Transcriptome-Wide Identification of RNA Targets of Arabidopsis SERINE/ARGININE-RICH45 Uncovers the Unexpected Roles of This RNA Binding Protein in RNA Processing

Chloroplast RNA processing requires a large number of nuclear-encoded RNA binding proteins (RBPs) that are imported post-translationally into the organelle. Most of these RBPs are highly specific for one or few target RNAs. By contrast, members of the chloroplast ribonucleoprotein family (cpRNPs) have a wider RNA target range. We here present a quantitative analysis of RNA targets of the cpRNP CP31A using digestion-optimized RNA co-immunoprecipitation with deep sequencing (DO-RIP-seq). This identifies the mRNAs coding for subunits of the chloroplast NAD(P)H dehydrogenase (NDH) complex as main targets for CP31A. We demonstrate using whole-genome gene expression analysis and targeted RNA gel blot hybridization that the ndh mRNAs are all down-regulated in cp31a mutants. This diminishes the activity of the NDH complex. Our findings demonstrate how a chloroplast RNA binding protein can combine functionally related RNAs into one post-transcriptional operon.

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Human cytomegalovirus induces and exploits Roquin to counteract the IRF1-mediated antiviral state

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1909314116 ◽

2019 ◽

Vol 116 (37) ◽

pp. 18619-18628 ◽

Cited By ~ 2

Author(s):

Jaewon Song ◽

Sanghyun Lee ◽

Dong-Yeon Cho ◽

Sungwon Lee ◽

Hyewon Kim ◽

...

Keyword(s):

Human Cytomegalovirus ◽

Rna Processing ◽

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Transcriptome Profiling ◽

Loss Of Function ◽

Antiviral Genes ◽

Cellular Antiviral Response ◽

Infected Cells

RNA represents a pivotal component of host–pathogen interactions. Human cytomegalovirus (HCMV) infection causes extensive alteration in host RNA metabolism, but the functional relationship between the virus and cellular RNA processing remains largely unknown. Through loss-of-function screening, we show that HCMV requires multiple RNA-processing machineries for efficient viral lytic production. In particular, the cellular RNA-binding protein Roquin, whose expression is actively stimulated by HCMV, plays an essential role in inhibiting the innate immune response. Transcriptome profiling revealed Roquin-dependent global down-regulation of proinflammatory cytokines and antiviral genes in HCMV-infected cells. Furthermore, using cross-linking immunoprecipitation (CLIP)-sequencing (seq), we identified IFN regulatory factor 1 (IRF1), a master transcriptional activator of immune responses, as a Roquin target gene. Roquin reduces IRF1 expression by directly binding to its mRNA, thereby enabling suppression of a variety of antiviral genes. This study demonstrates how HCMV exploits host RNA-binding protein to prevent a cellular antiviral response and offers mechanistic insight into the potential development of CMV therapeutics.

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RNA binding protein HuD promotes autophagy and tumor stress survival by suppressing mTORC1 activity and augmenting ARL6IP1 levels

Journal of Experimental & Clinical Cancer Research ◽

10.1186/s13046-021-02203-2 ◽

2022 ◽

Vol 41 (1) ◽

Author(s):

Kausik Bishayee ◽

Khadija Habib ◽

Uddin Md. Nazim ◽

Jieun Kang ◽

Aniko Szabo ◽

...

Keyword(s):

Cancer Survival ◽

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Neuroblastoma Cells ◽

Cancer Type ◽

Rna Targets ◽

Stress Survival ◽

Promote Cell Survival ◽

Rna Immunoprecipitation

Abstract Background Neuronal-origin HuD (ELAVL4) is an RNA binding protein overexpressed in neuroblastoma (NB) and certain other cancers. The RNA targets of this RNA binding protein in neuroblastoma cells and their role in promoting cancer survival have been unexplored. In the study of modulators of mTORC1 activity under the conditions of optimal cell growth and starvation, the role of HuD and its two substrates were studied. Methods RNA immunoprecipitation/sequencing (RIP-SEQ) coupled with quantitative real-time PCR were used to identify substrates of HuD in NB cells. Validation of the two RNA targets of HuD was via reverse capture of HuD by synthetic RNA oligoes from cell lysates and binding of RNA to recombinant forms of HuD in the cell and outside of the cell. Further analysis was via RNA transcriptome analysis of HuD silencing in the test cells. Results In response to stress, HuD was found to dampen mTORC1 activity and allow the cell to upregulate its autophagy levels by suppressing mTORC1 activity. Among mRNA substrates regulated cell-wide by HuD, GRB-10 and ARL6IP1 were found to carry out critical functions for survival of the cells under stress. GRB-10 was involved in blocking mTORC1 activity by disrupting Raptor-mTOR kinase interaction. Reduced mTORC1 activity allowed lifting of autophagy levels in the cells required for increased survival. In addition, ARL6IP1, an apoptotic regulator in the ER membrane, was found to promote cell survival by negative regulation of apoptosis. As a therapeutic target, knockdown of HuD in two xenograft models of NB led to a block in tumor growth, confirming its importance for viability of the tumor cells. Cell-wide RNA messages of these two HuD substrates and HuD and mTORC1 marker of activity significantly correlated in NB patient populations and in mouse xenografts. Conclusions HuD is seen as a novel means of promoting stress survival in this cancer type by downregulating mTORC1 activity and negatively regulating apoptosis.

