Abstract 362: Genomewide Assessment of Posttranscriptional Events Orchestrated by Quaking that Determine Monocyte Fate

2014 ◽  
Vol 34 (suppl_1) ◽  
Author(s):  
Eric P van der Veer
Keyword(s):  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Cellular Adhesion ◽  
Growth And Survival ◽  
Expression Levels ◽  
Protein Levels ◽  
Atherosclerotic Lesions ◽  
Genome Wide ◽  
A Genome

The post-transcriptional events that enable monocytes to home to sites of vascular injury, and subsequently differentiate into macrophages within atherosclerotic lesions are poorly understood. We discovered that the mRNA and protein levels of the RNA-binding protein Quaking (QKI) are augmented in CD14+ myeloid cells extracted from advanced human atherosclerotic plaques (4.2-fold upregulated vs. early lesions; p<0.01). This prompted us to investigate how the RNA-binding properties of QKI could influence monocyte fate. Our approach was to examine, at a genome-wide level, how altering the expression levels of QKI could impact pre-mRNA splicing, expression, and localization upon differentiation of human monocytes into Mf. For this, we employed both array-based gene expression analyses as well as next-generation sequencing techniques (RNA-seq) of THP-1 monocytic cells as well as CD14+ monocytes derived from the peripheral blood of a unique, QKI haploinsufficient subject (with sibling control). Despite low expression levels of QKI in monocytes, the abrogation of QKI in these cells perturbed cellular adhesion and the ensuing establishment of the cytoskeletal architecture. Interestingly, our investigation of post-transcriptional events that are associated with the conversion of the monocyte to a macrophage, uncovered: 1) 536 alternative splicing events (p<0.05) that are directly mediated by binding of QKI proximal to the splice site (QBS)(Fig. 1A); and 2) 1214 differentially expressed genes (minimally +/- 1.5-fold; p<0.05) that indicate that QKI modulates monocyte activation and differentiation by regulating inflammation, cell growth and survival, RNA editing and lipid metabolism via activation of the LXR/RXR pathway (Fig. 1B). Collectively, our data illustrate the post-transcriptional events that drive monocyte to macrophage differentiation, and identify the RNA-binding protein QKI as an orchestrator of this inflammatory response.

scholarly journals A genome-wide homologous recombination screen identifies the RNA-binding protein RBMX as a component of the DNA-damage response

2012 ◽  
Vol 14 (3) ◽  
pp. 318-328 ◽  
Author(s):  
Britt Adamson ◽  
Agata Smogorzewska ◽  
Frederic D. Sigoillot ◽  
Randall W. King ◽  
Stephen J. Elledge
Keyword(s):  
Dna Damage ◽  
Homologous Recombination ◽  
Dna Damage Response ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Genome Wide ◽  
A Genome ◽  
Damage Response

scholarly journals RNA-binding protein hnRNPLL regulates mRNA splicing and stability during B-cell to plasma-cell differentiation

2015 ◽  
Vol 112 (15) ◽  
pp. E1888-E1897 ◽  
Author(s):  
Xing Chang ◽  
Bin Li ◽  
Anjana Rao
Keyword(s):  
Cell Differentiation ◽  
B Cell ◽  
Plasma Cell ◽  
Rna Binding ◽  
Plasma Cells ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Plasma Cell Differentiation ◽  
Genome Wide ◽  
A Genome

Posttranscriptional regulation is a major mechanism to rewire transcriptomes during differentiation. Heterogeneous nuclear RNA-binding protein LL (hnRNPLL) is specifically induced in terminally differentiated lymphocytes, including effector T cells and plasma cells. To study the molecular functions of hnRNPLL at a genome-wide level, we identified hnRNPLL RNA targets and binding sites in plasma cells through integrated Photoactivatable-Ribonucleoside-Enhanced Cross-Linking and Immunoprecipitation (PAR-CLIP) and RNA sequencing. hnRNPLL preferentially recognizes CA dinucleotide-containing sequences in introns and 3′ untranslated regions (UTRs), promotes exon inclusion or exclusion in a context-dependent manner, and stabilizes mRNA when associated with 3′ UTRs. During differentiation of primary B cells to plasma cells, hnRNPLL mediates a genome-wide switch of RNA processing, resulting in loss of B-cell lymphoma 6 (Bcl6) expression and increased Ig production—both hallmarks of plasma-cell maturation. Our data identify previously unknown functions of hnRNPLL in B-cell to plasma-cell differentiation and demonstrate that the RNA-binding protein hnRNPLL has a critical role in tuning transcriptomes of terminally differentiating B lymphocytes.

