scholarly journals Computational Tools for Genome-Wide miRNA Prediction and Study

2012 ◽  
Vol 5 (1) ◽  
pp. 23-30 ◽  
Author(s):  
Tareq B. Malas ◽  
Timothy Ravasi
Keyword(s):  
Messenger Rna ◽  
Biological Processes ◽  
Computational Tools ◽  
Mirna Prediction ◽  
Advantages And Disadvantages ◽  
Non Coding Rna ◽  
Large Numbers ◽  
Genome Wide ◽  
Post Transcriptional Regulation ◽  
Generation Sequencing

MicroRNAs (miRNAs) are single-stranded non-coding RNA susually of 22 nucleotidesin length that play an important post-transcriptional regulation role in many organisms. MicroRNAs bind a seed sequence to the 3'-untranslated region (UTR) region of the target messenger RNA (mRNA), inducing degradation or inhibition of translation and resulting in a reduction in the protein level. This regulatory mechanism is central to many biological processes and perturbation could lead to diseases such as cancer. Given the biological importance, of miRNAs, there is a great need to identify and study their targets and functions. However, miRNAs are very difficult to clone in the lab and this has hindered the identification of novel miRNAs. Next-generation sequencing coupled with new computational tools has recently evolved to help researchers efficiently identify large numbers of novel miRNAs. In this review, we describe recent miRNA prediction tools and discuss their priorities, advantages and disadvantages.

scholarly journals Post-transcriptional regulation of microRNAs in cancer: From prediction to validation

2018 ◽  
Author(s):  
Sheril June Ankasha ◽  
Mohamad Nasir Shafiee ◽  
Norhazlina Abdul Wahab ◽  
Raja Affendi Raja Ali ◽  
Norfilza Mohd Mokhtar
Keyword(s):  
Transcriptional Regulation ◽  
Messenger Rna ◽  
Vital Role ◽  
Transcriptional Level ◽  
Rna Expression ◽  
Biological Processes ◽  
Target Region ◽  
Non Coding Rna ◽  
Target Sites ◽  
Post Transcriptional Regulation

MicroRNA (miRNA) is a small non-coding RNA with an established function to regulate genes at the post-transcriptional level leading to suppression or degradation of its messenger RNA expression (mRNA). Its dysregulation plays a vital role in a variety of biological and pathological processes including cancer. A lot of algorithms have been established to predict the target sites of miRNA, but experimentally identifying and validating its target region is still lacking. Guidance in experimental procedures is really needed to find genuine miRNA targets. Therefore, in this review, we provide an outline on the workflow in predicting and validating the targeted sites of miRNA using several methods as a guideline for the scientists. The final outcome of this type of experiment is essential to explore the major impact of miRNAmRNA interaction involved in the biological processes and to assist miRNA-based drug development in the future.

MicroRNAs: Key Regulators in Lung Cancer

MicroRNA ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Younes El Founini ◽  
Imane Chaoui ◽  
Hind Dehbi ◽  
Mohammed El Mzibri ◽  
Roger Abounader ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Messenger Rna ◽  
Recent Literature ◽  
Immune Surveillance ◽  
Rna Stability ◽  
Noncoding Rnas ◽  
Therapy Resistance ◽  
Biological Processes ◽  
Genome Wide ◽  
Stable Forms

: Noncoding RNAs have emerged as key regulators of the genome upon gene expression profiling and genome-wide sequencing. Among these noncoding RNAs, microRNAs are short noncoding RNAs that regulate a plethora of functions, biological processes and human diseases by targeting the messenger RNA stability through 3’UTR binding, leading to either mRNA cleavage or translation repression, depending on microRNA-mRNA complementarity degree. Additionally, strong evidence has suggested that dysregulation of miRNAs contribute to the etiology and progression of human cancers, such as lung cancer, the most common and deadliest cancer worldwide. Indeed, by acting as oncogenes or tumor suppressors, microRNAs control all aspects of lung cancer malignancy, including cell proliferation, survival, migration, invasion, angiogenesis, cancer stem cells, immune-surveillance escape, and therapy resistance; and their expressions are often associated with clinical parameters. Moreover, several deregulated microRNAs in lung cancer are carried by exosomes, microvesicles and secreted in body fluids, mainly the circulation where they conserve their stable forms. Subsequently, seminal efforts have been focused on extracellular microRNAs levels as noninvasive diagnostic and prognostic biomarkers in lung cancer. In this review, focusing on recent literature, we summarize the deregulation, mechanisms of action, functions and highlight clinical applications of miRNAs for better management and design of future lung cancer targeted therapies.

