells. This approach identified three RNA-binding proteins: the Tudor-staphylococcal nuclease domain 1 (SND1) protein and two proteins from the Drosophila behavior human splicing family, the paraspeckle protein component 1 and the splicing factor proline- and glutamine-rich protein. Since these proteins were partially pure after fractionation, truncated forms of these proteins were expressed in Escherichia coli and purified to near homogeneity. The specificity of their interaction with HCs was re-examined in vitro. The two truncated purified SND1 proteins exhibited specificity for HCs, opening the interesting possibility of a link between the basic transcription machinery and HC structures via SND1.

scholarly journals Edc3p and a glutamine/asparagine-rich domain of Lsm4p function in processing body assembly in Saccharomyces cerevisiae

2007 ◽  
Vol 179 (3) ◽  
pp. 437-449 ◽  
Author(s):  
Carolyn J. Decker ◽  
Daniela Teixeira ◽  
Roy Parker
Keyword(s):  
Protein Interactions ◽  
Messenger Rna ◽  
Mrna Decay ◽  
Processing Bodies ◽  
P Bodies ◽  
Rna Granules ◽  
Rich Domain ◽  
Cytoplasmic Rna ◽  
Processing Body ◽  
The Individual

Processing bodies (P-bodies) are cytoplasmic RNA granules that contain translationally repressed messenger ribonucleoproteins (mRNPs) and messenger RNA (mRNA) decay factors. The physical interactions that form the individual mRNPs within P-bodies and how those mRNPs assemble into larger P-bodies are unresolved. We identify direct protein interactions that could contribute to the formation of an mRNP complex that consists of core P-body components. Additionally, we demonstrate that the formation of P-bodies that are visible by light microscopy occurs either through Edc3p, which acts as a scaffold and cross-bridging protein, or via the “prionlike” domain in Lsm4p. Analysis of cells defective in P-body formation indicates that the concentration of translationally repressed mRNPs and decay factors into microscopically visible P-bodies is not necessary for basal control of translation repression and mRNA decay. These results suggest a stepwise model for P-body assembly with the initial formation of a core mRNA–protein complex that then aggregates through multiple specific mechanisms.

HuR and other turnover- and translation-regulatory RNA-binding proteins: implications for the kidney

2014 ◽  
Vol 306 (6) ◽  
pp. F569-F576 ◽  
Author(s):  
Rudolf Pullmann ◽  
Hamid Rabb
Keyword(s):  
Posttranscriptional Regulation ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Current Knowledge ◽  
Regulation Of Gene Expression ◽  
Regulatory Elements ◽  
Matrix Remodeling ◽  
Acid Base Balance ◽  
Renal Metabolism

The posttranscriptional regulation of gene expression occurs through cis RNA regulatory elements by the action of trans factors, which are represented by noncoding RNAs (especially microRNAs) and turnover- and translation-regulatory (TTR) RNA-binding proteins (RBPs). These multifactorial proteins are a group of heterogeneous RBPs primarily implicated in controlling the decay and translation rates of target mRNAs. TTR-RBPs usually shuttle between cellular compartments (the nucleus and cytoplasm) in response to various stimuli and undergo posttranslational modifications such as phosphorylation or methylation to ensure their proper subcellular localization and function. TTR-RBPs are emerging as key regulators of a wide variety of genes influencing kidney physiology and pathology. This review summarizes the current knowledge of TTR-RBPs that influence renal metabolism. We will discuss the role of TTR-RBPs as regulators of kidney ischemia, fibrosis and matrix remodeling, angiogenesis, membrane transport, immunity, vascular tone, hypertension, and acid-base balance as well as anemia, bone mineral disease, and vascular calcification.

scholarly journals RNA Recognition and Immunity—Innate Immune Sensing and Its Posttranscriptional Regulation Mechanisms

Cells ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 1701
Author(s):  
Takuya Uehata ◽  
Osamu Takeuchi
Keyword(s):  
Nuclear Export ◽  
Posttranscriptional Regulation ◽  
Rna Binding ◽  
Inflammatory Responses ◽  
Rna Binding Proteins ◽  
Mammalian Species ◽  
Regulation Of Gene Expression ◽  
Innate Immune ◽  
Type I ◽  
Immune Sensing

