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Janvier A, Hayek H, Alghoul F, Gross L, Allmang C, Martin F, Eriani G. Purification of In Vivo or In Vitro-Assembled RNA-Protein Complexes by RNA Centric Methods. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:17-29. [PMID: 38507197 DOI: 10.1007/978-3-031-52193-5_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Throughout their entire life cycle, RNAs are associated with RNA-binding proteins (RBPs), forming ribonucleoprotein (RNP) complexes with highly dynamic compositions and very diverse functions in RNA metabolism, including splicing, translational regulation, ribosome assembly. Many RNPs remain poorly characterized due to the challenges inherent in their purification and subsequent biochemical characterization. Therefore, developing methods to isolate specific RNA-protein complexes is an important initial step toward understanding their function. Many elegant methodologies have been developed to isolate RNPs. This chapter describes different approaches and methods devised for RNA-specific purification of a target RNP. We focused on general methods for selecting RNPs that target a given RNA under conditions favourable for the copurification of associated factors including RNAs and protein components of the RNP.
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Affiliation(s)
- Aurélie Janvier
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Hassan Hayek
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Fatima Alghoul
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Lauriane Gross
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Christine Allmang
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Franck Martin
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Gilbert Eriani
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France.
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Wang X, Liu Y, Zhou M, Yu L, Si Z. m6A modified BACE1-AS contributes to liver metastasis and stemness-like properties in colorectal cancer through TUFT1 dependent activation of Wnt signaling. J Exp Clin Cancer Res 2023; 42:306. [PMID: 37986103 PMCID: PMC10661562 DOI: 10.1186/s13046-023-02881-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/01/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Liver metastasis is one of the most important reasons for high mortality of colorectal cancer (CRC). Growing evidence illustrates that lncRNAs play a critical role in CRC liver metastasis. Here we described a novel function and mechanisms of BACE1-AS promoting CRC liver metastasis. METHODS qRT-PCR and in situ hybridization were performed to examine the BACE1-AS level in CRC. IGF2BP2 binding to m6A motifs in BACE1-AS was determined by RIP assay and S1m-tagged immunoprecipitation. Transwell assay and liver metastasis mice model experiments were performed to examine the metastasis capabilities of BACE1-AS knockout cells. Stemness-like properties was examined by tumor sphere assay and the expression of stemness biomarkers. Microarray data were acquired to analyze the signaling pathways involved in BACE1-AS promoting CRC metastasis. RESULTS BACE1-AS is the most up-regulated in metastatic CRC associated with unfavorable prognosis. Sequence blast revealed two m6A motifs in BACE1-AS. IGF2BP2 binding to these two m6A motifs is required for BACE1-AS boost in metastatic CRC. m6A modified BACE1-AS drives CRC cells migration and invasion and liver metastasis both in vitro and in vivo. Moreover, BACE1-AS maintains the stemness-like properties of CRC cells. Mechanically, BACE1-AS promoted TUFT1 expression by ceRNA network through miR-214-3p. CRC patients with such ceRNA network suffer poorer prognosis than ceRNA-negative patients. Depletion of TUFT1 mimics BACE1-AS loss. BACE1-AS activated Wnt signaling pathway in a TUFT1 dependent manner. BACE1-AS/miR-214-3p/TUFT1/Wnt signaling regulatory axis is essential for CRC liver metastasis. Pharmacologic inhibition of Wnt signaling pathway repressed liver metastasis and stemness-like features in BACE1-AS over-expressed CRC cells. CONCLUSION Our study demonstrated BACE1-AS as a novel target of IGF2BP2 through m6A modification. m6A modified BACE1-AS promotes CRC liver metastasis through TUFT1 dependent activation of Wnt signaling pathway. Thus, targeting BACE1-AS and its downstream Wnt signaling pathways may provide a new opportunity for metastatic CRC intervention and treatment.
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Affiliation(s)
- Xidi Wang
- Central Laboratory of the Medical Research Center, The First Affiliated Hospital of Ningbo University, 247 Renmin Road, Jiangbei District, Ningbo, 315020, P. R. China.
- Health Science Center, Ningbo University, 818 Fenghua Road, Jiangbei District, Ningbo, 315211, P. R. China.
| | - Yu Liu
- Health Science Center, Ningbo University, 818 Fenghua Road, Jiangbei District, Ningbo, 315211, P. R. China
| | - Miao Zhou
- Central Laboratory of the Medical Research Center, The First Affiliated Hospital of Ningbo University, 247 Renmin Road, Jiangbei District, Ningbo, 315020, P. R. China
| | - Lei Yu
- Department of Colorectal Cancer Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, P. R. China
| | - Zizhen Si
- Health Science Center, Ningbo University, 818 Fenghua Road, Jiangbei District, Ningbo, 315211, P. R. China.
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Kositanont U, Srisawat C, Sripinitchai S, Thawornkuno C, Chaibun T, Karunaithas S, Promptmas C, Lertanantawong B. Electrochemical aptasensor detection of electron transfer flavoprotein subunit beta for leptospirosis diagnosis. Analyst 2023; 148:4777-4786. [PMID: 37599631 DOI: 10.1039/d3an01064c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Electron transfer flavoprotein subunit beta (ETFB) of Leptospira interrogans is a biomarker for diagnosing leptospiral infection. Thus, the ETFB-specific nuclease-resistant RNA aptamer ETFB3-63 was developed and used in an electrochemical aptasensor to assay ETFB. Although the majority of reported biosensors detect various genes and antibodies of L. interrogans, this is the first attempt to construct an electrochemical biosensor to detect ETFB protein for the diagnosis of leptospiral infection. The ETFB protein can be detected without any extraction phase. In this assay, a single-stranded DNA probe complementary to the ETFB3-63 sequence was immobilized on a screen-printed carbon electrode (SPCE). The aptamer was then incubated and hybridized with the antisense probe on the SPCE. In the presence of ETFB, the aptamer dissociates from the aptamer/probe complex on the SPCE to bind with the protein. Methylene blue was then added to intercalate with the remaining hybridized aptamers, and its signal was measured using differential pulse voltammetry. The signal arising from the intercalated methylene blue decreased with increasing concentration of ETFB, showing a linear response in the range of 50-500 nM of ETFB and 10 to 109 leptospira cells per mL, respectively. The aptasensor signal was also specific to L. interrogans but not to 12 related bacteria tested. In addition, the aptasensor showed similar performance in detecting ETFB spiked in human serum to that in buffer, indicating that proteins in the serum do not interfere with the assay. Therefore, this assay has great potential to develop into a point-of-care electrochemical device that is accurate, cost-effective, and user-friendly for leptospirosis diagnosis.
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Affiliation(s)
- Uraiwan Kositanont
- Faculty of Public Health, Thammasat University, Pahol Yothin Rd., Klong Luang, Pathum Thani 12121, Thailand
| | - Chatchawan Srisawat
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Wang Lang Rd., Bangkok Noi, Bangkok 10700, Thailand
| | - Sirinapa Sripinitchai
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Wang Lang Rd., Bangkok Noi, Bangkok 10700, Thailand
| | - Charin Thawornkuno
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Ratchawithi Road, Ratchathewi, Bangkok 10400, Thailand
| | - Thanyarat Chaibun
- Biosensors Laboratory, Department of Biomedical Engineering, Faculty of Engineering, Mahidol University, Phutthamonthon 4 Road, Salaya, Nakhon Pathom 73170, Thailand.
| | - Sinthu Karunaithas
- Biosensors Laboratory, Department of Biomedical Engineering, Faculty of Engineering, Mahidol University, Phutthamonthon 4 Road, Salaya, Nakhon Pathom 73170, Thailand.
| | - Chamras Promptmas
- Biosensors Laboratory, Department of Biomedical Engineering, Faculty of Engineering, Mahidol University, Phutthamonthon 4 Road, Salaya, Nakhon Pathom 73170, Thailand.
| | - Benchaporn Lertanantawong
- Biosensors Laboratory, Department of Biomedical Engineering, Faculty of Engineering, Mahidol University, Phutthamonthon 4 Road, Salaya, Nakhon Pathom 73170, Thailand.
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Fang M, Li H, Xie X, Wang H, Jiang Y, Li T, Zhang B, Jiang X, Cao Y, Zhang R, Zhang D, Zhao Y, Zhu L, Chen X, Yang Y. Imaging intracellular metabolite and protein changes in live mammalian cells with bright fluorescent RNA-based genetically encoded sensors. Biosens Bioelectron 2023; 235:115411. [PMID: 37236014 DOI: 10.1016/j.bios.2023.115411] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/07/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023]
Abstract
Fluorescent RNA (FR)-based genetically encoded sensors have been engineered to detect various essential metabolites in living systems. However, the unfavorable characteristics of FR impede sensor applications. Here, we describe a strategy for converting Pepper fluorescent RNA into a series of fluorescent sensors to detect their cognate targets both in vitro and in live cells. Compared to previously developed FR-based sensors, Pepper-based sensors exhibited expanded emission of up to 620 nm and markedly improved cellular brightness, allowing robust and real-time monitoring of the pharmacologic-triggered dynamics changes in the intracellular level of S-adenosylmethionine (SAM) and the optogenetic manipulated protein translocation in live mammalian cells. Furthermore, signal amplification in fluorescence imaging of the target was achieved using the CRISPR-display strategy by incorporating a Pepper-based sensor into the sgRNA scaffold. Together, these results demonstrate that Pepper can be readily developed into high-performance FR-based sensors to detect various cellular targets.
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Affiliation(s)
- Mengyue Fang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China; Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Huiwen Li
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China; Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Xin Xie
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China; Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Hui Wang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Ying Jiang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China; Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Tianyu Li
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China; Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Bibi Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China; Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Xin Jiang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China; Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Yueyang Cao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China; Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Rui Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China; Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Dasheng Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China; Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Linyong Zhu
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China; School of Biomedical Engineering, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai, 200240, China
| | - Xianjun Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China; Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China.
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China; Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China.
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Charteau V, Derksen M, Pruijn GJM. A Novel Method to Isolate RNase MRP Using RNA Streptavidin Aptamer Tags. Bio Protoc 2023; 13:e4615. [PMID: 36845535 PMCID: PMC9947544 DOI: 10.21769/bioprotoc.4615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/05/2022] [Accepted: 01/23/2023] [Indexed: 02/17/2023] Open
Abstract
Interactions between RNA-binding proteins and RNA molecules are at the center of multiple biological processes. Therefore, accurate characterization of the composition of ribonucleoprotein complexes (RNPs) is crucial. Ribonuclease (RNase) for mitochondrial RNA processing (MRP) and RNase P are highly similar RNPs that play distinct roles at the cellular level; as a consequence, the specific isolation of either of these complexes is essential to study their biochemical function. Since their protein components are nearly identical, purification of these endoribonucleases using protein-centric methods is not feasible. Here, we describe a procedure employing an optimized high-affinity streptavidin-binding RNA aptamer, termed S1m, to purify RNase MRP free of RNase P. This report details all steps from the RNA tagging to the characterization of the purified material. We show that using the S1m tag allows efficient isolation of active RNase MRP.