scholarly journals The Long Noncoding RNA HEAL Regulates HIV-1 Replication through Epigenetic Regulation of the HIV-1 Promoter

mBio ◽  
2019 ◽  
Vol 10 (5) ◽  
Author(s):  
Ti-Chun Chao ◽  
Qiong Zhang ◽  
Zhonghan Li ◽  
Shashi Kant Tiwari ◽  
Yue Qin ◽  
...  
Keyword(s):  
T Cells ◽  
Noncoding Rna ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Hiv Replication ◽  
Genome Wide ◽  
Primary Monocyte ◽  
A Genome ◽  
Hiv 1

ABSTRACT A major challenge in finding a cure for HIV-1/AIDS is the difficulty in identifying and eradicating persistent reservoirs of replication-competent provirus. Long noncoding RNAs (lncRNAs, >200 nucleotides) are increasingly recognized to play important roles in pathophysiology. Here, we report the first genome-wide expression analysis of lncRNAs in HIV-1-infected primary monocyte-derived macrophages (MDMs). We identified an lncRNA, which we named HIV-1-enhanced lncRNA (HEAL), that is upregulated by HIV-1 infection of MDMs, microglia, and T lymphocytes. Peripheral blood mononuclear cells of HIV-1-infected individuals show elevated levels of HEAL. Importantly, HEAL is a broad enhancer of multiple HIV-1 strains because depletion of HEAL inhibited X4, R5, and dual-tropic HIV replications and the inhibition was rescued by HEAL overexpression. HEAL forms a complex with the RNA-binding protein FUS, which facilitates HIV replication through at least two mechanisms: (i) HEAL-FUS complex binds the HIV promoter and enhances recruitment of the histone acetyltransferase p300, which positively regulates HIV transcription by increasing histone H3K27 acetylation and P-TEFb enrichment on the HIV promoter, and (ii) HEAL-FUS complex is enriched at the promoter of the cyclin-dependent kinase 2 gene, CDK2, to enhance CDK2 expression. Notably, HEAL knockdown and knockout mediated by RNA interference (RNAi) and CRISPR-Cas9, respectively, prevent HIV-1 recrudescence in T cells and microglia upon cessation of azidothymidine treatment in vitro. Our results suggest that silencing of HEAL or perturbation of the HEAL-FUS ribonucleoprotein complex could provide a new epigenetic silencing strategy to eradicate viral reservoirs and effect a cure for HIV-1/AIDS. IMPORTANCE Despite our increased understanding of the functions of lncRNAs, their potential to develop HIV/AIDS cure strategies remains unexplored. A genome-wide analysis of lncRNAs in HIV-1-infected primary monocyte-derived macrophages (MDMs) was performed, and 1,145 differentially expressed lncRNAs were identified. An lncRNA named HIV-1-enhanced lncRNA (HEAL) is upregulated by HIV-1 infection and promotes HIV replication in T cells and macrophages. HEAL forms a complex with the RNA-binding protein FUS to enhance transcriptional coactivator p300 recruitment to the HIV promoter. Furthermore, HEAL knockdown and knockout prevent HIV-1 recrudescence in T cells and microglia upon cessation of azidothymidine treatment, suggesting HEAL as a potential therapeutic target to cure HIV-1/AIDS.

scholarly journals Genome-wide landscape of RNA-binding protein target site dysregulation reveals a major impact on psychiatric disorder risk

2021 ◽  
Vol 53 (2) ◽  
pp. 166-173
Author(s):  
Christopher Y. Park ◽  
Jian Zhou ◽  
Aaron K. Wong ◽  
Kathleen M. Chen ◽  
Chandra L. Theesfeld ◽  
...  
Keyword(s):  
Psychiatric Disorder ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Target Site ◽  
Protein Target ◽  
Genome Wide ◽  
Disorder Risk