scholarly journals Long Non-Coding RNAs as Endogenous Target Mimics and Exploration of Their Role in Low Nutrient Stress Tolerance in Plants

Genes ◽  
2018 ◽  
Vol 9 (9) ◽  
pp. 459 ◽  
Author(s):  
Priyanka Borah ◽  
Antara Das ◽  
Matthew Milner ◽  
Arif Ali ◽  
Alison Bentley ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Next Generation Sequencing ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Non Coding Rnas ◽  
Endogenous Target ◽  
Long Non Coding Rna ◽  
Nutrient Homeostasis ◽  
Generation Sequencing

Long non-coding RNA (lncRNA) research in plants has recently gained momentum taking cues from studies in animals systems. The availability of next-generation sequencing has enabled genome-wide identification of lncRNA in several plant species. Some lncRNAs are inhibitors of microRNA expression and have a function known as target mimicry with the sequestered transcript known as an endogenous target mimic (eTM). The lncRNAs identified to date show diverse mechanisms of gene regulation, most of which remain poorly understood. In this review, we discuss the role of identified putative lncRNAs that may act as eTMs for nutrient-responsive microRNAs (miRNAs) in plants. If functionally validated, these putative lncRNAs would enhance current understanding of the role of lncRNAs in nutrient homeostasis in plants.

scholarly journals Genome-wide screening of circadian and non-circadian impact of Neat1 genetic deletion

2021 ◽  
Author(s):  
Audrey Jacq ◽  
Denis Becquet ◽  
Maria-Montserrat Bello-Goutierrez ◽  
Bénédicte Boyer ◽  
Séverine Guillen ◽  
...  
Keyword(s):  
Biological Processes ◽  
Circadian Expression ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Independent Functions ◽  
Rat Pituitary ◽  
Genetic Deletion ◽  
The Impact ◽  
Long Non Coding Rna ◽  
Abundant Transcript

AbstractThe functions of the long non-coding RNA, Nuclear enriched abundant transcript 1 (Neat1), are poorly understood. Neat1 is required for the formation of paraspeckles, but its respective paraspeckle-dependent or independent functions are unknown. Several studies including ours reported that Neat1 is involved in the regulation of circadian rhythms. We characterized the impact of Neat1 genetic deletion in a rat pituitary cell line. The mRNAs whose circadian expression pattern or expression level is regulated by Neat1 were identified after high-throughput RNA sequencing of the circadian transcriptome of wild-type cells compared to cells in which Neat1 was deleted by CRISPR/Cas9. The numerous RNAs affected by Neat1 deletion were found to be circadian or non-circadian, targets or non-targets of paraspeckles, and to be associated with many key biological processes showing that Neat1, interacting or independently of the circadian system, could play crucial roles in key physiological functions through diverse mechanisms.

scholarly journals Platforms for Investigating LncRNA Functions

2018 ◽  
Vol 23 (6) ◽  
pp. 493-506 ◽  
Author(s):  
John Lalith Charles Richard ◽  
Pieter Johan Adam Eichhorn
Keyword(s):  
Next Generation Sequencing ◽  
Dosage Compensation ◽  
Messenger Rna ◽  
Noncoding Rnas ◽  
Rna Degradation ◽  
Biological Processes ◽  
Protein Kinetics ◽  
Heterogeneous Nature ◽  
Eukaryotic Genomes ◽  
Generation Sequencing

Prior to the sequencing of the human genome, it was presumed that most of the DNA coded for proteins. However, with the advent of next-generation sequencing, it has now been recognized that most complex eukaryotic genomes are in fact transcribed into noncoding RNAs (ncRNAs), including a family of transcripts referred to as long noncoding RNAs (lncRNAs). LncRNAs have been implicated in many biological processes ranging from housekeeping functions such as transcription to more specialized functions such as dosage compensation or genomic imprinting, among others. Interestingly, lncRNAs are not limited to a defined set of functions but can regulate varied activities such as messenger RNA degradation, translation, and protein kinetics or function as RNA decoys or scaffolds. Although still in its infancy, research into the biology of lncRNAs has demonstrated the importance of lncRNAs in development and disease. However, the specific mechanisms through which these lncRNAs act remain poorly defined. Focused research into a small number of these lncRNAs has provided important clues into the heterogeneous nature of this family of ncRNAs. Due to the complex diversity of lncRNA function, in this review, we provide an update on the platforms available for investigators to aid in the identification of lncRNA function.

