Global Analysis of the Human RNA Degradome Reveals Widespread Decapped and Endonucleolytic Cleaved Transcripts

RNA decay is an important regulatory mechanism for gene expression at the posttranscriptional level. Although the main pathways and major enzymes that facilitate this process are well defined, global analysis of RNA turnover remains under-investigated. Recent advances in the application of next-generation sequencing technology enable its use in order to examine various RNA decay patterns at the genome-wide scale. In this study, we investigated human RNA decay patterns using parallel analysis of RNA end-sequencing (PARE-seq) data from XRN1-knockdown HeLa cell lines, followed by a comparison of steady state and degraded mRNA levels from RNA-seq and PARE-seq data, respectively. The results revealed 1103 and 1347 transcripts classified as stable and unstable candidates, respectively. Of the unstable candidates, we found that a subset of the replication-dependent histone transcripts was polyadenylated and rapidly degraded. Additionally, we identified 380 endonucleolytically cleaved candidates by analyzing the most abundant PARE sequence on a transcript. Of these, 41.4% of genes were classified as unstable genes, which implied that their endonucleolytic cleavage might affect their mRNA stability. Furthermore, we identified 1877 decapped candidates, including HSP90B1 and SWI5, having the most abundant PARE sequences at the 5′-end positions of the transcripts. These results provide a useful resource for further analysis of RNA decay patterns in human cells.

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

10.1101/2021.07.07.451423 ◽

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.

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Genome-wide transcriptome analysis between Small-tail Han sheep and the Surabaya fur sheep using high-throughput RNA sequencing

Reproduction ◽

10.1530/rep-12-0507 ◽

2013 ◽

Vol 145 (6) ◽

pp. 587-596 ◽

Cited By ~ 40

Author(s):

Xiangyang Miao ◽

Qingmiao Luo

Keyword(s):

Candidate Genes ◽

Molecular Mechanisms ◽

Complex Trait ◽

Future Research ◽

Rna Seq ◽

Molecular Biology Technique ◽

High Fecundity ◽

Next Generation Sequencing Technology ◽

Genome Wide ◽

Generation Sequencing

The Small-tail Han sheep and the Surabaya fur sheep are two local breeds in North China, which are characterized by high-fecundity and low-prolificacy breed respectively. Significant genetic differences between these two breeds have provided increasing interests in the identification and utilization of major prolificacy genes in these sheep. High prolificacy is a complex trait, and it is difficult to comprehensively identify the candidate genes related to this trait using the single molecular biology technique. To understand the molecular mechanisms of fecundity and provide more information about high prolificacy candidate genes in high- and low-fecundity sheep, we explored the utility of next-generation sequencing technology in this work. A total of 1.8 Gb sequencing reads were obtained and resulted in more than 20 000 contigs that averaged ∼300 bp in length. Ten differentially expressed genes were further verified by quantitative real-time RT-PCR to confirm the reliability of RNA-seq results. Our work will provide a basis for the future research of the sheep reproduction.

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

Briefings in Bioinformatics ◽

10.1093/bib/bbaa322 ◽

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.

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Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data

BMC Biology ◽

10.1186/s12915-021-00949-x ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Amit Blumberg ◽

Yixin Zhao ◽

Yi-Fei Huang ◽

Noah Dukler ◽

Edward J. Rice ◽

...

Keyword(s):

Dna Sequences ◽

Structural Equation ◽

Dynamic Equilibrium ◽

Rna Stability ◽

Estimation Method ◽

Decay Rates ◽

Rna Decay ◽

Rna Seq ◽

Simple Method ◽

Genome Wide

Abstract Background The concentrations of distinct types of RNA in cells result from a dynamic equilibrium between RNA synthesis and decay. Despite the critical importance of RNA decay rates, current approaches for measuring them are generally labor-intensive, limited in sensitivity, and/or disruptive to normal cellular processes. Here, we introduce a simple method for estimating relative RNA half-lives that is based on two standard and widely available high-throughput assays: Precision Run-On sequencing (PRO-seq) and RNA sequencing (RNA-seq). Results Our method treats PRO-seq as a measure of transcription rate and RNA-seq as a measure of RNA concentration, and estimates the rate of RNA decay required for a steady-state equilibrium. We show that this approach can be used to assay relative RNA half-lives genome-wide, with good accuracy and sensitivity for both coding and noncoding transcription units. Using a structural equation model (SEM), we test several features of transcription units, nearby DNA sequences, and nearby epigenomic marks for associations with RNA stability after controlling for their effects on transcription. We find that RNA splicing-related features are positively correlated with RNA stability, whereas features related to miRNA binding and DNA methylation are negatively correlated with RNA stability. Furthermore, we find that a measure based on U1 binding and polyadenylation sites distinguishes between unstable noncoding and stable coding transcripts but is not predictive of relative stability within the mRNA or lincRNA classes. We also identify several histone modifications that are associated with RNA stability. Conclusion We introduce an approach for estimating the relative half-lives of individual RNAs. Together, our estimation method and systematic analysis shed light on the pervasive impacts of RNA stability on cellular RNA concentrations.

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Visualizing the periodic Ribo-seq reads with RiboPlotR

10.1101/694646 ◽

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.

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

10.1101/058339 ◽

2016 ◽

Cited By ~ 1

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.

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The velvet Regulator VosA Governs Survival and Secondary Metabolism of Sexual Spores in Aspergillus nidulans

Genes ◽

10.3390/genes11010103 ◽

2020 ◽

Vol 11 (1) ◽

pp. 103 ◽

Cited By ~ 1

Author(s):

Min-Ju Kim ◽

Mi-Kyung Lee ◽

Huy Quang Pham ◽

Myeong Ju Gu ◽

Bohan Zhu ◽

...

