Key Spec Table
|Description||EZ-Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit|
|Overview||RNA-binding protein immunoprecipitation (RIP) is the RNA analog of the more well-known ChIP application (chromatin immunoprecipitation), which identifies DNA targets of DNA-binding proteins in an in-vivo cellular context. RIP can be used to identify specific RNA molecules (of many types) associated with specific nuclear or cytoplasmic binding proteins. These experiments involve immunoprecipitation of endogenously formed complexes of RNA-binding proteins and co-isolation of any RNA species associated with that RNA-binding protein. Purification of these RNA species allows interrogation and identification of mRNAs (and potentially non-coding RNAs associated with them) and can be directly measured using down stream applications including quantitative reverse transcription polymerase chain reaction (RT-PCR), microarray analysis (RIP-chip) and “deep-sequencing” or 2nd-generation sequencing based platforms (RIP-Seq).
Features & Benefits:
-Protein A/G magnetic beads, optimized to bind nucleic acid-protein immune complexes
-RNAse inhibitors and RNAse-free reagents
-Positive and negative controls
|Materials Required but Not Delivered||Magna Grip™ Rack 8 well ( 20-400) (Now Available!) or similar magnetic rack.|
|Background Information||Gene regulation plays a critical role in complex cellular processes such as development, differentiation, and cellular response to environmental changes. In addition to transcriptional regulation of gene expression by transcription factors, cells utilize post-transcriptional regulatory mechanisms. One such mechanism involves use of certain RNA-binding proteins (RBPs) to temporally and coordinately regulate the rate of mRNA translation of functionally related gene
products. While the regulation of gene expression by transcription factors has been well studied over time, the post-transcriptional regulation of mRNAs by RBPs and the role of non-coding RNAs in this process is a relatively nascent field that remains to be thoroughly explored.
|Safety Information according to GHS|
|Storage and Shipping Information|
|Storage Conditions||Upon receipt, store components at the temperatures indicated on the labels. Kit components are stable for 6 months from date of shipment when stored as directed.|
|Material Size||12 assays|
|Material Package||RIP Kit capacity: 12 RNA-binding protein immunoprecipitation assays|
EZ-Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit SDS
|Reference overview||Application||Pub Med ID|
|LncRNA TUG1 sponges miR-204-5p to promote osteoblast differentiation through upregulating Runx2 in aortic valve calcification.|
Yu, C; Li, L; Xie, F; Guo, S; Liu, F; Dong, N; Wang, Y
Cardiovasc Res 114 168-179 2018
Emerging evidence indicates that long non-coding RNAs (lncRNAs) play a vital role in cardiovascular physiology and pathology. Although the lncRNA TUG1 is implicated in atherosclerosis, its function in calcific aortic valve disease (CAVD) remains unknown.In this study, we found that TUG1 was highly expressed in human aortic valves and primary valve interstitial cells (VICs). Moreover, TUG1 knockdown induced inhibition of osteoblast differentiation in CAVD both in vitro and in vivo. Mechanistically, silencing of TUG1 increased the expression of miR-204-5p and subsequently inhibited Runx2 expression at the post-transcriptional level. Importantly, TUG1 directly interacted with miR-204-5p and downregulation of miR-204-5p efficiently reversed the suppression of Runx2 induced by TUG1 short hairpin RNA (shRNA). Thus, TUG1 positively regulated the expression of Runx2, through sponging miR-204-5p, and promoted osteogenic differentiation in CAVD.All together, the evidence generated by our study elucidates the role of lncRNA TUG1 as a miRNA sponge in CAVD, and sheds new light on lncRNA-directed diagnostics and therapeutics in CAVD.
