Arabidopsis Apoplastic Fluid Contains sRNA- and Circular RNA-Protein Complexes that Are Located Outside Extracellular Vesicles

2021 ◽  
Author(s):  
Hana Zand Karimi ◽  
Patricia Baldrich ◽  
Brian D. Rutter ◽  
Lucia Borniego ◽  
Kamil K. Zajt ◽  
...  
Keyword(s):  
Extracellular Vesicles ◽  
Rna Binding ◽  
Protein Complexes ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Circular Rna ◽  
Rnase A ◽  
Circular Rnas ◽  
Apoplastic Fluid ◽  
Rna Protein Complexes

Previously, we have shown that apoplastic wash fluid purified from Arabidopsis leaves contains small RNAs (sRNAs). To investigate whether these sRNAs are encapsulated inside extracellular vesicles (EVs), we treated EVs isolated from Arabidopsis leaves with the protease trypsin and RNase A, which should degrade RNAs located outside EVs but not those located inside. These analyses revealed that apoplastic RNAs are mostly located outside EVs and are associated with proteins. Further analyses of these extracellular RNAs (exRNAs) revealed that they comprise both sRNAs and long non-coding RNAs (lncRNAs), including circular RNAs (circRNAs). We also found that exRNAs are highly enriched in the post-transcriptional modification N6-methyladenine (m(6)A). Consistent with this, we identified a putative m(6)A-binding protein in apoplastic wash fluid, GLYCINE-RICH RNA-BINDING PROTEIN 7 (GRP7), as well as the small RNA-binding protein ARGONAUTE2 (AGO2). These two proteins co-immunoprecipitated with each other, and with lncRNAs, including circRNAs. Mutation of GRP7 or AGO2 caused changes in both the sRNA and lncRNA content of apoplastic wash fluid, suggesting that these proteins contribute to the secretion and/or stabilization of exRNAs. We propose that these extravesicular RNAs mediate host-induced gene silencing, rather than RNA inside EVs.

scholarly journals Circular RNA and its mechanisms in diabetic retinopathy: a systematic review

2020 ◽  
Author(s):  
Miao He ◽  
Rouxi Zhou ◽  
Sen Liu ◽  
Weijing Cheng ◽  
Wei Wang
Keyword(s):  
Systematic Review ◽  
Diabetic Retinopathy ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Protein Complexes ◽  
Protein Translation ◽  
Circular Rna ◽  
Circular Rnas ◽  
Eye Tissues ◽  
Rna Protein Complexes

ABSTRACTCircular RNAs (CircRNAs) are endogenous long non-coding RNAs. Unlike linear RNAs, they are structurally continuous and covalently closed, without 5 ’caps or 3’ polyadenylation tails. High-throughput RNA sequencing has enabled people to find several endogenous circRNAs in different species and tissues. circRNA mainly acts as a sponge for microRNAs in cytoplasm to regulates protein translation, or interacts with RNA-binding proteins to generate RNA protein complexes that control transcription. circRNAs are closely associated with diseases such as diabetes, neurological disorders, cardiovascular diseases and cancer, which indicates that circRNAs are closely related to and also play an important functional role in the occurrence and development of human diseases. Recent studies have shown that they are differentially expressed in healthy and diseased eye tissues. There lacks of biomarkers for early detection of diabetic retinopathy, and the newly discovered circRNAs seem to be an ideal candidate of novel molecular markers and therapeutic targets. However, the molecular mechanism of circRNAs activity in the occurrence and development of diabetic retinopathy are not clear yet. This systematic review aims to summarize the research status on function and mechanism of circRNAs in regulating the occurrence of diabetic retinopathy.

Abstract 1373: Circular RNAs generated from theBRCA1pseudogene regulates the DNA damage response through SERBP1 RNA-binding protein

2018 ◽  
Author(s):  
Yoo J. Han ◽  
Jing Zhang ◽  
Jennifer M. Mason ◽  
Toshio F. Yoshimatsu ◽  
Xinxin Du ◽  
...  
Keyword(s):  
Dna Damage ◽  
Dna Damage Response ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Circular Rnas ◽  
Damage Response

scholarly journals The RNA-binding protein RBM3 promotes cell proliferation in hepatocellular carcinoma by regulating circular RNA SCD-circRNA 2 production

EBioMedicine ◽  
2019 ◽  
Vol 45 ◽  
pp. 155-167 ◽  
Author(s):  
Wei Dong ◽  
Zhi-hui Dai ◽  
Fu-chen Liu ◽  
Xing-gang Guo ◽  
Chun-mei Ge ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Cell Proliferation ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Circular Rna

scholarly journals Integrated analysis of RNA-binding protein complexes using in vitro selection and high-throughput sequencing and sequence specificity landscapes (SEQRS)

