Interpreting and integrating big data in non-coding RNA research

2019 ◽  
Vol 3 (4) ◽  
pp. 343-355
Author(s):  
Simona Cantarella ◽  
Elena Di Nisio ◽  
Davide Carnevali ◽  
Giorgio Dieci ◽  
Barbara Montanini
Keyword(s):  
Big Data ◽  
Regulatory Networks ◽  
Literature Mining ◽  
Data Sets ◽  
Protein Coding ◽  
Regulatory Interactions ◽  
Cell Responses ◽  
Non Coding Rna ◽  
Data Collection And Analysis ◽  
Molecular Information

Abstract In the last two decades, we have witnessed an impressive crescendo of non-coding RNA studies, due to both the development of high-throughput RNA-sequencing strategies and an ever-increasing awareness of the involvement of newly discovered ncRNA classes in complex regulatory networks. Together with excitement for the possibility to explore previously unknown layers of gene regulation, these advancements led to the realization of the need for shared criteria of data collection and analysis and for novel integrative perspectives and tools aimed at making biological sense of very large bodies of molecular information. In the last few years, efforts to respond to this need have been devoted mainly to the regulatory interactions involving ncRNAs as direct or indirect regulators of protein-coding mRNAs. Such efforts resulted in the development of new computational tools, allowing the exploitation of the information spread in numerous different ncRNA data sets to interpret transcriptome changes under physiological and pathological cell responses. While experimental validation remains essential to identify key RNA regulatory interactions, the integration of ncRNA big data, in combination with systematic literature mining, is proving to be invaluable in identifying potential new players, biomarkers and therapeutic targets in cancer and other diseases.

scholarly journals CircHIPK3 dysregulation of the miR-30c/DLL4 axis is essential for KSHV lytic replication

2021 ◽  
Author(s):  
Katherine L Harper ◽  
Timothy J Mottram ◽  
Chinedu A Arene ◽  
Becky Foster ◽  
Molly R Patterson ◽  
...  
Keyword(s):  
Gene Expression ◽  
B Cells ◽  
Regulatory Network ◽  
Regulatory Networks ◽  
Cell Cycle Control ◽  
Lytic Replication ◽  
Protein Coding ◽  
Non Coding Rna ◽  
Novel Host ◽  
Cellular Pathways

Non coding RNA (ncRNA) regulatory networks are emerging as critical regulators of gene expression. These intricate networks of ncRNA-ncRNA interactions modulate multiple cellular pathways and impact the development and progression of multiple diseases. Herpesviruses, including Kaposi's sarcoma-associated herpesvirus, are adept at utilising ncRNAs, encoding their own as well as dysregulating host ncRNAs to modulate virus gene expression and the host response to infection. Research has mainly focused on unidirectional ncRNA-mediated regulation of target protein-coding transcripts; however, we have identified a novel host ncRNA regulatory network essential for KSHV lytic replication in B cells. KSHV-mediated upregulation of the host cell circRNA, circHIPK3, is a key component of this network, functioning as a competing endogenous RNA of miR-30c, leading to increased levels of the miR-30c target, DLL4. Dysregulation of this network highlights a novel mechanism of cell cycle control during KSHV lytic replication in B cells. Importantly, disruption at any point within this novel ncRNA regulatory network has a detrimental effect on KSHV lytic replication, highlighting the essential nature of this network and potential for therapeutic intervention.

scholarly journals Highly Divergent Neuropeptide - non-coding RNA regulatory networks underpin variant host-finding behaviours in Steinernema species infective juveniles

2020 ◽  
Author(s):  
Neil D. Warnock ◽  
Erwan Atcheson ◽  
Ciaran McCoy ◽  
Johnathan J. Dalzell
Keyword(s):  
Gene Expression ◽  
Small Rna ◽  
Regulatory Networks ◽  
Host Finding ◽  
Protein Coding ◽  
Rna Analysis ◽  
New Family ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Shared Gene

AbstractWe conducted a transcriptomic and small RNA analysis of infective juveniles (IJs) from three behaviourally distinct Steinernema species. Substantial variation was found in the expression of shared gene orthologues, revealing gene expression signatures that correlate with behavioural states. 97% of predicted microRNAs are novel to each species. Surprisingly, our data provide evidence that isoform variation can effectively convert protein-coding neuropeptide genes into non-coding transcripts, which may represent a new family of long non-coding RNAs. These data suggest that differences in neuropeptide gene expression, isoform variation, and small RNA interactions could contribute to behavioural differences within the Steinernema genus.