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Affiliation(s)
- Violette Charteau
- Department of Biomolecular Chemistry, Institute for Molecules and Materials (IMM), Radboud University, Nijmegen, The Netherlands
| | - Merel Derksen
- Department of Biomolecular Chemistry, Institute for Molecules and Materials (IMM), Radboud University, Nijmegen, The Netherlands
| | - Ger J. M. Pruijn
- Department of Biomolecular Chemistry, Institute for Molecules and Materials (IMM), Radboud University, Nijmegen, The Netherlands;
,*For correspondence:
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6
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Jagodnik J, Tjaden B, Ross W, Gourse R. Identification and characterization of RNA binding sites for (p)ppGpp using RNA-DRaCALA. Nucleic Acids Res 2023; 51:852-869. [PMID: 36617997 PMCID: PMC9881157 DOI: 10.1093/nar/gkac1224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/30/2022] [Accepted: 01/04/2023] [Indexed: 01/10/2023] Open
Abstract
Ligand-binding RNAs (RNA aptamers) are widespread in the three domains of life, serving as sensors of metabolites and other small molecules. When aptamers are embedded within RNA transcripts as components of riboswitches, they can regulate gene expression upon binding their ligands. Previous methods for biochemical validation of computationally predicted aptamers are not well-suited for rapid screening of large numbers of RNA aptamers. Therefore, we utilized DRaCALA (Differential Radial Capillary Action of Ligand Assay), a technique designed originally to study protein-ligand interactions, to examine RNA-ligand binding, permitting rapid screening of dozens of RNA aptamer candidates concurrently. Using this method, which we call RNA-DRaCALA, we screened 30 ykkC family subtype 2a RNA aptamers that were computationally predicted to bind (p)ppGpp. Most of the aptamers bound both ppGpp and pppGpp, but some strongly favored only ppGpp or pppGpp, and some bound neither. Expansion of the number of biochemically verified sites allowed construction of more accurate secondary structure models and prediction of key features in the aptamers that distinguish a ppGpp from a pppGpp binding site. To demonstrate that the method works with other ligands, we also used RNA DRaCALA to analyze aptamer binding by thiamine pyrophosphate.
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Affiliation(s)
- Jonathan Jagodnik
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Brian Tjaden
- Department of Computer Science, Wellesley College, Wellesley, MA 02481, USA
| | - Wilma Ross
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Richard L Gourse
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI 53706, USA
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7
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He X, Chen X, Wang Y. Mass Spectrometry for Assessing Protein-Nucleic Acid Interactions. Anal Chem 2023; 95:115-127. [PMID: 36625126 PMCID: PMC9869667 DOI: 10.1021/acs.analchem.2c04353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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8
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Graczyk A, Radzikowska-Cieciura E, Kaczmarek R, Pawlowska R, Chworos A. Modified Nucleotides for Chemical and Enzymatic Synthesis of Therapeutic RNA. Curr Med Chem 2023; 30:1320-1347. [PMID: 36239720 DOI: 10.2174/0929867330666221014111403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/22/2022] [Accepted: 05/16/2022] [Indexed: 11/22/2022]
Abstract
In recent years, RNA has emerged as a medium with a broad spectrum of therapeutic potential, however, for years, a group of short RNA fragments was studied and considered therapeutic molecules. In nature, RNA plays both functions, with coding and non-coding potential. For RNA, like any other therapeutic, to be used clinically, certain barriers must be crossed. Among them, there are biocompatibility, relatively low toxicity, bioavailability, increased stability, target efficiency and low off-target effects. In the case of RNA, most of these obstacles can be overcome by incorporating modified nucleotides into its structure. This may be achieved by both, in vitro and in vivo biosynthetic methods, as well as chemical synthesis. Some advantages and disadvantages of each approach are summarized here. The wide range of nucleotide analogues has been tested for their utility as monomers for RNA synthesis. Many of them have been successfully implemented, and a lot of pre-clinical and clinical studies involving modified RNA have been carried out. Some of these medications have already been introduced into clinics. After the huge success of RNA-based vaccines that were introduced into widespread use in 2020, and the introduction to the market of some RNA-based drugs, RNA therapeutics containing modified nucleotides appear to be the future of medicine.
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Affiliation(s)
- Anna Graczyk
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Ewa Radzikowska-Cieciura
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Renata Kaczmarek
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Roza Pawlowska
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Arkadiusz Chworos
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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Minkner R, Boonyakida J, Park EY, Wätzig H. Oligonucleotide separation techniques for purification and analysis: What can we learn for today's tasks? Electrophoresis 2022; 43:2402-2427. [PMID: 36285667 DOI: 10.1002/elps.202200079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 09/09/2022] [Accepted: 09/23/2022] [Indexed: 11/07/2022]
Abstract
Nucleic acids are the blueprint of life. They are not only the construction plan of the single cell or higher associations of them, but also necessary for function, communication and regulation. Due to the pandemic, the attention shifted in particular to their therapeutic potential as a vaccine. As pharmaceutical oligonucleotides are unique in terms of their stability and application, special delivery systems were also considered. Oligonucleotide production systems can vary and depend on the feasibility, availability, price and intended application. To achieve good purity, reliable results and match the strict specifications in the pharmaceutical industry, the separation of oligonucleotides is always essential. Besides the separation required for production, additional and specifically different separation techniques are needed for analysis to determine if the product complies with the designated specifications. After a short introduction to ribonucleic acids (RNAs), messenger RNA vaccines, and their production and delivery systems, an overview regarding separation techniques will be provided. This not only emphasises electrophoretic separations but also includes spin columns, extractions, precipitations, magnetic nanoparticles and several chromatographic separation principles, such as ion exchange chromatography, ion-pair reversed-phase, size exclusion and affinity.
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Affiliation(s)
- Robert Minkner
- Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Jirayu Boonyakida
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan.,Laboratory of Biotechnology, Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Enoch Y Park
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan.,Laboratory of Biotechnology, Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Hermann Wätzig
- Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
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Singh M, Ye B, Kim JH. Dual Leucine Zipper Kinase Regulates Dscam Expression through a Noncanonical Function of the Cytoplasmic Poly(A)-Binding Protein. J Neurosci 2022; 42:6007-6019. [PMID: 35764381 PMCID: PMC9351639 DOI: 10.1523/jneurosci.0543-21.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/17/2022] [Accepted: 06/22/2022] [Indexed: 02/05/2023] Open
Abstract
Dual leucine zipper kinase (DLK) plays a pivotal role in the development, degeneration, and regeneration of neurons. DLK can regulate gene expression post-transcriptionally, but the underlying mechanism remains poorly understood. The Drosophila DLK, Wallenda (Wnd), regulates the expression of Down syndrome cell adhesion molecule (Dscam) to control presynaptic arbor growth. This regulation is mediated by the 3' untranslated region (3'UTR) of Dscam mRNA, which suggests that RNA binding proteins (RBPs) mediate DLK function. We performed a genome-wide cell-based RNAi screen of RBPs and identified the cytoplasmic poly(A)-binding protein, pAbp, as an RBP that mediates Wnd-induced increase in Dscam expression. Genetic analysis shows that Wnd requires pAbp for promoting presynaptic arbor growth and for enhancing Dscam expression. Our analysis revealed that Dscam mRNAs harbor short poly(A) tails. We identified a region in Dscam 3'UTR that specifically interacts with pAbp. Removing this region significantly reduced Wnd-induced increase in Dscam expression. These suggest that a noncanonical interaction of PABP with the 3'UTR of target transcripts is essential for DLK functions.SIGNIFICANCE STATEMENT The kinase DLK plays key roles in a multitude of neuronal responses, including axon development, neurodegeneration, and nerve injury. Previous studies show that DLK acts via mRNAs to regulate protein synthesis, but how DLK does so is poorly understood. This study demonstrates that DLK regulates the synthesis of Dscam through the poly(A)-binding protein PABP-C. Whereas PABP-C is known as a general translational activator, our study shows that DLK-mediated Dscam expression involves a noncanonical interaction between PABP-C and the Dscam mRNA, which leads to a selective regulation of Dscam translation by PABP-C. Thus, our study provides novel insights into the mechanisms that underlie the function of DLK and regulation of gene expression of PABP-C.
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Affiliation(s)
- Monika Singh
- Department of Biology, University of Nevada, Reno, Nevada 89557
| | - Bing Ye
- Life Sciences Institute and Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Jung Hwan Kim
- Department of Biology, University of Nevada, Reno, Nevada 89557,
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N6-methyladenosine modified LINC00901 promotes pancreatic cancer progression through IGF2BP2/MYC axis. Genes Dis 2022; 10:554-567. [DOI: 10.1016/j.gendis.2022.02.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 02/17/2022] [Indexed: 11/20/2022] Open
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Pheno-SELEX: Engineering Anti-Metastatic Aptamers through Targeting the Invasive Phenotype Using Systemic Evolution of Ligands by Exponential Enrichment. Bioengineering (Basel) 2021; 8:bioengineering8120212. [PMID: 34940365 PMCID: PMC8698736 DOI: 10.3390/bioengineering8120212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/06/2021] [Accepted: 12/10/2021] [Indexed: 11/24/2022] Open
Abstract
Multiple methods (e.g., small molecules and antibodies) have been engineered to target specific proteins and signaling pathways in cancer. However, many mediators of the cancer phenotype are unknown and the ability to target these phenotypes would help mitigate cancer. Aptamers are small DNA or RNA molecules that are designed for therapeutic use. The design of aptamers to target cancers can be challenging. Accordingly, to engineer functionally anti-metastatic aptamers we used a modification of systemic evolution of ligands by exponential enrichment (SELEX) we call Pheno-SELEX to target a known phenotype of cancer metastasis, i.e., invasion. A highly invasive prostate cancer (PCa) cell line was established and used to identify aptamers that bound to it with high affinity as opposed to a less invasive variant to the cell line. The anti-invasive aptamer (AIA1) was found to inhibit in vitro invasion of the original highly invasive PCa cell line, as well as an additional PCa cell line and an osteosarcoma cell line. AIA1 also inhibited in vivo development of metastasis in both a PCa and osteosarcoma model of metastasis. These results indicate that Pheno-SELEX can be successfully used to identify aptamers without knowledge of underlying molecular targets. This study establishes a new paradigm for the identification of functional aptamers.
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13
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He RZ, Jiang J, Hu X, Lei M, Li J, Luo W, Duan L, Hu Z, Mo YY, Luo DX, Peng WX. Stabilization of UCA1 by N6-methyladenosine RNA methylation modification promotes colorectal cancer progression. Cancer Cell Int 2021; 21:616. [PMID: 34809621 PMCID: PMC8609784 DOI: 10.1186/s12935-021-02288-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/21/2021] [Indexed: 02/07/2023] Open
Abstract
Background UCA1 is frequently upregulated in a variety of cancers, including CRC, and it can play an oncogenic role by various mechanisms. However, how UCA1 is regulated in cancer is largely unknown. In this study, we aimed to determine whether RNA methylation at N6-methyladenosine (m6A) can impact UCA1 expression in colorectal cancer (CRC). Methods qRT-PCR was performed to detect the level of UCA1 and IGF2BP2 in CRC samples. CRISPR/Cas9 was employed to knockout (KO) UCA1, METTL3 and WTAP in DLD-1 and HCT-116 cells, while rescue experiments were carried out to re-express METTL3 and WTAP in KO cells. Immunoprecipitation using m6A antibody was performed to determine the m6A modification of UCA1. In vivo pulldown assays using S1m tagging combined with site-direct mutagenesis was carried out to confirm the recognition of m6A-modified UCA1 by IGF2BP2. Cell viability was measured by MTT and colony formation assays. The expression of UCA1 and IGF2BP2 in TCGA CRC database was obtained from GEPIA (http://gepia.cancer-pku.cn). Results Our results revealed that IGF2BP2 serves as a reader for m6A modified UCA1 and that adenosine at 1038 of UCA1 is critical to the recognition by IGF2BP2. Importantly, we showed that m6A writers, METTL3 and WTAP positively regulate UCA1 expression. Mechanically, IGF2BP2 increases the stability of m6A-modified UCA1. Clinically, IGF2BP2 is upregulated in CRC tissues compared with normal tissues. Conclusion These results suggest that m6A modification is an important factor contributing to upregulation of UCA1 in CRC tissues. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02288-x.