Keyword(s):

Aspergillus Nidulans ◽

Gene Clusters ◽

Primary Metabolism ◽

Mrna Levels ◽

Rna Seq ◽

Spore Viability ◽

Oxidative Stresses ◽

Genome Wide ◽

Elevated Expression ◽

Trehalose Biosynthesis

The velvet regulator VosA plays a pivotal role in asexual sporulation in the model filamentous fungus Aspergillus nidulans. In the present study, we characterize the roles of VosA in sexual spores (ascospores) in A. nidulans. During ascospore maturation, the deletion of vosA causes a rapid decrease in spore viability. The absence of vosA also results in a lack of trehalose biogenesis and decreased tolerance of ascospores to thermal and oxidative stresses. RNA-seq-based genome-wide expression analysis demonstrated that the loss of vosA leads to elevated expression of sterigmatocystin (ST) biosynthetic genes and a slight increase in ST production in ascospores. Moreover, the deletion of vosA causes upregulation of additional gene clusters associated with the biosynthesis of other secondary metabolites, including asperthecin, microperfuranone, and monodictyphenone. On the other hand, the lack of vosA results in the downregulation of various genes involved in primary metabolism. In addition, vosA deletion alters mRNA levels of genes associated with the cell wall integrity and trehalose biosynthesis. Overall, these results demonstrate that the velvet regulator VosA plays a key role in the maturation and the cellular and metabolic integrity of sexual spores in A. nidulans.

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The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae

10.1101/2020.07.01.182956 ◽

2020 ◽

Author(s):

Natalia I. Reim ◽

James Chuang ◽

Dhawal Jain ◽

Burak H. Alver ◽

Peter J. Park ◽

...

Keyword(s):

Gene Expression ◽

Elongation Factor ◽

Mrna Levels ◽

Chromatin Dynamics ◽

Binding Partner ◽

Genome Wide ◽

A Genome ◽

Highly Expressed Genes ◽

Wide Scale

Spn1/Iws1 is a conserved protein involved in transcription and chromatin dynamics, yet its general in vivo requirement for these functions is unknown. Using a Spn1 depletion system in S. cerevisiae, we demonstrate that Spn1 broadly influences several aspects of gene expression on a genome-wide scale. We show that Spn1 is globally required for normal mRNA levels and for normal splicing of ribosomal protein transcripts. Furthermore, Spn1 maintains the localization of H3K36 and H3K4 methylation across the genome and is required for normal histone levels at highly expressed genes. Finally, we show that the association of Spn1 with the transcription machinery is strongly dependent on its binding partner, Spt6, while the association of Spt6 and Set2 with transcribed regions is partially dependent on Spn1. Taken together, our results show that Spn1 affects multiple aspects of gene expression and provide additional evidence that it functions as a histone chaperone in vivo.

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A comprehensive online database for exploring ~20,000 public Arabidopsis RNA-Seq libraries

10.1101/844522 ◽

2019 ◽

Author(s):

Hong Zhang ◽

Fei Zhang ◽

Li Feng ◽

Jinbu Jia ◽

Jixian Zhai

Keyword(s):

Transcriptional Regulation ◽

Transcriptome Profiling ◽

Research Community ◽

Online Database ◽

Rna Seq ◽

Huge Amount ◽

Genome Wide ◽

Wide Scale ◽

Computational Resources ◽

User Friendly

AbstractApplication of Next Generating Sequencing (NGS) technology in transcriptome profiling has greatly improved our understanding of transcriptional regulation at genome-wide scale in the last decade, and tens of thousands of RNA-sequencing (RNA-seq) libraries have been produced by the research community. However, accessing such huge amount of RNA-seq data poses a big challenge for groups that lack dedicated bioinformatic personnel or expensive computational resources. Here, we introduce the Arabidopsis RNA-seq database (ARS), a free, web-accessible, and user-friendly to quickly explore expression level of any gene in 20,000+ publicly available Arabidopsis RNA-seq libraries.

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The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae

Nucleic Acids Research ◽

10.1093/nar/gkaa745 ◽

2020 ◽

Vol 48 (18) ◽

pp. 10241-10258 ◽

Cited By ~ 1

Author(s):

Natalia I Reim ◽

James Chuang ◽

Dhawal Jain ◽

Burak H Alver ◽

Peter J Park ◽

...

Keyword(s):

Gene Expression ◽

Saccharomyces Cerevisiae ◽

Elongation Factor ◽

Mrna Levels ◽

Chromatin Dynamics ◽

Genome Wide ◽

A Genome ◽

Highly Expressed Genes ◽

Wide Scale

Abstract Spn1/Iws1 is a conserved protein involved in transcription and chromatin dynamics, yet its general in vivo requirement for these functions is unknown. Using a Spn1 depletion system in Saccharomyces cerevisiae, we demonstrate that Spn1 broadly influences several aspects of gene expression on a genome-wide scale. We show that Spn1 is globally required for normal mRNA levels and for normal splicing of ribosomal protein transcripts. Furthermore, Spn1 maintains the localization of H3K36 and H3K4 methylation across the genome and is required for normal histone levels at highly expressed genes. Finally, we show that the association of Spn1 with the transcription machinery is strongly dependent on its binding partner, Spt6, while the association of Spt6 and Set2 with transcribed regions is partially dependent on Spn1. Taken together, our results show that Spn1 affects multiple aspects of gene expression and provide additional evidence that it functions as a histone chaperone in vivo.

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