scholarly journals Prediction Of Novel Pirna Rat Clusters Based On Mouse Pirna Clusters Using Downstream and Upstream Analysis

10.29007/zwxg ◽  
2019 ◽  
Author(s):  
Tamer Aldwairi ◽  
Federico Hoffmann ◽  
Andy Perkins
Keyword(s):  
Gene Silencing ◽  
Danio Rerio ◽  
Repetitive Elements ◽  
Sequence Conservation ◽  
Animal Cells ◽  
Novel Approach ◽  
Non Coding Rna ◽  
Genomic Clusters

PiRNAs are a particular type of small non-coding RNA. They are distinct from miRNA in size as well as other characteristics, such as the lack of sequence conservation and increased complexity when compared to their miRNA counterparts. PiRNA is considered the largest class of sRNA that is expressed especially in the animal cells. piRNAs are derived from long single-stranded RNAs, which are transcribed from genomic clusters, in contrast to other small silencing RNAs. It has been speculated that one locus could generate more than one piRNA. PiRNA corresponding to repetitive elements is fewer in mammals than in other species like Drosophila and Danio rerio, which signifies that piRNA might have possessed or gained some additional functionality in mammals. While the functionality of piRNAs may not be fully understood, they are believed to be involved in gene silencing. In this paper, we will examine a novel approach to identify potential piRNA clusters based on genes downstream and upstream location and order.

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.

Cationic siRNAs Provide Carrier-Free Gene Silencing in Animal Cells

2009 ◽  
Vol 131 (49) ◽  
pp. 17730-17731 ◽  
Author(s):  
Marc Nothisen ◽  
Mitsuharu Kotera ◽  
Emilie Voirin ◽  
Jean-Serge Remy ◽  
Jean-Paul Behr
Keyword(s):  
Gene Silencing ◽  
Animal Cells ◽  
Carrier Free ◽  
Free Gene

scholarly journals The Strategy of Predator Evasion in Response to a Visual Looming Stimulus in Zebrafish (Danio rerio)

2020 ◽  
Vol 2 (1) ◽  
Author(s):  
A McKee ◽  
M J McHenry
Keyword(s):  
Danio Rerio ◽  
Visual Angle ◽  
Visual Cues ◽  
Adult Zebrafish ◽  
Fish Predator ◽  
Live Fish ◽  
Artificial Stimulus ◽  
Novel Approach ◽  
Escape Speed ◽  
Stimulus Angle

Synopsis A diversity of animals survive encounters with predators by escaping from a looming visual stimulus. Despite the importance of this behavior, it is generally unclear how visual cues facilitate a prey’s survival from predation. Therefore, the aim of this study was to understand how the visual angle subtended on the eye of the prey by the predator affects the distance of adult zebrafish (Danio rerio) from predators. We performed experiments to measure the threshold visual angle and mathematically modeled the kinematics of predator and prey. We analyzed the responses to the artificial stimulus with a novel approach that calculated relationships between hypothetical values for a threshold-stimulus angle and the latency between stimulus and response. These relationships were verified against the kinematic responses of zebrafish to a live fish predator (Herichthys cyanoguttatus). The predictions of our model suggest that the measured threshold visual angle facilitates escape when the predator’s approach is slower than approximately twice the prey’s escape speed. These results demonstrate the capacity and limits to how the visual angle provides a prey with the means to escape a predator.

MicroRNA-mediated gene silencing: are we close to a unifying model?

2012 ◽  
Vol 3 (1) ◽  
pp. 29-40 ◽  
Author(s):  
Victoria James ◽  
Sybil C.K. Wong ◽  
Tyson V. Sharp
Keyword(s):  
Gene Expression ◽  
Gene Silencing ◽  
Messenger Rna ◽  
Transcriptional Regulators ◽  
Effector Proteins ◽  
Specific Reference ◽  
Functional Studies ◽  
Non Coding Rna ◽  
Almost All ◽  
Terminal Effector

AbstractMicroRNAs (miRNAs) comprise a group of small non-coding RNA –21 nucleotides in length. They act as post-transcriptional regulators of gene expression by forming base pairing interactions with target messenger RNA (mRNA). At least 1000 miRNAs are predicted to be expressed in humans and are encoded for in the genome of almost all organisms. Functional studies indicate that every cellular process studied thus far is regulated at some level by miRNAs. Given this expansive role, it is not surprising that disruption of this crucial pathway underlies the initiation of, or in the least, contributes to the development and progression of numerous human diseases and physiological disorders. This review will focus on the latest developments in uncovering the mechanism(s) of miRNA-mediated silencing with specific reference to the function of terminal effector proteins, how translation of target mRNA is inhibited and whether we are moving towards understanding this fundamental gene silencing paradigm.

