scholarly journals Emerging Role of Circular RNA–Protein Interactions

2021 ◽  
Vol 7 (3) ◽  
pp. 48
Author(s):  
Arundhati Das ◽  
Tanvi Sinha ◽  
Sharmishtha Shyamal ◽  
Amaresh Chandra Panda
Keyword(s):  
Gene Expression ◽  
Protein Interactions ◽  
Nuclear Export ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Critical Role ◽  
Large Family ◽  
Circular Rnas ◽  
Protein Interaction Data ◽  
Cell Physiology

Circular RNAs (circRNAs) are emerging as novel regulators of gene expression in various biological processes. CircRNAs regulate gene expression by interacting with cellular regulators such as microRNAs and RNA binding proteins (RBPs) to regulate downstream gene expression. The accumulation of high-throughput RNA–protein interaction data revealed the interaction of RBPs with the coding and noncoding RNAs, including recently discovered circRNAs. RBPs are a large family of proteins known to play a critical role in gene expression by modulating RNA splicing, nuclear export, mRNA stability, localization, and translation. However, the interaction of RBPs with circRNAs and their implications on circRNA biogenesis and function has been emerging in the last few years. Recent studies suggest that circRNA interaction with target proteins modulates the interaction of the protein with downstream target mRNAs or proteins. This review outlines the emerging mechanisms of circRNA–protein interactions and their functional role in cell physiology.

scholarly journals Identification and Characterization of Circular Intronic RNAs Derived from Insulin Gene

2020 ◽  
Vol 21 (12) ◽  
pp. 4302 ◽  
Author(s):  
Debojyoti Das ◽  
Aniruddha Das ◽  
Mousumi Sahu ◽  
Smruti Sambhav Mishra ◽  
Shaheerah Khan ◽  
...  
Keyword(s):  
Rna Binding ◽  
Cell Function ◽  
Rna Binding Proteins ◽  
Critical Role ◽  
Large Family ◽  
Normal Diet ◽  
Circular Rnas ◽  
Sequencing Data ◽  
Reverse Transcription Pcr ◽  
Β Cell Function

Circular RNAs (circRNAs) are a large family of noncoding RNAs that have emerged as novel regulators of gene expression. However, little is known about the function of circRNAs in pancreatic β-cells. Here, transcriptomic analysis of mice pancreatic islet RNA-sequencing data identified 77 differentially expressed circRNAs between mice fed with a normal diet and a high-fat diet. Surprisingly, multiple circRNAs were derived from the intron 2 of the preproinsulin 2 (Ins2) gene and are termed as circular intronic (ci)-Ins2. The expression of ci-Ins2 transcripts in mouse pancreatic islets, and βTC6 cells were confirmed by reverse transcription PCR, DNA sequencing, and RNase R treatment experiments. The level of ci-Ins2 was altered in βTC6 cells upon exposure to elevated levels of palmitate and glucose. Computational analysis predicted the interaction of several RNA-binding proteins with ci-Ins2 and their flanking region, suggesting their role in the ci-Ins2 function or biogenesis. Additionally, bioinformatics analysis predicted the association of several microRNAs with ci-Ins2. Gene ontology and pathway analysis of genes targeted by miRNAs associated with ci-Ins2 suggested the regulation of several key biological processes. Together, our findings indicate that differential expression of circRNAs, especially ci-Ins2 transcripts, may regulate β-cell function and may play a critical role in the development of diabetes.

scholarly journals Compendium of Methods to Uncover RNA-Protein Interactions In Vivo

2021 ◽  
Vol 4 (1) ◽  
pp. 22
Author(s):  
Mrinmoyee Majumder ◽  
Viswanathan Palanisamy
Keyword(s):  
Gene Expression ◽  
Protein Interactions ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Expression Patterns ◽  
Control Of Gene Expression ◽  
Regulatory Pathways ◽  
Advantages And Disadvantages ◽  
Protein Nucleic Acid

Control of gene expression is critical in shaping the pro-and eukaryotic organisms’ genotype and phenotype. The gene expression regulatory pathways solely rely on protein–protein and protein–nucleic acid interactions, which determine the fate of the nucleic acids. RNA–protein interactions play a significant role in co- and post-transcriptional regulation to control gene expression. RNA-binding proteins (RBPs) are a diverse group of macromolecules that bind to RNA and play an essential role in RNA biology by regulating pre-mRNA processing, maturation, nuclear transport, stability, and translation. Hence, the studies aimed at investigating RNA–protein interactions are essential to advance our knowledge in gene expression patterns associated with health and disease. Here we discuss the long-established and current technologies that are widely used to study RNA–protein interactions in vivo. We also present the advantages and disadvantages of each method discussed in the review.

