scholarly journals Chromosome-associated RNA–protein complexes promote pairing of homologous chromosomes during meiosis in Schizosaccharomyces pombe

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Da-Qiao Ding ◽  
Kasumi Okamasa ◽  
Yuki Katou ◽  
Eriko Oya ◽  
Jun-ichi Nakayama ◽  
...  
Keyword(s):  
Phase Separation ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Protein Complexes ◽  
Homologous Pairing ◽  
Homologous Chromosomes ◽  
Rna Protein Complexes ◽  
Chromosomal Loci

AbstractPairing of homologous chromosomes in meiosis is essential for sexual reproduction. We have previously demonstrated that the fission yeast sme2 RNA, a meiosis-specific long noncoding RNA (lncRNA), accumulates at the sme2 chromosomal loci and mediates their robust pairing in meiosis. However, the mechanisms underlying lncRNA-mediated homologous pairing have remained elusive. In this study, we identify conserved RNA-binding proteins that are required for robust pairing of homologous chromosomes. These proteins accumulate mainly at the sme2 and two other chromosomal loci together with meiosis-specific lncRNAs transcribed from these loci. Remarkably, the chromosomal accumulation of these lncRNA–protein complexes is required for robust pairing. Moreover, the lncRNA–protein complexes exhibit phase separation properties, since 1,6-hexanediol treatment reversibly disassembled these complexes and disrupted the pairing of associated loci. We propose that lncRNA–protein complexes assembled at specific chromosomal loci mediate recognition and subsequent pairing of homologous chromosomes.

scholarly journals HOTAIRM1 regulates neuronal differentiation by modulating NEUROGENIN 2 and the downstream neurogenic cascade

2020 ◽  
Vol 11 (7) ◽  
Author(s):  
Jessica Rea ◽  
Valentina Menci ◽  
Paolo Tollis ◽  
Tiziana Santini ◽  
Alexandros Armaos ◽  
...  
Keyword(s):  
Neuronal Differentiation ◽  
Cell Fate ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Regulatory Networks ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Regulatory Cascade ◽  
Expression Control ◽  
Gene Expression Control

Abstract Neuronal differentiation is a timely and spatially regulated process, relying on precisely orchestrated gene expression control. The sequential activation/repression of genes driving cell fate specification is achieved by complex regulatory networks, where transcription factors and noncoding RNAs work in a coordinated manner. Herein, we identify the long noncoding RNA HOTAIRM1 (HOXA Transcript Antisense RNA, Myeloid-Specific 1) as a new player in neuronal differentiation. We demonstrate that the neuronal-enriched HOTAIRM1 isoform epigenetically controls the expression of the proneural transcription factor NEUROGENIN 2 that is key to neuronal fate commitment and critical for brain development. We also show that HOTAIRM1 activity impacts on NEUROGENIN 2 downstream regulatory cascade, thus contributing to the achievement of proper neuronal differentiation timing. Finally, we identify the RNA-binding proteins HNRNPK and FUS as regulators of HOTAIRM1 biogenesis and metabolism. Our findings uncover a new regulatory layer underlying NEUROGENIN 2 transitory expression in neuronal differentiation and reveal a previously unidentified function for the neuronal-induced long noncoding RNA HOTAIRM1.

The 5S RNA – protein complex from yeast: a model for the evolution and structure of the eukaryotic ribosome

1982 ◽  
Vol 60 (4) ◽  
pp. 490-496 ◽  
Author(s):  
Ross N. Nazar ◽  
Makoto Yaguchi ◽  
Gordon E. Willick
Keyword(s):  
Binding Site ◽  
Protein Complex ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Protein Complexes ◽  
Basic Structure ◽  
5S Rna ◽  
Chemical Studies ◽  
Physical And Chemical ◽  
Rna Protein Complexes

The ribosomal 5S RNA – protein complex appears to be an excellent model for studies on the evolution and structure of ribosomes. In eukaryotes this complex is composed of two components, the 5S rRNA and a single ribosomal protein which in yeast has a molecular weight of about 38 000. The primary protein-binding site is located in the 3′-end region of the 5S RNA together with a small portion of the 5′ end. The primary RNA-binding site appears to be situated in the C-terminal end of the protein (YL3 in yeast) but the binding specificity requires other structural elements in the N-terminal half of the molecule. When compared with prokaryotic 5S RNA – protein complexes, various physical and chemical studies suggest that the basic structure and interactions have been conserved in the course of evolution, but that the single larger eukaryotic 5S RNA binding protein has evolved through a fusion of genes for the multiple 5S RNA binding proteins in prokaryotes.

scholarly journals A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells

2015 ◽  
Author(s):  
Ailone Tichon ◽  
Noa Gil ◽  
Yoav Lubelsky ◽  
Tal Havkin Solomon ◽  
Doron Lemze ◽  
...  
Keyword(s):  
Cell Division ◽  
Human Genome ◽  
Chromosome Segregation ◽  
Binding Sites ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Mrna Levels ◽  
Pumilio Proteins