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Affiliation(s)
- Rong-Zhang He
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Through Molecular Diagnosis Technology, The First People's Hospital of Chenzhou, The First Affiliated Hospital of Xiangnan University, Chenzhou, 423000, China.,Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, Hunan, China.,Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA
| | - Jing Jiang
- Center of Medical Laboratory, The First People's Hospital of Chenzhou, University of South China, Chenzhou, 423000, China
| | - Xinglin Hu
- Department of Dermatology, Affiliated the First People's Hospital of Chenzhou of University of South China, Chenzhou, 423000, China
| | - Ming Lei
- Department of Clinical Laboratory, The First People's Hospital of Changde City, Changde, 415003, China
| | - Jia Li
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Through Molecular Diagnosis Technology, The First People's Hospital of Chenzhou, The First Affiliated Hospital of Xiangnan University, Chenzhou, 423000, China
| | - Weihao Luo
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Through Molecular Diagnosis Technology, The First People's Hospital of Chenzhou, The First Affiliated Hospital of Xiangnan University, Chenzhou, 423000, China
| | - Lili Duan
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Through Molecular Diagnosis Technology, The First People's Hospital of Chenzhou, The First Affiliated Hospital of Xiangnan University, Chenzhou, 423000, China
| | - Zheng Hu
- Translational Medicine Institute, National and Local Joint Engineering Laboratory for High-Through Molecular Diagnosis Technology, The First People's Hospital of Chenzhou, The First Affiliated Hospital of Xiangnan University, Chenzhou, 423000, China
| | - Yin-Yuan Mo
- Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA
| | - Di-Xian Luo
- Department of Laboratory Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital), Guangdong, 518000, China.
| | - Wan-Xin Peng
- Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA. .,National Clinical Research Center for Child Health, National Children's Regional Medical Center, the Children's Hospital, Zhejiang University School of Medicine, No. 3333, Binsheng Road, Hangzhou, 310052, China.
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14
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Neiswender H, Goldman CH, Veeranan-Karmegam R, Gonsalvez GB. Dynein light chain-dependent dimerization of Egalitarian is essential for maintaining oocyte fate in Drosophila. Dev Biol 2021; 478:76-88. [PMID: 34181915 DOI: 10.1016/j.ydbio.2021.06.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/02/2021] [Accepted: 06/17/2021] [Indexed: 11/28/2022]
Abstract
Egalitarian (Egl) is an RNA adaptor for the Dynein motor and is thought to link numerous, perhaps hundreds, of mRNAs with Dynein. Dynein, in turn, is responsible for the transport and localization of these mRNAs. Studies have shown that efficient mRNA binding by Egl requires the protein to dimerize. We recently demonstrated that Dynein light chain (Dlc) is responsible for facilitating the dimerization of Egl. Mutations in Egl that fail to interact with Dlc do not dimerize, and as such, are defective for mRNA binding. Consequently, this mutant does not efficiently associate with BicaudalD (BicD), the factor responsible for linking the Egl/mRNA complex with Dynein. In this report, we tested whether artificially dimerizing this Dlc-binding mutant using a leucine zipper would restore mRNA binding and rescue mutant phenotypes in vivo. Interestingly, we found that although artificial dimerization of Egl restored BicD binding, it only partially restored mRNA binding. As a result, Egl-dependent phenotypes, such as oocyte specification and mRNA localization, were only partially rescued. We hypothesize that Dlc-mediated dimerization of Egl results in a three-dimensional conformation of the Egl dimer that is best suited for mRNA binding. Although the leucine zipper restores Egl dimerization, it likely does not enable Egl to assemble into the conformation required for maximal mRNA binding activity.
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Affiliation(s)
- Hannah Neiswender
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA, 30912, USA
| | - Chandler H Goldman
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA, 30912, USA
| | - Rajalakshmi Veeranan-Karmegam
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA, 30912, USA
| | - Graydon B Gonsalvez
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1460 Laney Walker Blvd, Augusta, GA, 30912, USA.
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15
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Weissinger R, Heinold L, Akram S, Jansen RP, Hermesh O. RNA Proximity Labeling: A New Detection Tool for RNA-Protein Interactions. Molecules 2021; 26:2270. [PMID: 33919831 PMCID: PMC8070807 DOI: 10.3390/molecules26082270] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/09/2021] [Accepted: 04/10/2021] [Indexed: 12/26/2022] Open
Abstract
Multiple cellular functions are controlled by the interaction of RNAs and proteins. Together with the RNAs they control, RNA interacting proteins form RNA protein complexes, which are considered to serve as the true regulatory units for post-transcriptional gene expression. To understand how RNAs are modified, transported, and regulated therefore requires specific knowledge of their interaction partners. To this end, multiple techniques have been developed to characterize the interaction between RNAs and proteins. In this review, we briefly summarize the common methods to study RNA-protein interaction including crosslinking and immunoprecipitation (CLIP), and aptamer- or antisense oligonucleotide-based RNA affinity purification. Following this, we focus on in vivo proximity labeling to study RNA-protein interactions. In proximity labeling, a labeling enzyme like ascorbate peroxidase or biotin ligase is targeted to specific RNAs, RNA-binding proteins, or even cellular compartments and uses biotin to label the proteins and RNAs in its vicinity. The tagged molecules are then enriched and analyzed by mass spectrometry or RNA-Seq. We highlight the latest studies that exemplify the strength of this approach for the characterization of RNA protein complexes and distribution of RNAs in vivo.
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Affiliation(s)
| | | | | | | | - Orit Hermesh
- Interfaculty Institute for Biochemistry (IFIB), Tübingen University, 72076 Tübingen, Germany; (R.W.); (L.H.); (S.A.); (R.-P.J.)
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16
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Opposing roles for Egalitarian and Staufen in transport, anchoring and localization of oskar mRNA in the Drosophila oocyte. PLoS Genet 2021; 17:e1009500. [PMID: 33798193 PMCID: PMC8046350 DOI: 10.1371/journal.pgen.1009500] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/14/2021] [Accepted: 03/19/2021] [Indexed: 11/19/2022] Open
Abstract
Localization of oskar mRNA includes two distinct phases: transport from nurse cells to the oocyte, a process typically accompanied by cortical anchoring in the oocyte, followed by posterior localization within the oocyte. Signals within the oskar 3' UTR directing transport are individually weak, a feature previously hypothesized to facilitate exchange between the different localization machineries. We show that alteration of the SL2a stem-loop structure containing the oskar transport and anchoring signal (TAS) removes an inhibitory effect such that in vitro binding by the RNA transport factor, Egalitarian, is elevated as is in vivo transport from the nurse cells into the oocyte. Cortical anchoring within the oocyte is also enhanced, interfering with posterior localization. We also show that mutation of Staufen recognized structures (SRSs), predicted binding sites for Staufen, disrupts posterior localization of oskar mRNA just as in staufen mutants. Two SRSs in SL2a, one overlapping the Egalitarian binding site, are inferred to mediate Staufen-dependent inhibition of TAS anchoring activity, thereby promoting posterior localization. The other three SRSs in the oskar 3' UTR are also required for posterior localization, including two located distant from any known transport signal. Staufen, thus, plays multiple roles in localization of oskar mRNA.
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17
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Compendium of Methods to Uncover RNA-Protein Interactions In Vivo. Methods Protoc 2021; 4:mps4010022. [PMID: 33808611 PMCID: PMC8006020 DOI: 10.3390/mps4010022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/11/2021] [Accepted: 03/17/2021] [Indexed: 01/01/2023] Open
Abstract
Control of gene expression is critical in shaping the pro-and eukaryotic organisms’ genotype and phenotype. The gene expression regulatory pathways solely rely on protein–protein and protein–nucleic acid interactions, which determine the fate of the nucleic acids. RNA–protein interactions play a significant role in co- and post-transcriptional regulation to control gene expression. RNA-binding proteins (RBPs) are a diverse group of macromolecules that bind to RNA and play an essential role in RNA biology by regulating pre-mRNA processing, maturation, nuclear transport, stability, and translation. Hence, the studies aimed at investigating RNA–protein interactions are essential to advance our knowledge in gene expression patterns associated with health and disease. Here we discuss the long-established and current technologies that are widely used to study RNA–protein interactions in vivo. We also present the advantages and disadvantages of each method discussed in the review.
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18
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DNA origami signposts for identifying proteins on cell membranes by electron cryotomography. Cell 2021; 184:1110-1121.e16. [PMID: 33606980 PMCID: PMC7895908 DOI: 10.1016/j.cell.2021.01.033] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 09/14/2020] [Accepted: 01/20/2021] [Indexed: 12/21/2022]
Abstract
Electron cryotomography (cryoET), an electron cryomicroscopy (cryoEM) modality, has changed our understanding of biological function by revealing the native molecular details of membranes, viruses, and cells. However, identification of individual molecules within tomograms from cryoET is challenging because of sample crowding and low signal-to-noise ratios. Here, we present a tagging strategy for cryoET that precisely identifies individual protein complexes in tomograms without relying on metal clusters. Our method makes use of DNA origami to produce “molecular signposts” that target molecules of interest, here via fluorescent fusion proteins, providing a platform generally applicable to biological surfaces. We demonstrate the specificity of signpost origami tags (SPOTs) in vitro as well as their suitability for cryoET of membrane vesicles, enveloped viruses, and the exterior of intact mammalian cells. Asymmetric DNA signpost origami tags (SPOTs) precisely localize proteins SPOTs identify specific proteins in electron cryomicroscopy SPOTs have a high contrast “sign” and functionalized “post” base for targeting SPOTs recognize fluorescent fusion proteins on vesicles, viruses, and cell surfaces
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19
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Daneshvar K, Ardehali MB, Klein IA, Hsieh FK, Kratkiewicz AJ, Mahpour A, Cancelliere SOL, Zhou C, Cook BM, Li W, Pondick JV, Gupta SK, Moran SP, Young RA, Kingston RE, Mullen AC. lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation. Nat Cell Biol 2020; 22:1211-1222. [PMID: 32895492 PMCID: PMC8008247 DOI: 10.1038/s41556-020-0572-2] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/05/2020] [Indexed: 01/19/2023]
Abstract
Cooperation between DNA, RNA and protein regulates gene expression and controls differentiation through interactions that connect regions of nucleic acids and protein domains and through the assembly of biomolecular condensates. Here, we report that endoderm differentiation is regulated by the interaction between the long non-coding RNA (lncRNA) DIGIT and the bromodomain and extraterminal domain protein BRD3. BRD3 forms phase-separated condensates of which the formation is promoted by DIGIT, occupies enhancers of endoderm transcription factors and is required for endoderm differentiation. BRD3 binds to histone H3 acetylated at lysine 18 (H3K18ac) in vitro and co-occupies the genome with H3K18ac. DIGIT is also enriched in regions of H3K18ac, and the depletion of DIGIT results in decreased recruitment of BRD3 to these regions. Our findings show that cooperation between DIGIT and BRD3 at regions of H3K18ac regulates the transcription factors that drive endoderm differentiation and suggest that protein-lncRNA phase-separated condensates have a broader role as regulators of transcription.