scholarly journals The role of transposable elements in the ecological morphogenesis under the influence of stress

2019 ◽  
Vol 23 (4) ◽  
pp. 380-389 ◽  
Author(s):  
R. N. Mustafin ◽  
E. K. Khusnutdinova
Keyword(s):  
Transcription Factors ◽  
Regulatory Networks ◽  
Insertional Mutagenesis ◽  
Specific Protein ◽  
Regulatory Sequences ◽  
Rapid Variability ◽  
Protein Coding ◽  
Genome Variability ◽  
Protein Coding Genes ◽  
Non Coding Rna

In natural selection, insertional mutagenesis is an important source of genome variability. Transposons are sensors of environmental stress effects, which contribute to adaptation and speciation. These effects are due to changes in the mechanisms of morphogenesis, since transposons contain regulatory sequences that have cis and trans effects on specific protein-coding genes. In variability of genomes, the horizontal transfer of transposons plays an important role, because it contributes to changing the composition of transposons and the acquisition of new properties. Transposons are capable of site-specific transpositions, which lead to the activation of stress response genes. Transposons are sources of non-coding RNA, transcription factors binding sites and protein-coding genes due to domestication, exonization, and duplication. These genes contain nucleotide sequences that interact with non-coding RNAs processed from transposons transcripts, and therefore they are under the control of epigenetic regulatory networks involving transposons. Therefore, inherited features of the location and composition of transposons, along with a change in the phenotype, play an important role in the characteristics of responding to a variety of environmental stressors. This is the basis for the selection and survival of organisms with a specific composition and arrangement of transposons that contribute to adaptation under certain environmental conditions. In evolution, the capability to transpose into specific genome sites, regulate gene expression, and interact with transcription factors, along with the ability to respond to stressors, is the basis for rapid variability and speciation by altering the regulation of ontogenesis. The review presents evidence of tissue-specific and stage-specific features of transposon activation and their role in the regulation of cell differentiation to confirm their role in ecological morphogenesis.

The origins and evolutionary history of human non-coding RNA regulatory networks

2017 ◽  
Vol 15 (02) ◽  
pp. 1750005 ◽  
Author(s):  
Masih Sherafatian ◽  
Seyed Javad Mowla
Keyword(s):  
Cell Cycle ◽  
Regulatory Network ◽  
Regulatory Networks ◽  
Evolutionary History ◽  
Regulatory Function ◽  
Protein Coding ◽  
Evolutionary Pattern ◽  
Non Coding Rna ◽  
History Of ◽  
Non Coding Rnas

The evolutionary history and origin of the regulatory function of animal non-coding RNAs are not well understood. Lack of conservation of long non-coding RNAs and small sizes of microRNAs has been major obstacles in their phylogenetic analysis. In this study, we tried to shed more light on the evolution of ncRNA regulatory networks by changing our phylogenetic strategy to focus on the evolutionary pattern of their protein coding targets. We used available target databases of miRNAs and lncRNAs to find their protein coding targets in human. We were able to recognize evolutionary hallmarks of ncRNA targets by phylostratigraphic analysis. We found the conventional 3′-UTR and lesser known 5′-UTR targets of miRNAs to be enriched at three consecutive phylostrata. Firstly, in eukaryata phylostratum corresponding to the emergence of miRNAs, our study revealed that miRNA targets function primarily in cell cycle processes. Moreover, the same overrepresentation of the targets observed in the next two consecutive phylostrata, opisthokonta and eumetazoa, corresponded to the expansion periods of miRNAs in animals evolution. Coding sequence targets of miRNAs showed a delayed rise at opisthokonta phylostratum, compared to the 3′ and 5′ UTR targets of miRNAs. LncRNA regulatory network was the latest to evolve at eumetazoa.

Construction of 3-D Terrain Models from BIG Data Sets

2014 ◽  
Author(s):  
Pankaj K. Agarwal ◽  
Thomas Moelhave
Keyword(s):  
Big Data ◽  
Data Sets ◽  
Terrain Models

Big Data Security Challenges and Solution of Distributed Computing in Hadoop Environment: A Security Framework

2020 ◽  
Vol 13 (4) ◽  
pp. 790-797
Author(s):  
Gurjit Singh Bhathal ◽  
Amardeep Singh Dhiman
Keyword(s):  
Big Data ◽  
Data Security ◽  
Data Sets ◽  
Security Framework ◽  
Hadoop Distributed File System ◽  
Current Scenario ◽  
Hadoop Cluster ◽  
Ciphertext Policy ◽  
In Transit ◽  
Hadoop Framework