A Potential Therapeutic Target RNA-binding Protein, Arid5a for the Treatment of Inflammatory Disease Associated with Aberrant Cytokine Expression

2018 ◽  
Vol 24 (16) ◽  
pp. 1766-1771 ◽  
Author(s):  
Kazuya Masuda ◽  
Tadamitsu Kishimoto
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
Severe Sepsis ◽  
Inflammatory Cytokines ◽  
Binding Proteins ◽  
Rna Binding ◽  
Cytokine Production ◽  
Rna Binding Proteins ◽  
Critical Role ◽  
Transcriptional Level

Background: Infection, tissue damage and aging can cause inflammation with high levels of inflammatory cytokines. Overproduction of inflammatory cytokines often leads to systemic inflammatory response syndrome (SIRS), severe sepsis, and septic shock. However, prominent therapeutic targets have not been found, although the incidence of sepsis is likely to increase annually. Our recent studies indicate that some RNA-binding proteins, which control gene expression of inflammatory cytokines at the post-transcriptional level, may play a critical role in inflammatory diseases such as sepsis. Results: 1) One of the RNA-binding proteins, AT-rich interactive domain-containing 5a (Arid5a) promotes cytokine production through control of mRNA half-lives of pro-inflammatory molecules such as IL-6, STAT3, T-bet, and OX40 in activated macrophages and T cells. Arid5a KO mice are refractory to endotoxin shock, bleomycininduced lung injury, and inflammatory autoimmune disease. 2) Chlorpromazine (CPZ), which is recognized as a psychotic drug, impairs post-transcriptional gene expression of Il6 in LPS-stimulated macrophages: CPZ inhibits the binding activity of Arid5a to the 3’UTR of Il6 mRNA, thereby destabilizing Il6 mRNA possibly through suppression of Arid5a expression. 3) CPZ has strong suppressive effects on cytokine production such as TNF-α in vivo. Mice with treatment of CPZ are resistant to lipopolysaccharide (LPS)-induced shock. Conclusion: Thus, Arid5a contributes to the activation of macrophages and T cells through positive control of mRNA half-lives of inflammatory cytokines and its related molecules, which might lead to cytokine storm. Interestingly, Arid5a was identified from an inhibitory effect of CPZ on IL-6 production in macrophages activated by LPS. Therefore, CPZ derivatives or Arid5a inhibitors may have a potential to suppress severe sepsis through control of post-transcriptional gene expression.

scholarly journals A potential role for a novel ZC3H5 complex in regulating mRNA translation in Trypanosoma brucei

2020 ◽  
Vol 295 (42) ◽  
pp. 14291-14304
Author(s):  
Kathrin Bajak ◽  
Kevin Leiss ◽  
Christine Clayton ◽  
Esteban Erben
Keyword(s):  
Gene Expression ◽  
Trypanosoma Brucei ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Protein ◽  
Affinity Purification ◽  
Critical Role ◽  
Rna Binding Protein ◽  
Mrna Translation

In Trypanosoma brucei and related kinetoplastids, gene expression regulation occurs mostly posttranscriptionally. Consequently, RNA-binding proteins play a critical role in the regulation of mRNA and protein abundance. Yet, the roles of many RNA-binding proteins are not understood. Our previous research identified the RNA-binding protein ZC3H5 as possibly involved in gene repression, but its role in controlling gene expression was unknown. We here show that ZC3H5 is an essential cytoplasmic RNA-binding protein. RNAi targeting ZC3H5 causes accumulation of precytokinetic cells followed by rapid cell death. Affinity purification and pairwise yeast two-hybrid analysis suggest that ZC3H5 forms a complex with three other proteins, encoded by genes Tb927.11.4900, Tb927.8.1500, and Tb927.7.3040. RNA immunoprecipitation revealed that ZC3H5 is preferentially associated with poorly translated, low-stability mRNAs, the 5′-untranslated regions and coding regions of which are enriched in the motif (U/A)UAG(U/A). As previously found in high-throughput analyses, artificial tethering of ZC3H5 to a reporter mRNA or other complex components repressed reporter expression. However, depletion of ZC3H5 in vivo caused only very minor decreases in a few targets, marked increases in the abundances of very stable mRNAs, an increase in monosomes at the expense of large polysomes, and appearance of “halfmer” disomes containing two 80S subunits and one 40S subunit. We speculate that the ZC3H5 complex might be implicated in quality control during the translation of suboptimal open reading frames.