AbstractThousands of long noncoding RNA (lncRNA) genes are encoded in the human genome, and hundreds of them are evolutionary conserved, but their functions and modes of action remain largely obscure. Particularly enigmatic lncRNAs are those that are exported to the cytoplasm, including NORAD – an abundant and highly conserved cytoplasmic lncRNA. Most of the sequence of NORAD is comprised of repetitive units that together contain at least 17 functional binding sites for the two Pumilio homologs in mammals. Through binding to PUM1 and PUM2, NORAD modulates the mRNA levels of their targets, which are enriched for genes involved in chromosome segregation during cell division. Our results suggest that some cytoplasmic lncRNAs function by modulating the activities of RNA binding proteins, an activity which positions them at key junctions of cellular signaling pathways.

scholarly journals Long Noncoding RNA UCA1 Promotes Glutamine-Driven Anaplerosis of Bladder Cancer by Interacting With hnRNP I/L to Upregulate GPT2 Expression

2020 ◽  
Author(s):  
Hua Zhao ◽  
Wenjing Wu ◽  
Xu Li ◽  
Wei Chen
Keyword(s):  
Bladder Cancer ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Metabolic Flux ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Tca Cycle ◽  
Metabolic Reprogramming ◽  
Luciferase Reporter ◽  
Flux Analysis

Abstract Background: Glutamine-driven anaplerosis maintains the tricarboxylic acid (TCA) cycle by replenishing its carbon source of intermediates with the glutamine-derived carbons in cancer cells. Long noncoding RNA urothelial cancer associated 1 (UCA1), initially identified in bladder cancer, is associated with multiple cellular processes, including metabolic reprogramming. However, its characteristics in the anaplerosis context of bladder cancer (BLCA) remains elusive. Methods: The mechanism of UCA1 bound to and facilitated the combination of hnRNP I/L to the promoter of GPT2 gene was investigated by RNA pulldown, qRT-PCR, western blot, dual luciferase reporter assays, immunohistochemical staining, chromatin immunoprecipitation and chromatin isolation by RNA purification. Metabolomics analysis and metabolic flux analysis were conducted to assess the effects of UCA1, hnRNP I/L, and GPT2 on metabolic reprogramming of BLCA.Results: We identified UCA1 as a binding partner of heterogeneous nuclear ribonucleoproteins (hnRNPs) I and L, RNA-binding proteins with no previously known role in metabolic reprogramming. UCA1 and hnRNP I/L profoundly affected glycolysis, TCA cycle, glutaminolysis, and viability of BLCA cells. Importantly, UCA1 specifically bound to and facilitated the combination of hnRNP I/L to the promoter of glutamic pyruvate transaminase 2 (GPT2) gene, resulting in upregulated expression of GPT2 and enhanced glutamine-derived carbons in the TCA cycle. We also systematically confirmed the influence of UCA1, hnRNP I/L, and GPT2 on metabolism and proliferation via glutamine-driven anaplerosis in BLCA cells. Conclusions: Our study reveals the critical mechanism by which UCA1 forms a functional UCA1-hnRNP I/L complex that upregulates GPT2 expression to promote glutamine-driven TCA cycle anaplerosis, providing novel evidence that lncRNA regulates metabolic reprogramming in tumor cells.

scholarly journals System-wide analyses of the fission yeast poly(A)+ RNA interactome reveal insights into organisation and function of RNA-protein complexes

2019 ◽  
Author(s):  
Cornelia Kilchert ◽  
Tea Kecman ◽  
Emily Priest ◽  
Svenja Hester ◽  
Krzysztof Kus ◽  
...  
Keyword(s):  
Fission Yeast ◽  
Protein Interactions ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Protein Complexes ◽  
Rna Degradation ◽  
Binding Activity ◽  
Rna Exosome ◽  
And Function ◽  
Rna Protein Complexes

AbstractProduction, function, and turnover of mRNA are orchestrated by multi-subunit machineries that play a central role in gene expression. Within these molecular machines, interactions with the target mRNA are mediated by RNA-binding proteins (RBPs), and the accuracy and dynamics of these RNA-protein interactions are essential for their function. Here, we show that fission yeast whole cell poly(A)+ RNA-protein crosslinking data provides system-wide information on the organisation and function of the RNA-protein complexes. We evaluate relative enrichment of cellular RBPs on poly(A)+ RNA to identify interactors with high RNA-binding activity and provide key information about the RNA-binding properties of large multi-protein complexes, such as the mRNA 3’ end processing machinery (cleavage and polyadenylation factor, CPF) and the RNA exosome. We demonstrate that different functional modules within CPF differ in their ability to interact with RNA. Importantly, we reveal that CPF forms additional contacts with RNA via the Fip1 subunit of the polyadenylation module and two subunits of the nuclease module. In addition, our data highlights the central role of the RNA helicase Mtl1 in RNA degradation by the exosome as mutations in Mtl1 lead to disengagement of the exosome from RNA. We examine how routes of substrate access to the complex are affected upon mutation of exosome subunits. Our results provide important insights into how different components of the exosome contribute to engagement of the complex with substrate RNA. Overall, our data uncover how multi-subunit cellular machineries interact with RNA, on a proteome-wide scale.