Background: In current scenario of internet, large amounts of data are generated and processed. Hadoop framework is widely used to store and process big data in a highly distributed manner. It is argued that Hadoop Framework is not mature enough to deal with the current cyberattacks on the data. Objective: The main objective of the proposed work is to provide a complete security approach comprising of authorisation and authentication for the user and the Hadoop cluster nodes and to secure the data at rest as well as in transit. Methods: The proposed algorithm uses Kerberos network authentication protocol for authorisation and authentication and to validate the users and the cluster nodes. The Ciphertext-Policy Attribute- Based Encryption (CP-ABE) is used for data at rest and data in transit. User encrypts the file with their own set of attributes and stores on Hadoop Distributed File System. Only intended users can decrypt that file with matching parameters. Results: The proposed algorithm was implemented with data sets of different sizes. The data was processed with and without encryption. The results show little difference in processing time. The performance was affected in range of 0.8% to 3.1%, which includes impact of other factors also, like system configuration, the number of parallel jobs running and virtual environment. Conclusion: The solutions available for handling the big data security problems faced in Hadoop framework are inefficient or incomplete. A complete security framework is proposed for Hadoop Environment. The solution is experimentally proven to have little effect on the performance of the system for datasets of different sizes.

scholarly journals Transcriptomic and chemical analyses to identify candidate genes involved in color variation of sainfoin flowers

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yu Qiao ◽  
Qiming Cheng ◽  
Yutong Zhang ◽  
Wei Yan ◽  
Fengyan Yi ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Flower Color ◽  
Color Variation ◽  
Anthocyanin Synthesis ◽  
Flower Formation ◽  
Factors Affecting ◽  
Phenylpropanoid Biosynthesis ◽  
Molecular Information ◽  
Illumina Hiseq4000 ◽  
Insight Into

Abstract Background Sainfoin (Onobrychis viciifolia Scop) is not only a high-quality legume forage, but also a nectar-producing plant. Therefore, the flower color of sainfoin is an important agronomic trait, but the factors affecting its flower phenotype are still unclear. To gain insights into the regulatory networks associated with metabolic pathways of coloration compounds (flavonoids or anthocyanins) and identify the key genes, we conducted a comprehensive analysis of the phenotype, metabolome and transcriptome of WF and AF of sainfoin. Results Delphinidin, petunidin and malvidin derivatives were the main anthocyanin compounds in the AF of sainfoin. These substances were not detected in the WF of sainfoin. The transcriptomes of WF and AF in sainfoin at the S1 and S3 stages were obtained using the Illumina HiSeq4000 platform. Overall, 10,166 (4273 upregulated and 5893 downregulated) and 15,334 (8174 upregulated and 7160 downregulated) DEGs were identified in flowers at S1 and S3 stages, respectively (WF-VS-AF). KEGG pathway annotations showed that 6396 unigenes were annotated to 120 pathways and contained 866 DEGs at S1 stages, and 6396 unigenes were annotated to 131 pathways and included 1546 DEGs at the S3 stage. Nine DEGs belonging to the “flavonoid biosynthesis”and “phenylpropanoid biosynthesis” pathways involved in flower color formation were identified and verified by RT-qPCR analyses. Among these DEGs, 4CL3, FLS, ANS, CHS, DFR and CHI2 exhibited downregulated expression, and F3H exhibited upregulated expression in the WF compared to the AF, resulting in a decrease in anthocyanin synthesis and the formation of WF in sainfoin. Conclusions This study is the first to use transcriptome technology to study the mechanism of white flower formation in sainfoin. Our transcriptome data will be a great enrichment of the genetic information for sainfoin. In addition, the data presented herein will provide valuable molecular information for genetic breeding and provide insight into the future study of flower color polymorphisms in sainfoin.

scholarly journals Integrated whole transcriptome and small RNA analysis revealed multiple regulatory networks in colorectal cancer

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hibah Shaath ◽  
Salman M. Toor ◽  
Mohamed Abu Nada ◽  
Eyad Elkord ◽  
Nehad M. Alajez
Keyword(s):  
Colorectal Cancer ◽  
Messenger Rna ◽  
Regulatory Networks ◽  
Potential Interaction ◽  
Therapeutic Interventions ◽  
Signaling Networks ◽  
Protein Coding ◽  
Paired Samples ◽  
And Migration ◽  
Whole Transcriptome

