RNA-Seq defines novel genes, RNA processing patterns and enhancer maps for the early stages of nephrogenesis: Hox supergenes

Somatic cell nuclear transfer (SCNT) is not only a valuable tool for understanding nuclear reprogramming, but it also facilitates the generation of genetically modified animals. However, the development of SCNT embryos has remained an uncontrollable process. It was reported that the SCNT embryos that complete the first cell division sooner are more likely to develop to the blastocyst stage, suggesting their better developmental competence. Therefore, to better understand the underlying molecular mechanisms, RNA-seq of pig SCNT embryos that were early-dividing (24 h postactivation) and late-dividing (36 h postactivation) was performed. Our analysis revealed that early- and late-dividing embryos have distinct RNA profiles, and, in all, 3077 genes were differentially expressed. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that early-dividing embryos exhibited higher expression in genes that participated in the meiotic cell cycle, while enrichment of RNA processing- and translation-related genes was found in late-dividing embryos. There are also fewer somatic memory genes such as FLRT2, ADAMTS1, and FOXR1, which are abnormally activated or suppressed in early-dividing cloned embryos. These results show that early-dividing SCNT embryos have different transcriptional profiles than late-dividing embryos. Early division of SCNT embryos may be associated with their better reprogramming capacity, and somatic memory genes may act as a reprogramming barrier in pig SCNT reprogramming.

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RJunBase: a database of RNA splice junctions in human normal and cancerous tissues

Nucleic Acids Research ◽

10.1093/nar/gkaa1056 ◽

2020 ◽

Vol 49 (D1) ◽

pp. D201-D211

Author(s):

Qin Li ◽

Hongyan Lai ◽

Yuchen Li ◽

Bing Chen ◽

Siyuan Chen ◽

...

Keyword(s):

Cancer Treatment ◽

Expression Profile ◽

Rna Processing ◽

Human Cells ◽

Rna Seq ◽

Essential Step ◽

Splicing Pattern ◽

Gene Level ◽

Precursor Rna ◽

Splice Junctions

Abstract Splicing is an essential step of RNA processing for multi-exon genes, in which introns are removed from a precursor RNA, thereby producing mature RNAs containing splice junctions. Here, we develope the RJunBase (www.RJunBase.org), a web-accessible database of three types of RNA splice junctions (linear, back-splice, and fusion junctions) that are derived from RNA-seq data of non-cancerous and cancerous tissues. The RJunBase aims to integrate and characterize all RNA splice junctions of both healthy or pathological human cells and tissues. This new database facilitates the visualization of the gene-level splicing pattern and the junction-level expression profile, as well as the demonstration of unannotated and tumor-specific junctions. The first release of RJunBase contains 682 017 linear junctions, 225 949 back-splice junctions and 34 733 fusion junctions across 18 084 non-cancerous and 11 540 cancerous samples. RJunBase can aid researchers in discovering new splicing-associated targets and provide insights into the identification and assessment of potential neoepitopes for cancer treatment.

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RNA-Seq Analysis of lncRNAs and cisNATs in the Tomato Genome

IU Journal of Undergraduate Research ◽

10.14434/iujur.v1i1.13244 ◽

2015 ◽

Vol 1 (1) ◽

pp. 34

Author(s):

S. Hussain Ather

Keyword(s):