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Affiliation(s)
- Kaveh Daneshvar
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - M Behfar Ardehali
- Department of Molecular Biology and MGH Research Institute, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Isaac A Klein
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Fu-Kai Hsieh
- Department of Molecular Biology and MGH Research Institute, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Arcadia J Kratkiewicz
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Amin Mahpour
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | - Chan Zhou
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | - Wenyang Li
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Joshua V Pondick
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sweta K Gupta
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sean P Moran
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Robert E Kingston
- Department of Molecular Biology and MGH Research Institute, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Alan C Mullen
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
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20
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Jaiswal A, Singh AK, Tamrakar A, Kodgire P. Unfolding the Role of Splicing Factors and RNA Debranching in AID Mediated Antibody Diversification. Int Rev Immunol 2020; 40:289-306. [PMID: 32924658 DOI: 10.1080/08830185.2020.1815725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Activated B-cells diversify their antibody repertoire via somatic hypermutation (SHM) and class switch recombination (CSR). SHM is restricted to the variable region, whereas, CSR is confined to the constant region of immunoglobulin (Ig) genes. Activation-induced cytidine deaminase (AID) is a crucial player in the diversification of antibodies in the activated B-cell. AID catalyzes the deamination of cytidine (C) into uracil (U) at Ig genes. Subsequently, low fidelity repair of U:G mismatches may lead to mutations. Transcription is essential for the AID action, as it provides a transient single-strand DNA substrate. Since splicing is a co-transcriptional event, various splicing factors or regulators influence the transcription. Numerous splicing factors are known to regulate the AID targeting, function, Ig transcription, and AID splicing, which eventually influence antibody diversification processes. Splicing regulator SRSF1-3, a splicing isoform of serine arginine-rich splicing factor (SRSF1), and CTNNBL1, a spliceosome interacting factor, interact with AID and play a critical role in SHM. Likewise, a splicing regulator polypyrimidine tract binding protein-2 (PTBP2) and the debranching enzyme (DBR1) debranches primary switch transcripts which later forms G-quadruplex structures, and the S region guide RNAs direct AID to S region DNA. Moreover, AID shows several alternate splicing isoforms, like AID devoid of exon-4 (AIDΔE4) that is expressed in various pathological conditions. Interestingly, RBM5, a splicing regulator, is responsible for the skipping of AID exon 4. In this review, we discuss the role and significance of splicing factors in the AID mediated antibody diversification.
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Affiliation(s)
- Ankit Jaiswal
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Amit Kumar Singh
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Anubhav Tamrakar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Prashant Kodgire
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
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21
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Ray J, Kruse A, Ozer A, Kajitani T, Johnson R, MacCoss M, Heck M, Lis JT. RNA aptamer capture of macromolecular complexes for mass spectrometry analysis. Nucleic Acids Res 2020; 48:e90. [PMID: 32609809 PMCID: PMC7470977 DOI: 10.1093/nar/gkaa542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 06/03/2020] [Accepted: 06/27/2020] [Indexed: 12/25/2022] Open
Abstract
Specific genomic functions are dictated by macromolecular complexes (MCs) containing multiple proteins. Affinity purification of these complexes, often using antibodies, followed by mass spectrometry (MS) has revolutionized our ability to identify the composition of MCs. However, conventional immunoprecipitations suffer from contaminating antibody/serum-derived peptides that limit the sensitivity of detection for low-abundant interacting partners using MS. Here, we present AptA-MS (aptamer affinity-mass spectrometry), a robust strategy primarily using a specific, high-affinity RNA aptamer against Green Fluorescent Protein (GFP) to identify interactors of a GFP-tagged protein of interest by high-resolution MS. Utilizing this approach, we have identified the known molecular chaperones that interact with human Heat Shock Factor 1 (HSF1), and observed an increased association with several proteins upon heat shock, including translation elongation factors and histones. HSF1 is known to be regulated by multiple post-translational modifications (PTMs), and we observe both known and new sites of modifications on HSF1. We show that AptA-MS provides a dramatic target enrichment and detection sensitivity in evolutionarily diverse organisms and allows identification of PTMs without the need for modification-specific enrichments. In combination with the expanding libraries of GFP-tagged cell lines, this strategy offers a general, inexpensive, and high-resolution alternative to conventional approaches for studying MCs.
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Affiliation(s)
- Judhajeet Ray
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Angela Kruse
- Department of Plant Pathology and Plant-microbe Biology, Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute, Ithaca, NY, USA
| | - Abdullah Ozer
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Takuya Kajitani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Richard Johnson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Michael MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Michelle Heck
- Department of Plant Pathology and Plant-microbe Biology, Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute, Ithaca, NY, USA
- Emerging Pests and Pathogens Research Unit, Robert W. Holley Center, United States Department of Agriculture Agricultural Research Service (USDA ARS), Ithaca, NY, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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22
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Hu X, Peng WX, Zhou H, Jiang J, Zhou X, Huang D, Mo YY, Yang L. IGF2BP2 regulates DANCR by serving as an N6-methyladenosine reader. Cell Death Differ 2020; 27:1782-1794. [PMID: 31804607 PMCID: PMC7244758 DOI: 10.1038/s41418-019-0461-z] [Citation(s) in RCA: 198] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 11/02/2019] [Accepted: 11/11/2019] [Indexed: 12/31/2022] Open
Abstract
The major function of Insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) is to regulate cell metabolism. However, emerging evidence indicates that IGF2BP2 plays a role in cancer, but the underlying mechanism is largely unknown. Here we showed that upregulation of IGF2BP2 is associated with poor outcomes of pancreatic cancer patients and suppression of IGF2BP2 inhibits cell proliferation. We further showed that IGF2BP2 regulates lncRNA DANCR. Ectopic expression IGF2BP2 enhances, whereas knockdown (KD) or knockout (KO) of IGF2BP2 suppresses DANCR expression. Moreover, in vivo RNA precipitation and reciprocal RNA immunoprecipitation revealed that IGF2BP2 interacts with DANCR. DANCR promotes cell proliferation and stemness-like properties. Experiments with xenograft models revealed that while ectopic expression of DANCR promotes, DANCR KO suppresses tumor growth. Mechanistically, DANCR is modified at N6-methyladenosine (m6A) and mutagenesis assay identified that adenosine at 664 of DANCR is critical to the interaction between IGF2BP2 and DANCR where IGF2BP2 serves a reader for m6A modified DANCR and stabilizes DANCR RNA. Together, these results suggest that DANCR is a novel target for IGF2BP2 through m6A modification, and IGF2BP2 and DANCR work together to promote cancer stemness-like properties and pancreatic cancer pathogenesis.
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Affiliation(s)
- Xiaoge Hu
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
- Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA
| | - Wan-Xin Peng
- Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA
- Department of Cell biology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Huaixiang Zhou
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
| | - Jiahong Jiang
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
| | - Xinchun Zhou
- Department of Pathology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Dongsheng Huang
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
| | - Yin-Yuan Mo
- Cancer Institute, University of Mississippi Medical Center, Jackson, MS, USA.
- Department of Pharmacology/Toxicology, University of Mississippi Medical Center, Jackson, MS, USA.
| | - Liu Yang
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China.
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23
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Scherer M, Levin M, Butter F, Scheibe M. Quantitative Proteomics to Identify Nuclear RNA-Binding Proteins of Malat1. Int J Mol Sci 2020; 21:ijms21031166. [PMID: 32050583 PMCID: PMC7037011 DOI: 10.3390/ijms21031166] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/03/2020] [Accepted: 02/05/2020] [Indexed: 01/02/2023] Open
Abstract
The long non-coding RNA Malat1 has been implicated in several human cancers, while the mechanism of action is not completely understood. As RNAs in cells function together with RNA-binding proteins (RBPs), the composition of their RBP complex can shed light on their functionality. We here performed quantitative interactomics of 14 non-overlapping fragments covering the full length of Malat1 to identify possible nuclear interacting proteins. Overall, we identified 35 candidates including 14 already known binders, which are able to interact with Malat1 in the nucleus. Furthermore, the use of fragments along the full-length RNA allowed us to reveal two hotspots for protein binding, one in the 5′-region and one in the 3′-region of Malat1. Our results provide confirmation on previous RNA-protein interaction studies and suggest new candidates for functional investigations.
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Smith TS, Zoltek MA, Simon MD. Reengineering a tRNA Methyltransferase To Covalently Capture New RNA Substrates. J Am Chem Soc 2019; 141:17460-17465. [PMID: 31626536 DOI: 10.1021/jacs.9b08529] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Covalent RNA modifications can alter the function and metabolism of RNA transcripts. Altering the RNA substrate specificities of the enzymes that install these modifications can provide powerful tools to study and manipulate RNA. To develop new tools and probe the plasticity of the substrate specificity of one of these enzymes, we examined the engineerability of the uridine-54 tRNA methyltransferase, TrmA. Starting from a mutant that remains covalently bound to its substrate RNA (E358Q, TrmA*), we were able to use both rational design and a high-throughput sequencing assay to examine the RNA substrates of TrmA*. Although rational engineering substantially changed TrmA* specificity, the rationally designed substrate mutants we developed still retained activity with the wild-type protein. Using high-throughput substrate screening of additional TrmA* mutants, we identified a triple mutant of the substrate RNA (C56A;A58G;C60U) that is efficiently trapped by a TrmA* double mutant (E49R;R51E) but not by the wild-type TrmA*. This work establishes a foundation for using protein engineering to reconfigure substrate specificities of RNA-modifying enzymes and covalently trap RNAs with engineered proteins.
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Affiliation(s)
- Tyler S Smith
- Department of Molecular Biophysics & Biochemistry , Yale University , New Haven , Connecticut 06511 , United States.,Chemical Biology Institute , Yale University , West Haven , Connecticut 06516 , United States
| | - Madeline A Zoltek
- Department of Molecular Biophysics & Biochemistry , Yale University , New Haven , Connecticut 06511 , United States.,Chemical Biology Institute , Yale University , West Haven , Connecticut 06516 , United States
| | - Matthew D Simon
- Department of Molecular Biophysics & Biochemistry , Yale University , New Haven , Connecticut 06511 , United States.,Chemical Biology Institute , Yale University , West Haven , Connecticut 06516 , United States
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25
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Kikuchi Y, Umekage S. Extracellular nucleic acids of the marine bacterium Rhodovulum sulfidophilum and recombinant RNA production technology using bacteria. FEMS Microbiol Lett 2019; 365:4705897. [PMID: 29228187 DOI: 10.1093/femsle/fnx268] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 12/05/2017] [Indexed: 12/21/2022] Open
Abstract
Extracellular nucleic acids of high molecular weight are detected ubiquitously in seawater. Recent studies have indicated that these nucleic acids are, at least in part, derived from active production by some bacteria. The marine bacterium Rhodovulum sulfidophilum is one of those bacteria. Rhodovulumsulfidophilum is a non-sulfur phototrophic marine bacterium that is known to form structured communities of cells called flocs, and to produce extracellular nucleic acids in culture media. Recently, it has been revealed that this bacterium produces gene transfer agent-like particles and that this particle production may be related to the extracellular nucleic acid production mechanism. This review provides a summary of recent physiological and genetic studies of these phenomena and also introduces a new method for extracellular production of artificial and biologically functional RNAs using this bacterium. In addition, artificial RNA production using Escherichia coli, which is related to this topic, will also be described.
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Affiliation(s)
- Yo Kikuchi
- Department of Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - So Umekage
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan
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26
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Henderson CA, Rail CA, Butt LE, Vincent HA, Callaghan AJ. Generation of small molecule-binding RNA arrays and their application to fluorogen-binding RNA aptamers. Methods 2019; 167:39-53. [PMID: 31055072 PMCID: PMC7068705 DOI: 10.1016/j.ymeth.2019.04.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 04/04/2019] [Accepted: 04/29/2019] [Indexed: 12/23/2022] Open
Abstract
The discovery and engineering of more and more functions of RNA has highlighted the utility of RNA-targeting small molecules. Recently, several fluorogen-binding RNA aptamers have been developed that have been applied to live cell imaging of RNA and metabolites as RNA tags or biosensors, respectively. Although the design and application of these fluorogen-binding RNA aptamer-based devices is straightforward in theory, in practice, careful optimisation is required. For this reason, high throughput in vitro screening techniques, capable of quantifying fluorogen-RNA aptamer interactions, would be beneficial. We recently developed a method for generating functional-RNA arrays and demonstrated that they could be used to detect fluorogen-RNA aptamer interactions. Specifically, we were able to visualise the interaction between malachite green and the malachite green-binding aptamer. Here we expand this study to demonstrate that functional-RNA arrays can be used to quantify fluorogen-aptamer interactions. As proof-of-concept, we provide detailed protocols for the production of malachite green-binding RNA aptamer and DFHBI-binding Spinach RNA aptamer arrays. Furthermore, we discuss the potential utility of the technology to fluorogen-binding RNA aptamers, including application as a molecular biosensor platform. We anticipate that functional-RNA array technology will be beneficial for a wide variety of biological disciplines.
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Affiliation(s)
- Charlotte A Henderson
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Callum A Rail
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Louise E Butt
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Helen A Vincent
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom.
| | - Anastasia J Callaghan
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom.
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27
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Phillips JO, Butt LE, Henderson CA, Devonshire M, Healy J, Conway SJ, Locker N, Pickford AR, Vincent HA, Callaghan AJ. High-density functional-RNA arrays as a versatile platform for studying RNA-based interactions. Nucleic Acids Res 2019; 46:e86. [PMID: 29846708 PMCID: PMC6101487 DOI: 10.1093/nar/gky410] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 05/02/2018] [Indexed: 12/13/2022] Open
Abstract
We are just beginning to unravel the myriad of interactions in which non-coding RNAs participate. The intricate RNA interactome is the foundation of many biological processes, including bacterial virulence and human disease, and represents unexploited resources for the development of potential therapeutic interventions. However, identifying specific associations of a given RNA from the multitude of possible binding partners within the cell requires robust high-throughput systems for their rapid screening. Here, we present the first demonstration of functional-RNA arrays as a novel platform technology designed for the study of such interactions using immobilized, active RNAs. We have generated high-density RNA arrays by an innovative method involving surface-capture of in vitro transcribed RNAs. This approach has significant advantages over existing technologies, particularly in its versatility in regards to binding partner character. Indeed, proof-of-principle application of RNA arrays to both RNA–small molecule and RNA–RNA pairings is demonstrated, highlighting their potential as a platform technology for mapping RNA-based networks and for pharmaceutical screening. Furthermore, the simplicity of the method supports greater user-accessibility over currently available technologies. We anticipate that functional-RNA arrays will find broad utility in the expanding field of RNA characterization.
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Affiliation(s)
- Jack O Phillips
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Louise E Butt
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Charlotte A Henderson
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Martin Devonshire
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Jess Healy
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Stuart J Conway
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Nicolas Locker
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford GU2 7HX, UK
| | - Andrew R Pickford
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Helen A Vincent
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Anastasia J Callaghan
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
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28
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Colognori D, Sunwoo H, Kriz AJ, Wang CY, Lee JT. Xist Deletional Analysis Reveals an Interdependency between Xist RNA and Polycomb Complexes for Spreading along the Inactive X. Mol Cell 2019; 74:101-117.e10. [PMID: 30827740 DOI: 10.1016/j.molcel.2019.01.015] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/21/2018] [Accepted: 01/10/2019] [Indexed: 12/16/2022]
Abstract
During X-inactivation, Xist RNA spreads along an entire chromosome to establish silencing. However, the mechanism and functional RNA elements involved in spreading remain undefined. By performing a comprehensive endogenous Xist deletion screen, we identify Repeat B as crucial for spreading Xist and maintaining Polycomb repressive complexes 1 and 2 (PRC1/PRC2) along the inactive X (Xi). Unexpectedly, spreading of these three factors is inextricably linked. Deleting Repeat B or its direct binding partner, HNRNPK, compromises recruitment of PRC1 and PRC2. In turn, ablating PRC1 or PRC2 impairs Xist spreading. Therefore, Xist and Polycomb complexes require each other to propagate along the Xi, suggesting a positive feedback mechanism between RNA initiator and protein effectors. Perturbing Xist/Polycomb spreading causes failure of de novo Xi silencing, with partial compensatory downregulation of the active X, and also disrupts topological Xi reconfiguration. Thus, Repeat B is a multifunctional element that integrates interdependent Xist/Polycomb spreading, silencing, and changes in chromosome architecture.
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Affiliation(s)
- David Colognori
- Howard Hughes Medical Institute; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Hongjae Sunwoo
- Howard Hughes Medical Institute; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Andrea J Kriz
- Howard Hughes Medical Institute; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Chen-Yu Wang
- Howard Hughes Medical Institute; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jeannie T Lee
- Howard Hughes Medical Institute; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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29
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Bachtiar BM, Srisawat C, Bachtiar EW. RNA aptamers selected against yeast cells inhibit Candida albicans biofilm formation in vitro. Microbiologyopen 2019; 8:e00812. [PMID: 30779315 PMCID: PMC6692556 DOI: 10.1002/mbo3.812] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/14/2019] [Accepted: 01/15/2019] [Indexed: 11/24/2022] Open
Abstract
Aptamers that bind live bacterial cells have been widely investigated, but their potential to inhibit Candida albicans biofilm formation needs to be further explored. The aims of this study were to evaluate the binding of C. albicans to RNA aptamers and to examine the potential of aptamers to inhibit C. albicans biofilm formation in vitro. In this study, RNA aptamers selected against yeast cells of C. albicans ATCC 10231 were developed using the systematic evolution of ligands by exponential enrichment (SELEX) technique. The binding affinity of the resulting aptamers was then determined by an aptamer‐linked immobilized sorbent assay (ALISA), and a colorimetric (MTT) assay was used to measure the metabolic activity of Candida biofilms. After 11 rounds of SELEX, two candidate aptamers, Ca‐apt‐1 and Ca‐apt‐12, were identified. The Ca‐apt‐1 aptamer also recognized C. albicans isolated from clinical specimens but did not recognize other oral microorganisms (i.e., Streptococcus mutans and Saccharomyces cerevisiae). The ALISA results showed that the binding affinity of these aptamers was comparable to that of an anti‐C. albicans monoclonal antibody. In addition, Ca‐apt‐1 could inhibit biofilm and hyphal formation of C. albicans in vitro, as demonstrated using biofilm assays. This study shows that RNA aptamers could potentially be used in diagnostic and therapeutic applications for C. albicans‐related disease in the future.
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Affiliation(s)
- Boy M Bachtiar
- Department of Oral Biology, Faculty of Dentistry, Universitas Indonesia, Jakarta, Indonesia.,Oral Research Science Center, Faculty of Dentistry, Universitas Indonesia, Jakarta, Indonesia
| | - Chatchawan Srisawat
- Department of Biochemistry and NANOTEC-Mahidol University Center of Excellence in Nanotechnology for Cancer Diagnosis and Treatment, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkoknoi, Bangkok, Thailand
| | - Endang W Bachtiar
- Department of Oral Biology, Faculty of Dentistry, Universitas Indonesia, Jakarta, Indonesia.,Oral Research Science Center, Faculty of Dentistry, Universitas Indonesia, Jakarta, Indonesia
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30
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Sauvageau M. Diverging RNPs: Toward Understanding lncRNA-Protein Interactions and Functions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1203:285-312. [PMID: 31811638 DOI: 10.1007/978-3-030-31434-7_10] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
RNA-protein interactions are essential to a variety of biological processes. The realization that mammalian genomes are pervasively transcribed brought a tidal wave of tens of thousands of newly identified long noncoding RNAs (lncRNAs) and raised questions about their purpose in cells. The vast majority of lncRNAs have yet to be studied, and it remains to be determined to how many of these transcripts a function can be ascribed. However, results gleaned from studying a handful of these macromolecules have started to reveal common themes of biological function and mechanism of action involving intricate RNA-protein interactions. Some lncRNAs were shown to regulate the chromatin and transcription of distant and neighboring genes in the nucleus, while others regulate the translation or localization of proteins in the cytoplasm. Some lncRNAs were found to be crucial during development, while mutations and aberrant expression of others have been associated with several types of cancer and a plethora of diseases. Over the last few years, the establishment of new technologies has been key in providing the tools to decode the rules governing lncRNA-protein interactions and functions. This chapter will highlight the general characteristics of lncRNAs, their function, and their mode of action, with a special focus on protein interactions. It will also describe the methods at the disposition of scientists to help them cross this next frontier in our understanding of lncRNA biology.
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Affiliation(s)
- Martin Sauvageau
- Montreal Clinical Research Institute (IRCM), Montréal, QC, Canada. .,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, Canada.
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31
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Xu C, Li H, Zhang K, Binzel DW, Yin H, Chiu W, Guo P. Photo-controlled release of paclitaxel and model drugs from RNA pyramids. NANO RESEARCH 2019; 12:41-48. [PMID: 31258852 PMCID: PMC6599617 DOI: 10.1007/s12274-018-2174-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Stimuli-responsive release of drugs from a nanocarrier in spatial-, temporal-, and dosage-controlled fashions is of great interest in the pharmaceutical industry. Paclitaxel is one of the most effective and popular chemotherapeutic drugs against a number of cancers such as metastatic or nonmetastatic breast cancer, non-small cell lung cancer, refractory ovarian cancer, AIDS-related Kaposi's sarcoma, and head and neck cancers. Here, by taking the advantage of RNA nanotechnology in biomedical and material science, we developed a three-dimensional pyramid-shaped RNA nanocage for a photocontrolled release of cargo, using paclitaxel as a model drug. The light-triggered release of paclitaxel or fluorophore Cy5 was achieved by incorporation of photocleavable spacers into the RNA nanoparticles. Upon irradiation with ultraviolet light, cargos were rapidly released (within 5 min). In vitro treatment of breast cancer cells with the RNA nanoparticles harboring photocleavable paclitaxel showed higher cytotoxicity as compared to RNA nanoparticles without the photocleavable spacer. The methodology provides proof of concept for the application of the light-triggered controlled release of drugs from RNA nanocages.
