A Sequence determinant in 3’UTR of mRNAs for Nuclear Retention by Paraspeckles

Jacq, Audrey; Becquet, Denis; Boyer, Brigitte; Guillen, Séverine; Bello-Goutierrez, Maria-Montserrat; Blanchard, Marie-Pierre; Villard, Claude; Belghazi, Maya; Torres, Manon; Franc, Jean‐Louis; François‐Bellan, Anne‐Marie

doi:10.1101/2020.07.19.206417

Cited by 2 publications

(5 citation statements)

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“…The first one corresponds to an IRAlu sequence whereas the second one is a 15-nucleotide sequence, and both are located in 3'UTR of some mRNAs that are paraspeckles targets. The IRAlu sequence and the 15-nucleotide sequence bind RBPs, NONO (25) and HNRNPK (18), respectively. However, while we have previously established that in the GH4C1 cells, 4268 RNAs are targeted by paraspeckles, no IRSINE-like structure, the rat equivalent of primate IRAlus, has been found in the 3'UTR of these RNAs and only 30% of them displayed the 15-nucleotide sequence recognized by HNRNPK (18).…”

Section: Discussionmentioning

confidence: 99%

“…The IRAlu sequence and the 15-nucleotide sequence bind RBPs, NONO (25) and HNRNPK (18), respectively. However, while we have previously established that in the GH4C1 cells, 4268 RNAs are targeted by paraspeckles, no IRSINE-like structure, the rat equivalent of primate IRAlus, has been found in the 3'UTR of these RNAs and only 30% of them displayed the 15-nucleotide sequence recognized by HNRNPK (18). This indicates that other mechanisms are the support of the binding of RNAs to paraspeckles.…”

Section: Discussionmentioning

confidence: 99%

“…However, unexpectedly we didn't find IRSINEs in 3'-UTR of the 4268 RNAs, we previously identified as paraspeckle RNAs targets using a Neat1 RNA pull-down procedure (17) followed by RNA-sequencing in GH4C1 cells (12). By contrast, a sequence motive of 15 nucleotides identified in the 3'UTR of more than 30% of the 4268 RNAs that are paraspeckle targets may be involved in the nuclear retention of RNAs by paraspeckles through its binding by PSP component HNRNPK (18). However, whereas PSPs probably play a crucial role in binding RNA targets, it is also possible that the lncRNA Neat1, in addition to its structural role, may also be directly involved in the binding by base pairing of RNAs and consequently in their retention in paraspeckles.…”

Section: Introductionmentioning

confidence: 93%

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Direct RNA–RNA interaction between Neat1 and RNA targets, as a mechanism for RNAs paraspeckle retention

et al. 2021

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Paraspeckles are nuclear ribonucleic complex formed of a long non-coding RNA, nuclearenriched abundant transcript one (Neat1) and associated RNA-binding proteins (RBP) whose cellular known functions are to sequester in the nucleus both proteins and RNAs. However, how RNAs are bound to paraspeckles is largely unknown. It is highly likely that binding of RNAs may occur via interactions with RBPs and accordingly, two structures present in the 3'UTR of some RNAs have been shown to allow their association to paraspeckles via protein binding. However, Neat1 could also be involved in the targeting of RNAs through direct RNA-RNA interactions. Using a RNA pull-down procedure adapted to select only RNAs engaged in direct RNA-RNA interactions and followed by RNA-seq we showed that in a rat pituitary cell line, GH4C1 cells, 1791 RNAs were associated with paraspeckles by direct interaction with Neat1. Neat1 was actually found able to bind more than 30% of the total transcripts targeted by the paraspeckles, we have identified in this cell line in a previous study. Furthermore, given the biological processes in which direct RNAs targets of Neat1 were involved as determined by gene ontology analysis, it was proposed that Neat1 played a major role in paraspeckle functions such as circadian rhythms, mRNA processing, RNA splicing and regulation of cell cycle. Finally, we provided evidence that direct RNA targets of Neat1 were preferentially bound to the 5' end of Neat1 demonstrating that they are located in the shell region of paraspeckles.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 93%

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Direct RNA–RNA interaction between Neat1 and RNA targets, as a mechanism for RNAs paraspeckle retention

et al. 2021

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show abstract

“…The first one corresponds to an IRAlu sequence whereas the second one is a 15-nucleotide sequence, and both are located in 3’UTR of some mRNAs that are paraspeckles targets. The IRAlu sequence and the 15-nucleotide sequence bind RBPs, NONO (25) and HNRNPK (18), respectively. However, while we have previously established that in the GH4C1 cells, 4268 RNAs are targeted by paraspeckles, no IRSINE-like structure, the rat equivalent of primate IRAlus, has been found in the 3’UTR of these RNAs and only 30% of them displayed the 15-nucleotide sequence recognized by HNRNPK (18).…”

Section: Discussionmentioning

confidence: 99%

“…The IRAlu sequence and the 15-nucleotide sequence bind RBPs, NONO (25) and HNRNPK (18), respectively. However, while we have previously established that in the GH4C1 cells, 4268 RNAs are targeted by paraspeckles, no IRSINE-like structure, the rat equivalent of primate IRAlus, has been found in the 3’UTR of these RNAs and only 30% of them displayed the 15-nucleotide sequence recognized by HNRNPK (18). This indicates that other mechanisms are the support of the binding of RNAs to paraspeckles.…”

Section: Discussionmentioning

confidence: 99%

Direct RNA-RNA interaction between Neat1 and RNA targets, as a mechanism for RNAs paraspeckle retention

Jacq¹,

Becquet²,

Guillen³

et al. 2020

Preprint

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Paraspeckles are nuclear ribonucleic complex formed of a long non-coding RNA, nuclear-enriched abundant transcript one (Neat1) and associated RNA-binding proteins (RBP) whose cellular known functions are to sequester in the nucleus both proteins and RNAs. However, how RNAs are bound to paraspeckles is largely unknown. It is highly likely that binding of RNAs may occur via interactions with RBPs and accordingly, two structures present in the 3'UTR of some RNAs have been shown to allow their association to paraspeckles via protein binding. However, Neat1 could also be involved in the targeting of RNAs through direct RNA-RNA interactions. Using a RNA pull-down procedure adapted to select only RNAs engaged in direct RNA-RNA interactions and followed by RNA-seq we showed that in a rat pituitary cell line, GH4C1 cells, 1791 RNAs were associated with paraspeckles by direct interaction with Neat1. Neat1 was actually found able to bind more than 30% of the total transcripts targeted by the paraspeckles, we have identified in this cell line in a previous study. Furthermore, given the biological processes in which direct RNAs targets of Neat1 were involved as determined by gene ontology analysis, it was proposed that Neat1 played a major role in paraspeckle functions such as circadian rhythms, mRNA processing, RNA splicing and regulation of cell cycle. Finally, we provided evidence that direct RNA targets of Neat1 were preferentially bound to the 5'end of Neat1 demonstrating that they are located in the shell region of paraspeckles.

show abstract

A Sequence determinant in 3’UTR of mRNAs for Nuclear Retention by Paraspeckles

Cited by 2 publications

References 32 publications

Direct RNA–RNA interaction between Neat1 and RNA targets, as a mechanism for RNAs paraspeckle retention

Direct RNA–RNA interaction between Neat1 and RNA targets, as a mechanism for RNAs paraspeckle retention

Direct RNA-RNA interaction between Neat1 and RNA targets, as a mechanism for RNAs paraspeckle retention

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