A computational framework to study sub-cellular RNA localization

Samacoïts, Aubin; Chouaib, Racha; Safieddine, Adham; Traboulsi, Abdel-Meneem; Ouyang, Wei; Zimmer, Christophe; Peter, Matthias; Bertrand, Édouard; Walter, Thomas; Mueller, Florian

doi:10.1038/s41467-018-06868-w

Cited by 53 publications

(56 citation statements)

References 29 publications

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“…Detection of RNA molecules was performed in the 3D image stacks using FISH-quant (Mueller et al, 2013). Positions of individual RNA molecules within dense clusters were determined with a recently developed approach using the signal of isolated RNAs to decompose these clusters (Samacoits et al, 2018). Post-processing to calculate the different location metrics was performed as described below with custom-written Matlab and Python code.…”

Section: Quantification Of Rna Clusteringmentioning

confidence: 99%

mRNA localization is linked to translation regulation in theCaenorhabditis elegansgerm lineage

et al. 2020

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Caenorhabditis elegans early embryos generate cell-specific transcriptomes despite lacking active transcription, thereby presenting an opportunity to study mechanisms of post-transcriptional regulatory control. We observed that some cell-specific mRNAs accumulate nonhomogenously within cells, localizing to membranes, P granules (associated with progenitor germ cells in the P lineage) and P-bodies (associated with RNA processing). The subcellular distribution of transcripts differed in their dependence on 3′UTRs and RNA binding proteins, suggesting diverse regulatory mechanisms. Notably, we found strong but imperfect correlations between low translational status and P granule localization within the progenitor germ lineage. By uncoupling translation from mRNA localization, we untangled a long-standing question: Are mRNAs directed to P granules to be translationally repressed, or do they accumulate there as a consequence of this repression? We found that translational repression preceded P granule localization and could occur independently of it. Further, disruption of translation was sufficient to send homogenously distributed mRNAs to P granules. These results implicate transcriptional repression as a means to deliver essential maternal transcripts to the progenitor germ lineage for later translation.

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Section: Quantification Of Rna Clusteringmentioning

confidence: 99%

mRNA localization is linked to translation regulation in theCaenorhabditis elegansgerm lineage

et al. 2020

Self Cite

View full text Add to dashboard Cite

show abstract

“…Detection of RNA molecules was performed in the 3D image stacks with FISH-quant [Mueller et al, 2013]. Positions of individual RNA molecules within dense clusters, were determined with a recently developed approach using the signal of isolated RNAs to decompose these clusters [Samacoits et al, 2018]. Post-processing to calculate the different location metrics was performed as described below with custom written Matlab and Python code.…”

Section: Quantification Of Rna Clusteringmentioning

confidence: 99%

mRNA localization is linked to translation regulation in the Caenorhabditis elegans germ lineage

Parker¹

2020

Preprint

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Caenorhabditis elegans early embryos generate cell-specific transcriptomes despite lacking active transcription. This presents an opportunity to study mechanisms of post-transcriptional regulatory control. In seeking the mechanisms behind this patterning, we discovered that some cell-specific mRNAs accumulate non-homogenously within cells, localizing to membranes, P granules (associated with progenitor germ cells in the P lineage), and P-bodies (associated with RNA processing). Transcripts differed in their dependence on 3'UTRs and RNA Binding Proteins, suggesting diverse regulatory mechanisms. Notably, we found strong but imperfect correlations between low translational status and P granule localization within the progenitor germ lineage. By uncoupling these, we untangled a long-standing question: Are mRNAs directed to P granules for translational repression or do they accumulate there as a downstream step? We found translational repression preceded P granule localization and could occur independent of it. Further, disruption of translation was sufficient to send homogenously distributed mRNAs to P granules. Overall, we show transcripts important for germline development are directed to P granules by translational repression, and this, in turn, directs their accumulation in the progenitor germ lineage where their repression can ultimately be relieved.

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“…This method is based on tracking the target RNA with multiple short DNA probes, which are complementary to the target and are conjugated with a fluorescent dye [ 83 ]. For imaging intracellular localization of single RNA transcripts in fixed cells or tissues, FISH is still regarded as the gold-standard approach [ 84 , 85 ]. For live-cell imaging of the RNA of interest, stem-loop labeling and fluorescence protein tagging by the MS2-MCP system are useful [ 86 , 87 ].…”

Section: The Subcellular Localization and Stability Of Lncrnasmentioning

confidence: 99%

Challenges and Strategies in Ascribing Functions to Long Noncoding RNAs

Zhao

Teng

Yao

et al. 2020

Cancers

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Long noncoding RNAs (lncRNAs) are involved in many physiological and pathological processes, such as development, aging, immunity, and cancer. Mechanistically, lncRNAs exert their functions through interaction with proteins, genomic DNA, and other RNA, leading to transcriptional and post-transcriptional regulation of gene expression, either in cis or in trans; it is often difficult to distinguish between these two regulatory mechanisms. A variety of approaches, including RNA interference, antisense oligonucleotides, CRISPR-based methods, and genetically engineered mouse models, have yielded abundant information about lncRNA functions and underlying mechanisms, albeit with many discrepancies. In this review, we elaborate on the challenges in ascribing functions to lncRNAs based on the features of lncRNAs, including the genomic location, copy number, domain structure, subcellular localization, stability, evolution, and expression pattern. We also describe a framework for the investigation of lncRNA functions and mechanisms of action. Rigorous characterization of cancer-implicated lncRNAs is critical for the identification of bona fide anticancer targets.

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A computational framework to study sub-cellular RNA localization

Cited by 53 publications

References 29 publications

mRNA localization is linked to translation regulation in theCaenorhabditis elegansgerm lineage

mRNA localization is linked to translation regulation in theCaenorhabditis elegansgerm lineage

mRNA localization is linked to translation regulation in the Caenorhabditis elegans germ lineage

Challenges and Strategies in Ascribing Functions to Long Noncoding RNAs

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