scholarly journals CLIPreg: Constructing translational regulatory networks from CLIP-, Ribo- and RNA-seq

2021 ◽  
Author(s):  
Baptiste Kerouanton ◽  
Sebastian Schafer ◽  
Lena Ho ◽  
Sonia Chothani ◽  
Owen JL Rackham
Keyword(s):  
Protein Interactions ◽  
Translational Regulation ◽  
Regulatory Networks ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Critical Role ◽  
Sequencing Data ◽  
Data Types ◽  
Network Resources ◽  
Gene Regulatory

Motivation: The creation and analysis of gene regulatory networks have been the focus of bioinformatic research and underpins much of what is known about gene regulation. However, as a result of a bias in the availability of data-types that are collected, the vast majority of gene regulatory network resources and tools have focused on either transcriptional regulation or protein-protein interactions. This has left other areas of regulation, for instance translational regulation, vastly underrepresented despite them having been shown to play a critical role in both health and disease. Results: In order to address this we have developed CLIPreg, a package that integrates RNA, Ribo and CLIP- sequencing data in order to construct translational regulatory networks coordinated by RNA-binding proteins. This is the first tool of its type to be created, allowing for detailed investigation into a previously unseen layer of regulation.

scholarly journals Transcriptome-wide profiles of circular RNA and RNA binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expression

2020 ◽  
Author(s):  
Trine Line Hauge Okholm ◽  
Shashank Sathe ◽  
Samuel S. Park ◽  
Andreas Bjerregaard Kamstrup ◽  
Asta Mannstaedt Rasmussen ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Protein Interactions ◽  
Binding Sites ◽  
Target Genes ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Circular Rna ◽  
Circular Rnas ◽  
Cancer Genes

AbstractCircular RNAs (circRNAs) are stable, often highly expressed RNA transcripts with potential to modulate other regulatory RNAs. A few circRNAs have been shown to bind RNA binding proteins (RBPs), however, little is known about the prevalence and strength of these interactions in different biological contexts. Here, we comprehensively evaluate the interplay between circRNAs and RBPs in the ENCODE cell lines, HepG2 and K562, by profiling the expression of circRNAs in fractionated total RNA-sequencing samples and analyzing binding sites of 150 RBPs in large eCLIP data sets. We show that KHSRP binding sites are enriched in flanking introns of circRNAs in both HepG2 and K562 cells, and that KHSRP depletion affects circRNA biogenesis. Additionally, we show that exons forming circRNAs are generally enriched with RBP binding sites compared to non-circularizing exons. To detect individual circRNAs with regulatory potency, we computationally identify circRNAs that are highly covered by RBP binding sites and experimentally validate circRNA-RBP interactions by RNA immunoprecipitations. We characterize circCDYL, a highly expressed circRNA with clinical and functional implications in bladder cancer, which is covered with GRWD1 binding sites. We confirm that circCDYL binds GRWD1 in vivo and functionally characterizes the effect of circCDYL-GRWD1 interactions on target genes in HepG2. Furthermore, we confirm interactions between circCDYL and RBPs in bladder cancer cells and demonstrate that circCDYL depletion affects hallmarks of cancer and perturbs the expression of key cancer genes, e.g. TP53 and MYC. Finally, we show that elevated levels of highly RBP-covered circRNAs, including circCDYL, are associated with overall survival of bladder cancer patients. Our study demonstrates transcriptome-wide and cell-type-specific circRNA-RBP interactions that could play important regulatory roles in tumorigenesis.

scholarly journals Delineating the Role of Interplay between m6A Machinery Genes and IGF2BP Group of RNA-Binding Proteins in B-Cell Acute Lymphoblastic Leukemia (B-ALL)