|Down-regulation of LncRNA CCAT1 enhances radiosensitivity via regulating miR-148b in breast cancer.|
Lai, Y; Chen, Y; Lin, Y; Ye, L
Cell Biol Int 42 227-236 2018
LncRNA colon-cancer-associated transcript-1 (CCAT1) was proved to be a potential prognostic biomarker for breast cancer progression. However, the role of CCAT1 in regulating radiosensitivity of breast cancer and its underlying mechanism have not been investigated. The present study showed that CCAT1 was up-regulated and miR-148b was down-regulated in radioresistant breast cancer tissues compared with radiosensitive breast cancer tissues. Radiation treatment triggered a significant increase in CCAT1 and an obvious decrease in miR-148b. CCAT1 down-regulation reduced colony formation rates and caspase3 activity in breast cancer cells under irradiation. Moreover, CCAT1 could negatively regulate miR-148b expression. Furthermore, overexpression of miR-148b suppressed colony survival fraction and caspase3 expression under irradiation in breast cancer cells, which was exacerbated by CCAT1 knockdown. Taken together, this study demonstrated that CCAT1 down-regulation improved radiosensitivity of breast cancer cells via negatively regulating miR-148b expression, providing a crucial clue for lncRNA-miRNA interaction in the mechanism of radiosensitivity of breast cancer.
|High-content hydrogen water-induced downregulation of miR-136 alleviates non-alcoholic fatty liver disease by regulating Nrf2 via targeting MEG3.|
Wang, X; Wang, J
Biol Chem 399 397-406 2018
This study was aimed to investigate the potential regulatory mechanism of high-content hydrogen water (HHW) in non-alcoholic fatty liver disease (NAFLD). A high-fat diet (HFD)-induced NAFLD mice model and cellular model were prepared. The serum levels of alanine transaminase (ALT), aspartate transaminase (AST), total cholesterol (TCH) and triglycerides (TG) were measured. The expression levels of representative five microRNA (miRNAs) (miR-103, miR-488, miR-136, miR-505 and miR-148a) in liver tissues were determined by quantitative real-time PCR (qRT-PCR). The target of miR-136 was validated by RNA immunoprecipitation (RIP) and pull-down assay. MiR-136, MEG3 and nuclear factor erythroid 2-related factor 2 (Nrf2) expression levels following cell treatment were detected in hepatocytes using qRT-PCR and Western blotting. Moreover, cell viability and TG content were conducted. MiR-136 was downregulated, MEG3 as well as Nrf2 was upregulated and serum lipid level was reduced in NAFLD mice model after HHW treatment, which exerted the same effect in cellular model. RIP and RNA pull-down assay confirmed that MEG2 was a downstream target of miR-136. What's more, HHW ameliorated lipid accumulation by regulating miR-136/MEG3/Nrf2 axis in vitro and in vivo. Hence, HHW alleviated NAFLD by downregulation of miR-136 through mediating Nrf2 via targeting MEG3.
|Dual regulation of HMGB1 by combined JNK1/2-ATF2 axis with miR-200 family in nonalcoholic steatohepatitis in mice.|
Chen, X; Ling, Y; Wei, Y; Tang, J; Ren, Y; Zhang, B; Jiang, F; Li, H; Wang, R; Wen, W; Lv, G; Wu, M; Chen, L; Li, L; Wang, H
FASEB J 32 2722-2734 2018
In the context of diabetes, obesity, and metabolic syndrome, the inflammatory signaling has critical roles in the pathogenesis of nonalcoholic fatty liver disease (NAFLD), but the underlying mechanisms remain poorly delineated. Herein, early and persistently elevated, proinflammatory cytokine HMGB1 expression was detected in a high-fat diet (HFD)-induced NAFLD model in C57BL/6 mice. The expression and extracellular release of HMGB1 was rapidly and dramatically induced by saturated palmitic acid in vitro. HFD-induced inflammatory response and liver function impairment were both mitigated after the inhibition of endogenous HMGB1 by neutralizing antibody in vivo. The up-regulation of HMGB1 was thought to be modified by dual channels: in the transcriptional level, it was regulated by JNK1/JNK2-ATF2 axis; post-transcriptionally, it was regulated by the microRNA (miR)-200 family, especially miR-429. miR-429 liver conditional knockout mice (miR-429Δhep), fed either a normal diet or an HFD, showed severe liver inflammation and dysfunction, accompanied by greater expression of HMGB1. Intriguingly, the up-regulation and release of HMGB1 could in turn self-activate TLR4-JNK1/JNK2-ATF2 signaling, thus forming a positive feedback. Our findings reveal a novel mechanism by which HMGB1 expression was regulated by both the JNK1/2-ATF2 axis and the miR-200 family, which provides a potential new approach for the treatment of NAFLD.-Chen, X., Ling, Y., Wei, Y., Tang, J., Ren, Y., Zhang, B., Jiang, F., Li, H., Wang, R., Wen, W., Lv, G., Wu, M., Chen, L., Li, L., Wang, H. Dual regulation of HMGB1 by combined JNK1/2-ATF2 axis with miR-200 family in nonalcoholic steatohepatitis in mice.