Rna Processing ◽

De Novo ◽

Rna Seq ◽

Tomato Genome ◽

Biological Mechanisms ◽

Global Issues ◽

Tomato Species ◽

And Function ◽

Two Stages ◽

Coding Potential

Since the sequencing of the human genome, it has been revealed that the vast majority of DNA does not code for proteins. Instead, these regions of DNA produce long noncoding RNAs (lncRNAs), which have recently been reported to play important roles such as protein regulation and small RNA processing (Wilusz, Sunwoo, & Spector, 2009). The catalog and functions of lncRNAs in the ripening of tomato species (Solanum lycopersicum) are largely unknown. Similarly, the mechanisms of cis-natural antisense transcripts (cisNATs) of proximal complementary RNA strings, which function to inhibit transcription, are also poorly understood (Wang, Gaasterland, & Chua, 2005). Global issues in food production and malnutrition exacerbate the relevance of understanding these biological mechanisms central to the development of fruit. We identified certain functions of lncRNAs and cisNATs in the tomato ripening process using an RNA-Seq pipeline (Wang, Gerstein, & Snyder, 2005). Raw reads from two different stages in the tomato ripening cycle were aligned to a reference genome to test the hypothesis that there would be different expression levels for certain lncRNAs and cis-NATs between the two stages. The two stages were Mature Green, the stage in which the tomato is completely green, and Breaker, the stage in which the tomato shows initial colors of red. Then, the reads were de novo assembled, assessed for coding potential, and annotated by transcript and function. Finally, the results were filtered for lncRNAs (length > 200 bp, ORF < 100 bp, noncoding, expression value > 0) and cis-NATs (sense-antisense pairs, overlap length > 50 bp, differential splice patterns, expression value = 0). Differentially-expressed lncRNAs and cis-NATs between the two stages of development were identified, and their functions were analyzed. However, experimental evidence is necessary to confirm our findings and hypothesize models of cis-NAT mechanisms for further classification and identification.

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Transcriptome-wide splicing quantification in single cells

10.1101/098517 ◽

2017 ◽

Cited By ~ 1

Author(s):

Yuanhua Huang ◽

Guido Sanguinetti

Keyword(s):

Rna Processing ◽

Single Cells ◽

Bayesian Hierarchical Model ◽

Bayesian Regression ◽

Data Sets ◽

Rna Seq ◽

Bayesian Hierarchical ◽

Informative Prior Distribution ◽

Comprehensive Measurement ◽

Isoform Quantification

AbstractSingle cell RNA-seq (scRNA-seq) has revolutionised our understanding of transcriptome variability, with profound implications both fundamental and translational. While scRNA-seq provides a comprehensive measurement of stochasticity in transcription, the limitations of the technology have prevented its application to dissect variability in RNA processing events such as splicing. Here we present BRIE (Bayesian Regression for Isoform Estimation), a Bayesian hierarchical model which resolves these problems by learning an informative prior distribution from sequence features. We show that BRIE yields reproducible estimates of exon inclusion ratios in single cells and provides an effective tool for differential isoform quantification between scRNA-seq data sets. BRIE therefore expands the scope of scRNA-seq experiments to probe the stochasticity of RNA-processing.

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Metabolic labeling of RNAs uncovers hidden features and dynamics of the Arabidopsis thaliana transcriptome

10.1101/588780 ◽

2019 ◽

Author(s):

Emese Xochitl Szabo ◽

Philipp Reichert ◽

Marie-Kristin Lehniger ◽

Marilena Ohmer ◽

Marcella de Francisco Amorim ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Transcriptome Analysis ◽

Rna Processing ◽

Rna Synthesis ◽

Rna Stability ◽

Metabolic Labeling ◽

Rna Seq ◽

Genome Wide ◽

Stability Measurement ◽

Chemical Inhibition

AbstractTranscriptome analysis by RNA sequencing (RNA-seq) has become an indispensable core research tool in modern plant biology. Virtually all RNA-seq studies provide a snapshot of the steady-state transcriptome, which contains valuable information about RNA populations at a given time, but lacks information about the dynamics of RNA synthesis and degradation. Only a few specialized sequencing techniques, such as global run-on sequencing (GRO-seq), have been applied in plants and provide information about RNA synthesis rates. Here, we demonstrate that RNA labeling with a modified, non-toxic uridine analog, 5-ethynyl uridine (5-EU), in Arabidopsis thaliana seedlings provides insight into the dynamic nature of a plant transcriptome. Pulse-labeling with 5-EU allowed the detection and analysis of nascent and unstable RNAs, of RNA processing intermediates generated by splicing, and of chloroplast RNAs. We also conducted pulse-chase experiments with 5-EU, which allowed us to determine RNA stabilities without the need for chemical inhibition of transcription using compounds such as actinomycin and cordycepin. Genome-wide analysis of RNA stabilities by 5-EU pulse-chase experiments revealed that this inhibitor-free RNA stability measurement results in RNA half-lives much shorter than those reported after chemical inhibition of transcription. In summary, our results show that the Arabidopsis nascent transcriptome contains unstable RNAs and RNA processing intermediates, and suggest that half-lives of plant RNAs are largely overestimated. Our results lay the ground for an easy and affordable nascent transcriptome analysis and inhibitor-free analysis of RNA stabilities in plants.