scholarly journals Studying RNA–DNA interactome by Red-C identifies noncoding RNAs associated with repressed chromatin compartment and reveals transcription dynamics

2019 ◽  
Author(s):  
Alexey A. Gavrilov ◽  
Anastasiya A. Zharikova ◽  
Aleksandra A. Galitsyna ◽  
Artem V. Luzhin ◽  
Natalia M. Rubanova ◽  
...  
Keyword(s):  
Messenger Rna ◽  
K562 Cells ◽  
Biological Processes ◽  
Rna Molecules ◽  
Proximity Ligation ◽  
Genome Wide ◽  
Non Coding Rnas ◽  
Genomic Regions ◽  
Kinetics Of ◽  
Inactive Chromatin

AbstractNon-coding RNAs (ncRNAs) participate in various biological processes, including regulating transcription and sustaining genome 3D organization. Here, we present a method termed Red-C that exploits proximity ligation to identify contacts with the genome for all RNA molecules present in the nucleus. Using Red-C, we uncovered the RNA–DNA interactome of human K562 cells and identified hundreds of ncRNAs enriched in active or repressed chromatin, including previously undescribed RNAs. We found two microRNAs—MIR3648 and MIR3687 transcribed from the rRNA locus—that are associated with inactive chromatin genome wide. These miRNAs favor bulk heterochromatin over Polycomb-repressed chromatin and interact preferentially with late-replicating genomic regions. Analysis of the RNA–DNA interactome also allowed us to trace the kinetics of messenger RNA production. Our data support the model of co-transcriptional intron splicing, but not the hypothesis of the circularization of actively transcribed genes.

scholarly journals Noninvasive characterization of Alzheimer’s disease by circulating, cell-free messenger RNA next-generation sequencing

2020 ◽  
Vol 6 (50) ◽  
pp. eabb1654
Author(s):  
Shusuke Toden ◽  
Jiali Zhuang ◽  
Alexander D. Acosta ◽  
Amy P. Karns ◽  
Neeraj S. Salathia ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Messenger Rna ◽  
Biological Processes ◽  
Molecular Alterations ◽  
Gene Transcripts ◽  
Noninvasive Characterization ◽  
The Brain ◽  
Generation Sequencing

The lack of accessible noninvasive tools to examine the molecular alterations occurring in the brain limits our understanding of the causes and progression of Alzheimer’s disease (AD), as well as the identification of effective therapeutic strategies. Here, we conducted a comprehensive profiling of circulating, cell-free messenger RNA (cf-mRNA) in plasma of 126 patients with AD and 116 healthy controls of similar age. We identified 2591 dysregulated genes in the cf-mRNA of patients with AD, which are enriched in biological processes well known to be associated with AD. Dysregulated genes included brain-specific genes and resembled those identified to be dysregulated in postmortem AD brain tissue. Furthermore, we identified disease-relevant circulating gene transcripts that correlated with the severity of cognitive impairment. These data highlight the potential of high-throughput cf-mRNA sequencing to evaluate AD-related pathophysiological alterations in the brain, leading to precision healthcare solutions that could improve AD patient management.

scholarly journals Revisiting criteria for plant miRNA annotation in the era of big data

2017 ◽  
Author(s):  
Michael J. Axtell ◽  
Blake C. Meyers
Keyword(s):  
Big Data ◽  
Transcriptional Regulation ◽  
Dna Sequencing ◽  
Small Rnas ◽  
Next Generation ◽  
Large Numbers ◽  
Plant Mirna ◽  
Post Transcriptional Regulation ◽  
Generation Sequencing ◽  
Sheer Number

