scholarly journals A conserved sequence signature is essential for robust plant miRNA biogenesis

2020 ◽  
Vol 48 (6) ◽  
pp. 3103-3118 ◽  
Author(s):  
Anushree Narjala ◽  
Ashwin Nair ◽  
Varsha Tirumalai ◽  
G Vivek Hari Sundar ◽  
Padubidri V Shivaprasad
Keyword(s):  
Rna Binding ◽  
Mirna Biogenesis ◽  
Complementary Sequence ◽  
Stem Loop ◽  
Rna Molecules ◽  
Conserved Sequence ◽  
Non Coding Rna ◽  
Sequence Signature ◽  
Genomic Studies ◽  
High Base

Abstract Micro (mi)RNAs are 20–22nt long non-coding RNA molecules involved in post-transcriptional silencing of targets having high base-pair complementarity. Plant miRNAs are processed from long Pol II-transcripts with specific stem-loop structures by Dicer-like (DCL) 1 protein. Although there were reports indicating how a specific region is selected for miRNA biogenesis, molecular details were unclear. Here, we show that the presence of specific GC-rich sequence signature within miRNA/miRNA* region is required for the precise miRNA biogenesis. The involvement of GC-rich signatures in precise processing and abundance of miRNAs was confirmed through detailed molecular and functional analysis. Consistent with the presence of the miRNA-specific GC signature, target RNAs of miRNAs also possess conserved complementary sequence signatures in their miRNA binding motifs. The selection of these GC signatures was dependent on an RNA binding protein partner of DCL1 named HYL1. Finally, we demonstrate a direct application of this discovery for enhancing the abundance and efficiency of artificial miRNAs that are popular in plant functional genomic studies.

scholarly journals MAC5, an RNA-binding protein, protects pri-miRNAs from SERRATE-dependent exoribonuclease activities

2020 ◽  
Vol 117 (38) ◽  
pp. 23982-23990 ◽  
Author(s):  
Shengjun Li ◽  
Mu Li ◽  
Kan Liu ◽  
Huimin Zhang ◽  
Shuxin Zhang ◽  
...  
Keyword(s):  
Rna Binding ◽  
Rna Binding Protein ◽  
Dual Role ◽  
Mirna Biogenesis ◽  
Core Component ◽  
Stem Loop ◽  
Loop Region ◽  
Nuclear Rna ◽  
Efficient Processing ◽  
The Stability

MAC5 is a component of the conserved MOS4-associated complex. It plays critical roles in development and immunity. Here we report that MAC5 is required for microRNA (miRNA) biogenesis. MAC5 interacts with Serrate (SE), which is a core component of the microprocessor that processes primary miRNA transcripts (pri-miRNAs) into miRNAs and binds the stem-loop region of pri-miRNAs. MAC5 is essential for both the efficient processing and the stability of pri-miRNAs. Interestingly, the reduction of pri-miRNA levels inmac5is partially caused by XRN2/XRN3, the nuclear-localized 5′-to-3′ exoribonucleases, and depends on SE. These results reveal that MAC5 plays a dual role in promoting pri-miRNA processing and stability through its interaction with SE and/or pri-miRNAs. This study also uncovers that pri-miRNAs need to be protected from nuclear RNA decay machinery, which is connected to the microprocessor.

scholarly journals Accurate Detection of RNA Stem-Loops in Structurome Data Reveals Widespread Association with Protein Binding Sites

2021 ◽  
Author(s):  
Pierce Radecki ◽  
Rahul Uppuluri ◽  
Kaustubh Deshpande ◽  
Sharon Aviran
Keyword(s):  
Rna Structure ◽  
Nearest Neighbor ◽  
Rna Binding ◽  
Learning Algorithm ◽  
Accurate Method ◽  
Stem Loop ◽  
Rna Molecules ◽  
Computational Overhead ◽  
Local Sequence ◽  
Functional Relevance

