Computational methods for annotation of plant regulatory non-coding RNAs using RNA-seq

2020 ◽  
Author(s):  
A T Vivek ◽  
Shailesh Kumar
Keyword(s):  
Computational Methods ◽  
High Throughput ◽  
Rna Seq ◽  
Physiological Mechanisms ◽  
Software Packages ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale ◽  
Plant Transcriptome ◽  
Non Coding Rnas

Abstract Plant transcriptome encompasses numerous endogenous, regulatory non-coding RNAs (ncRNAs) that play a major biological role in regulating key physiological mechanisms. While studies have shown that ncRNAs are extremely diverse and ubiquitous, the functions of the vast majority of ncRNAs are still unknown. With ever-increasing ncRNAs under study, it is essential to identify, categorize and annotate these ncRNAs on a genome-wide scale. The use of high-throughput RNA sequencing (RNA-seq) technologies provides a broader picture of the non-coding component of transcriptome, enabling the comprehensive identification and annotation of all major ncRNAs across samples. However, the detection of known and emerging class of ncRNAs from RNA-seq data demands complex computational methods owing to their unique as well as similar characteristics. Here, we discuss major plant endogenous, regulatory ncRNAs in an RNA sample followed by computational strategies applied to discover each class of ncRNAs using RNA-seq. We also provide a collection of relevant software packages and databases to present a comprehensive bioinformatics toolbox for plant ncRNA researchers. We assume that the discussions in this review will provide a rationale for the discovery of all major categories of plant ncRNAs.

scholarly journals Visualizing the periodic Ribo-seq reads with RiboPlotR

2019 ◽  
Author(s):  
Hsin-Yen Larry Wu ◽  
Polly Yingshan Hsu
Keyword(s):  
Mrna Translation ◽  
Open Reading Frames ◽  
Untranslated Regions ◽  
Rna Seq ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale ◽  
Non Coding Rnas ◽  
Reading Frames ◽  
Small Open Reading Frames

ABSTRACTBackgroundRibo-seq has revolutionized the study of mRNA translation in a genome-wide scale. High-quality Ribo-seq data display strong 3-nucleotide (nt) periodicity, which corresponds to translating ribosomes decipher three nucleotides each time. While the 3-nt periodicity has been widely used to study novel translation events and identify small open reading frames on presumed non-coding RNAs, tools which allow the visualization of those events remain underdeveloped.FindingsRiboPlotR is a visualization package written in R that presents both RNA-seq coverage and Ribo-seq reads for all annotated transcript isoforms in a context of a given gene. In particular, RiboPlotR plots Ribo-seq reads mapped in three reading frames using three colors for one isoform model at a time. Moreover, RiboPlotR shows Ribo-seq reads on upstream ORFs, 5’ and 3’ untranslated regions and introns, which is critical for observing new translation events and potential regulatory mechanisms.ConclusionsRiboPlotR is freely available (https://github.com/hsinyenwu/RiboPlotR) and allows the visualization of the translating features in Ribo-seq data.

scholarly journals Study strategies for long non-coding RNAs and their roles in regulating gene expression

2015 ◽  
Vol 20 (2) ◽  
Author(s):  
Dan Qin ◽  
Cunshuan Xu
Keyword(s):  
Gene Expression ◽  
Regulatory Network ◽  
Experimental Methods ◽  
Study Strategies ◽  
Mechanisms Of Action ◽  
Cellular Processes ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale ◽  
Non Coding Rnas

AbstractLong non-coding RNAs (lncRNAs) have attracted considerable attention recently due to their involvement in numerous key cellular processes and in the development of various disorders. New high-throughput methods enable their study on a genome-wide scale. Numerous lncRNAs have been identified and characterized as important members of the biological regulatory network, with significant roles in regulating gene expression at the epigenetic, transcriptional and post-transcriptional levels. This paper summarizes the diverse mechanisms of action of these lncRNAs and looks at the study strategies in this field. A major challenge in future study is to establish more effective bioinformatics and experimental methods to explore the functions, detailed mechanisms of action and structures deciding the functional diversity of lncRNAs, since the vast majority remain unresolved.

scholarly journals Characterization of the radiation desiccation response regulon of the radioresistant bacterium Deinococcus radiodurans by integrative genomic analyses.

2021 ◽  
Author(s):  
Nicolas Eugenie ◽  
Yvan Zivanovic ◽  
Gaelle Lelandais ◽  
Genevieve Coste ◽  
Claire Bouthier de la Tour ◽  
...  
Keyword(s):  
Deinococcus Radiodurans ◽  
Normal Growth ◽  
Growth Conditions ◽  
Rna Seq ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Analyses ◽  
Number Of Genes ◽  
Wide Scale

Numerous genes are overexpressed in the radioresistant bacterium Deinococcus radiodurans after exposure to radiation or prolonged desiccation. The DdrO and IrrE proteins play a major role in regulating the expression of approximately predicted twenty of these genes. The transcriptional repressor DdrO blocks the expression of these genes under normal growth conditions. After exposure to genotoxic agents, the IrrE metalloprotease cleaves DdrO and relieves gene repression. Bioinformatic analyzes showed that this mechanism seems to be conserved in several species of Deinococcus, but many questions remain as such the number of genes regulated by DdrO. Here, by RNA-seq and CHiP-seq assays performed at a genome-wide scale coupled with bioinformatic analyses, we show that, the DdrO regulon in D. radiodurans includes many other genes than those previously described. These results thus pave the way to better understand the radioresistance mechanisms encoded by this bacterium.

