RNA Biology最新文献_第2页

Recent progress in miRNA biogenesis and decay. miRNA生物发生与衰变研究进展。

IF 4.1 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2023-11-29 DOI: 10.1080/15476286.2023.2288741

Xavier Bofill-De Ros, Ulf Andersson Vang Ørom

引用次数: 0

CCAR-1 works together with the U2AF large subunit UAF-1 to regulate alternative splicing. CCAR-1 与 U2AF 大亚基 UAF-1 共同调节替代剪接。

IF 4.1 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2023-12-21 DOI: 10.1080/15476286.2023.2289707

Doreen I Lugano, Lindsey N Barrett, Dale Chaput, Margaret A Park, Sandy D Westerheide

{"title":"CCAR-1 works together with the U2AF large subunit UAF-1 to regulate alternative splicing.","authors":"Doreen I Lugano, Lindsey N Barrett, Dale Chaput, Margaret A Park, Sandy D Westerheide","doi":"10.1080/15476286.2023.2289707","DOIUrl":"10.1080/15476286.2023.2289707","url":null,"abstract":"The Cell Division Cycle and Apoptosis Regulator (CCAR) protein family members have recently emerged as regulators of alternative splicing and transcription, as well as having other key physiological functions. For example, mammalian CCAR2/DBC1 forms a complex with the zinc factor protein ZNF326 to integrate alternative splicing with RNA polymerase II transcriptional elongation in AT-rich regions of the DNA. Additionally, Caenorhabditis elegans CCAR-1, a homolog to mammalian CCAR2, facilitates the alternative splicing of the perlecan unc-52 gene. However, much about the CCAR family's role in alternative splicing is unknown. Here, we have examined the role of CCAR-1 in genome-wide alternative splicing in Caenorhabditis elegans and have identified new alternative splicing targets of CCAR-1 using RNA sequencing. Also, we found that CCAR-1 interacts with the spliceosome factors UAF-1 and UAF-2 using mass spectrometry, and that knockdown of ccar-1 affects alternative splicing patterns, motility, and proteostasis of UAF-1 mutant worms. Collectively, we demonstrate the role of CCAR-1 in regulating global alternative splicing in C. elegans and in conjunction with UAF-1.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10761121/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138831335","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Extracellular RNA in oncogenesis, metastasis and drug resistance. 肿瘤发生、转移和耐药性中的细胞外 RNA。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-08-06 DOI: 10.1080/15476286.2024.2385607

Hannah Nelson, Sherman Qu, Jeffrey L Franklin, Qi Liu, Heather H Pua, Kasey C Vickers, Alissa M Weaver, Robert J Coffey, James G Patton

引用次数: 0

Gas-sensing riboceptors. 气体感应核素受体

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-07-17 DOI: 10.1080/15476286.2024.2379607

Savani Anbalagan

引用次数: 0

Structures and functions of short argonautes. 短吻鳄的结构和功能。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-09-01 DOI: 10.1080/15476286.2024.2380948

Chen Wang, Zhangfei Shen, Xiao-Yuan Yang, Tian-Min Fu

引用次数: 0

Mature microRNA-binding protein QKI promotes microRNA-mediated gene silencing. 成熟的 microRNA 结合蛋白 QKI 可促进 microRNA 介导的基因沉默。

IF 4.1 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-02-19 DOI: 10.1080/15476286.2024.2314846

Kyung-Won Min, Myung Hyun Jo, Minseok Song, Ji Won Lee, Min Ji Shim, Kyungmin Kim, Hyun Bong Park, Shinwon Ha, Hyejin Mun, Ahsan Polash, Markus Hafner, Jung-Hyun Cho, Dongsan Kim, Ji-Hoon Jeong, Seungbeom Ko, Sungchul Hohng, Sung-Ung Kang, Je-Hyun Yoon

{"title":"Mature microRNA-binding protein QKI promotes microRNA-mediated gene silencing.","authors":"Kyung-Won Min, Myung Hyun Jo, Minseok Song, Ji Won Lee, Min Ji Shim, Kyungmin Kim, Hyun Bong Park, Shinwon Ha, Hyejin Mun, Ahsan Polash, Markus Hafner, Jung-Hyun Cho, Dongsan Kim, Ji-Hoon Jeong, Seungbeom Ko, Sungchul Hohng, Sung-Ung Kang, Je-Hyun Yoon","doi":"10.1080/15476286.2024.2314846","DOIUrl":"10.1080/15476286.2024.2314846","url":null,"abstract":"Although Argonaute (AGO) proteins have been the focus of microRNA (miRNA) studies, we observed AGO-free mature miRNAs directly interacting with RNA-binding proteins, implying the sophisticated nature of fine-tuning gene regulation by miRNAs. To investigate microRNA-binding proteins (miRBPs) globally, we analyzed PAR-CLIP data sets to identify RBP quaking (QKI) as a novel miRBP for let-7b. Potential existence of AGO-free miRNAs were further verified by measuring miRNA levels in genetically engineered AGO-depleted human and mouse cells. We have shown that QKI regulates miRNA-mediated gene silencing at multiple steps, and collectively serves as an auxiliary factor empowering AGO2/let-7b-mediated gene silencing. Depletion of QKI decreases interaction of AGO2 with let-7b and target mRNA, consequently controlling target mRNA decay. This finding indicates that QKI is a complementary factor in miRNA-mediated mRNA decay. QKI, however, also suppresses the dissociation of let-7b from AGO2, and slows the assembly of AGO2/miRNA/target mRNA complexes at the single-molecule level. We also revealed that QKI overexpression suppresses cMYC expression at post-transcriptional level, and decreases proliferation and migration of HeLa cells, demonstrating that QKI is a tumour suppressor gene by in part augmenting let-7b activity. Our data show that QKI is a new type of RBP implicated in the versatile regulation of miRNA-mediated gene silencing.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10878027/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139900373","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Single-cell analysis of the epitranscriptome: RNA modifications under the microscope. 表转录组的单细胞分析：显微镜下的 RNA 修饰。

