Analysis of RNA processing and m6A modification using nanopore direct RNA sequencing.

Yanocomp: robust prediction of m6A modifications in individual nanopore direct RNA reads.

10.1101/2021.06.15.448494 ◽

2021 ◽

Author(s):

Matthew T Parker ◽

Geoffrey J Barton ◽

Gordon G Simpson

Keyword(s):

Rna Sequencing ◽

Mixture Models ◽

Single Molecule ◽

Rna Processing ◽

Sequencing Data ◽

Rna Modifications ◽

Robust Prediction ◽

Good Support

Yanocomp is a tool for predicting the positions and stoichiometries of RNA modifications in Nanopore direct RNA sequencing data. It uses general mixture models to identify differentially modified sites between two conditions, with good support for replicates. Yanocomp models across adjacent kmers and uses a uniform component to account for outliers, improving the accuracy of single molecule predictions. Consequently, Yanocomp can be used to measure modification stoichiometry, and correlate modifications with other RNA processing events. Yanocomp is available under an MIT license at www.github.com/bartongroup/yanocomp.

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Investigating Mitochondrial Transcriptomes and RNA Processing Using Circular RNA Sequencing

Methods in Molecular Biology - Mitochondrial Gene Expression ◽

10.1007/978-1-0716-0834-0_4 ◽

2020 ◽

pp. 43-57

Author(s):

Irina Kuznetsova ◽

Oliver Rackham ◽

Aleksandra Filipovska

Keyword(s):

Rna Sequencing ◽

Rna Processing ◽

Circular Rna

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Altered levels of hsromega lncRNAs further enhance Ras signaling during ectopically activated Ras induced R7 differentiation in Drosophila

10.1101/224543 ◽

2017 ◽

Author(s):

Mukulika Ray ◽

Gunjan Singh ◽

Subhash C. Lakhotia

Keyword(s):

Signaling Pathway ◽

Rna Sequencing ◽

Rna Processing ◽

Rna Binding ◽

Rna Binding Proteins ◽

Ras Signaling ◽

Transcript Levels ◽

Cone Cells ◽

Ras Signaling Pathway ◽

Transcriptional Changes

AbstractWe exploited the high Ras activity induced differentiation of supernumerary R7 cells in Drosophila eyes to examine if hsrω lncRNAs influence active Ras signaling. Surprisingly, either down- or up-regulation of hsrω lncRNAs in sev-GAL4>RasV12 expressing eye discs resulted in complete pupal lethality and substantially greater increase in R7 photoreceptor number at the expense of cone cells. Enhanced nuclear p-MAPK and presence of sev-GAL4 driven RasV12 bound RafRBDFLAG in cells not expressing the sev-GAL4 driver indicated non-cell autonomous spread of Ras signaling when hsrω levels were co-altered. RNA-sequencing revealed that down-and up-regulation of hsrω transcripts in sev-GAL4>RasV12 expressing eye discs elevated transcripts of positive or negative modulators, respectively, of Ras signaling so that either condition enhances it. Altered hsrω transcript levels in sev-GAL4>RasV12 expressing discs also affected sn/sno/sca RNAs and some other RNA processing transcript levels. Post-transcriptional changes due to the disrupted intra-cellular dynamicity of omega speckle associated hnRNPs and other RNA-binding proteins that follow down- or up-regulation of hsrω lncRNAs appear to be responsible for the further elevated Ras signaling. Cell autonomous and non-autonomous enhancement of Ras signaling by lncRNAs like hsrω has implications for cell signaling during high Ras activity commonly associated with some cancers.HighlightsOur findings highlight roles of hsrω lncRNAs in conditionally modulating the important Ras signaling pathway and provide evidence for cell non-autonomous Ras signaling in Drosophila eye discs.