Whole human exome capture for high-throughput sequencing

Genome ◽  
2010 ◽  
Vol 53 (7) ◽  
pp. 568-574 ◽  
Author(s):  
Dae-Won Kim ◽  
Seong-Hyeuk Nam ◽  
Ryong Nam Kim ◽  
Sang-Haeng Choi ◽  
Hong-Seog Park
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Exome Capture ◽  
Microarray Design ◽  
Genome Wide ◽  
Human Genes ◽  
Practical Usefulness ◽  
A Genome ◽  
Wide Scale ◽  
Total Base

We captured the whole human exome by hybridization using synthesized oligonucleotides, based on a high-density microarray design, and we sequenced those captured human exons using high-throughput sequencing on a Genome Sequencer FLX instrument. Of the uniquely mapped reads, 71% fell within target regions, and these corresponded to coverage of 94% of human genes, 87% of exons, and 70% of the total base-pair length of the CCDS set. Our study provides strong evidence for the practical usefulness of this method on a genome-wide scale, showing the resequenced whole human exome database with 501 microRNAs and 307 novel SNPs.

scholarly journals Functional Genomics–Linking Genotype with Phenotype on Genome-wide Scale

2019 ◽  
Vol 4 (01) ◽  
pp. 4-12
Author(s):  
Nida Tabassum Khan ◽  
Namra Jameel ◽  
Maham Jamil Khan
Keyword(s):  
Functional Genomics ◽  
High Throughput ◽  
Genomic Data ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Studies ◽  
Wide Scale

Functional genomics manipulates genomic data to study genes and its expression on a genome wide scale involving high-throughput methods. The keyobjective of Functional genomics is to exploit the data acquired from transcriptomic and genomic studies to explain the functions and interfaces of a genome and its corresponding phenotype.

scholarly journals Genome-Wide Technologies to Study RNA–Chromatin Interactions

2020 ◽  
Vol 6 (2) ◽  
pp. 20 ◽  
Author(s):  
Masaki Kato ◽  
Piero Carninci
Keyword(s):  
Nuclear Organization ◽  
Oligonucleotide Probes ◽  
Hybridization Capture ◽  
Proximity Ligation ◽  
Advantages And Disadvantages ◽  
Chromatin Interactions ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale ◽  
Non Coding Rnas

An increasing number of studies have revealed that long non-coding RNAs (lncRNAs) play important roles in gene regulation and nuclear organization. Although the mechanisms are still largely unknown, many lncRNAs have been shown to interact with chromatin. Thus, one approach to understanding the function of these lncRNAs is to identify their sites of genomic interaction. Hybridization capture methods using oligonucleotide probes have been used for years to study chromatin-associated RNA. Recently, several groups have developed novel methods based on proximity ligation to investigate RNA–chromatin interactions at a genome-wide scale. This review discusses these technologies and highlights their advantages and disadvantages for the consideration of potential users.

scholarly journals Regulation of global transcription inE. coliby Rsd and 6S RNA

2016 ◽  
Author(s):  
Avantika Lal ◽  
Sandeep Krishna ◽  
Aswin Sai Narain Seshasayee
Keyword(s):  
Rna Polymerase ◽  
Sigma Factor ◽  
Global Gene Expression ◽  
Rna Seq ◽  
Genome Wide ◽  
A Genome ◽  
6S Rna ◽  
Wide Scale ◽  
Five Phases ◽  
First Time

ABSTRACTInEscherichia coli, the sigma factor σ70directs RNA polymerase to transcribe growth-related genes, while σ38directs transcription of stress response genes during stationary phase. Two molecules hypothesized to regulate RNA polymerase are the protein Rsd, which binds to σ70, and the non-coding 6S RNA which binds to the RNA polymerase- σ70holoenzyme. Despite multiple studies, the functions of Rsd and 6S RNA remain controversial. Here we use RNA-Seq in five phases of growth to elucidate their function on a genome-wide scale. We show for the first time that Rsd and 6S RNA facilitate σ38activity throughout bacterial growth, while 6S RNA also regulates widely different genes depending upon growth phase. We discover novel interactions between 6S RNA and Rsd and show widespread expression changes in a strain lacking both regulators. Finally, we present a mathematical model of transcription which highlights the crosstalk between Rsd and 6S RNA as a crucial factor in controlling sigma factor competition and global gene expression.

scholarly journals CRISPRi-Seq for the Identification and Characterisation of Essential Mycobacterial Genes and Transcriptional Units

2018 ◽  
Author(s):  
Timothy J. de Wet ◽  
Irene Gobe ◽  
Musa M. Mhlanga ◽  
Digby F. Warner
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Essential Gene ◽  
Experimental Models ◽  
Bacterial Gene ◽  
Growth And Survival ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale ◽  
Transcriptional Units

AbstractHigh-throughput essentiality screens have enabled genome-wide assessments of the genetic requirements for growth and survival of a variety of bacteria in different experimental models. The reliance in many of these studies on transposon (Tn)-based gene inactivation has, however, limited the ability to probe essential gene function or design targeted screens. We interrogated the potential of targeted, large-scale, pooled CRISPR interference (CRISPRi)-based screens to extend conventional Tn approaches in mycobacteria through the capacity for positionally regulable gene repression. Here, we report the utility of the “CRISPRi-Seq” method for targeted, pooled essentiality screening, confirming strong overlap with Tn-Seq datasets. In addition, we exploit this high-throughput approach to provide insight into CRISPRi functionality. By interrogating polar effects and combining image-based phenotyping with CRISPRi-mediated depletion of selected essential genes, we demonstrate that CRISPRi-Seq can functionally validate Transcriptional Units within operons. Together, these observations suggest the utility of CRISPRi-Seq to provide insights into (myco)bacterial gene regulation and expression on a genome-wide scale.

Sign in / Sign up

Export Citation Format

Share Document