Single particle imaging of mRNAs crossing the nuclear pore: Surfing on the edge

Palazzo, Alexander F.; Truong, Matthew

doi:10.1002/bies.201600038

Cited by 9 publications

(9 citation statements)

References 87 publications

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“…To observe mRNA transport from the nucleus to the cytoplasm the MS2 or PP7 systems have been employed in S. cerevisiae , the fly Chironomus tentans , mouse, and human cells (Summarized in Table , and reviewed in ). Whereas some studies observe similar mRNA behaviors (e.g.…”

Section: Visualization Of Mrnas In Vivo Reveals Their Spatiotemporal mentioning

confidence: 99%

Section: Visualization Of Mrnas In Vivo Reveals Their Spatiotemporal mentioning

confidence: 99%

“…In the following sections we discuss some of the major questions and highlight how SMI technologies can be used and/or adapted to answering such questions in vivo. For additional discussions of mRNA transport kinetics the reader is directed to a number of other recent reviews [33,[35][36][37]. Single molecule techniques can overcome limitations in understanding cellular mRNP function obtained from ensemble composition data from large-scale sequencing and proteomic approaches.…”

Section: Introductionmentioning

confidence: 99%

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Temporal and spatial regulation of mRNA export: Single particle RNA‐imaging provides new tools and insights

et al. 2017

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The transport of messenger RNAs (mRNAs) from the nucleus to cytoplasm is an essential step in the gene expression program of all eukaryotes. Recent technological advances in the areas of RNA-labeling, microscopy, and sequencing are leading to novel insights about mRNA biogenesis and export. This includes quantitative single molecule imaging (SMI) of RNA molecules in live cells, which is providing knowledge of the spatial and temporal dynamics of the export process. As this information becomes available, it leads to new questions, the reinterpretation of previous findings, and revised models of mRNA export. In this review, we will briefly highlight some of these recent findings and discuss how live cell SMI approaches may be used to further our current understanding of mRNA export and gene expression.

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Section: Visualization Of Mrnas In Vivo Reveals Their Spatiotemporal mentioning

confidence: 99%

Section: Visualization Of Mrnas In Vivo Reveals Their Spatiotemporal mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Temporal and spatial regulation of mRNA export: Single particle RNA‐imaging provides new tools and insights

et al. 2017

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“…This interaction may promote the docking of mRNP complexes with the nucleoplasmic face of the yeast nuclear pore (42,43). TREX-Mlp1/2 interactions and mRNP docking could facilitate the exchange of proteins in the mRNP to prepare it for nuclear export (44). Whether TPR associates with TREX components or regulates mRNP remodelling in mammalian cells remains unclear.…”

Section: Introductionmentioning

confidence: 99%

TPR is required for the nuclear export of mRNAs and lncRNAs from intronless and intron-poor genes

Lee

Wolf

Smith

et al. 2019

Preprint

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While splicing has been shown to enhance nuclear export, it has remained unclear whether mRNAs generated from intronless genes use specific machinery to promote their export. Here we investigate the role of the major nuclear pore basket protein, TPR, in regulating mRNA and lncRNA nuclear export in human cells. By sequencing mRNA from the nucleus and cytosol of control and TPR-depleted cells, we provide evidence that TPR is required for the nuclear export of mRNAs and lncRNAs that are generated from intronless and intron-poor genes, and we validate this with reporter constructs. Moreover, in TPRdepleted cells reporter mRNAs generated from intronless genes accumulate in nuclear speckles and are bound to Nxf1. These observations suggest that TPR acts downstream of Nxf1 recruitment, and may allow mRNAs to leave nuclear speckles and properly dock with the nuclear pore. In summary, our study provides one of the first examples of a factor that is required for the nuclear export of intronless and intron-poor mRNAs and lncRNAs.

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“…Then, the nuclear export receptor composed of Nuclear RNA Export Factor 1 (Nxf1) and Nuclear Transport Factor 2 Like Export Factor 1 (Nxt1) (also known as TAP and p15) associates with Aly and allows the transport at the nuclear pore of its cargo physically interacting with the phenylalanine (F) and glycine (G) repeats of proteins in the interior of nuclear pore. After the transport through the nuclear pore the RNP is remodeled to remove certain nuclear associated exported factors, recycled back into the nucleus, and to make the mRNA or the lncRNA stably located in the cytoplasm [96].…”

Section: Cytoplasmic Lncrnasmentioning

confidence: 99%

A Single Cell but Many Different Transcripts: A Journey into the World of Long Non-Coding RNAs

Alessio

Bonadio

Buson

et al. 2020

IJMS

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In late 2012 it was evidenced that most of the human genome is transcribed but only a small percentage of the transcripts are translated. This observation supported the importance of non-coding RNAs and it was confirmed in several organisms. The most abundant non-translated transcripts are long non-coding RNAs (lncRNAs). In contrast to protein-coding RNAs, they show a more cell-specific expression. To understand the function of lncRNAs, it is fundamental to investigate in which cells they are preferentially expressed and to detect their subcellular localization. Recent improvements of techniques that localize single RNA molecules in tissues like single-cell RNA sequencing and fluorescence amplification methods have given a considerable boost in the knowledge of the lncRNA functions. In recent years, single-cell transcription variability was associated with non-coding RNA expression, revealing this class of RNAs as important transcripts in the cell lineage specification. The purpose of this review is to collect updated information about lncRNA classification and new findings on their function derived from single-cell analysis. We also retained useful for all researchers to describe the methods available for single-cell analysis and the databases collecting single-cell and lncRNA data. Tables are included to schematize, describe, and compare exposed concepts.Int. J. Mol. Sci. 2020, 21, 302 2 of 32 not achieved by transcription factors (TFs) alone because of their low number (approximately 1500 in mammals [4]) compared to genes to regulate (90% of the genome is transcribed in human [5]). A single TF is estimated to regulate only ten thousand genes according to Chromatin immunoprecipitation and DNA sequencing experiments (ChIp-seq) [6]. Moreover, the involvement of non-coding RNAs in gene expression regulation was evident [7,8]. The evidence that the non-protein coding component of the human genome is actively transcribed and carries out crucial functions limits the importance of coding genes in genome regulation. Non-coding transcripts become one of the stars of modern biology, especially because of their involvement in a wide range of regulatory processes and changed the association of non-coding regions to junk DNA [3].The genome of multicellular eukaryotes is mostly comprised of non-coding DNA (less than 2% of the human genome codes for proteins [9] while 90% of the human genome is transcribed). Non-coding DNA is transcribed into different classes of non-coding RNAs (ncRNAs) that include structural RNAs (rRNAs and tRNAs) and regulatory RNAs [10]. rRNAs and tRNAs are involved in mRNA translation and can be long or short in size. Regulatory RNAs are further divided into three classes: Small, medium, and long non-coding RNAs. Small non-coding RNAs are between 20 and 50 nucleotides long and include microRNAs (miRNAs) that participate in post-transcriptional regulation [11], small interfering RNAs (siRNAs) that are double-stranded RNAs involved in gene silencing through RNA interfering pathway [12], piwi interacting R...

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Single particle imaging of mRNAs crossing the nuclear pore: Surfing on the edge

Cited by 9 publications

References 87 publications

Temporal and spatial regulation of mRNA export: Single particle RNA‐imaging provides new tools and insights

Temporal and spatial regulation of mRNA export: Single particle RNA‐imaging provides new tools and insights

TPR is required for the nuclear export of mRNAs and lncRNAs from intronless and intron-poor genes

A Single Cell but Many Different Transcripts: A Journey into the World of Long Non-Coding RNAs

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