|LncRNA GAS5 regulates ischemic stroke as a competing endogenous RNA for miR-137 to regulate the Notch1 signaling pathway.|
Chen, F; Zhang, L; Wang, E; Zhang, C; Li, X
Biochem Biophys Res Commun 496 184-190 2018
Ischemic stroke is related to a variety of physiological and pathological processes including autophagy and apoptosis. Growth arrest-specific 5 (GAS5), a long non-coding RNA (lncRNA), is known to negatively regulate cell survival and plays a key role in the pathogenesis of numerous diseases. However, the function and molecular mechanism of lncRNA GAS5 in ischemic stroke have not been reported. Real-time PCR was used to detect GAS5 and microRNA-137 (miR-137) expression in the brain tissues of mice underwent middle cerebral artery occlusion (MCAO) surgery and oxygen-glucose deprivation (OGD)-treated mouse primary brain neurons. Gain- or loss-of-function approaches were used to manipulate GAS5, miR-137, and Notch1. The mechanism of GAS5 in ischemic stroke was evaluated both in vivo and in vitro via bioinformatics analysis, MTT, flow cytometry, luciferase assay, RNA immunoprecipitation, and Western blot. GAS5 level was up-regulated and negatively correlated with miR-137 expression in MACO-injured brain and in OGR-stimulated primary brain neurons. GAS5 siRNA notably increased the cell viability, suppressed the activation of caspase-3 and cell apoptosis in neurons subjected to OGD. Furthermore, we also found that GAS5 functioned as a competing endogenous RNA (ceRNA) for miR-137 to regulate the de-repression of its endogenous target Notch1 and decrease neuron survival through inactivation of the Notch1 signaling pathway. Taken together, these findings indicate that GAS5 may promote the progression of ischemic stroke through acting as a ceRNA for miR-137 to mediate the Notch1 signaling pathway, which contributes to an extensive understanding of ischemic stroke and may provide novel therapeutic options for this disease.
|The long non-coding RNA ENST00000547547 reduces 5-fluorouracil resistance of colorectal cancer cells via competitive binding to microRNA-31.|
Li, J; Li, X; Cen, C; Ai, X; Lin, C; Hu, G
Oncol Rep 39 217-226 2018
Colorectal cancer (CRC) is one of the most common cancers and the third leading cause of cancer-related deaths due to its rapid progression and poor prognosis. 5-Fluorouracil (5-FU)-based chemotherapies are the standard treatment for locally advanced CRC. However, a considerable percentage of CRCs have inherent or acquired 5-FU resistance, which critically impedes clinical outcomes. In the present study, we reported that the expression level ENST00000547547 was downregulated in 5-FU-resistant CRC cells in comparison with the parental cells, While rising with the treatment of 5-FU in parental cells. Overexpression of ENST00000547547 promoted 5-FU-induced cell apoptosis and reduced the chemoresistance of 5-FU in vitro. Moreover, we found that ENST00000547547 was a target of miR-31, as confirmed by dual-luciferase reporter assay and RNA immunoprecipitation assay. Notably, miR-31 was upregulated in 5-FU-resistant CRC cells, and knockdown of miR-31 increased the chemosensitivity of 5-FU-resistant CRC cells. Furthermore, we demonstrated that ENST00000547547 reduced the chemoresistance of 5-FU via competitive binding to miR-31 in 5-FU-resistant CRC cell lines. Collectively, our findings revealed that ENST00000547547 reduced chemoresistance in 5-FU of 5-FU-resistant CRC cells through competitive binding to miR-31 and has the potential to serve as a therapeutic target in CRC patients.
