2021年表观遗传学技术资讯——第一期 RIP技术及最新成果_

2021年表观遗传学技术资讯——第一期 RIP技术及最新成果

发布时间：2021-01-12| BY ：伯信官网

2021年，新年新开始。伯信生物聚焦行业资讯，本期给大家带来表观遗传学研究中使用RIP技术的最新研究成果；本期从PubMed中检索收集最新发布的使用RIP技术的文献共计39篇，下面我们一起来看看，最近的研究中哪些技术路线选用了RIP技术以及对结果分析起到什么样的作用。检索式：(rip[Title/Abstract]) OR (RNA immunoprecipitation[Title/Abstract])

1、环状RNA circDLC1通过与HuR相互作用抑制MMP1介导的肝癌发展

标题：Circular RNA circDLC1 inhibits MMP1-mediated liver cancer progression via interaction with HuR

杂志：Theranostics

影响因子：8.579

通讯作者：曾勇，袁克非，黄继伟（四川大学华西医院生物治疗国家重点实验室）

环状RNA（circRNA）已被证明在癌症发展中起关键作用。最近有报道说，KIAA1429是m6A甲基转移酶复合物的关键成分，可通过调节m6A甲基化来促进肝细胞癌（HCC）的发展。在这里研究者报道了环状RNA在KIAA1429介导的HCC发展中的作用。研究者发现，circDLC1在肝癌组织中下调，与良好的预后密切相关。进一步的研究表明，circDLC1的过表达在体外和体内抑制肝癌细胞的增殖和运动，而circDLC1的沉默发挥相反的作用。此外，机理研究表明，circDLC1可以与RNA结合蛋白HuR结合，从而减少HuR与MMP1 mRNA之间的相互作用，从而抑制MMP1的表达，最终有助于抑制HCC发展。研究者证明了KIAA1429的下游靶标circDLC1是HCC患者有希望的预后标志物，而circDLC1-HuR-MMP1可作为HCC治疗的潜在治疗靶标。

文中运用RIP分析和生物素标记RNA下拉分析用于研究circDLC1的下游效应器；

2、使用纳米孔直接RNA测序技术在毛果杨的茎分化木质部中以单碱基分辨率定量分析N 6-甲基腺苷

标题：Quantitative profiling of N6-methyladenosine at single-base resolution in stem-differentiating xylem of Populustrichocarpa using Nanopore direct RNA sequencing

杂志： Genome Biol

.影响因子：10.806

通讯作者：顾连峰（福建农林大学林学院基础林学与蛋白质组学研究中心）

对于每一个转录本，目前尚没有综合的方法以单碱基分辨率鉴定N6-甲基腺苷（m6A），这对于估计m6A丰度是必需的。研究者使用基于XGBoost模型的Nanopore直接RNA测序技术，开发了一种名为Nanom6A的新管线，用于鉴定和定量单碱基分辨率的m 6 A修饰。研究者使用甲基化的RNA免疫沉淀测序（MeRIP-Seq）和m6A敏感的RNA-核糖核酸内切酶促进测序（m6A-REF-seq）验证了我们的方法，证实了其准确性。使用此方法，研究者提供了在茎分化木质部中m6A修饰的转录组范围内的定量分析，并揭示了不同的替代聚腺苷酸化（APA）用法显示了不同的m6A比值

文中使用MeRIP-Seq和m6验证Nanom6A参考序列

3、在神经退行性变过程中使用环状rna标记的研究表明，视网膜是大脑功能障碍的窗口

标题：Retina as a window to cerebral dysfunction following studies with circRNA signature during neurodegeneration