Long Non-Coding RNA GATA6-AS1 Inhibits Proliferation and Promotes Apoptosis of Lung Adenocarcinoma Through Sponging miR-331-3p and Regulating SOCS1/JAK2/STAT3 Pathway

2020 ◽  
Author(s):  
Xiaodong Huo ◽  
Huixing Wang ◽  
Ning Jiang ◽  
Kuo Yang ◽  
Bin Huo ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Lung Adenocarcinoma ◽  
Cell Apoptosis ◽  
Luciferase Reporter ◽  
Stat3 Signaling ◽  
Novel Approach ◽  
Non Coding Rna ◽  
Stat3 Signaling Pathway ◽  
Reporter Assays ◽  
Long Non Coding Rna

Abstract Background: Accumulating evidence has indicated the remarkable roles of long non-coding RNAs (lncRNAs) as oncogenes or tumor suppressors in many malignancies. The involvement of lncRNA GATA6-AS1 in cancers remains largely undiscovered. Herein, our research was aimed at elucidating the function and mechanism of GATA6-AS1 in lung adenocarcinoma (LUAD).Methods: Gene expression was measured through qRT-PCR and WB. Cell proliferation ratio was determined using CCK-8 and EdU assays. Cell apoptosis ratio was determined using TUNEL and flow cytometry assays. Molecular interactions were examined through RIP, RNA pull-down and luciferase reporter assays.Results: GATA6-AS1 expression was markedly down-regulated in LUAD cell lines. GATA6-AS1 could inhibit LUAD cell proliferation and promote cell apoptosis. Mechanistically, GATA6-AS1 was identified as the molecular sponge for miR-331-3p, whose knockdown in LUAD cells could reinforce the tumor-suppressing effects of GATA6-AS1 overexpression. Moreover, GATA6-AS1 functions as a competing endogenous RNA (ceRNA) through sequestering miR-331-3p to deregulate SOCS1, thus inhibiting JAK2/STAT3 signaling pathway and suppressing LUAD cell viability.Conclusions: These results demonstrate the tumor-suppressing function and mechanism of lncRNA GATA6-AS1 in LUAD cells. The axis of GATA6-AS1/miR-331-3p/SOCS1/JAK2/STAT3 can be adopted as a novel approach for LUAD treatment.

scholarly journals X chromosome inactivation: new players in the initiation of gene silencing

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 344 ◽  
Author(s):  
Ines Pinheiro ◽  
Edith Heard
Keyword(s):  
Gene Silencing ◽  
X Chromosome ◽  
Gene Dosage ◽  
X Chromosome Inactivation ◽  
Chromosome Inactivation ◽  
Crucial Importance ◽  
Compensation Process ◽  
Repressive Chromatin ◽  
Non Coding Rna ◽  
Recent Developments

X chromosome inactivation (XCI) is a dosage compensation process that was adopted by female mammals to balance gene dosage between XX females and XY males. XCI starts with the upregulation of the non-coding RNA Xist, after which most X-linked genes are silenced and acquire a repressive chromatin state. Even though the chromatin marks of the inactive X have been fairly well described, the mechanisms responsible for the initiation of XCI remain largely unknown. In this review, we discuss recent developments that revealed unexpected factors playing a role in XCI and that might be of crucial importance to understand the mechanisms responsible for the very first steps of this chromosome-wide gene-silencing event.

scholarly journals Xist-seeded nucleation sites form local concentration gradients of silencing proteins to inactivate the X-chromosome

2020 ◽  
Author(s):  
Yolanda Markaki ◽  
Johnny Gan Chong ◽  
Christy Luong ◽  
Shawn Y.X. Tan ◽  
Yuying Wang ◽  
...  
Keyword(s):  
Gene Silencing ◽  
X Chromosome ◽  
Effector Proteins ◽  
Local Concentration ◽  
Concentration Gradients ◽  
Rna Molecules ◽  
Intrinsically Disordered ◽  
Chromatin Interactions ◽  
Non Coding Rna ◽  
Xist Rna

AbstractThe long non-coding RNA Xist exploits numerous effector proteins to progressively induce gene silencing across the X chromosome and form the inactive X (Xi)-compartment. The mechanism underlying formation of the chromosome-wide Xi-compartment is poorly understood. Here, we find that formation of the Xi-compartment is induced by ∼50 locally confined granules, where two Xist RNA molecules nucleate supra-molecular complexes (SMCs) of interacting proteins. Xist-SMCs are transient structures that concentrate rapidly recycling proteins in the X by increasing protein binding affinity. We find that gene silencing originates at Xist-SMCs and propagates across the entire chromosome over time, achieved by Polycomb-mediated coalescence of chromatin regions and aggregation, via its intrinsically disordered domains, of the critical silencing factor SPEN. Our results suggest a new model for X chromosome inactivation, in which Xist RNA induces macromolecular crowding of heterochromatinizing proteins near distinct sites which ultimately increases their density throughout the chromosome. This mechanism enables deterministic gene silencing without the need for Xist ribonucleoprotein complex-chromatin interactions at each target gene.