IF 4.1 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-02-18 DOI: 10.1080/15476286.2024.2315385

Eva Crespo-García, Alberto Bueno-Costa, Manel Esteller

引用次数: 0

Expression of RNautophagy/DNautophagy-related genes is regulated under control of an innate immune receptor. RNautophagy/DNautophagy 相关基因的表达受先天性免疫受体的调控。

IF 4.1 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-01-10 DOI: 10.1080/15476286.2023.2291610

Yuuki Fujiwara, Kazuki Oroku, Yinping Zhou, Masayuki Takahashi, Taiichi Katayama, Keiji Wada, Nobuyuki Tsutsumi, Tetsuo Sato, Tomohiro Kabuta

{"title":"Expression of RNautophagy/DNautophagy-related genes is regulated under control of an innate immune receptor.","authors":"Yuuki Fujiwara, Kazuki Oroku, Yinping Zhou, Masayuki Takahashi, Taiichi Katayama, Keiji Wada, Nobuyuki Tsutsumi, Tetsuo Sato, Tomohiro Kabuta","doi":"10.1080/15476286.2023.2291610","DOIUrl":"10.1080/15476286.2023.2291610","url":null,"abstract":"Double-stranded RNA (dsRNA) is a molecular pattern uniquely produced in cells infected with various viruses as a product or byproduct of replication. Cells detect such molecules, which indicate non-self invasion, and induce diverse immune responses to eliminate them. The degradation of virus-derived molecules can also play a role in the removal of pathogens and suppression of their replication. RNautophagy and DNautophagy are cellular degradative pathways in which RNA and DNA are directly imported into a hydrolytic organelle, the lysosome. Two lysosomal membrane proteins, SIDT2 and LAMP2C, mediate nucleic acid uptake via this pathway. Here, we showed that the expression of both SIDT2 and LAMP2C is selectively upregulated during the intracellular detection of poly(I:C), a synthetic analog of dsRNA that mimics viral infection. The upregulation of these two gene products upon poly(I:C) introduction was transient and synchronized. We also observed that the induction of SIDT2 and LAMP2C expression by poly(I:C) was dependent on MDA5, a cytoplasmic innate immune receptor that directly recognizes poly(I:C) and induces various antiviral responses. Finally, we showed that lysosomes can target viral RNA for degradation via RNautophagy and may suppress viral replication. Our results revealed a novel degradative pathway in cells as a downstream component of the innate immune response and provided evidence suggesting that the degradation of viral nucleic acids via RNautophagy/DNautophagy contributes to the suppression of viral replication.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10793664/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139417980","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The nexus of long noncoding RNAs, splicing factors, alternative splicing and their modulations. 长链非编码rna，剪接因子，选择性剪接及其调节的联系。

IF 4.1 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2023-11-28 DOI: 10.1080/15476286.2023.2286099

Pushkar Malakar, Sudhanshu Shukla, Meghna Mondal, Rajesh Kumar Kar, Jawed Akhtar Siddiqui

引用次数: 0

Rapid and scalable detection of synthetic mRNA byproducts using polynucleotide phosphorylase and polythymidine oligonucleotides. 使用多核苷酸磷酸化酶和多胸苷寡核苷酸快速、可扩展地检测合成 mRNA 副产品。

IF 4.1 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-06-05 DOI: 10.1080/15476286.2024.2363029

Francis Combes, Thanh-Huong Bui, Frida J Pettersson, Sjoerd Hak

{"title":"Rapid and scalable detection of synthetic mRNA byproducts using polynucleotide phosphorylase and polythymidine oligonucleotides.","authors":"Francis Combes, Thanh-Huong Bui, Frida J Pettersson, Sjoerd Hak","doi":"10.1080/15476286.2024.2363029","DOIUrl":"10.1080/15476286.2024.2363029","url":null,"abstract":"Production and storage of synthetic mRNA can introduce a variety of byproducts which reduce the overall integrity and functionality of mRNA vaccines and therapeutics. mRNA integrity is therefore designated as a critical quality attribute which must be evaluated with state-of-the-art analytical methods before clinical use. The current study first demonstrates the effect of heat degradation on transcript translatability and then describes a novel enzymatic approach to assess the integrity of conventional mRNA and long self-amplifying mRNA. By first hybridizing oligo-T to the poly(A) tail of intact mRNA and subsequently digesting the unhybridized RNA fragments with a 3'-5' exoribonuclease, individual nucleotides can be selectively released from RNA fragments. The adenosine-based fraction of these nucleotides can then be converted into ATP and detected by luminescence as a sensitive indicator of mRNA byproducts. We developed a polynucleotide phosphorylase (PNPase)-based assay that offers fast and sensitive evaluation of mRNA integrity, regardless of its length, thus presenting a novel and fully scalable alternative to chromatographic-, electrophoresis-, or sequencing-based techniques.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":null,"pages":null},"PeriodicalIF":4.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11155706/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141248427","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0