|Long non-coding RNA TCONS_00041960 enhances osteogenesis and inhibits adipogenesis of rat bone marrow mesenchymal stem cell by targeting miR-204-5p and miR-125a-3p.|
Shang, G; Wang, Y; Xu, Y; Zhang, S; Sun, X; Guan, H; Zhao, X; Wang, Y; Li, Y; Zhao, G
J Cell Physiol 233 6041-6051 2018
A growing number of long non-coding RNAs (lncRNAs) have been found to be involved in diverse biological processes such as cell cycle regulation, embryonic development, and cell differentiation. However, limited knowledge is available concerning the underlying mechanisms of lncRNA functions. In this study, we found down-regulation of TCONS_00041960 during adipogenic and osteogenic differentiation of glucocorticoid-treated bone marrow mesenchymal stem cells (BMSCs). Furthermore, up-regulation of TCONS_00041960 promoted expression of osteogenic genes Runx2, osterix, and osteocalcin, and anti-adipogenic gene glucocorticoid-induced leucine zipper (GILZ). Conversely, expression of adipocyte-specific markers was decreased in the presence of over-expressed TCONS_00041960. Mechanistically, we determined that TCONS_00041960 as a competing endogenous RNA interacted with miR-204-5p and miR-125a-3p to regulate Runx2 and GILZ, respectively. Overall, we identified a new TCONS_00041960-miR-204-5p/miR-125a-3p-Runx2/GILZ axis involved in regulation of adipogenic and osteogenic differentiation of glucocorticoid-treated BMSCs.
|LncRNA myocardial infarction-associated transcript (MIAT) contributed to cardiac hypertrophy by regulating TLR4 via miR-93.|
Li, Y; Wang, J; Sun, L; Zhu, S
Eur J Pharmacol 818 508-517 2018
It has been reported that lncRNA myocardial infarction-associated transcript (MIAT) facilitated the pathological development in angiotensin II (AngII)-induced cardiac hypertrophy. Nevertheless, the underlying mechanism of MIAT involved in cardiac hypertrophy is largely unknown. In this study, AngII-treated cardiomyocytes were applied as a cardiac hypertrophy model in vitro. The expressions of MIAT and miR-93 were detected by qRT-PCR. The protein levels of toll-like receptor 4 (TLR4), atrial natriuretic factor (ANF), beta-myosin heavy chain (β-MHC), phosphoinositide-3 kinase (PI3K), protein kinase B (Akt), phosphorylated Akt (p-Akt), mammalian target of rapamycin (mTOR), and phosphorylated mTOR (p-mTOR) were determined by western blot. Luciferase reporter assay and RNA immunoprecipitation (RIP) were performed to explore the relationship between MIAT, TLR4 and miR-93. Hypertrophic response was assessed by measuring cell surface area and quantifying the expressions of ANF and β-MHC. The results demonstrated that MIAT was upregulated and miR-93 was downregulated in AngII-treated cardiomyocytes. MIAT functioned as a molecular sponge of miR-93 in cardiomyocytes. Additionally, TLR4 was identified as a target of miR-93 and MIAT promoted TLR4 expression by sponging miR-93. MIAT knockdown decreased cell surface area and the expression levels of ANF and β-MHC in AngII-treated cardiomyocytes by modulating miR-93. Moreover, enforced expression of TLR4 partially reversed the protective effect of miR-93 overexpression on AngII-induced cardiac hypertrophy. Furthermore, MIAT knockdown or miR-93 overexpression inactivated the PI3K/Akt/mTOR pathway via TLR4 in AngII-induced cardiac hypertrophy. Taken together, these data suggested that MIAT knockdown inhibited AngII-induced cardiac hypertrophy by regulating miR-93/TLR4 axis, highlighting a promising therapy target for cardiac hypertrophy.