ABSTRACTRNA molecules are known to fold into specific structures which often play a central role in their functions and regulation. In silico folding of RNA transcripts, especially when assisted with structure profiling (SP) data, is capable of accurately elucidating relevant structural conformations. However, such methods scale poorly to the swaths of SP data generated by transcriptome-wide experiments, which are becoming more commonplace and advancing our understanding of RNA structure and its regulation at global and local levels. This has created a need for tools capable of rapidly deriving structural assessments from SP data in a scalable manner. One such tool we previously introduced that aims to process such data is patteRNA, a statistical learning algorithm capable of rapidly mining big SP datasets for structural elements. Here, we present a reformulation of patteRNA’s pattern recognition scheme that sees significantly improved precision without major compromises to computational overhead. Specifically, we developed a data-driven logistic classifier which interprets patteRNA’s statistical characterizations of SP data in addition to local sequence properties as measured with a nearest neighbor thermodynamic model. Application of the classifier to human structurome data reveals a marked association between detected stem-loops and RNA binding protein (RBP) footprints. The results of our application demonstrate that upwards of 30% of RBP footprints occur within loops of stable stem-loop elements. Overall, our work arrives at a rapid and accurate method for automatically detecting families of RNA structure motifs and demonstrates the functional relevance of identifying them transcriptome-wide.

How to find small non-coding RNAs in bacteria

2005 ◽  
Vol 386 (12) ◽  
pp. 1219-1238 ◽  
Author(s):  
Jörg Vogel ◽  
Cynthia Mira Sharma
Keyword(s):  
Small Rnas ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Critical Role ◽  
Rna Molecules ◽  
Regulatory Circuit ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Response To Stress ◽  
Non Coding Rnas

AbstractSmall non-coding RNAs (sRNAs) have attracted considerable attention as an emerging class of gene expression regulators. In bacteria, a few regulatory RNA molecules have long been known, but the extent of their role in the cell was not fully appreciated until the recent discovery of hundreds of potential sRNA genes in the bacteriumEscherichia coli. Orthologs of theseE. colisRNA genes, as well as unrelated sRNAs, were also found in other bacteria. Here we review the disparate experimental approaches used over the years to identify sRNA molecules and their genes in prokaryotes. These include genome-wide searches based on the biocomputational prediction of non-coding RNA genes, global detection of non-coding transcripts using microarrays, and shotgun cloning of small RNAs (RNomics). Other sRNAs were found by either co-purification with RNA-binding proteins, such as Hfq or CsrA/RsmA, or classical cloning of abundant small RNAs after size fractionation in polyacrylamide gels. In addition, bacterial genetics offers powerful tools that aid in the search for sRNAs that may play a critical role in the regulatory circuit of interest, for example, the response to stress or the adaptation to a change in nutrient availability. Many of the techniques discussed here have also been successfully applied to the discovery of eukaryotic and archaeal sRNAs.

scholarly journals CSDE1 controls gene expression through the miRNA-mediated decay machinery

2020 ◽  
Vol 3 (4) ◽  
pp. e201900632
Author(s):  
Pavan Kumar Kakumani ◽  
Louis-Mathieu Harvey ◽  
François Houle ◽  
Tanit Guitart ◽  
Fátima Gebauer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Silencing ◽  
Rna Binding ◽  
Control Of Gene Expression ◽  
Rna Molecules ◽  
Stem Cell Maintenance ◽  
Argonaute Proteins ◽  
Posttranscriptional Gene Regulation ◽  
Non Coding Rna ◽  
Mirna Pathway

In animals, miRNAs are the most prevalent small non-coding RNA molecules controlling posttranscriptional gene regulation. The Argonaute proteins (AGO) mediate miRNA-guided gene silencing by recruiting multiple factors involved in translational repression, deadenylation, and decapping. Here, we report that CSDE1, an RNA-binding protein linked to stem cell maintenance and metastasis in cancer, interacts with AGO2 within miRNA-induced silencing complex and mediates gene silencing through its N-terminal domains. We show that CSDE1 interacts with LSM14A, a constituent of P-body assembly and further associates to the DCP1–DCP2 decapping complex, suggesting that CSDE1 could promote the decay of miRNA-induced silencing complex-targeted mRNAs. Together, our findings uncover a hitherto unknown mechanism used by CSDE1 in the control of gene expression mediated by the miRNA pathway.

scholarly journals Mining of miRNAs using Next Generation Sequencing (NGS) data generated for Okra (Abelmoschus esculentus)

2018 ◽  
Vol 13 (2) ◽  
pp. 137-145
Author(s):  
Rekha Gupta ◽  
M Gayathri ◽  
V Radhika ◽  
M Pichaimuthu ◽  
K V Ravishankar
Keyword(s):  
Gene Expression ◽  
Mirna Family ◽  
Abelmoschus Esculentus ◽  
Stem Loop ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Precursor Rna ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

