Changes in mRNA abundance drive shuttling of RNA binding proteins, linking cytoplasmic RNA degradation to transcription

Gilbertson, Sarah; Federspiel, Joel D.; Hartenian, Ella; Cristea, Ileana M.; Glaunsinger, Britt A.

doi:10.1101/295972

Cited by 3 publications

(2 citation statements)

References 58 publications

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“…The increase of PAR level is more pronounced when HA-FUS-expressing cells were treated for at least 45 min with ActD before H 2 O 2 , which may correspond to the time required for releasing FUS from its mRNA targets after transcription inhibition (Figures S6A and S6C). Consistently, the nucleocytoplasmic shuttling of mRNAbinding proteins such as FUS, TDP-43, and HuR, which relies on their binding to nuclear mRNAs, 61 occurs after ActD treatment (Figure S6B).…”

Section: Inhibiting Mrna Transcription Increases Par Level In Ha-fus-...supporting

confidence: 56%

FUS RRM Regulates Poly(ADP)-Ribose Levels After Transcriptional Arrest and PARP-1 Activation on DNA Damage

Mamontova

Clément

Sukhanova

et al. 2023

Preprint

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Section: Inhibiting Mrna Transcription Increases Par Level In Ha-fus-...supporting

confidence: 56%

FUS RRM Regulates Poly(ADP)-Ribose Levels After Transcriptional Arrest and PARP-1 Activation on DNA Damage

Mamontova

Clément

Sukhanova

et al. 2023

Preprint

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“…Exploring these questions from a protein-centric viewpoint could offer more insights, examining how post-translational modifications of HuR or alterations in the availability of proteins that bind cooperatively or competitively to similar motifs in the cytoplasm and stress granules affect these interactions. Additionally, it is worth exploring whether this observed binding pattern shift is exclusive to HuR or represents a shared behavior across other nucleocytoplasmic shuttling RBPs 41 in additional stress contests, 42 which could further enrich our understanding of RBP:RNA interaction networks. Another important question is the relationships between changes in HuR binding and downstream functional roles within different cellular compartments.…”

Section: Discussionmentioning

confidence: 99%

Mapping RNA-Protein Interactions with Subcellular Resolution Using Colocalization CLIP

Yi,

Singh,

Rozen-Gagnon

et al. 2023

Preprint

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RNA binding proteins (RBPs) are essential for RNA metabolism and profoundly impact health and disease. The subcellular organization of RBP interaction networks with target RNAs remains largely unexplored. Here, we develop colocalization CLIP, a method that combines CrossLinking and ImmunoPrecipitation (CLIP) with proximity labeling, to explore in-depth the subcellular RNA interactions of the well-studied RNA-binding protein HuR. Using this method, we uncover HuR's dynamic and location-specific interactions with RNA, revealing alterations in sequence preferences and interactions in the nucleus, cytosol, or stress granule compartments. We uncover HuR's unique binding preferences within stress granules during arsenite stress, illuminating intricate interactions that conventional methodologies cannot capture. Overall, coCLIP provides a powerful method for revealing RBP:RNA interactions based on localization and lays the foundation for an advanced understanding of RBP models that incorporate subcellular location as a critical determinant of their functions.

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Herpesvirus infection reduces Pol II occupancy of host promoters but spares viral promoters

2019

Preprint

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In mammalian cells, widespread acceleration of cytoplasmic mRNA degradation is linked to impaired RNA polymerase II (Pol II) transcription. This mRNA decay-induced transcriptional repression occurs during infection with gammaherpesviruses including Kaposi’s sarcoma-associated herpesvirus (KSHV) and murine gammaherpesvirus 68 (MHV68), which encode an mRNA endonuclease that initiates widespread RNA decay. Here, we show that MHV68-induced mRNA decay leads to a genome-wide reduction of Pol II occupancy at mammalian promoters. Viral genes, despite the fact that they require Pol II for transcription, escape this transcriptional repression. Protection is not governed by viral promoter sequences; instead, location on the viral genome is both necessary and sufficient to escape the transcriptional repression effects of mRNA decay. We hypothesize that the ability to escape from transcriptional repression is linked to the localization of viral DNA in replication compartments, providing a means for these viruses to counteract decay-induced viral transcript loss.

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Changes in mRNA abundance drive shuttling of RNA binding proteins, linking cytoplasmic RNA degradation to transcription

Cited by 3 publications

References 58 publications

FUS RRM Regulates Poly(ADP)-Ribose Levels After Transcriptional Arrest and PARP-1 Activation on DNA Damage

FUS RRM Regulates Poly(ADP)-Ribose Levels After Transcriptional Arrest and PARP-1 Activation on DNA Damage

Mapping RNA-Protein Interactions with Subcellular Resolution Using Colocalization CLIP

Herpesvirus infection reduces Pol II occupancy of host promoters but spares viral promoters

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