|Long non-coding RNA ZFAS1 sponges miR-484 to promote cell proliferation and invasion in colorectal cancer.|
Xie, S; Ge, Q; Wang, X; Sun, X; Kang, Y
Cell Cycle 17 154-161 2018
The incidence and mortality rate of colorectal cancer (CRC) have been significantly increasing. However, mechanisms involved in CRC progression are still unclear. LncRNA ZFAS1 has been verified as oncogenic molecular in a series of tumors, including CRC. However, the underlying mechanism of ZFAS1 in CRC carcinogenesis remains unclear. In the present study, our data showed that ZFAS1 expression was significantly upregulated in CRC tissues and cell lines. Correlation analysis showed that high ZFAS1 expression was significantly associated with Helicobacter pylori infection, lymph nodes metastasis, advanced TNM stage and poor overall survival of CRC patients. Loss-of-function experiments revealed that ZFAS1 inhibition could markedly suppress CRC cells proliferation and invasion both in vitro and in vivo. Bioinformatics analysis and luciferase reporter assay revealed that ZFAS1 directly interacted with miR-484. Rescue experiments showed that miR-484 inhibitor reversed the tumor suppressing roles of ZFAS1 knockdown on CRC cells. Therefore, our study suggested that ZFAS1 could act as an oncogene in CRC tumorigenesis, and discovered the functional regulatory pathway of ZFAS1 sponging miR-484.
|Nkx2-2as Suppression Contributes to the Pathogenesis of Sonic Hedgehog Medulloblastoma.|
Zhang, Y; Wang, T; Wang, S; Xiong, Y; Zhang, R; Zhang, X; Zhao, J; Yang, AG; Wang, L; Jia, L
Cancer Res 78 962-973 2018
Aberrant Hedgehog signaling and excessive activation of the Gli family of transcriptional activators are key drivers of medulloblastoma (MB), the most common human pediatric brain malignancy. MB originates mainly from cerebellar granule neuron progenitors (CGNP), but the mechanisms underlying CGNP transformation remain largely obscure. In this study, we found that suppression of the noncoding RNA Nkx2-2as promoted Sonic Hedgehog (Shh)-potentiated MB development. Nkx2-2as functioned as a competing endogenous RNA against miR-103 and miR-107, sequestering them and thereby derepressing their tumor suppressive targets BTG2 and LATS1 and impeding cell division and migration. We also found that Nkx2-2as tethered miR-548m and abrogated its LATS2 targeting activity. Shh signaling impaired Nkx2-2as expression by upregulating the transcriptional repressor FoxD1. In clinical specimens of Shh-subgroup MB, we validated coordinated expression of the aforementioned proteins. Notably, exogenous expression of Nkx2-2as suppressed tumorigenesis and prolonged animal survival in MB mouse models. Our findings illuminate the role of noncoding RNAs in Hedgehog signaling and MB occurrence, with implications for identifying candidate therapeutic targets for MB treatment.Significance: These findings illuminate the role of noncoding RNAs in Hedgehog signaling and an interplay between the Hedgehog and Hippo pathways in medulloblastoma pathogenesis. Cancer Res; 78(4); 962-73. ©2017 AACR.
|RNA-Binding Protein Immunoprecipitation|
|White Paper - The Message in the Marks: Deciphering Cancer Epigenetics|
|Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit|