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

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

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":"21 1","pages":"1-11"},"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

Origin & influence of autocatalytic reaction networks at the advent of the RNA world. RNA 世界出现时自催化反应网络的起源和影响。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-10-02 DOI: 10.1080/15476286.2024.2405757

Stephen A Zorc, Raktim N Roy

{"title":"Origin & influence of autocatalytic reaction networks at the advent of the RNA world.","authors":"Stephen A Zorc, Raktim N Roy","doi":"10.1080/15476286.2024.2405757","DOIUrl":"10.1080/15476286.2024.2405757","url":null,"abstract":"Research on the origin of life investigates the transition from abiotic chemistry to the emergence of biology, with the 'RNA world hypothesis' as the leading theory. RNA's dual role in storage and catalysis suggests its importance in this narrative. The discovery of natural ribozymes emphasizes RNA's catalytic capabilities in prebiotic environments, supporting the plausibility of an RNA world and prompting exploration of precellular evolution. Collective autocatalytic sets (CASs) mark a crucial milestone in this transition, fostering complexity through autocatalysis. While modern biology emphasizes sequence-specific polymerases, remnants of CASs persist in primary metabolism highlighting their significance. Autocatalysis, driven by CASs, promotes complexity through mutually interdependent catalytic sets. Yet, the transition from ribonucleotides to complex RNA oligomers remains puzzling. Questions persist about the genesis of the first self-replicating RNA molecule, RNA's stability in prebiotic conditions, and the shift to complex molecular reproduction. This review delves into diverse facets of the RNA world's emergence, addressing critical bottlenecks and scientific advances. Integrating insights from simulation and in vitro evolution research, we illuminate the multistep biogenesis of catalytic RNA from the abiotic world. Through this exploration, we aim to elucidate the journey from the primordial soup to the dawn of life, emphasizing the interplay between chemistry and biology in understanding life's origins.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"21 1","pages":"78-92"},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11451275/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142366418","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

Both host and parasite non-coding RNAs co-ordinate the regulation of macrophage gene expression to reduce pro-inflammatory immune responses and promote tissue repair pathways during infection with fasciola hepatica. 在感染法氏肝包虫期间，宿主和寄生虫的非编码 RNA 可协调调节巨噬细胞基因的表达，以减少促炎免疫反应并促进组织修复途径。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-09-30 DOI: 10.1080/15476286.2024.2408706

Dayna Sais, Sumaiya Chowdhury, John P Dalton, Nham Tran, Sheila Donnelly

{"title":"Both host and parasite non-coding RNAs co-ordinate the regulation of macrophage gene expression to reduce pro-inflammatory immune responses and promote tissue repair pathways during infection with fasciola hepatica.","authors":"Dayna Sais, Sumaiya Chowdhury, John P Dalton, Nham Tran, Sheila Donnelly","doi":"10.1080/15476286.2024.2408706","DOIUrl":"10.1080/15476286.2024.2408706","url":null,"abstract":"Parasitic worms (helminths) establish chronic infection within mammalian hosts by strategically regulating their host's immune responses. Deciphering the mechanisms by which host non-coding RNAs (ncRNA) co-ordinate the activation and regulation of immune cells is essential to understanding host immunity and immune-related pathology. It is also important to comprehend how pathogens secrete specific ncRNAs to manipulate gene expression of host immune cells and influence their response to infection. To investigate the contribution of both host and helminth derived ncRNAs to the activation and/or regulation of innate immune responses during a parasite infection, we examined ncRNA expression in the peritoneal macrophages from mice infected with Fasciola hepatica. We discovered the presence of several parasitic-derived miRNAs within host macrophages at 6 hrs and 18 hrs post infection. Target prediction analysis showed that these Fasciola miRNAs regulate host genes associated with the activation of host pro-inflammatory macrophages. Concomitantly, there was a distinct shift in host ncRNA expression, which was significant at 5 days post-infection. Prediction analysis suggested that these host ncRNAs target a different cohort of host genes compared to the parasite miRNAs, although the functional outcome was predicted to be similar i.e. reduced pro-inflammatory response and the promotion of a reparative/tolerant phenotype. Taken together, these observations uncover the interplay between host and parasitic ncRNAs and reveal a complementary regulation of the immune response that allows the parasite to evade immune detection and promote tissue repair for the host. These findings will provide a new understanding of the molecular interaction between parasites and host.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"21 1","pages":"62-77"},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11445894/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142353015","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

