RIPiT-Seq: A tandem immunoprecipitation approach to reveal global binding landscape of multisubunit ribonucleoproteins

Yi, Zhongxia; Singh, Guramrit

doi:10.1016/bs.mie.2021.03.019

Cited by 2 publications

(3 citation statements)

References 29 publications

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“…RIPiT‐Seq was performed as described (Yi & Singh, 2021 ). Four biological replicates each were performed for FLAG‐MAGOH:EIF4A3, FLAG‐UPF3B:EIF4A3, and FLAG‐CASC3:EIF4A3 and sequenced on the HiSeq4000 (Novogene) platform.…”

Section: Methodsmentioning

confidence: 99%

Mammalian UPF3A and UPF3B can activate nonsense‐mediated mRNA decay independently of their exon junction complex binding

Arvola

Myers

et al. 2022

The EMBO Journal

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Nonsense‐mediated mRNA decay (NMD) is governed by the three conserved factors—UPF1, UPF2, and UPF3. While all three are required for NMD in yeast, UPF3B is dispensable for NMD in mammals, and its paralog UPF3A is suggested to only weakly activate or even repress NMD due to its weaker binding to the exon junction complex (EJC). Here, we characterize the UPF3A/B‐dependence of NMD in human cell lines deleted of one or both UPF3 paralogs. We show that in human colorectal cancer HCT116 cells, NMD can operate in a UPF3B‐dependent and ‐independent manner. While UPF3A is almost dispensable for NMD in wild‐type cells, it strongly activates NMD in cells lacking UPF3B. Notably, NMD remains partially active in cells lacking both UPF3 paralogs. Complementation studies in these cells show that EJC‐binding domain of UPF3 paralogs is dispensable for NMD. Instead, the conserved “mid” domain of UPF3 paralogs is consequential for their NMD activity. Altogether, our results demonstrate that the mammalian UPF3 proteins play a more active role in NMD than simply bridging the EJC and the UPF complex.

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Section: Methodsmentioning

confidence: 99%

Mammalian UPF3A and UPF3B can activate nonsense‐mediated mRNA decay independently of their exon junction complex binding

Arvola

Myers

et al. 2022

The EMBO Journal

Self Cite

View full text Add to dashboard Cite

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“…These pathways (along with MLKL mediated necroptosis) lead to PANoptosis or inflammatory cell death (78)(79)(80)(81)(82)(83)(84)(85). (39,(45)(46)(47)(48). It also has the advantage to be reversible upon incubation of samples at high temperature, which can facilitate RNA recovery and downstream processing such as reversetranscription.…”

Section: Technical Approaches To Study Rbpsmentioning

confidence: 99%

“…It intercalates between RNA bases of a dsRNA structure and allow efficient dsRBP/RNA crosslinking through visible light, thus overcoming the poor cross-linking activity of UV ( 38 , 44 ). Formaldehyde can also be used to cross-link single-strand and double-strand RBPs to their RNA targets ( 39 , 45 – 48 ). It also has the advantage to be reversible upon incubation of samples at high temperature, which can facilitate RNA recovery and downstream processing such as reverse-transcription.…”

Section: Technical Approaches To Study Rbpsmentioning

confidence: 99%

Shaping the Innate Immune Response Through Post-Transcriptional Regulation of Gene Expression Mediated by RNA-Binding Proteins

et al. 2022

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Innate immunity is the frontline of defense against infections and tissue damage. It is a fast and semi-specific response involving a myriad of processes essential for protecting the organism. These reactions promote the clearance of danger by activating, among others, an inflammatory response, the complement cascade and by recruiting the adaptive immunity. Any disequilibrium in this functional balance can lead to either inflammation-mediated tissue damage or defense inefficiency. A dynamic and coordinated gene expression program lies at the heart of the innate immune response. This expression program varies depending on the cell-type and the specific danger signal encountered by the cell and involves multiple layers of regulation. While these are achieved mainly via transcriptional control of gene expression, numerous post-transcriptional regulatory pathways involving RNA-binding proteins (RBPs) and other effectors play a critical role in its fine-tuning. Alternative splicing, translational control and mRNA stability have been shown to be tightly regulated during the innate immune response and participate in modulating gene expression in a global or gene specific manner. More recently, microRNAs assisting RBPs and post-transcriptional modification of RNA bases are also emerging as essential players of the innate immune process. In this review, we highlight the numerous roles played by specific RNA-binding effectors in mediating post-transcriptional control of gene expression to shape innate immunity.

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RIPiT-Seq: A tandem immunoprecipitation approach to reveal global binding landscape of multisubunit ribonucleoproteins

Cited by 2 publications

References 29 publications

Mammalian UPF3A and UPF3B can activate nonsense‐mediated mRNA decay independently of their exon junction complex binding

Mammalian UPF3A and UPF3B can activate nonsense‐mediated mRNA decay independently of their exon junction complex binding

Shaping the Innate Immune Response Through Post-Transcriptional Regulation of Gene Expression Mediated by RNA-Binding Proteins

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