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Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts

eLife ◽

10.7554/elife.27024 ◽

2018 ◽

Vol 7 ◽

Cited By ~ 45

Author(s):

Jason C Bell ◽

David Jukam ◽

Nicole A Teran ◽

Viviana I Risca ◽

Owen K Smith ◽

...

Keyword(s):

Rna Sequencing ◽

Rna Processing ◽

De Novo ◽

Critical Component ◽

Proximity Ligation ◽

Ribonucleoprotein Complexes ◽

Genome Wide ◽

Sequencing Method ◽

Nascent Transcripts ◽

Drosophila Cells

RNA is a critical component of chromatin in eukaryotes, both as a product of transcription, and as an essential constituent of ribonucleoprotein complexes that regulate both local and global chromatin states. Here, we present a proximity ligation and sequencing method called Chromatin-Associated RNA sequencing (ChAR-seq) that maps all RNA-to-DNA contacts across the genome. Using Drosophila cells, we show that ChAR-seq provides unbiased, de novo identification of targets of chromatin-bound RNAs including nascent transcripts, chromosome-specific dosage compensation ncRNAs, and genome-wide trans-associated RNAs involved in co-transcriptional RNA processing.

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Extent and complexity of RNA processing in the development of honey bee queen and worker castes revealed by Nanopore direct RNA sequencing

10.1101/2021.08.08.455492 ◽

2021 ◽

Author(s):

Xu Jiang He ◽

Andrew B. Barron ◽

Liu Yang ◽

Hu Chen ◽

Yu Zhu He ◽

...

Keyword(s):

Alternative Splicing ◽

Phenotypic Plasticity ◽

Larval Development ◽

Rna Sequencing ◽

Honey Bee ◽

Rna Processing ◽

Caste Differentiation ◽

A Genome ◽

Honey Bee Queen ◽

Isoform Expression

The distinct honey bee (Apis mellifera) worker and queen castes have become a model for the study of genomic mechanisms of phenotypic plasticity. Prior studies have explored differences in gene expression and methylation during development of the two castes, but thus far no study has performed a genome-wide analysis of differences in RNA processing. To address this here we performed a Nanopore-based direct RNA sequencing with exceptionally long reads to compare the mRNA transcripts between honey bee queen and workers at three points during their larval development. We found thousands of significantly differentially expressed isoforms (DEIs) between queen and worker larvae. Most DEIs contained alternative splicing, and many of them contained at least two types of alternative splicing patterns, indicating complex RNA processing in honey bee caste differentiation. We found a negative correlation between poly(A) length and DEI expression, suggesting that poly(A) tails participate in the regulation of isoform expression. Hundreds of isoforms uniquely expressed in either queens or workers during their larval development, and isoforms were expressed at different points in queen and worker larval development demonstrating a dynamic relationship between isoform expression and developmental mechanisms. These findings show the full complexity of RNA processing and transcript expression in honey bee phenotypic plasticity.

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Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts

10.1101/118786 ◽

2017 ◽

Author(s):

Jason C. Bell ◽

David Jukam ◽

Nicole A. Teran ◽

Viviana I. Risca ◽

Owen K. Smith ◽

...

Keyword(s):

Rna Sequencing ◽

Dosage Compensation ◽

Rna Processing ◽

De Novo ◽

Critical Component ◽

Proximity Ligation ◽

Ribonucleoprotein Complexes ◽

Genome Wide ◽

Sequencing Method ◽

Nascent Transcripts

AbstractRNA is a critical component of chromatin in eukaryotes, both as a product of transcription, and as an essential constituent of ribonucleoprotein complexes that regulate both local and global chromatin states. Here we present a proximity ligation and sequencing method called Chromatin-Associated RNA sequencing (ChAR-seq) that maps all RNA-to-DNA contacts across the genome. ChAR-seq provides unbiased, de novo identification of targets of chromatin-bound RNAs including nascent transcripts, chromosome-specific dosage compensation ncRNAs, and genome-wide trans-associated RNAs involved in co-transcriptional RNA processing.

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