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Pseudo-Location: A novel predictor for predicting pseudo-temporal gene expression patterns using spatial functional regression

10.1101/2020.06.11.145565 ◽

2020 ◽

Author(s):

Kyungmin Ahn ◽

Hironobu Fujiwara

Keyword(s):

Gene Expression ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Functional Regression ◽

Rna Seq ◽

Temporal Gene Expression ◽

Early Stages ◽

The Future

Statement of withdrawalThe authors have withdrawn version 1 of this manuscript because a draft manuscript, which was still in the early stages of preparation and required major revisions including the replacement of the source RNA-seq datasets, was erroneously submitted. The authors do not wish this version to be cited as reference for this study. We will post a revised manuscript in the future. If you have any questions, please contact the corresponding author.

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Frontiers in RNA biology: advances from a small fly Drosophila melanogaster

The Biochemist ◽

10.1042/bio03802021 ◽

2016 ◽

Vol 38 (2) ◽

pp. 21-25

Author(s):

James B. Brown ◽

Susan E. Celniker

Keyword(s):

Rna Processing ◽

Small Sample ◽

Rna Seq ◽

Ribonucleoprotein Complexes ◽

Rna Biology ◽

Cell Type Specific ◽

Exciting Time ◽

Small Sample Sizes ◽

Analytical Tools ◽

Processing Mechanisms

In this article, we discuss emerging frontiers in RNA biology from a historical perspective. The field is currently undergoing yet another transformative expansion. RNA-seq has revealed that splicing, and, more generally, RNA processing is far more complex than expected, and the mechanisms of regulation are correspondingly sophisticated. Our understanding of the molecular machines involved in RNA metabolism is incomplete and derives from small sample sizes. Even if we manage to complete a catalogue of molecular species, RNA isoforms and the ribonucleoprotein complexes that drive their genesis, the horizons of molecular dynamics and cell-type-specific processing mechanisms await. This is an exciting time to enter into the study of RNA biology; analytical tools, wet and dry, are advancing rapidly, and each new measurement modality brings into view another new function or activity of versatile RNA. Since the dawn of sequence-based RNA biology, we have come a long way.

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Functional categorization of de novo transcriptome assembly of Vanilla planifolia Jacks. potentially points to a translational regulation during early stages of infection by Fusarium oxysporum f. sp. vanillae

10.21203/rs.2.12054/v3 ◽

2019 ◽

Author(s):

Marco Tulio Solano-De la Cruz ◽

Jacel Adame-García ◽

Josefat Gregorio-Jorge ◽

Verónica Jiménez-Jacinto ◽

Leticia Vega-Alvarado ◽

...

Keyword(s):