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 4472-4472
Author(s):  
Sumedha Saluja ◽  
Jay Singh ◽  
Ayushi Jain ◽  
Shilpi Chaudhary ◽  
Karthikeyan Pethusamy ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bone Marrow ◽  
Cancer Progression ◽  
Rna Binding ◽  
Conflicts Of Interest ◽  
Rna Binding Proteins ◽  
Colorimetric Assay ◽  
Lymphoblastic Leukemia ◽  
Critical Role ◽  
Cell Renewal

Abstract Introduction: N-6-methyladenosine (m6A) is the most common, dynamic and reversible RNA modification with implications in various cancers including leukemia. Deregulation of m6A writer METTL3 has been shown to promote disease progression in various cancers, including Acute Myeloid Leukemia(AML). Overexpression of METTL3 led to increase in cell growth and inhibition of apoptosis, thereby promoting leukemia progression. Interestingly, m6A demethylases (erasers) ALKBH5 and FTO have also seen to play a critical role in progression of AML by mediating cancer stem cell renewal. The IGF2BP family of RNA binding, oncofetal proteins have recently been identified as m6A readers and have also been shown to be deregulated in B-ALL. In this work, we have studied the expression of m6A machinery (writers, erasers and readers) in primary (naïve and relapsed) B-ALL patient samples. The percentage of methylated RNA (m6A%) was also evaluated in B-ALL patient samples. Materials and Methods: 91 newly diagnosed (naïve) and 47 relapsed B-ALL pediatric patient bone marrow samples were collected from BRAIRCH, AIIMS, New Delhi. Gene expression of m6A writer (METTL3), readers (IGF2BP1/3) and erasers (ALKBH5, FTO) was studied by RT-qPCR. Peripheral blood (PB) of 20 healthy individuals and 18 uninvolved bone marrow (BM) samples of patients with other malignancies were used as controls. m6A% was also measured in B-ALL patients (naïve n=47, relapsed n=43,) and controls (PB n=20, BM n=16, CD34+ cells from normal donors n=5) by an anti-m6A based colorimetric assay. Results: The ratio of m6A writer METTL3 to m6A eraser ALKBH5 was significantly higher in the naïve and relapsed B-ALL patients as compared to all controls. Interestingly, the ratio of the m6A writer METTL3 to m6A eraser FTO was also significantly high in naïve BM patient sample than controls. The expression of m6A readers IGF2BP1/3 that stabilize the methylated target mRNA, was also studied. IGF2BP1/3 m6A reader was significantly higher in naïve and relapsed patient samples. Increased expression of the writers and readers implied an increase in the m6A levels in B-ALL patients. The m6A% assay showed that the percentage of m6A was significantly higher in naïve and relapsed BM patient samples than both controls corroborating the RT-qPCR data. Discussion: METTL3 m6A methyl transferase has been identified a key factor in mediating the pathogenesis of AML. In our data, we have shown overexpression of METTL3 in B-ALL patient BM samples compared to controls. We have also seen an overexpression of m6A demethylase FTO in B-ALL patient samples. In order to identify the major factor among m6A writers and erasers that might play a role in pathogenesis of B-ALL, we calculated the ratio of m6A writer to m6A eraser. We have observed that ratio of METTL3 to ALKBH5 and METTL3 to FTO was significantly higher in B-ALL patient samples than both the controls. This signifies that overexpression of METTL3 subsequently leading to dysregulated methylation of its targets might influence the development and onset of relapse in B-ALL. It is well known that m6A bound target mRNAs are read by m6A readers like IGF2BPs that stabilize these m6A bound mRNAs leading to overexpression and thereby cancer progression. We have also studied expression of IGF2BP1/3 in B-ALL and seen significant overexpression of both IGF2BP1 and IGF2BP3 in B-ALL samples. These findings indicate a combined dysregulation of m6A writers, erasers and readers in B-ALL. This corroborates with the findings seen in AML, which also shows overexpression of METTL3, ALKBH5 and FTO. Our gene expression studies together point towards an increased percentage of m6A methylated RNA in B-ALL. We have evaluated the percentage of m6A in B-ALL patient samples to confirm our gene expression findings. We observed presence of significantly higher percentage of m6A in B-ALL patient samples (naïve and relapse) than both the controls. m6A% was significantly higher in naïve B-ALL patient samples compared to CD34+ HSCs also. Our findings reveal overall high m6A% in B-ALL, attributed to overexpression of m6A writer METTL3 and m6A readers IGF2BP1/3. This RNA methylation and stabilization might be dysregulated and concentrated in oncogenic genes leading to leukemogenesis. Our results provide a rationale for targeting of these m6A machinery genes dysregulation of which can be instrumental in pathogenesis of B-ALL. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.