scholarly journals Genome-wide detection and sequence conservation analysis of long non-coding RNA during hair follicle cycle of yak

2020 ◽  
Author(s):  
Xiaolan Zhang ◽  
Qi Bao ◽  
Congjun Jia ◽  
Chen Li ◽  
Yongfang Chang ◽  
...  
Keyword(s):  
Hair Follicle ◽  
Signaling Pathway ◽  
Expression Profile ◽  
Differential Expression Analysis ◽  
Hair Follicles ◽  
Sequence Conservation ◽  
Cashmere Goat ◽  
Non Coding Rna ◽  
Long Non Coding Rna ◽  
Ncbi Blast

Abstract Background: Long non-coding RNA (lncRNA) as an important regulator has been demonstrated playing an indispensable role in the biological process of hair follicles (HFs) growth. However, their function and expression profile in the HFs cycle of yak are yet unknown. Only a few functional lncRNAs have been identified, partly due to the low sequence conservation and lack of identified conserved properties in lncRNAs. Here, lncRNA-seq was employed to detect the expression profile of lncRNAs during the HFs cycle of yak, and the sequence conservation of two datasets between yak and cashmere goat during the HFs cycle was analyzed. Results: A total of 2884 lncRNAs were identified in 5 phases (Jan., Mar., Jun., Aug., and Oct.) during the HFs cycle of yak. Then, differential expression analysis between 3 phases (Jan., Mar., and Oct.) was performed, revealing that 198 differentially expressed lncRNAs (DELs) were obtained in the Oct.-vs-Jan. group, 280 DELs were obtained in the Jan.-vs-Mar. group, and 340 DELs were obtained in Mar.-vs-Oct. group. Subsequently, the nearest genes of lncRNAs were searched as the potential target genes and used to explore the function of DELs by GO and KEGG enrichment analysis. Several critical pathways involved in HFs development such as Wnt signaling pathway, VEGF signaling pathway, and Signaling pathways regulating pluripotency of stem cells, were enriched. To further screen key lncRNAs influencing the HFs cycle, 24 DELs with differ degree of sequence conservation were obtained via a comparative analysis of partial DELs with previously published lncRNA-seq data of cashmere goat in the HFs cycle using NCBI BLAST-2.9.0+, and 3 DELs of them were randomly selected for further detailed analysis of the sequence conservation properties. Conclusions: This study revealed the expression pattern and potential function of lncRNAs during HFs cycle of yak, which would expand the knowledge about the role of lncRNAs in the HFs cycle. The findings related to sequence conservation properties of lncRNAs in the HFs cycle between the two species may provide valuable insights into the study of lncRNA functionality and mechanism. Keywords: Hair follicle cycling, lncRNA, NCBI blast-2.9.0+, Yak

scholarly journals A novel binary k-mer approach for classification of coding and non-coding RNAs across diverse species

2021 ◽  
Author(s):  
Neha Periwal ◽  
Priya Sharma ◽  
Pooja Arora ◽  
Saurabh Pandey ◽  
Baljeet Kaur ◽  
...  
Keyword(s):  
Performance Metrics ◽  
Binary Sequences ◽  
C Elegans ◽  
Diverse Species ◽  
Novel Approach ◽  
Non Coding Rna ◽  
Binary Approach ◽  
Non Coding Rnas ◽  
Nearest Neighbour Classifier

Classification among coding (CDS) and non-coding RNA (ncRNA) sequences is a challenge and several machine learning models have been developed for the same. Since the frequency of curated coding sequences is many-folds as compared to that of the ncRNAs, we devised a novel approach to work with the complete datasets from fifteen diverse species. In our proposed novel binary approach, we replaced all the A,T with 0 and G,C with 1 to obtain a binary form of coding and ncRNAs. The k-mer analysis of these binary sequences revealed that the frequency of binary patterns among the coding and ncRNAs can be used as features to distinguish among them. Using insights from these distinguishing frequencies, we used k-nearest neighbour classifier to classify among them. Our strategy is not only time-efficient but leads to significantly increased performance metrics including Matthews correlation coefficient (MCC) for some species like P. paniscus, M. mulatta, M. lucifugus, G. gallus, C. japonica, C. abingdonii, A. carolinensis, D. melanogaster and C. elegans when compared with the conventional ATGC approach. Additionally, we also show that the values of MCC obtained for diverse species tested on the model based on H. sapiens correlated with the geological evolutionary timeline thereby further strengthening our approach. Therefore, we propose that CDS and ncRNAs can be efficiently classified using 2-character frequency as compared to 4-character frequency of ATGC approach. Thus, our highly efficient binary approach can replace the more complex ATGC approach successfully.

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