Fusarium Oxysporum ◽

Translational Regulation ◽

Transcriptome Assembly ◽

Transcriptional Level ◽

Post Inoculation ◽

Molecular Response ◽

Vanilla Planifolia ◽

Rna Seq ◽

Early Stages ◽

Transcriptional Changes

Abstract Background Upon exposure to unfavorable environmental conditions, plants need to respond quickly to maintain their homeostasis. For instance, physiological, biochemical and transcriptional changes occur during plant-pathogen interaction. In the case of Vanilla planifolia Jacks., a worldwide economically important crop, it is susceptible to Fusarium oxysporum f. sp. vanillae (Fov). This pathogen causes root and stem rot (RSR) in vanilla plants that lead to plant death. To investigate how vanilla plants, respond at the transcriptional level upon infection with Fov, here we employed the RNA-Seq approach to analyze the dynamics of whole-transcriptome changes during two-time frames of the infection. Results Analysis of global gene expression profiles upon infection by Fov indicated that the major transcriptional change occurred at 2 days post-inoculation (dpi), in comparison to 10 dpi. Briefly, the RNA-Seq analysis carried out in roots found that 3420 and 839 differentially expressed genes (DEGs) were detected at 2 and 10 dpi, respectively, as compared to the control. In the case of DEGs at 2 dpi, 1563 genes were found to be up-regulated, whereas 1857 genes were down-regulated. Moreover, functional categorization of DEGs at 2 dpi indicated that up-regulated genes are mainly associated to translation, whereas down-regulated genes are involved in cell wall remodeling. Among the translational-related transcripts, ribosomal proteins (RPs) were found increased their expression exclusively at 2 dpi. Conclusions The screening of transcriptional changes of V. planifolia Jacks upon infection by Fov provides insights into the plant molecular response, particularly at early stages of infection. The accumulation of translational-related transcripts at early stages of infection potentially points to a transcriptional reprogramming coupled with a translational regulation in vanilla plants upon infection by Fov. Altogether, the results presented here highlight potential molecular players that might be further studied to improve Fov-induced resistance in vanilla plants.

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Functional categorization of de novo transcriptome assembly of Vanilla planifolia Jacks. potentially points to a translational regulation during early stages of infection by Fusarium oxysporum f. sp. vanillae

10.21203/rs.2.12054/v2 ◽

2019 ◽

Author(s):

Marco Tulio Solano-De la Cruz ◽

Jacel Adame-García ◽

Josefat Gregorio-Jorge ◽

Verónica Jiménez-Jacinto ◽

Leticia Vega-Alvarado ◽

...

Keyword(s):

Fusarium Oxysporum ◽

Translational Regulation ◽

Transcriptome Assembly ◽

Transcriptional Level ◽

Post Inoculation ◽

Molecular Response ◽

Vanilla Planifolia ◽

Rna Seq ◽

Early Stages ◽

Transcriptional Changes

Abstract Background Upon exposure to unfavorable environmental conditions, plants need to respond quickly to maintain their homeostasis. For instance, physiological, biochemical and transcriptional changes occur during plant-pathogen interaction. In the case of Vanilla planifolia Jacks., a worldwide economically important crop, it is susceptible to Fusarium oxysporum f. sp. vanillae (Fov). This pathogen causes root and stem rot (RSR) in vanilla plants that lead to plant death. To investigate how vanilla plants, respond at the transcriptional level upon infection with Fov, here we employed the RNA-Seq approach to analyze the dynamics of whole-transcriptome changes during two-time frames of the infection. Results Analysis of global gene expression profiles upon infection by Fov indicated that the major transcriptional change occurred at 2 days post-inoculation (dpi), in comparison to 10 dpi. Briefly, the RNA-Seq analysis carried out in roots found that 3420 and 839 differentially expressed genes (DEGs) were detected at 2 and 10 dpi, respectively, as compared to the control. In the case of DEGs at 2 dpi, 1563 genes were found to be up-regulated, whereas 1857 genes were down-regulated. Moreover, functional categorization of DEGs at 2 dpi indicated that up-regulated genes are mainly associated to translation, whereas down-regulated genes are involved in cell wall remodeling. Among the translational-related transcripts, ribosomal proteins (RPs) were found increased their expression exclusively at 2 dpi. Conclusions The screening of transcriptional changes of V. planifolia Jacks upon infection by Fov provides insights into the plant molecular response, particularly at early stages of infection. The accumulation of translational-related transcripts at early stages of infection potentially points to a transcriptional reprogramming coupled with a translational regulation in vanilla plants upon infection by Fov. Altogether, the results presented here highlight potential molecular players that might be further studied to improve Fov-induced resistance in vanilla plants.

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Detection of generic differential RNA processing events from RNA-seq data

RNA Biology ◽

10.1080/15476286.2015.1118604 ◽

2016 ◽

Vol 13 (1) ◽

pp. 59-67 ◽

Cited By ~ 9

Author(s):

Van Du T Tran ◽

Oussema Souiai ◽

Natali Romero-Barrios ◽

Martin Crespi ◽

Daniel Gautheret

Keyword(s):

Rna Processing ◽

Rna Seq

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