Identification and functional characterization of lncRNAs involved in human monocyte-to-macrophage differentiation. 参与人类单核细胞向巨噬细胞分化的 lncRNAs 的鉴定和功能表征。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-10-21 DOI: 10.1080/15476286.2024.2417155

Christy Montano, Sergio Covarrubias, Eric Malekos, Sol Katzman, Susan Carpenter

{"title":"Identification and functional characterization of lncRNAs involved in human monocyte-to-macrophage differentiation.","authors":"Christy Montano, Sergio Covarrubias, Eric Malekos, Sol Katzman, Susan Carpenter","doi":"10.1080/15476286.2024.2417155","DOIUrl":"10.1080/15476286.2024.2417155","url":null,"abstract":"Although long noncoding RNAs (lncRNAs) constitute the majority of the human transcriptome, the functional roles of most remain elusive. While protein-coding genes in macrophage biology have been extensively studied, the contribution of lncRNAs in this context is poorly understood. Given the vast number of lncRNAs (>20,000), identifying candidates for functional characterization poses a significant challenge. Here, we present two complementary approaches to pinpoint and investigate lncRNAs involved in monocyte-to-macrophage differentiation: RNA-seq for functional inference and a high-throughput functional screen. These strategies enabled us to identify four lncRNA regulators of monocyte differentiation: lincRNA-JADE1, lincRNA-ANXA3, GATA2-AS1, and PPP2R5C-AS1. Preliminary insights suggest these lncRNAs may act in cis through neighbouring protein-coding genes, although their precise mechanisms remain to be elucidated. We further discuss the strengths and weaknesses of these methodologies, along with validation pipelines crucial for establishing lncRNA functionality.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"21 1","pages":"39-51"},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11497951/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142473693","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

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

A high-throughput search for intracellular factors that affect RNA folding identifies E. coli proteins PepA and YagL as RNA chaperones that promote RNA remodelling. 通过高通量搜索影响 RNA 折叠的细胞内因子，发现大肠杆菌蛋白 PepA 和 YagL 是促进 RNA 重塑的 RNA 合子。

IF 3.6 3区生物学

RNA Biology Pub Date : 2024-01-01 Epub Date: 2024-11-22 DOI: 10.1080/15476286.2024.2429956

Alejandra Matsuri Rojano-Nisimura, Lucas G Miller, Aparna Anantharaman, Aaron T Middleton, Elroi Kibret, Sung H Jung, Rick Russell, Lydia M Contreras

{"title":"A high-throughput search for intracellular factors that affect RNA folding identifies E. coli proteins PepA and YagL as RNA chaperones that promote RNA remodelling.","authors":"Alejandra Matsuri Rojano-Nisimura, Lucas G Miller, Aparna Anantharaman, Aaron T Middleton, Elroi Kibret, Sung H Jung, Rick Russell, Lydia M Contreras","doi":"10.1080/15476286.2024.2429956","DOIUrl":"10.1080/15476286.2024.2429956","url":null,"abstract":"General RNA chaperones are RNA-binding proteins (RBPs) that interact transiently and non-specifically with RNA substrates and assist in their folding into their native state. In bacteria, these chaperones impact both coding and non-coding RNAs and are particularly important for large, structured RNAs which are prone to becoming kinetically trapped in misfolded states. Currently, due to the limited number of well-characterized examples and the lack of a consensus structural or sequence motif, it is difficult to identify general RNA chaperones in bacteria. Here, we adapted a previously published in vivo RNA regional accessibility probing assay to screen genome wide for intracellular factors in E. coli affecting RNA folding, among which we aimed to uncover novel RNA chaperones. Through this method, we identified eight proteins whose deletion gives changes in regional accessibility within the exogenously expressed Tetrahymena group I intron ribozyme. Furthermore, we purified and measured in vitro properties of two of these proteins, YagL and PepA, which were especially attractive as general chaperone candidates. We showed that both proteins bind RNA and that YagL accelerates native refolding of the ribozyme from a long-lived misfolded state. Further dissection of YagL showed that a putative helix-turn-helix (HTH) domain is responsible for most of its RNA-binding activity, but only the full protein shows chaperone activity. Altogether, this work expands the current repertoire of known general RNA chaperones in bacteria.","PeriodicalId":21351,"journal":{"name":"RNA Biology","volume":"21 1","pages":"13-30"},"PeriodicalIF":3.6,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11587861/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142688565","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

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":"21 1","pages":"1-15"},"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