杂志： Theranostics

影响因子：8.579

通讯作者：biao.yan （复旦大学）

缺血性中风是中枢神经系统中由缺血引起的神经退行性疾病。如今，中风诊断仍基于临床标准和根据组织病变发生情况的影像数据。在这一点上，疾病已经发展到晚期或晚期。中风的治疗主要是通过阻塞动脉的早期再灌注或者是机械再通。但是，疗效受到狭窄的时间范围，出血风险和其他因素的限制。缺血性中风还伴有视力障碍和丧失。通常，视网膜被认为是大脑的延伸。视网膜和大脑可能共享相同的调节器，并具有类似的神经退行性变化。此外，眼部症状有时先于中风症状。因此，视网膜的可及性和组织性使其成为卒中研究的方便且非侵入性的工具。

circRNAs已显示出巨大的潜力，可作为疾病诊断和预后的生物标志物和靶标。circRNA在中风中的作用已得到公认。circDLGAP4可通过调节内皮-间质转化改善缺血性卒中的结果。circTLK1可通过miR-335-3p / TIPARP加剧缺血性中风后的神经元损伤和神经功能缺损。circRNA在视网膜疾病中的作用也已得到认可。circZNF609通过充当miR-615海绵来调节视网膜神经变性。circZRANB1是治疗视网膜神经变性的有前途的靶标。然而，尚不清楚大脑神经变性和视网膜神经变性是否受普通circRNA调控。研究者使用了两种不同的模型，即缺血性中风和缺血性视网膜病，来研究circRNA在神经变性中的表达谱和功能意义。研究者还确定了视网膜和大脑是否共享共同的circRNA调节剂和共同的circRNA疾病标记。