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Affiliation(s)
- Congcong Xu
- Center for RNA Nanobiotechnology and Nanomedicine; Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy; Dorothy M. Davis Heart and Lung Research Institute, College of Medicine and James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Hui Li
- Center for RNA Nanobiotechnology and Nanomedicine; Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy; Dorothy M. Davis Heart and Lung Research Institute, College of Medicine and James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Kaiming Zhang
- Departments of Bioengineering, Microbiology and Immunology, and James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Daniel W Binzel
- Center for RNA Nanobiotechnology and Nanomedicine; Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy; Dorothy M. Davis Heart and Lung Research Institute, College of Medicine and James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Hongran Yin
- Center for RNA Nanobiotechnology and Nanomedicine; Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy; Dorothy M. Davis Heart and Lung Research Institute, College of Medicine and James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Wah Chiu
- Departments of Bioengineering, Microbiology and Immunology, and James H. Clark Center, Stanford University, Stanford, CA 94305, USA
- SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine; Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy; Dorothy M. Davis Heart and Lung Research Institute, College of Medicine and James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
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32
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Harvey RF, Smith TS, Mulroney T, Queiroz RML, Pizzinga M, Dezi V, Villenueva E, Ramakrishna M, Lilley KS, Willis AE. Trans-acting translational regulatory RNA binding proteins. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1465. [PMID: 29341429 PMCID: PMC5947564 DOI: 10.1002/wrna.1465] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/31/2017] [Accepted: 12/04/2017] [Indexed: 12/13/2022]
Abstract
The canonical molecular machinery required for global mRNA translation and its control has been well defined, with distinct sets of proteins involved in the processes of translation initiation, elongation and termination. Additionally, noncanonical, trans-acting regulatory RNA-binding proteins (RBPs) are necessary to provide mRNA-specific translation, and these interact with 5' and 3' untranslated regions and coding regions of mRNA to regulate ribosome recruitment and transit. Recently it has also been demonstrated that trans-acting ribosomal proteins direct the translation of specific mRNAs. Importantly, it has been shown that subsets of RBPs often work in concert, forming distinct regulatory complexes upon different cellular perturbation, creating an RBP combinatorial code, which through the translation of specific subsets of mRNAs, dictate cell fate. With the development of new methodologies, a plethora of novel RNA binding proteins have recently been identified, although the function of many of these proteins within mRNA translation is unknown. In this review we will discuss these methodologies and their shortcomings when applied to the study of translation, which need to be addressed to enable a better understanding of trans-acting translational regulatory proteins. Moreover, we discuss the protein domains that are responsible for RNA binding as well as the RNA motifs to which they bind, and the role of trans-acting ribosomal proteins in directing the translation of specific mRNAs. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Translation > Translation Regulation Translation > Translation Mechanisms.
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Affiliation(s)
| | - Tom S. Smith
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | - Rayner M. L. Queiroz
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | | | - Eneko Villenueva
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, Department of BiochemistryUniversity of CambridgeCambridgeUK
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33
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Identification and characterization of nucleobase-modified aptamers by click-SELEX. Nat Protoc 2018; 13:1153-1180. [PMID: 29700486 DOI: 10.1038/nprot.2018.023] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Aptamers are single-stranded oligonucleotides that are in vitro-selected to recognize their target molecule with high affinity and specificity. As they consist of the four canonical nucleobases, their chemical diversity is limited, which in turn limits the addressable target spectrum. Introducing chemical modifications into nucleic acid libraries increases the interaction capabilities of the DNA and thereby the target spectrum. Here, we describe a protocol to select nucleobase-modified aptamers by using click chemistry (CuAAC) to introduce the preferred chemical modification. The use of click chemistry to modify the DNA library enables the introduction of a wide range of possible functionalities, which can be customized to the requirements of the target molecule and the desired application. This protocol yields modified DNA aptamers with extended interaction properties that are not accessible with the canonical set of nucleotides. After synthesis of the starting library containing a commercially available, alkyne-modified uridine (5-ethynyl-deoxyuridine (EdU)) instead of thymidine, the library is functionalized with the modification of choice by CuAAC. The thus-modified DNA is incubated with the target molecule and the best binding sequences are recovered. The chemical modification is removed during the amplification process. Therefore, this protocol is compatible with conventional amplification procedures and avoids enzymatic incompatibility problems associated with more extensive nucleobase modifications. After single-strand generation, the modification is reintroduced into the enriched library, which can then be subjected to the subsequent selection cycle. The duration of each selection cycle as outlined in the protocol is ∼1 d.
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34
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Schwarz-Schilling M, Dupin A, Chizzolini F, Krishnan S, Mansy SS, Simmel FC. Optimized Assembly of a Multifunctional RNA-Protein Nanostructure in a Cell-Free Gene Expression System. NANO LETTERS 2018; 18:2650-2657. [PMID: 29564885 DOI: 10.1021/acs.nanolett.8b00526] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Molecular complexes composed of RNA molecules and proteins are promising multifunctional nanostructures for a wide variety of applications in biological cells or in artificial cellular systems. In this study, we systematically address some of the challenges associated with the expression and assembly of such hybrid structures using cell-free gene expression systems. As a model structure, we investigated a pRNA-derived RNA scaffold functionalized with four distinct aptamers, three of which bind to proteins, streptavidin and two fluorescent proteins, while one binds the small molecule dye malachite green (MG). Using MG fluorescence and Förster resonance energy transfer (FRET) between the RNA-scaffolded proteins, we assess critical assembly parameters such as chemical stability, binding efficiency, and also resource sharing effects within the reaction compartment. We then optimize simultaneous expression and coassembly of the RNA-protein nanostructure within a single-compartment cell-free gene expression system. We demonstrate expression and assembly of the multicomponent nanostructures inside of emulsion droplets and their aptamer-mediated localization onto streptavidin-coated substrates, plus the successful assembly of the hybrid structures inside of bacterial cells.
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Affiliation(s)
| | - Aurore Dupin
- Physics Department E14 , Technical University Munich , 85748 Garching , Germany
| | - Fabio Chizzolini
- CIBIO , University of Trento , Via Sommarive 9 , 38123 Povo , Italy
| | - Swati Krishnan
- Physics Department E14 , Technical University Munich , 85748 Garching , Germany
| | - Sheref S Mansy
- CIBIO , University of Trento , Via Sommarive 9 , 38123 Povo , Italy
| | - Friedrich C Simmel
- Physics Department E14 , Technical University Munich , 85748 Garching , Germany
- Nanosystems Initiative Munich , 80539 Munich , Germany
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35
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Cipriano A, Ballarino M. The Ever-Evolving Concept of the Gene: The Use of RNA/Protein Experimental Techniques to Understand Genome Functions. Front Mol Biosci 2018; 5:20. [PMID: 29560353 PMCID: PMC5845540 DOI: 10.3389/fmolb.2018.00020] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 02/20/2018] [Indexed: 12/12/2022] Open
Abstract
The completion of the human genome sequence together with advances in sequencing technologies have shifted the paradigm of the genome, as composed of discrete and hereditable coding entities, and have shown the abundance of functional noncoding DNA. This part of the genome, previously dismissed as “junk” DNA, increases proportionally with organismal complexity and contributes to gene regulation beyond the boundaries of known protein-coding genes. Different classes of functionally relevant nonprotein-coding RNAs are transcribed from noncoding DNA sequences. Among them are the long noncoding RNAs (lncRNAs), which are thought to participate in the basal regulation of protein-coding genes at both transcriptional and post-transcriptional levels. Although knowledge of this field is still limited, the ability of lncRNAs to localize in different cellular compartments, to fold into specific secondary structures and to interact with different molecules (RNA or proteins) endows them with multiple regulatory mechanisms. It is becoming evident that lncRNAs may play a crucial role in most biological processes such as the control of development, differentiation and cell growth. This review places the evolution of the concept of the gene in its historical context, from Darwin's hypothetical mechanism of heredity to the post-genomic era. We discuss how the original idea of protein-coding genes as unique determinants of phenotypic traits has been reconsidered in light of the existence of noncoding RNAs. We summarize the technological developments which have been made in the genome-wide identification and study of lncRNAs and emphasize the methodologies that have aided our understanding of the complexity of lncRNA-protein interactions in recent years.
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Affiliation(s)
- Andrea Cipriano
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
| | - Monica Ballarino
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy
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36
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Das M, Renganathan A, Dighe SN, Bhaduri U, Shettar A, Mukherjee G, Kondaiah P, Satyanarayana Rao MR. DDX5/p68 associated lncRNA LOC284454 is differentially expressed in human cancers and modulates gene expression. RNA Biol 2018; 15:214-230. [PMID: 29227193 PMCID: PMC5798960 DOI: 10.1080/15476286.2017.1397261] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/04/2017] [Accepted: 10/22/2017] [Indexed: 12/21/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are emerging as important players in regulation of gene expression in higher eukaryotes. DDX5/p68 RNA helicase protein which is involved in splicing of precursor mRNAs also interacts with lncRNAs like, SRA and mrhl, to modulate gene expression. We performed RIP-seq analysis in HEK293T cells to identify the complete repertoire of DDX5/p68 interacting transcripts including 73 single exonic (SE) lncRNAs. The LOC284454 lncRNA is the second top hit of the list of SE lncRNAs which we have characterized in detail for its molecular features and cellular functions. The RNA is located in the same primary transcript harboring miR-23a∼27a∼24-2 cluster. LOC284454 is a stable, nuclear restricted and chromatin associated lncRNA. The sequence is conserved only in primates among 26 different species and is expressed in multiple human tissues. Expression of LOC284454 is significantly reduced in breast, prostate, uterus and kidney cancer and also in breast cancer cell lines (MCF7 and T47D). Global gene expression studies upon loss and gain of function of LOC284454 revealed perturbation of genes related to cancer-related pathways. Focal adhesion and cell migration pathway genes are downregulated under overexpression condition, and these genes are significantly upregulated in breast cancer cell lines as well as breast cancer tissue samples suggesting a functional role of LOC284454 lncRNA in breast cancer pathobiology.
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Affiliation(s)
- Monalisa Das
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advance Scientific Research, Bangalore, Karnataka, India
| | - Arun Renganathan
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advance Scientific Research, Bangalore, Karnataka, India
| | - Shrinivas Nivrutti Dighe
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advance Scientific Research, Bangalore, Karnataka, India
| | - Utsa Bhaduri
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advance Scientific Research, Bangalore, Karnataka, India
| | - Abhijith Shettar
- Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, Karnataka, India
| | | | - Paturu Kondaiah
- Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, Karnataka, India
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Brandariz-Núñez A, Zeng F, Lam QN, Jin H. Sbp1 modulates the translation of Pab1 mRNA in a poly(A)- and RGG-dependent manner. RNA (NEW YORK, N.Y.) 2018; 24:43-55. [PMID: 28986506 PMCID: PMC5733569 DOI: 10.1261/rna.062547.117] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/29/2017] [Indexed: 05/13/2023]
Abstract
RNA-binding protein Sbp1 facilitates the decapping pathway in mRNA metabolism and inhibits global mRNA translation by an unclear mechanism. Here we report molecular interactions responsible for Sbp1-mediated translation inhibition of mRNA encoding the polyadenosine-binding protein (Pab1), an essential translation factor that stimulates mRNA translation and inhibits mRNA decapping in eukaryotic cells. We demonstrate that the two distal RRMs of Sbp1 bind to the poly(A) sequence in the 5'UTR of the Pab1 mRNA specifically and cooperatively while the central RGG domain of the protein interacts directly with Pab1. Furthermore, methylation of arginines in the RGG domain abolishes the protein-protein interaction and the inhibitory effect of Sbp1 on translation initiation of Pab1 mRNA. Based on these results, the underlying mechanism for Sbp1-specific translational regulation is proposed. The functional differences of Sbp1 and RGG repeats alone on transcript-specific translation were observed, and a comparison of the results suggests the importance of remodeling the 5'UTR by RNA-binding proteins in mRNA translation.