MicroRNAs (miRNAs) are small, highly conserved non-coding RNA molecules involved in theregulation of gene expression in eukaryotes. Gene expression involves post-transcriptionalgene regulation by miRNAs. miRNAs are formed from precursor RNA molecules that fold intoa stem loop secondary structure. The mature miRNA is one end of the precursor miRNA,defined by the cut from ‘Drosha’ on either the 5’ or 3’ arm. In this study, we have used abioinformatics approach to identify miRNAs in 3,361 contigs obtained from partial genomesequence data of Abelmoschus esculentus (okra) sequenced by NGS technology. Using C-miiand psRNA Target tools, we identified two miRNAs and their target RNAs for which a regulatorymiRNA binding has been verified. Their targets consisted of transcription factors involved ingrowth and development, gene regulation and metabolism. Phylogenetic analysis of the newlyidentified miRNA family has been done to compare their level of conservation with respect tothe other members of the plant kingdom.

scholarly journals Investigating the Underlying Mechanisms of Circular RNAs and Their Application in Clinical Research of Cervical Cancer

2021 ◽  
Vol 12 ◽  
Author(s):  
Jian Liu ◽  
He Zhu ◽  
Li Fu ◽  
Tianmin Xu
Keyword(s):  
Cervical Cancer ◽  
Rna Binding ◽  
Regulation Of Gene Expression ◽  
Rna Binding Protein ◽  
Circular Rnas ◽  
Rna Molecules ◽  
Innovative Strategies ◽  
Non Coding Rna ◽  
Underlying Mechanisms

Circular RNAs (circRNAs) are non-coding RNA molecules, and these are differentially expressed in various diseases, including cancer, suggesting that circRNAs can regulate certain diseases. CircRNAs can act as miRNAs sponges, RNA-binding protein (RBP) sponges, and translation regulators, and they can become an important part of the regulation of gene expression. Furthermore, because of their biomedical features in body fluids, such as high abundance, conservation, and stability, circRNAs are seen as potential biomarkers for various cancers. Cervical cancer (CC) is one of the main causes of cancer-related death in women, and there have been a large number of studies that analyze circRNAs as a new object to be evaluated in CC. Therefore, this review, by understanding the role of circRNAs in CC, may create innovative strategies in the future clinical diagnosis, treatment, and prognosis of CC and promote the development of personalized and highly accurate cancer therapy.

scholarly journals The Role of Extracellular Vesicles as Shuttles of RNA and Their Clinical Significance as Biomarkers in Hepatocellular Carcinoma

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 902
Author(s):  
Eva Costanzi ◽  
Carolina Simioni ◽  
Gabriele Varano ◽  
Cinzia Brenna ◽  
Ilaria Conti ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Extracellular Vesicles ◽  
Tumor Metastasis ◽  
Biological Processes ◽  
Rna Molecules ◽  
Expression Of Genes ◽  
Non Coding Rna ◽  
Donor Cells ◽  
Relevant Role

Extracellular vesicles (EVs) have attracted interest as mediators of intercellular communication following the discovery that EVs contain RNA molecules, including non-coding RNA (ncRNA). Growing evidence for the enrichment of peculiar RNA species in specific EV subtypes has been demonstrated. ncRNAs, transferred from donor cells to recipient cells, confer to EVs the feature to regulate the expression of genes involved in differentiation, proliferation, apoptosis, and other biological processes. These multiple actions require accuracy in the isolation of RNA content from EVs and the methodologies used play a relevant role. In liver, EVs play a crucial role in regulating cell–cell communications and several pathophysiological events in the heterogeneous liver class of cells via horizontal transfer of their cargo. This review aims to discuss the rising role of EVs and their ncRNAs content in regulating specific aspects of hepatocellular carcinoma development, including tumorigenesis, angiogenesis, and tumor metastasis. We analyze the progress in EV-ncRNAs’ potential clinical applications as important diagnostic and prognostic biomarkers for liver conditions.

scholarly journals Architecture of RNA influences plant biology

2021 ◽  
Author(s):  
Jiaying Zhu ◽  
Changhao Li ◽  
Xu Peng ◽  
Xiuren Zhang
Keyword(s):  
Rna Binding ◽  
Rna Binding Proteins ◽  
Mirna Biogenesis ◽  
Plant Responses ◽  
Tertiary Structures ◽  
Rna Transcripts ◽  
Environmental Variations ◽  
Living Organisms ◽  
Processing Stability

Abstract The majority of the genome is transcribed to RNA in living organisms. RNA transcripts can form astonishing arrays of secondary and tertiary structures via Watson-Crick, Hoogsteen or wobble base pairing. In vivo, RNA folding is not a simple thermodynamics event of minimizing free energy. Instead, the process is constrained by transcription, RNA binding proteins (RBPs), steric factors and micro-environment. RNA secondary structure (RSS) plays myriad roles in numerous biological processes, such as RNA processing, stability, transportation and translation in prokaryotes and eukaryotes. Emerging evidence has also implicated RSS in RNA trafficking, liquid-liquid phase separation and plant responses to environmental variations such as temperature and salinity. At the molecular level, RSS is correlated with regulating splicing, polyadenylation, protein systhsis, and miRNA biogenesis and functions. In this review, we summarized newly reported methods for probing RSS in vivo and functions and mechanisms of RSS in plant physiology.

scholarly journals Identification of the conserved long non-coding RNAs in myogenesis

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Anupam Bhattacharya ◽  
Simang Champramary ◽  
Tanya Tripathi ◽  
Debajit Thakur ◽  
Ilya Ioshikhes ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Muscle Development ◽  
Three Dimensional ◽  
C2c12 Cells ◽  
Mouse Muscle ◽  
Rna Molecules ◽  
Expression Of Genes ◽  
Novel Approach ◽  
Non Coding Rna ◽  
Topologically Associated Domains

Abstract Background Our understanding of genome regulation is ever-evolving with the continuous discovery of new modes of gene regulation, and transcriptomic studies of mammalian genomes have revealed the presence of a considerable population of non-coding RNA molecules among the transcripts expressed. One such non-coding RNA molecule is long non-coding RNA (lncRNA). However, the function of lncRNAs in gene regulation is not well understood; moreover, finding conserved lncRNA across species is a challenging task. Therefore, we propose a novel approach to identify conserved lncRNAs and functionally annotate these molecules. Results In this study, we exploited existing myogenic transcriptome data and identified conserved lncRNAs in mice and humans. We identified the lncRNAs expressing differentially between the early and later stages of muscle development. Differential expression of these lncRNAs was confirmed experimentally in cultured mouse muscle C2C12 cells. We utilized the three-dimensional architecture of the genome and identified topologically associated domains for these lncRNAs. Additionally, we correlated the expression of genes in domains for functional annotation of these trans-lncRNAs in myogenesis. Using this approach, we identified conserved lncRNAs in myogenesis and functionally annotated them. Conclusions With this novel approach, we identified the conserved lncRNAs in myogenesis in humans and mice and functionally annotated them. The method identified a large number of lncRNAs are involved in myogenesis. Further studies are required to investigate the reason for the conservation of the lncRNAs in human and mouse while their sequences are dissimilar. Our approach can be used to identify novel lncRNAs conserved in different species and functionally annotated them.

scholarly journals Tandem Repeats in Bacillus: Unique Features and Taxonomic Distribution

2021 ◽  
Vol 22 (10) ◽  
pp. 5373
Author(s):  
Juan A. Subirana ◽  
Xavier Messeguer
Keyword(s):  
Tandem Repeats ◽  
Bacterial Species ◽  
Individual Species ◽  
Large Set ◽  
Bacterial Genomes ◽  
Rna Molecules ◽  
Variable Sequence ◽  
Repeat Size ◽  
Genomic Studies ◽  
Dna Tandem Repeats

Little is known about DNA tandem repeats across prokaryotes. We have recently described an enigmatic group of tandem repeats in bacterial genomes with a constant repeat size but variable sequence. These findings strongly suggest that tandem repeat size in some bacteria is under strong selective constraints. Here, we extend these studies and describe tandem repeats in a large set of Bacillus. Some species have very few repeats, while other species have a large number. Most tandem repeats have repeats with a constant size (either 52 or 20–21 nt), but a variable sequence. We characterize in detail these intriguing tandem repeats. Individual species have several families of tandem repeats with the same repeat length and different sequence. This result is in strong contrast with eukaryotes, where tandem repeats of many sizes are found in any species. We discuss the possibility that they are transcribed as small RNA molecules. They may also be involved in the stabilization of the nucleoid through interaction with proteins. We also show that the distribution of tandem repeats in different species has a taxonomic significance. The data we present for all tandem repeats and their families in these bacterial species will be useful for further genomic studies.

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