scholarly journals RNA Proximity Labeling: A New Detection Tool for RNA–Protein Interactions

Molecules ◽  
2021 ◽  
Vol 26 (8) ◽  
pp. 2270
Author(s):  
Ronja Weissinger ◽  
Lisa Heinold ◽  
Saira Akram ◽  
Ralf-Peter Jansen ◽  
Orit Hermesh
Keyword(s):  
Protein Interactions ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Protein Complexes ◽  
Affinity Purification ◽  
Cellular Functions ◽  
Cellular Compartments ◽  
Rna Protein Complexes

Multiple cellular functions are controlled by the interaction of RNAs and proteins. Together with the RNAs they control, RNA interacting proteins form RNA protein complexes, which are considered to serve as the true regulatory units for post-transcriptional gene expression. To understand how RNAs are modified, transported, and regulated therefore requires specific knowledge of their interaction partners. To this end, multiple techniques have been developed to characterize the interaction between RNAs and proteins. In this review, we briefly summarize the common methods to study RNA–protein interaction including crosslinking and immunoprecipitation (CLIP), and aptamer- or antisense oligonucleotide-based RNA affinity purification. Following this, we focus on in vivo proximity labeling to study RNA–protein interactions. In proximity labeling, a labeling enzyme like ascorbate peroxidase or biotin ligase is targeted to specific RNAs, RNA-binding proteins, or even cellular compartments and uses biotin to label the proteins and RNAs in its vicinity. The tagged molecules are then enriched and analyzed by mass spectrometry or RNA-Seq. We highlight the latest studies that exemplify the strength of this approach for the characterization of RNA protein complexes and distribution of RNAs in vivo.

scholarly journals Circular RNA and its mechanisms in diabetic retinopathy: a systematic review

2020 ◽  
Author(s):  
Miao He ◽  
Rouxi Zhou ◽  
Sen Liu ◽  
Weijing Cheng ◽  
Wei Wang
Keyword(s):  
Systematic Review ◽  
Diabetic Retinopathy ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Protein Complexes ◽  
Protein Translation ◽  
Circular Rna ◽  
Circular Rnas ◽  
Eye Tissues ◽  
Rna Protein Complexes

ABSTRACTCircular RNAs (CircRNAs) are endogenous long non-coding RNAs. Unlike linear RNAs, they are structurally continuous and covalently closed, without 5 ’caps or 3’ polyadenylation tails. High-throughput RNA sequencing has enabled people to find several endogenous circRNAs in different species and tissues. circRNA mainly acts as a sponge for microRNAs in cytoplasm to regulates protein translation, or interacts with RNA-binding proteins to generate RNA protein complexes that control transcription. circRNAs are closely associated with diseases such as diabetes, neurological disorders, cardiovascular diseases and cancer, which indicates that circRNAs are closely related to and also play an important functional role in the occurrence and development of human diseases. Recent studies have shown that they are differentially expressed in healthy and diseased eye tissues. There lacks of biomarkers for early detection of diabetic retinopathy, and the newly discovered circRNAs seem to be an ideal candidate of novel molecular markers and therapeutic targets. However, the molecular mechanism of circRNAs activity in the occurrence and development of diabetic retinopathy are not clear yet. This systematic review aims to summarize the research status on function and mechanism of circRNAs in regulating the occurrence of diabetic retinopathy.

scholarly journals Purification of Cross-linked RNA-Protein Complexes by Phenol-Toluol Extraction

2018 ◽  
Author(s):  
Erika C Urdaneta ◽  
Carlos H Vieira-Vieira ◽  
Timon Hick ◽  
Hans-Herrmann Wessels ◽  
Davide Figini ◽  
...  
Keyword(s):  
Physicochemical Properties ◽  
Binding Sites ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Protein Complexes ◽  
Bacterial Species ◽  
Animal Tissue ◽  
Hek293 Cells ◽  
Rna Protein Complexes ◽  
Polyadenylated Rnas

Recent methodological advances allowed the identification of an increasing number of RNA-binding proteins (RBPs) and their RNA-binding sites. Most of those methods rely, however, on capturing proteins associated to polyadenylated RNAs which neglects RBPs bound to non-adenylate RNA classes (tRNA, rRNA, pre-mRNA) as well as the vast majority of species that lack poly-A tails in their mRNAs (including all archea and bacteria). To overcome these limitations, we have developed a novel protocol, Phenol Toluol extraction (PTex), that does not rely on a specific RNA sequence or motif for isolation of cross-linked ribonucleoproteins (RNPs), but rather purifies them based entirely on their physicochemical properties. PTex captures RBPs that bind to RNA as short as 30 nt, RNPs directly from animal tissue and can be used to simplify complex workflows such as PAR-CLIP. Finally, we provide a first global RNA-bound proteome of human HEK293 cells and Salmonella Typhimurium as a bacterial species.

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