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Abstract 204: Molecular function of the RNA binding protein EWS in RNA processing

10.1158/1538-7445.am2012-204 ◽

2012 ◽

Author(s):

Bethsaida I. Nieves ◽

Shuang Niu ◽

Dedeepya Vaka ◽

Julia Salzman ◽

Patrick Brown ◽

...

Keyword(s):

Rna Processing ◽

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Molecular Function

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The chaperonin of the archaeon Sulfolobus solfataricus is an RNA-binding protein that participates in ribosomal RNA processing

The EMBO Journal ◽

10.1093/emboj/17.12.3471 ◽

1998 ◽

Vol 17 (12) ◽

pp. 3471-3477 ◽

Cited By ~ 33

Author(s):

D. Ruggero

Keyword(s):

Ribosomal Rna ◽

Rna Processing ◽

Rna Binding ◽

Binding Protein ◽

Sulfolobus Solfataricus ◽

Rna Binding Protein ◽

Ribosomal Rna Processing

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RBD-1, a nucleolar RNA-binding protein, is essential for Caenorhabditis elegans early development through 18S ribosomal RNA processing

Nucleic Acids Research ◽

10.1093/nar/gkh264 ◽

2004 ◽

Vol 32 (3) ◽

pp. 1028-1036 ◽

Cited By ~ 16

Author(s):

E. Saijou

Keyword(s):

Caenorhabditis Elegans ◽

Early Development ◽

Ribosomal Rna ◽

Rna Processing ◽

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

18S Ribosomal Rna ◽

Ribosomal Rna Processing ◽

Nucleolar Rna

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FASTKD2 is an RNA-binding protein required for mitochondrial RNA processing and translation

RNA ◽

10.1261/rna.052365.115 ◽

2015 ◽

Vol 21 (11) ◽

pp. 1873-1884 ◽

Cited By ~ 49

Author(s):

Johannes Popow ◽

Anne-Marie Alleaume ◽

Tomaz Curk ◽

Thomas Schwarzl ◽

Sven Sauer ◽

...

Keyword(s):

Rna Processing ◽

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Mitochondrial Rna

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R-loop resolution promotes co-transcriptional chromatin silencing

Nature Communications ◽

10.1038/s41467-021-22083-6 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Congyao Xu ◽

Zhe Wu ◽

Hong-Chao Duan ◽

Xiaofeng Fang ◽

Guifang Jia ◽

...

Keyword(s):

Dna Damage ◽

Rna Processing ◽

Antisense Transcript ◽

Rna Binding ◽

Binding Protein ◽

Rna Binding Protein ◽

Arabidopsis Genome ◽

Nascent Transcript ◽

Genome Regulation ◽

Processing Factors

AbstractRNA-mediated chromatin silencing is central to genome regulation in many organisms. However, how nascent non-coding transcripts regulate chromatin is poorly understood. Here, through analysis of Arabidopsis FLC, we show that resolution of a nascent-transcript-induced R-loop promotes chromatin silencing. Stabilization of an antisense-induced R-loop at the 3′ end of FLC enables an RNA binding protein FCA, with its direct partner FY/WDR33 and other 3′-end processing factors, to polyadenylate the nascent antisense transcript. This clears the R-loop and recruits the chromatin modifiers demethylating H3K4me1. FCA immunoprecipitates with components of the m6A writer complex, and m6A modification affects dynamics of FCA nuclear condensates, and promotes FLC chromatin silencing. This mechanism also targets other loci in the Arabidopsis genome, and consistent with this fca and fy are hypersensitive to a DNA damage-inducing drug. These results show how modulation of R-loop stability by co-transcriptional RNA processing can trigger chromatin silencing.

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