AbstractColorectal cancer (CRC) remains a global disease burden and a leading cause of cancer related deaths worldwide. The identification of aberrantly expressed messenger RNA (mRNA), long non-coding RNA (lncRNA), and microRNA (miRNA), and the resulting molecular interactions and signaling networks is essential for better understanding of CRC, identification of novel diagnostic biomarkers and potential development of therapeutic interventions. Herein, we performed microRNA (miRNA) sequencing on fifteen CRC and their non-tumor adjacent tissues and whole transcriptome RNA-Seq on six paired samples from the same cohort and identified alterations in miRNA, mRNA, and lncRNA expression. Computational analyses using Ingenuity Pathway Analysis (IPA) identified multiple activated signaling networks in CRC, including ERBB2, RABL6, FOXM1, and NFKB networks, while functional annotation highlighted activation of cell proliferation and migration as the hallmark of CRC. IPA in combination with in silico prediction algorithms and experimentally validated databases gave insight into the complex associations and interactions between downregulated miRNAs and upregulated mRNAs in CRC and vice versa. Additionally, potential interaction between differentially expressed lncRNAs such as H19, SNHG5, and GATA2-AS1 with multiple miRNAs has been revealed. Taken together, our data provides thorough analysis of dysregulated protein-coding and non-coding RNAs in CRC highlighting numerous associations and regulatory networks thus providing better understanding of CRC.

scholarly journals Long non-coding RNA LINC00665 promotes gemcitabine resistance of Cholangiocarcinoma cells via regulating EMT and stemness properties through miR-424-5p/BCL9L axis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Min Lu ◽  
Xinglei Qin ◽  
Yajun Zhou ◽  
Gang Li ◽  
Zhaoyang Liu ◽  
...  
Keyword(s):  
Acquired Resistance ◽  
Transcriptional Regulators ◽  
First Line ◽  
Protein Coding ◽  
Gemcitabine Resistance ◽  
Non Coding Rna ◽  
Sphere Formation ◽  
Long Non Coding Rna ◽  
Line Chemotherapy

AbstractGemcitabine is the first-line chemotherapy drug for cholangiocarcinoma (CCA), but acquired resistance has been frequently observed in CCA patients. To search for potential long noncoding RNAs (lncRNAs) involved in gemcitabine resistance, two gemcitabine resistant CCA cell lines were established and dysregulated lncRNAs were identified by lncRNA microarray. Long intergenic non-protein coding RNA 665 (LINC00665) were found to rank the top 10 upregulated lncRNAs in our study, and high LINC00665 expression was closely associated with poor prognosis and chemoresistance of CCA patients. Silencing LINC00665 in gemcitabine resistant CCA cells impaired gemcitabine tolerance, while enforced LINC00665 expression increased gemcitabine resistance of sensitive CCA cells. The gemcitabine resistant CCA cells showed increased EMT and stemness properties, and silencing LINC00665 suppressed sphere formation, migration, invasion and expression of EMT and stemness markers. In addition, Wnt/β-Catenin signaling was activated in gemcitabine resistant CCA cells, but LINC00665 knockdown suppressed Wnt/β-Catenin activation. B-cell CLL/lymphoma 9-like (BCL9L), the nucleus transcriptional regulators of Wnt/β-Catenin signaling, plays a key role in the nucleus translocation of β-Catenin and promotes β-Catenin-dependent transcription. In our study, we found that LINC00665 regulated BCL9L expression by acting as a molecular sponge for miR-424-5p. Moreover, silencing BCL9L or miR-424-5p overexpression suppressed gemcitabine resistance, EMT, stemness and Wnt/β-Catenin activation in resistant CCA cells. In conclusion, our results disclosed the important role of LINC00665 in gemcitabine resistance of CCA cells, and provided a new biomarker or therapeutic target for CCA treament.

scholarly journals Thinking about police data: Analysts’ perceptions of data quality in Canadian policing

2021 ◽  
pp. 0032258X2110214
Author(s):  
Christopher D O’Connor ◽  
John Ng ◽  
Dallas Hill ◽  
Tyler Frederick
Keyword(s):  
Big Data ◽  
Data Collection ◽  
Data Quality ◽  
Research Culture ◽  
Police Services ◽  
Police Data ◽  
Data Collection And Analysis ◽  
Quality Issues

Policing is increasingly being shaped by data collection and analysis. However, we still know little about the quality of the data police services acquire and utilize. Drawing on a survey of analysts from across Canada, this article examines several data collection, analysis, and quality issues. We argue that as we move towards an era of big data policing it is imperative that police services pay more attention to the quality of the data they collect. We conclude by discussing the implications of ignoring data quality issues and the need to develop a more robust research culture in policing.

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