High‐throughput identification of
            <scp>RNA</scp>
            nuclear enrichment sequences

Shukla, Chinmay; McCorkindale, Alexandra L.; Gerhardinger, Chiara; Korthauer, Keegan; Cabili, Moran N.; Shechner, David M; Irizarry, Rafael A.; Maass, Philipp G.; Rinn, John L.

doi:10.15252/embj.201798452

Cited by 103 publications

(73 citation statements)

References 47 publications

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“…The last piece of evidence which suggests that nuclear export is the default pathway is that when nuclear localized lncRNAs were analyzed, it was observed that they contained nuclear retention elements ( Miyagawa et al, 2012 ; Zhang et al, 2014a ; Lubelsky and Ulitsky, 2018 ; Shukla et al, 2018 ). When these nuclear retention elements were removed or mutated, the altered lncRNAs were exported.…”

Section: What Is the Default Pathway?mentioning

confidence: 99%

Sequence Determinants for Nuclear Retention and Cytoplasmic Export of mRNAs and lncRNAs

Palazzo

Lee

2018

Front. Genet.

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Eukaryotes are divided into two major compartments: the nucleus where RNA is synthesized and processed, and the cytoplasm, where mRNA is translated into proteins. Although many different RNAs are made, only a subset is allowed access to the cytoplasm, primarily RNAs involved in protein synthesis (mRNA, tRNA, and rRNA). In contrast, nuclear retained transcripts are mostly long non-coding RNAs (lncRNAs) whose role in cell physiology has been a source of much investigation in the past few years. In addition, it is likely that many non-functional RNAs, which arise by spurious transcription and misprocessing of functional RNAs, are also retained in the nucleus and degraded. In this review, the main sequence features that dictate whether any particular mRNA or lncRNA is a substrate for retention in the nucleus, or export to the cytoplasm, are discussed. Although nuclear export is promoted by RNA-splicing due to the fact that the spliceosome can help recruit export factors to the mature RNA, nuclear export does not require splicing. Indeed, most stable unspliced transcripts are well exported and associate with these same export factors in a splicing-independent manner. In contrast, nuclear retention is promoted by specialized cis-elements found in certain RNAs. This new understanding of the determinants of nuclear retention and cytoplasmic export provides a deeper understanding of how information flow is regulated in eukaryotic cells. Ultimately these processes promote the evolution of complexity in eukaryotes by shaping the genomic content through constructive neutral evolution.

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Section: What Is the Default Pathway?mentioning

confidence: 99%

Sequence Determinants for Nuclear Retention and Cytoplasmic Export of mRNAs and lncRNAs

Palazzo

Lee

2018

Front. Genet.

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“…Indeed, despite these examples, it has been well-studied that Pol II transcription and the 3′-end alternative processing of the NEAT1 lncRNA act together to modulate paraspeckle morphology and function (Mao et al 2011;Naganuma et al 2012;Hirose et al 2014;Wang et al 2018;Yamazaki et al 2018). Emerging studies have also revealed both cis-and trans-factors are required for the subcellular localization of Pol II-transcribed mRNA-like lincRNAs and functions (Hacisuleyman et al 2014;Zhang et al 2014b;Lubelsky and Ulitsky 2018;Shukla et al 2018).…”

Section: Resultsmentioning

confidence: 99%

Linking RNA Processing and Function

Yao

Liu

2019

Cold Spring Harb Symp Quant Biol

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RNA processing is critical for eukaryotic mRNA maturation and function. It appears there is no exception for other types of RNAs. Long noncoding RNAs (lncRNAs) represent a subclass of noncoding RNAs, have sizes of >200 nucleotides (nt), and participate in various aspects of gene regulation. Although many lncRNAs are capped, polyadenylated, and spliced just like mRNAs, others are derived from primary transcripts of RNA polymerase II and stabilized by forming circular structures or by ending with small nucleolar RNA-protein complexes. Here we summarize the recent progress in linking the processing and function of these unconventionally processed lncRNAs; we also discuss how directional RNA movement is achieved using the radial flux movement of nascent precursor ribosomal RNA (pre-rRNA) in the human nucleolus as an example.

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“…LncRNAs that are only found in the nucleus are classified as nuclear lncRNAs. These lncRNAs contain specific sequences to indicate that they have to be retained in the nucleus [90,91]. Most of the nuclear lncRNAs are regulators of transcription or influence mRNA processing; they can both enhance or silence the transcription of genes, for example, by recruiting transcription factors or by acting as decoy impeding the binding of transcription factors to DNA.…”

Section: Nuclear 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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High‐throughput identification of RNA nuclear enrichment sequences

Cited by 103 publications

References 47 publications

Sequence Determinants for Nuclear Retention and Cytoplasmic Export of mRNAs and lncRNAs

Sequence Determinants for Nuclear Retention and Cytoplasmic Export of mRNAs and lncRNAs

Linking RNA Processing and Function

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

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