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Affiliation(s)
- Alberto Brandariz-Núñez
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA
| | - Fuxing Zeng
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA
| | - Quan Ngoc Lam
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA
| | - Hong Jin
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA
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Rogell B, Fischer B, Rettel M, Krijgsveld J, Castello A, Hentze MW. Specific RNP capture with antisense LNA/DNA mixmers. RNA (NEW YORK, N.Y.) 2017; 23:1290-1302. [PMID: 28476952 PMCID: PMC5513073 DOI: 10.1261/rna.060798.117] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 04/25/2017] [Indexed: 05/07/2023]
Abstract
RNA-binding proteins (RBPs) play essential roles in RNA biology, responding to cellular and environmental stimuli to regulate gene expression. Important advances have helped to determine the (near) complete repertoires of cellular RBPs. However, identification of RBPs associated with specific transcripts remains a challenge. Here, we describe "specific ribonucleoprotein (RNP) capture," a versatile method for the determination of the proteins bound to specific transcripts in vitro and in cellular systems. Specific RNP capture uses UV irradiation to covalently stabilize protein-RNA interactions taking place at "zero distance." Proteins bound to the target RNA are captured by hybridization with antisense locked nucleic acid (LNA)/DNA oligonucleotides covalently coupled to a magnetic resin. After stringent washing, interacting proteins are identified by quantitative mass spectrometry. Applied to in vitro extracts, specific RNP capture identifies the RBPs bound to a reporter mRNA containing the Sex-lethal (Sxl) binding motifs, revealing that the Sxl homolog sister of Sex lethal (Ssx) displays similar binding preferences. This method also revealed the repertoire of RBPs binding to 18S or 28S rRNAs in HeLa cells, including previously unknown rRNA-binding proteins.
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Affiliation(s)
- Birgit Rogell
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Bernd Fischer
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Mandy Rettel
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Jeroen Krijgsveld
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Alfredo Castello
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Matthias W Hentze
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
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Walton BM, Jackson GW, Deutz N, Cote G. Surface-enhanced Raman spectroscopy competitive binding biosensor development utilizing surface modification of silver nanocubes and a citrulline aptamer. JOURNAL OF BIOMEDICAL OPTICS 2017; 22:75002. [PMID: 28732094 PMCID: PMC5521305 DOI: 10.1117/1.jbo.22.7.075002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/30/2017] [Indexed: 05/15/2023]
Abstract
A point-of-care (PoC) device with the ability to detect biomarkers at low concentrations in bodily fluids would have an enormous potential for medical diagnostics outside the central laboratory. One method to monitor analytes at low concentrations is by using surface-enhanced Raman spectroscopy (SERS). In this preliminary study toward using SERS for PoC biosensing, the surface of colloidal silver (Ag) nanocubes has been modified to test the feasibility of a competitive binding SERS assay utilizing aptamers against citrulline. Specifically, Ag nanocubes were functionalized with mercaptobenzoic acid, as well as a heterobifunctional polyethylene glycol linker that forms an amide bond with the amino acid citrulline. After the functionalization, the nanocubes were characterized by zeta-potential, transmission electron microscopy images, ultraviolet/visible spectroscopy, and by SERS. The citrulline aptamers were developed and tested using backscattering interferometry. The data show that our surface modification method does work and that the functionalized nanoparticles can be detected using SERS down to a 24.5 picomolar level. Last, we used microscale thermophoresis to show that the aptamers bind to citrulline with at least a 50 times stronger affinity than other amino acids. Download PDF SAVE FOR LATER
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Affiliation(s)
- Brian M. Walton
- Texas A&M University, Department of Biomedical Engineering, College Station, Texas, United States
| | - George W. Jackson
- BioTex, Inc., Houston, Texas, United States
- Base Pair Biotechnologies, Inc., Pearland, Texas, United States
| | - Nicolaas Deutz
- Texas A&M University, Center for Translational Research in Aging & Longevity, Department of Health and Kinesiology, Texas, United States
| | - Gerard Cote
- Texas A&M University, Department of Biomedical Engineering, College Station, Texas, United States
- Texas A&M University, Texas A&M Engineering Experiment Station Center for Remote Health Technologies and Systems, Department of Biomedical Engineering, College Station, Texas, United States
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Chaudhary R, Gryder B, Woods WS, Subramanian M, Jones MF, Li XL, Jenkins LM, Shabalina SA, Mo M, Dasso M, Yang Y, Wakefield LM, Zhu Y, Frier SM, Moriarity BS, Prasanth KV, Perez-Pinera P, Lal A. Prosurvival long noncoding RNA PINCR regulates a subset of p53 targets in human colorectal cancer cells by binding to Matrin 3. eLife 2017; 6. [PMID: 28580901 PMCID: PMC5470874 DOI: 10.7554/elife.23244] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 05/20/2017] [Indexed: 12/19/2022] Open
Abstract
Thousands of long noncoding RNAs (lncRNAs) have been discovered, yet the function of the vast majority remains unclear. Here, we show that a p53-regulated lncRNA which we named PINCR (p53-induced noncoding RNA), is induced ~100-fold after DNA damage and exerts a prosurvival function in human colorectal cancer cells (CRC) in vitro and tumor growth in vivo. Targeted deletion of PINCR in CRC cells significantly impaired G1 arrest and induced hypersensitivity to chemotherapeutic drugs. PINCR regulates the induction of a subset of p53 targets involved in G1 arrest and apoptosis, including BTG2, RRM2B and GPX1. Using a novel RNA pulldown approach that utilized endogenous S1-tagged PINCR, we show that PINCR associates with the enhancer region of these genes by binding to RNA-binding protein Matrin 3 that, in turn, associates with p53. Our findings uncover a critical prosurvival function of a p53/PINCR/Matrin 3 axis in response to DNA damage in CRC cells. DOI:http://dx.doi.org/10.7554/eLife.23244.001 Though DNA contains the information needed to build the proteins that keep cells alive, only 2% of the DNA in a human cell codes for proteins. The remaining 98% is referred to as non-coding DNA. The information in some of these non-coding regions can still be copied into molecules of RNA, including long molecules called lncRNAs. Little is known about what lncRNAs actually do, but growing evidence suggests that these molecules are important for a number of vital processes including cell growth and survival. When the DNA in an animal cell gets damaged, the cell needs to decide whether to pause growth and repair the damage, or to kill itself if the harm is too great. One of the best-studied proteins guiding this decision is the p53 protein, which increases the number of protein-coding genes needed to carry out either option in this decision. That is to say that, p53 regulates the genes needed to kill the cell and the genes needed to temporarily pause its growth and repair the damage, which instead keeps the cell alive. So, how does the p53 protein guide the decision, and are lncRNA molecules involved? Using human colon cancer cells, Chaudhary et al. now report that when DNA is damaged, the levels of a specific lncRNA increase 100-fold. Further experiments showed that this lncRNA – named PINCR, which refers to p53-induced noncoding RNA – promotes the survival of cells. Chaudhary et al. showed that PINCR molecules do this by recruiting a protein called Matrin 3 to a certain region in the DNA called an enhancer and then links it to promoter region in the DNA of specific genes that temporarily pause cell growth but keep the cell alive. This in turn activates these ‘pro-survival genes’. In further experiments, when the PINCR molecules were essentially deleted, p53 was not able to fully activate these genes and as a result more of the cells died. Together these findings increase our knowledge of how lncRNAs can work, especially in the context of DNA damage in cancer cells. A next important step will be to uncover other roles for the PINCR molecule in both cancer and healthy cells. DOI:http://dx.doi.org/10.7554/eLife.23244.002
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Affiliation(s)
- Ritu Chaudhary
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Berkley Gryder
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Wendy S Woods
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Murugan Subramanian
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Matthew F Jones
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Xiao Ling Li
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Min Mo
- Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Mary Dasso
- Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Yuan Yang
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Lalage M Wakefield
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Yuelin Zhu
- Molecular Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | | | - Branden S Moriarity
- Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Twin Cities, United States
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Pablo Perez-Pinera
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Ashish Lal
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
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Köster T, Marondedze C, Meyer K, Staiger D. RNA-Binding Proteins Revisited - The Emerging Arabidopsis mRNA Interactome. TRENDS IN PLANT SCIENCE 2017; 22:512-526. [PMID: 28412036 DOI: 10.1016/j.tplants.2017.03.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 02/10/2017] [Accepted: 03/09/2017] [Indexed: 06/07/2023]
Abstract
RNA-protein interaction is an important checkpoint to tune gene expression at the RNA level. Global identification of proteins binding in vivo to mRNA has been possible through interactome capture - where proteins are fixed to target RNAs by UV crosslinking and purified through affinity capture of polyadenylated RNA. In Arabidopsis over 500 RNA-binding proteins (RBPs) enriched in UV-crosslinked samples have been identified. As in mammals and yeast, the mRNA interactomes came with a few surprises. For example, a plethora of the proteins caught on RNA had not previously been linked to RNA-mediated processes, for example proteins of intermediary metabolism. Thus, the studies provide unprecedented insights into the composition of the mRNA interactome, highlighting the complexity of RNA-mediated processes.
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Affiliation(s)
- Tino Köster
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Claudius Marondedze
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Cambridge, UK; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Katja Meyer
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Dorothee Staiger
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany.
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Pereira P, Queiroz JA, Figueiras A, Sousa F. Current progress on microRNAs-based therapeutics in neurodegenerative diseases. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27882692 DOI: 10.1002/wrna.1409] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/07/2016] [Accepted: 10/17/2016] [Indexed: 12/17/2022]
Abstract
MicroRNAs (miRNAs)-based therapy has recently emerged as a promising strategy in the treatments of neurodegenerative diseases. Thus, in this review, the most recent and important challenges and advances on the development of miRNA therapeutics for brain targeting are discussed. In particular, this review highlights current knowledge and progress in the field of manufacturing, recovery, isolation, purification, and analysis of these therapeutic oligonucleotides. Finally, the available miRNA delivery systems are reviewed and an analysis is presented in what concerns to the current challenges that have to be addressed to ensure their specificity and efficacy. Overall, it is intended to provide a perspective on the future of miRNA-based therapeutics, focusing the biotechnological approach to obtain miRNAs. WIREs RNA 2017, 8:e1409. doi: 10.1002/wrna.1409 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Patrícia Pereira
- CICS-UBI - Health Sciences Research Centre, Universidade da Beira Interior, Covilhã, Portugal
| | - João A Queiroz
- CICS-UBI - Health Sciences Research Centre, Universidade da Beira Interior, Covilhã, Portugal
| | - Ana Figueiras
- CICS-UBI - Health Sciences Research Centre, Universidade da Beira Interior, Covilhã, Portugal.,REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy, Universidade de Coimbra, Coimbra, Portugal
| | - Fani Sousa
- CICS-UBI - Health Sciences Research Centre, Universidade da Beira Interior, Covilhã, Portugal
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Mi L, Zhao XY, Li S, Yang G, Lin JD. Conserved function of the long noncoding RNA Blnc1 in brown adipocyte differentiation. Mol Metab 2016; 6:101-110. [PMID: 28123941 PMCID: PMC5220282 DOI: 10.1016/j.molmet.2016.10.010] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 10/27/2016] [Accepted: 10/27/2016] [Indexed: 01/23/2023] Open
Abstract
OBJECTIVE Long noncoding RNAs (lncRNAs) are emerging as important regulators of diverse biological processes. Recent work has demonstrated that the inducible lncRNA Blnc1 stimulates thermogenic gene expression during brown and beige adipocyte differentiation. However, whether Blnc1 is functionally conserved in humans has not been explored. In addition, the molecular basis of the Blnc1 ribonucleoprotein complex in thermogenic gene induction remains incompletely understood. The aims of the current study were to: i) investigate functional conservation of Blnc1 in mice and humans and ii) elucidate the molecular mechanisms by which Blnc1 controls the thermogenic gene program in brown adipocytes. METHODS Full-length human Blnc1 was cloned and examined for its ability to stimulate brown adipocyte differentiation. Different truncation mutants of Blnc1 were generated to identify functional RNA domains responsible for thermogenic gene induction. RNA-protein interaction studies were performed to delineate the molecular features of the Blnc1 ribonucleoprotein complex. RESULTS Blnc1 is highly conserved in mice and humans at the sequence and function levels, both capable of stimulating brown adipocyte gene expression. A conserved RNA domain was identified to be required and sufficient for the biological activity of Blnc1. We identified hnRNPU as an RNA-binding protein that facilitates the assembly and augments the transcriptional function of the Blnc1/EBF2 ribonucleoprotein complex. CONCLUSIONS Blnc1 is a conserved lncRNA that promotes thermogenic gene expression in brown adipocytes through formation of the Blnc1/hnRNPU/EBF2 ribonucleoprotein complex.
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Key Words
- ATP5A, ATP synthase, H+ transporting, mitochondrial F1 complex, alpha 1
- BAT, brown adipose tissue
- Blnc1
- Brown adipocyte differentiation
- Brown fat
- Cox7a1, cytochrome c oxidase subunit 7A1
- Dio2, deiodinase, iodothyronine type II
- EBF2
- EBF2, early B cell factor 2
- Elovl3, elongation of very long chain fatty acids like 3
- FABP4, fatty acid binding protein 4
- PPARγ, peroxisome proliferator-activated receptor gamma
- Ppargc1a, peroxisome proliferator-activated receptor gamma coactivator 1-alpha
- Pparα, peroxisome proliferator-activated receptor alpha
- Prdm16, PR domain zinc finger protein 16
- RACE, rapid amplification of cDNA ends
- SDHB, succinate dehydrogenase complex iron sulfur subunit B
- Thermogenesis
- UQCRC2, ubiquinol-cytochrome c reductase core protein II
- Ucp1, uncoupling protein 1
- lncRNA
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Affiliation(s)
- Lin Mi
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling, China; Life Sciences Institute and Department of Cell & Developmental Biology, University of Michigan Medical Center, Ann Arbor, MI 48109, USA
| | - Xu-Yun Zhao
- Life Sciences Institute and Department of Cell & Developmental Biology, University of Michigan Medical Center, Ann Arbor, MI 48109, USA
| | - Siming Li
- Life Sciences Institute and Department of Cell & Developmental Biology, University of Michigan Medical Center, Ann Arbor, MI 48109, USA
| | - Gongshe Yang
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling, China.
| | - Jiandie D Lin
- Life Sciences Institute and Department of Cell & Developmental Biology, University of Michigan Medical Center, Ann Arbor, MI 48109, USA.
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Jazurek M, Ciesiolka A, Starega-Roslan J, Bilinska K, Krzyzosiak WJ. Identifying proteins that bind to specific RNAs - focus on simple repeat expansion diseases. Nucleic Acids Res 2016; 44:9050-9070. [PMID: 27625393 PMCID: PMC5100574 DOI: 10.1093/nar/gkw803] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/01/2016] [Indexed: 12/11/2022] Open
Abstract
RNA–protein complexes play a central role in the regulation of fundamental cellular processes, such as mRNA splicing, localization, translation and degradation. The misregulation of these interactions can cause a variety of human diseases, including cancer and neurodegenerative disorders. Recently, many strategies have been developed to comprehensively analyze these complex and highly dynamic RNA–protein networks. Extensive efforts have been made to purify in vivo-assembled RNA–protein complexes. In this review, we focused on commonly used RNA-centric approaches that involve mass spectrometry, which are powerful tools for identifying proteins bound to a given RNA. We present various RNA capture strategies that primarily depend on whether the RNA of interest is modified. Moreover, we briefly discuss the advantages and limitations of in vitro and in vivo approaches. Furthermore, we describe recent advances in quantitative proteomics as well as the methods that are most commonly used to validate robust mass spectrometry data. Finally, we present approaches that have successfully identified expanded repeat-binding proteins, which present abnormal RNA–protein interactions that result in the development of many neurological diseases.
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Affiliation(s)
- Magdalena Jazurek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Adam Ciesiolka
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Julia Starega-Roslan
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Katarzyna Bilinska
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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Svensen N, Peersen OB, Jaffrey SR. Peptide Synthesis on a Next-Generation DNA Sequencing Platform. Chembiochem 2016; 17:1628-35. [PMID: 27385640 PMCID: PMC5183537 DOI: 10.1002/cbic.201600298] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Indexed: 11/11/2022]
Abstract
Methods for displaying large numbers of peptides on solid surfaces are essential for high-throughput characterization of peptide function and binding properties. Here we describe a method for converting the >10(7) flow cell-bound clusters of identical DNA strands generated by the Illumina DNA sequencing technology into clusters of complementary RNA, and subsequently peptide clusters. We modified the flow-cell-bound primers with ribonucleotides thus enabling them to be used by poliovirus polymerase 3D(pol) . The primers hybridize to the clustered DNA thus leading to RNA clusters. The RNAs fold into functional protein- or small molecule-binding aptamers. We used the mRNA-display approach to synthesize flow-cell-tethered peptides from these RNA clusters. The peptides showed selective binding to cognate antibodies. The methods described here provide an approach for using DNA clusters to template peptide synthesis on an Illumina flow cell, thus providing new opportunities for massively parallel peptide-based assays.
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Affiliation(s)
- Nina Svensen
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, 10065, USA
| | - Olve B Peersen
- Department of Biochemistry, Colorado State University, Fort Collins, CO, 80523, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, 10065, USA.
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Li H, Zhang K, Pi F, Guo S, Shlyakhtenko L, Chiu W, Shu D, Guo P. Controllable Self-Assembly of RNA Tetrahedrons with Precise Shape and Size for Cancer Targeting. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:7501-7. [PMID: 27322097 PMCID: PMC5059845 DOI: 10.1002/adma.201601976] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 05/11/2016] [Indexed: 05/20/2023]
Abstract
RNA tetrahedral nanoparticles with two different sizes are successfully assembled by a one-pot bottom-up approach with high efficiency and thermal stability. The reported design principles can be extended to construct higher-order polyhedral RNA architectures for various applications such as targeted cancer imaging and therapy.
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Affiliation(s)
- Hui Li
- College of Pharmacy/Division of Pharmaceutics and Pharmaceutical Chemistry, College of Medicine/Department of Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Kaiming Zhang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Fengmei Pi
- College of Pharmacy/Division of Pharmaceutics and Pharmaceutical Chemistry, College of Medicine/Department of Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Sijin Guo
- College of Pharmacy/Division of Pharmaceutics and Pharmaceutical Chemistry, College of Medicine/Department of Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Luda Shlyakhtenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Wah Chiu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Dan Shu
- College of Pharmacy/Division of Pharmaceutics and Pharmaceutical Chemistry, College of Medicine/Department of Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Peixuan Guo
- College of Pharmacy/Division of Pharmaceutics and Pharmaceutical Chemistry, College of Medicine/Department of Physiology and Cell Biology/Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210, USA.
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47
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Li Z, Lau C, Lu J. Effect of the Concentration Difference between Magnesium Ions and Total Ribonucleotide Triphosphates in Governing the Specificity of T7 RNA Polymerase-Based Rolling Circle Transcription for Quantitative Detection. Anal Chem 2016; 88:6078-83. [PMID: 27167591 DOI: 10.1021/acs.analchem.6b01460] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
T7 RNA polymerase-based rolling circle transcription (RCT) is a more powerful tool than universal runoff transcription and traditional DNA polymerase-based rolling circle amplification (RCA). However, RCT is rarely employed in quantitative detection due to its poor specificity for small single-stranded DNA (ssDNA), which can be transcribed efficiently by T7 RNA polymerase even without a promoter. Herein we show that the concentration difference between Mg(2+) and total ribonucleotide triphosphates (rNTPs) radically governs the specificity of T7 RNA polymerase. Only when the total rNTP concentration is 9 mM greater than the Mg(2+) concentration can T7 RNA polymerase transcribe ssDNA specifically and efficiently. This knowledge improves our traditional understanding of T7 RNA polymerase and makes convenient application of RCT in quantitative detection possible. Subsequently, an RCT-based label-free chemiluminescence method for microRNA detection was designed to test the capability of this sensing platform. Using this simple method, microRNA as low as 20 amol could be quantitatively detected. The results reveal that the developed sensing platform holds great potential for further applications in the quantitative detection of a variety of targets.
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Affiliation(s)
- Zhiyan Li
- School of Pharmacy, Fudan University , 826 Zhangheng Road, Shanghai 201203, China
| | - Choiwan Lau
- School of Pharmacy, Fudan University , 826 Zhangheng Road, Shanghai 201203, China
| | - Jianzhong Lu
- School of Pharmacy, Fudan University , 826 Zhangheng Road, Shanghai 201203, China
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48
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Patel KA, Sethi R, Dhara AR, Roy I. Challenges with osmolytes as inhibitors of protein aggregation: Can nucleic acid aptamers provide an answer? Int J Biol Macromol 2016; 100:75-88. [PMID: 27156694 DOI: 10.1016/j.ijbiomac.2016.05.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 02/07/2023]
Abstract
Protein aggregation follows some common motifs. Whether in the formation of inclusion bodies in heterologous overexpression systems or inclusions in protein conformational diseases, or aggregation during storage or transport of protein formulations, aggregates form cross beta-sheet structures and stain with amyloidophilic dyes like Thioflavin T and Congo Red, irrespective of the concerned protein. Traditionally, osmolytes are used to stabilize proteins against stress conditions. They are employed right from protein expression, through production and purification, to formulation and administration. As osmolytes interact with the solvent, the differential effect of the stress condition on the solvent mostly determines the effect of the osmolyte on protein stability. Nucleic acid aptamers, on the other hand, are highly specific for their targets. When selected against monomeric, natively folded proteins, they bind to them with very high affinity. This binding inhibits the unfolding of the protein and/or monomer-monomer interaction which are the initial common steps of protein aggregation. Thus, by changing the approach to a protein-centric model, aptamers are able to function as universal stabilizers of proteins. The review discusses cases where osmolytes were unable to provide stabilization to proteins against different stress conditions, a gap which the aptamers seem to be able to fill.
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Affiliation(s)
- Kinjal A Patel
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Ratnika Sethi
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Anita R Dhara
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160 062, India.
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Affinity approaches in RNAi-based therapeutics purification. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1021:45-56. [DOI: 10.1016/j.jchromb.2016.01.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 01/05/2016] [Accepted: 01/12/2016] [Indexed: 02/07/2023]
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Abstract
In the last few decades, small regulatory RNA (sRNA) molecules emerged as key regulators in every kingdom of life. Resolving the full targetome of sRNAs has however remained a challenge. To address this, we used an in vivo tagging MS2-affinity purification protocol coupled with RNA sequencing technology, namely MAPS, to assemble full bacterial small RNAs targetomes. The impressive potential of MAPS has been supported by a number of reports. Here, we concisely overview RNA-tagging history that preceded the development of the MAPS assay and expose the range of possible uses of this technology.
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Affiliation(s)
- Marie-Claude Carrier
- a Department of Biochemistry , RNA Group, Université de Sherbrooke , Sherbrooke, Québec , Canada
| | - David Lalaouna
- a Department of Biochemistry , RNA Group, Université de Sherbrooke , Sherbrooke, Québec , Canada
| | - Eric Massé
- a Department of Biochemistry , RNA Group, Université de Sherbrooke , Sherbrooke, Québec , Canada
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