Control of HIV-1 gene expression by SR proteins

2016 ◽  
Vol 44 (5) ◽  
pp. 1417-1425 ◽  
Author(s):  
Charlotte Mahiet ◽  
Chad M. Swanson
Keyword(s):  
Gene Expression ◽  
Nuclear Export ◽  
Rna Splicing ◽  
Drug Targets ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Antiviral Drug ◽  
Sr Proteins ◽  
Immunodeficiency Virus ◽  
Hiv 1

Cellular proteins are required for all steps of human immunodeficiency virus type 1 (HIV-1) gene expression including transcription, splicing, 3′-end formation/polyadenylation, nuclear export and translation. SR proteins are a family of cellular RNA-binding proteins that regulate and functionally integrate multiple steps of gene expression. Specific SR proteins are best characterised for regulating HIV-1 RNA splicing by binding specific locations in the viral RNA, though recently they have also been shown to control transcription, 3′-end formation, and translation. Due to their importance in regulating HIV-1 gene expression, SR proteins and their regulatory factors are potential antiviral drug targets.

scholarly journals The search for RNA-binding proteins: a technical and interdisciplinary challenge

2021 ◽  
Author(s):  
Jeffrey M. Smith ◽  
Jarrod J. Sandow ◽  
Andrew I. Webb
Keyword(s):  
Gene Expression ◽  
Protein Interactions ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Target Validation ◽  
Binding Function ◽  
Technical Features ◽  
Post Transcriptional Regulation ◽  
The Impact

RNA-binding proteins are customarily regarded as important facilitators of gene expression. In recent years, RNA–protein interactions have also emerged as a pervasive force in the regulation of homeostasis. The compendium of proteins with provable RNA-binding function has swelled from the hundreds to the thousands astride the partnership of mass spectrometry-based proteomics and RNA sequencing. At the foundation of these advances is the adaptation of RNA-centric capture methods that can extract bound protein that has been cross-linked in its native environment. These methods reveal snapshots in time displaying an extensive network of regulation and a wealth of data that can be used for both the discovery of RNA-binding function and the molecular interfaces at which these interactions occur. This review will focus on the impact of these developments on our broader perception of post-transcriptional regulation, and how the technical features of current capture methods, as applied in mammalian systems, create a challenging medium for interpretation by systems biologists and target validation by experimental researchers.

scholarly journals Plant Ribonuclease J: An Essential Player in Maintaining Chloroplast RNA Quality Control for Gene Expression

Plants ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 334
Author(s):  
Amber M. Hotto ◽  
David B. Stern ◽  
Gadi Schuster
Keyword(s):  
Gene Expression ◽  
Quality Control ◽  
Protein Interactions ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Land Plant ◽  
Protein Protein Interactions ◽  
Rna Quality ◽  
Rna Quality Control ◽  
Chloroplast Rna

RNA quality control is an indispensable but poorly understood process that enables organisms to distinguish functional RNAs from nonfunctional or inhibitory ones. In chloroplasts, whose gene expression activities are required for photosynthesis, retrograde signaling, and plant development, RNA quality control is of paramount importance, as transcription is relatively unregulated. The functional RNA population is distilled from this initial transcriptome by a combination of RNA-binding proteins and ribonucleases. One of the key enzymes is RNase J, a 5′→3′ exoribonuclease and an endoribonuclease that has been shown to trim 5′ RNA termini and eliminate deleterious antisense RNA. In the absence of RNase J, embryo development cannot be completed. Land plant RNase J contains a highly conserved C-terminal domain that is found in GT-1 DNA-binding transcription factors and is not present in its bacterial, archaeal, and algal counterparts. The GT-1 domain may confer specificity through DNA and/or RNA binding and/or protein–protein interactions and thus be an element in the mechanisms that identify target transcripts among diverse RNA populations. Further understanding of chloroplast RNA quality control relies on discovering how RNase J is regulated and how its specificity is imparted.

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