Methods ◽  
2017 ◽  
Vol 118-119 ◽  
pp. 171-181 ◽  
Author(s):  
Tzu-Fang Lou ◽  
Chase A. Weidmann ◽  
Jordan Killingsworth ◽  
Traci M. Tanaka Hall ◽  
Aaron C. Goldstrohm ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
In Vitro Selection ◽  
Rna Binding ◽  
Protein Complexes ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Integrated Analysis ◽  
Sequence Specificity

scholarly journals Multiple RNA Binding Protein Complexes Interact with the Rice Prolamine RNA Cis-Localization Zipcode Sequences

2014 ◽  
Vol 164 (3) ◽  
pp. 1271-1282 ◽  
Author(s):  
Yongil Yang ◽  
Andrew J. Crofts ◽  
Naoko Crofts ◽  
Thomas W. Okita
Keyword(s):  
Rna Binding ◽  
Protein Complexes ◽  
Binding Protein ◽  
Rna Binding Protein

scholarly journals The SRSF1/circATP5B/miR-185-5p/HOXB5 Feedback Loop Regulates the Proliferation of Glioma Stem Cells via the IL6-mediated JAK2/STAT3 Signaling Pathway

2020 ◽  
Author(s):  
Junshuang Zhao ◽  
Yang Jiang ◽  
Haiying Zhang ◽  
Jinpeng Zhou ◽  
Lian Chen ◽  
...  
Keyword(s):  
Stem Cells ◽  
Feedback Loop ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Bioinformatic Analysis ◽  
Luciferase Reporter ◽  
Circular Rnas ◽  
Glioma Stem Cells ◽  
Stat3 Signaling

Abstract BackgroundGlioma is the most common and malignant tumor of central nervous system. The tumor initiation, self-renewal, and multi-lineage differentiation abilities of glioma stem cells (GSCs) are responsible for glioma proliferation and recurrence. Although circular RNAs (circRNAs) play vital roles in the progression of glioma, the detailed mechanisms remain unknown. MethodsqRT-PCR, western blotting, immunohistochemistry, and bioinformatic analysis were performed to detect the expression of circATP5B, miR-185-5p, HOXB5, and SRSF1. Patient-derived GSCs were established, and MTS, EDU, neurosphere formation, and limiting dilution assays were used to detect the proliferation of GSCs. RNA-binding protein immunoprecipitation, RNA pull-down, luciferase reporter assays, and chromatin immunoprecipitation assays were used to detect these molecules' regulation mechanisms. ResultsWe found circATP5B expression was significantly upregulated in GSCs and promoted the proliferation of GSCs. Mechanistically, circATP5B acted as miR-185-5p sponge to upregulate HOXB5 expression. HOXB5 was overexpressed in glioma and transcriptionally regulated IL6 expression and promoted the proliferation of GSCs via JAK2/STAT3 signaling. Moreover, RNA binding protein SRSF1 could bind to and promote circATP5B expression and regulate the proliferation of GSCs, while HOXB5 also transcriptionally regulated SRSF1 expression. ConclusionsOur study identified the SRSF1/circATP5B/miR-185-5p/HOXB5 feedback loop in GSCs. This provides an effective biomarker for glioma diagnosis and prognostic evaluation.

scholarly journals hnRNPA2B1-Mediated Extracellular Vesicles Sorting of miR-122-5p Potentially Promotes Lung Cancer Progression

2021 ◽  
Vol 22 (23) ◽  
pp. 12866
Author(s):  
Chuang Li ◽  
Fang Qin ◽  
Wei Wang ◽  
Yifan Ni ◽  
Mingyu Gao ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Extracellular Vesicles ◽  
Cancer Progression ◽  
Tumor Metastasis ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Small Cell ◽  
Small Cell Lung ◽  
Non Coding Rna

Extracellular vesicles (EVs) released by tumor cells play important roles on the remodeling of the tumor–stromal environment and on promoting tumor metastasis. Our earlier studies revealed that miR-122-5p, a type of small non-coding RNA, was dysregulated in non-small cell lung cancer (NSCLC) cell-derived EVs. In this study, we found that miR-122-5p was selectively sorted and secreted into lung cancer EVs through binding to RNA-binding protein hnRNPA2B1. In addition, we found that hnRNPA2B1 interacted with miR-122-5p through the EXO-motif. The delivering of lung cancer EVs-miR-122-5p promoted the migration of liver cells, which may play roles in establishing a pre-metastatic micro-environment and hepatic metastasis of lung cancer. Importantly, our findings revealed the molecular mechanism that RNA-binding protein controls the selective sorting of tumor-derived EV miR-122-5p, which potentially promotes lung cancer progression.

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