AbstractMicroRNAs (miRNAs) are ~21 nucleotide-long regulatory RNAs that arise from endonucleolytic processing of hairpin precursors. Many function as essential post-transcriptional regulators of target mRNAs and long non-coding RNAs. Alongside miRNAs, plants also produce large numbers of short interfering RNAs (siRNAs), which are distinguished from miRNAs primarily by their biogenesis (typically processed from long double-stranded RNA instead of single-stranded hairpins) and functions (typically via roles in transcriptional regulation instead of post-transcriptional regulation). Next-generation DNA sequencing methods have yielded extensive datasets of plant small RNAs, resulting in many miRNA annotations, occasionally inaccurately curated. The sheer number of endogenous siRNAs compared to miRNAs has been a major factor in the erroneous annotation of siRNAs as miRNAs. Here, we provide updated criteria for the confident annotation of plant miRNAs, suitable for the era of “big data” from DNA sequencing. The updated criteria emphasize replication, the minimization of false positives, and they require next-generation sequencing of small RNAs. We argue that improved annotation systems are needed for miRNAs and all other classes of plant small RNAs. Finally, to illustrate the complexities of miRNA and siRNA annotation, we review the evolution and functions of miRNAs and siRNAs in plants.

scholarly journals Efficient and accurate detection of splice junctions from RNAseq with Portcullis

2017 ◽  
Author(s):  
Daniel Mapleson ◽  
Luca Venturini ◽  
Gemy Kaithakottil ◽  
David Swarbreck
Keyword(s):  
Rna Seq ◽  
Accurate Identification ◽  
Large Numbers ◽  
Genome Wide ◽  
Exon Junctions ◽  
Next Generation Sequencing Ngs ◽  
Error Profiles ◽  
High Degree ◽  
Splice Junctions ◽  
Generation Sequencing

ABSTRACTNext generation sequencing (NGS) technologies enable rapid and cheap genome-wide transcriptome analysis, providing vital information about gene structure, transcript expression and alternative splicing. Key to this is the the accurate identification of exon-exon junctions from RNA sequenced (RNA-seq) reads. A number of RNA-seq aligners capable of splitting reads across these splice junctions (SJs) have been developed, however, it has been shown that while they correctly identify most genuine SJs available in a given sample, they also often produce large numbers of incorrect SJs. Herein we describe the extent of this problem using popular RNA-seq mapping tools, and present a new method, called Portcullis, to rapidly filter false SJs junctions from spliced alignments produced by any RNA-seq mapper capable of creating SAM/BAM files. We show that Portcullis distinguishes between genuine and false positive junctions to a high-degree of accuracy across different species, samples, expression levels, error profiles and read lengths. Portcullis makes efficient use of memory and threading and, to our knowledge, is currently the only SJ prediction tool that reliably scales for use with large RNAseq datasets and large highly fragmented genomes, whilst delivering highly accurate SJs.AvailabilityPortcullis is available under the GPLv3 license at: http://maplesond.github.io/portcullis/[email protected]

scholarly journals Halobacterium salinarum and Haloferax volcanii Comparative Transcriptomics Reveals Conserved Transcriptional Processing Sites

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1018
Author(s):  
Amr Galal Abd El-Raheem Ibrahim ◽  
Ricardo Z. N. Vêncio ◽  
Alan P. R. Lorenzetti ◽  
Tie Koide
Keyword(s):  
Messenger Rna ◽  
Comparative Transcriptomics ◽  
Halobacterium Salinarum ◽  
Haloferax Volcanii ◽  
Model Organisms ◽  
Genome Wide ◽  
Regulatory Strategy ◽  
Processing Signal ◽  
Processing Site ◽  
Post Transcriptional Regulation

Post-transcriptional processing of messenger RNA is an important regulatory strategy that allows relatively fast responses to changes in environmental conditions. In halophile systems biology, the protein perspective of this problem (i.e., ribonucleases which implement the cleavages) is generally more studied than the RNA perspective (i.e., processing sites). In the present in silico work, we mapped genome-wide transcriptional processing sites (TPS) in two halophilic model organisms, Halobacterium salinarum NRC-1 and Haloferax volcanii DS2. TPS were established by reanalysis of publicly available differential RNA-seq (dRNA-seq) data, searching for non-primary (monophosphorylated RNAs) enrichment. We found 2093 TPS in 43% of H. salinarum genes and 3515 TPS in 49% of H. volcanii chromosomal genes. Of the 244 conserved TPS sites found, the majority were located around start and stop codons of orthologous genes. Specific genes are highlighted when discussing antisense, ribosome and insertion sequence associated TPS. Examples include the cell division gene ftsZ2, whose differential processing signal along growth was detected and correlated with post-transcriptional regulation, and biogenesis of sense overlapping transcripts associated with IS200/IS605. We hereby present the comparative, transcriptomics-based processing site maps with a companion browsing interface.

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