CHMP2B regulates TDP-43 phosphorylation and cytotoxicity independent of autophagy via CK1

2021 ◽  
Vol 221 (1) ◽  
Author(s):  
Xue Deng ◽  
Xing Sun ◽  
Wenkai Yue ◽  
Yongjia Duan ◽  
Rirong Hu ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Down Regulation ◽  
Protein Levels ◽  
Modifying Effect

The ESCRT protein CHMP2B and the RNA-binding protein TDP-43 are both associated with ALS and FTD. The pathogenicity of CHMP2B has mainly been considered a consequence of autophagy–endolysosomal dysfunction, whereas protein inclusions containing phosphorylated TDP-43 are a pathological hallmark of ALS and FTD. Intriguingly, TDP-43 pathology has not been associated with the FTD-causing CHMP2BIntron5 mutation. In this study, we identify CHMP2B as a modifier of TDP-43–mediated neurodegeneration in a Drosophila screen. Down-regulation of CHMP2B reduces TDP-43 phosphorylation and toxicity in flies and mammalian cells. Surprisingly, although CHMP2BIntron5 causes dramatic autophagy dysfunction, disturbance of autophagy does not alter TDP-43 phosphorylation levels. Instead, we find that inhibition of CK1, but not TTBK1/2 (all of which are kinases phosphorylating TDP-43), abolishes the modifying effect of CHMP2B on TDP-43 phosphorylation. Finally, we uncover that CHMP2B modulates CK1 protein levels by negatively regulating ubiquitination and the proteasome-mediated turnover of CK1. Together, our findings propose an autophagy-independent role and mechanism of CHMP2B in regulating CK1 abundance and TDP-43 phosphorylation.

Cold-induced RNA-binding protein (CIRBP) regulates the expression of Src-associated during mitosis of 68 kDa (Sam68) and extracellular signal-regulated kinases (ERK) during heat stress-induced testicular injury

2020 ◽  
Vol 32 (18) ◽  
pp. 1357
Author(s):  
Chengcheng Xu ◽  
Dandan Ke ◽  
Liping Zou ◽  
Nianyu Li ◽  
Yingying Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Heat Stress ◽  
Protein Expression ◽  
Rna Binding ◽  
Cell Model ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Protein Levels ◽  
Extracellular Signal ◽  
Testicular Injury

In this study, the ability of cold-induced RNA-binding protein (CIRBP) to regulate the expression of Src-associated during mitosis of 68 kDa (Sam68) and extracellular signal-regulated kinases (ERK) in the mouse testis and mouse primary spermatocytes (GC-2spd cell line) before and after heat stress was examined to explore the molecular mechanism by which CIRBP decreases testicular injury. A mouse testicular hyperthermia model, a mouse primary spermatocyte hyperthermia model and a low CIRBP gene-expression cell model were constructed and their relevant parameters were analysed. The mRNA and protein levels of CIRBP and Sam68 were significantly decreased in the 3-h and 12-h testicular heat-stress groups, extracellular signal-regulated kinase 1/2 (ERK1/2) protein expression was not significantly affected but phospho-ERK1/2 protein levels were significantly decreased. GC-2spd cellular heat-stress results showed that the mRNA and protein concentrations of CIRBP and Sam68 were reduced 48h after heat stress. In the low CIRBP gene-expression cell model, CIRBP protein expression was significantly decreased. Sam68 mRNA expression was significantly decreased only at the maximum transfection concentration of 50nM and Sam68 protein expression was not significantly affected. These findings suggest that CIRBP may regulate the expression of Sam68 at the transcriptional level and the expression of phospho-ERK1/2 protein, both of which protect against heat-stress-induced testicular injury in mice.

Genome-wide survey of putative RNA-binding proteins encoded in the human proteome

2016 ◽  
Vol 12 (2) ◽  
pp. 532-540 ◽  
Author(s):  
Pritha Ghosh ◽  
R. Sowdhamini
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Human Proteome ◽  
Genome Wide ◽  
Genome Wide Survey

We have classified the existing RNA-binding protein (RBP) structures into different structural families. Here, we report ∼2600 proteins with RBP signatures in humans.

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