文中运用RIP技术来确定circRNA在神经退行性变中的调节机制。

序号	标题	杂志	影响因子
1	Qki is an essential regulator of microglial phagocytosis in demyelination.	J Exp Med	11.743
2	RNA-Binding Protein Immunoprecipitation and High-Throughput Sequencing.	Methods Mol Biol	0
3	Hsa_circ_001988 attenuates GC progression in vitro and in vivo via sponging miR-197-3p.	J Cell Physiol	5.546
4	Long Noncoding RNA SNHG16 Facilitates Abdominal Aortic Aneurysm Progression through the miR-106b-5p/STAT3 Feedback Loop.	J Atheroscler Thromb	3.876
5	LncRNA miR503HG inhibits epithelial-mesenchymal transition and angiogenesis in hepatocellular carcinoma by enhancing PDCD4 via regulation of miR-15b.	Dig Liver Dis	3.57
6	Long non-coding RNA XIST regulates chondrogenic differentiation of synovium-derived mesenchymal stem cells from temporomandibular joint via miR-27b-3p/ADAMTS-5 axis.	Cytokine	2.952
7	LINC00565 promotes the progression of colorectal cancer by upregulating EZH2.	Oncol Lett	2.311
8	Long non-coding RNA 01126 promotes periodontitis pathogenesis of human periodontal ligament cells via miR-518a-5p/HIF-1alpha/MAPK pathway.	Cell Prolif	5.753
9	Circular RNA circDLC1 inhibits MMP1-mediated liver cancer progression via interaction with HuR.	Theranostics	8.579
10	Long non-coding maternally expressed gene 3 regulates cigarette smoke extract-induced apoptosis, inflammation and cytotoxicity by sponging miR-181a-2-3p in 16HBE cells.	Oncol Lett	2.311
11	Hsa_circ_0006872 promotes cigarette smoke-induced apoptosis, inflammation and oxidative stress in HPMECs and BEAS-2B cells through the miR-145-5p/NF-κB axis.	Biochem Biophys Res Commun	2.985
12	Amniotic fluid mesenchymal stem cells repair mouse corneal cold injury by promoting mRNA N4-acetylcytidine modification and ETV4/JUN/CCND2 signal axis activation.	Hum Cell	3.463
13	A novel long intergenic non-coding RNA, Nostrill, regulates iNOS gene transcription and neurotoxicity in microglia.	J Neuroinflammation	5.793
14	Involvement of circHIPK3 in the pathogenesis of diabetic cardiomyopathy in mice.	Diabetologia	7.518
15	MiR-23b-3p promotes postmenopausal osteoporosis by targeting MRC2 and regulating the Wnt/β-catenin signaling pathway.	J Pharmacol Sci	2.835
16	Overexpression of long non-coding RNA00355 enhances proliferation, chemotaxis, and metastasis in colon cancer via promoting GTF2B-mediated ITGA2.	Transl Oncol	3.558
17	Lidocaine inhibits glioma cell proliferation, migration and invasion by modulating the circEZH2/miR-181b-5p pathway.	Neuroreport	1.394
18	MiR-30a suppresses clear cell renal cell carcinoma proliferation and metastasis by targeting LRP6.	Hum Cell	3.463
19	Oscillating lncRNA Platr4 regulates NLRP3 inflammasome to ameliorate nonalcoholic steatohepatitis in mice.	Theranostics	8.579
20	CircNOL10 suppresses breast cancer progression by sponging miR-767-5p to regulate SOCS2/JAK/STAT signaling.	J Biomed Sci	5.762
21	Methods for the Study of Long Noncoding RNA in Cancer Cell Signaling.	Methods Mol Biol	0
22	Hypermethylation-mediated downregulation of lncRNA PVT1 promotes granulosa cell apoptosis in premature ovarian insufficiency via interacting with Foxo3a.	J Cell Physiol	5.546
23	LINC01255 combined with BMI1 to regulate human mesenchymal stromal senescence and acute myeloid leukemia cell proliferation through repressing transcription of MCP-1.	Clin Transl Oncol	2.737
24	CircRNA DNA methyltransferase 1 silence inhibits breast cancer development by regulating micoRNA-485-3p/zinc finger E-box binding homeobox 1 axis.	J Obstet Gynaecol Res	1.392
25	Dynamic regulation of CTCF stability and sub-nuclear localization in response to stress.	PLoS Genet	5.174
26	CircRNA PIP5K1A promotes the progression of glioma through upregulation of the TCF12/PI3K/AKT pathway by sponging miR-515-5p.	Cancer Cell Int	4.175
27	CircWHSC1 serves as an oncogene to promote hepatocellular carcinoma progression.	Eur J Clin Invest	3.481
28	LncRNA H19 suppresses pyroptosis of cardiomyocytes to attenuate myocardial infarction in a PBX3/CYP1B1-dependent manner.	Mol Cell Biochem	2.795
29	Extracellular vesicles derived from hypoxic glioma stem-like cells confer temozolomide resistance on glioblastoma by delivering miR-30b-3p.	Theranostics	8.579
30	Protective Effect of miR-193a-5p and miR-320-5p on Caerulein-Induced Injury in AR42J Cells.	Dig Dis Sci	2.751
31	A chromatin-associated splicing isoform of OIP5-AS1 acts in cis to regulate the OIP5 oncogene.	RNA Biol	5.35
32	LncRNA PCAT6 regulates the progression of pituitary adenomas by regulating the miR-139-3p/BRD4 axis.	Cancer Cell Int	4.175
33	circ_0044516 functions in the progression of gastric cancer by modulating MicroRNA-149-5p/HuR axis.	Mol Cell Biochem	2.795
34	Circ-LDLRAD3 Enhances Cell Growth, Migration, and Invasion and Inhibits Apoptosis by Regulating MiR-224-5p/NRP2 Axis in Gastric Cancer.	Dig Dis Sci	2.751
35	CircNEIL3 promotes cervical cancer cell proliferation by adsorbing miR-137 and upregulating KLF12.	Cancer Cell Int	4.175
36	Knockdown of RMST Impedes Neuronal Apoptosis and Oxidative Stress in OGD/R-Induced Ischemic Stroke Via Depending on the miR-377/SEMA3A Signal Network.	Neurochem Res	3.038
37	LINC00665 enhances tumorigenicity of endometrial carcinoma by interacting with high mobility group AT-hook 1.	Cancer Cell Int	4.175
38	Quantitative profiling of N(6)-methyladenosine at single-base resolution in stem-differentiating xylem of Populus trichocarpa using Nanopore direct RNA sequencing.	Genome Biol	10.806
39	Exosomal LINC00161 promotes angiogenesis and metastasis via regulating miR-590-3p/ROCK axis in hepatocellular carcinoma.	Cancer Gene Ther	4.534

另外1月7-9日在广州中山大学举办的第二届全国核糖核酸（RNA）青年学术会议上，国内RNA领域多位资深专家学者给大家带来了RNA研究领域的最新研究，其中多项前沿研究中均运用到RIP技术，感兴趣的小伙伴可以多了解一下该项技术的魅力及功能！