RNA acts as an immunostimulatory molecule in the innate immune system to activate nucleic acid sensors. It functions as an intermediate, conveying genetic information to control inflammatory responses. A key mechanism for RNA sensing is discriminating self from non-self nucleic acids to initiate antiviral responses reliably, including the expression of type I interferon (IFN) and IFN-stimulated genes. Another important aspect of the RNA-mediated inflammatory response is posttranscriptional regulation of gene expression, where RNA-binding proteins (RBPs) have essential roles in various RNA metabolisms, including splicing, nuclear export, modification, and translation and mRNA degradation. Recent evidence suggests that the control of mRNA stability is closely involved in signal transduction and orchestrates immune responses. In this study, we review the current understanding of how RNA is sensed by host RNA sensing machinery and discuss self/non-self-discrimination in innate immunity focusing on mammalian species. Finally, we discuss how posttranscriptional regulation by RBPs shape immune reactions.

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 Involvement of a tissue-specific RNA recognition motif protein in Drosophila spermatogenesis.

1997 ◽  
Vol 17 (5) ◽  
pp. 2708-2715 ◽  
Author(s):  
S R Haynes ◽  
M T Cooper ◽  
S Pype ◽  
D T Stolow
Keyword(s):  
Posttranscriptional Regulation ◽  
Rna Binding ◽  
Protein Gene ◽  
Germ Line ◽  
Rna Binding Proteins ◽  
Regulation Of Gene Expression ◽  
Rna Recognition Motif ◽  
Rna Recognition ◽  
Two Dimensional Gel Electrophoresis ◽  
Recognition Motif

RNA binding proteins mediate posttranscriptional regulation of gene expression via their roles in nuclear and cytoplasmic mRNA metabolism. Many of the proteins involved in these processes have a common RNA binding domain, the RNA recognition motif (RRM). We have characterized the Testis-specific RRM protein gene (Tsr), which plays an important role in spermatogenesis in Drosophila melanogaster. Disruption of Tsr led to a dramatic reduction in male fertility due to the production of spermatids with abnormalities in mitochondrial morphogenesis. Tsr is located on the third chromosome at 87F, adjacent to the nuclear pre-mRNA binding protein gene Hrb87F. A 1.7-kb Tsr transcript was expressed exclusively in the male germ line. It encoded a protein containing two RRMs similar to those found in HRB87F as well as a unique C-terminal domain. TSR protein was located in the cytoplasm of spermatocytes and young spermatids but was absent from mature sperm. The cellular proteins expressed in premeiotic primary spermatocytes from Tsr mutant and wild-type males were assessed by two-dimensional gel electrophoresis. Lack of TSR resulted in the premature expression of a few proteins prior to meiosis; this was abolished by a transgenic copy of Tsr. These data demonstrate that TSR negatively regulated the expression of some testis proteins and, in combination with its expression pattern and subcellular localization, suggest that TSR regulates the stability or translatability of some mRNAs during spermatogenesis.

scholarly journals Identification of hemicatenane-specific binding proteins by fractionation of Hela nuclei extracts

2019 ◽  
Author(s):  
Oumayma Rouis ◽  
Cédric Broussard ◽  
François Guillonneau ◽  
Jean-Baptiste Boulé ◽  
Emmanuelle Delagoutte
Keyword(s):  
Spatial Organization ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Specific Binding ◽  
Regulation Of Gene Expression ◽  
High Specificity ◽  
E Coli ◽  
Nuclear Extracts

AbstractDNA hemicatenanes (HCs) are DNA structures in which one strand of a double stranded helix passes through the two strands of another double stranded DNA. Frequently mentioned as DNA replication, recombination and repair intermediates, they have been proposed to participate in the spatial organization of chromosomes and in the regulation of gene expression. To explore potential roles of HCs in genome metabolism, proteins capable of binding specifically HCs were purified by fractionating nuclear extracts from Hela cells. This approach identified three RNA-binding proteins: the Tudor-Staphylococcal Nuclease Domain 1 (SND1) protein and two proteins from the Drosophila behavior human splicing family, the ParaSpeckle Protein Component 1 and the Splicing Factor Proline- and Glutamine- rich protein. Since these proteins were partially pure after fractionation, truncated forms of these proteins were expressed in E. coli and purified to near homogeneity. The specificity of their interaction with HCs was re-examined in vitro. The two truncated purified SND1 proteins exhibited a high specificity for HCs, suggesting a role of SND1 protein in targeting the basic transcription machinery to HC structures.

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