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For: Zhang J, Tan D, DeRose EF, Perera L, Dominski Z, Marzluff WF, Tong L, Hall TM. Molecular mechanisms for the regulation of histone mRNA stem-loop-binding protein by phosphorylation. Proc Natl Acad Sci U S A 2014;111:E2937-46. [PMID: 25002523 DOI: 10.1073/pnas.1406381111] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]  Open
Number Cited by Other Article(s)
1
Hegazy YA, Dhahri H, El Osmani N, George S, Chandler DP, Fondufe-Mittendorf YN. Histone variants: The bricks that fit differently. J Biol Chem 2025;301:108048. [PMID: 39638247 PMCID: PMC11742582 DOI: 10.1016/j.jbc.2024.108048] [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: 08/06/2024] [Revised: 10/28/2024] [Accepted: 10/31/2024] [Indexed: 12/07/2024]  Open
2
Qiu C, Zhang Z, Wine RN, Campbell ZT, Zhang J, Hall TMT. Intra- and inter-molecular regulation by intrinsically-disordered regions governs PUF protein RNA binding. Nat Commun 2023;14:7323. [PMID: 37953271 PMCID: PMC10641069 DOI: 10.1038/s41467-023-43098-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/30/2023] [Indexed: 11/14/2023]  Open
3
Imdad MJ, Khan MN, Alam HS, Khan AB, Mirani ZA, Khan A, Ahmed F. Design and in silico analysis of mRNA vaccine construct against Salmonella. J Biomol Struct Dyn 2023;41:7248-7264. [PMID: 36093938 DOI: 10.1080/07391102.2022.2119280] [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: 05/31/2022] [Accepted: 08/24/2022] [Indexed: 10/14/2022]
4
Christoffer C, Kihara D. Modeling protein-nucleic acid complexes with extremely large conformational changes using Flex-LZerD. Proteomics 2023;23:e2200322. [PMID: 36529945 PMCID: PMC10448949 DOI: 10.1002/pmic.202200322] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
5
Zaharias S, Fargason T, Greer R, Song Y, Zhang J. Electronegative clusters modulate folding status and RNA binding of unstructured RNA-binding proteins. Protein Sci 2023;32:e4643. [PMID: 37060324 PMCID: PMC10127258 DOI: 10.1002/pro.4643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/02/2023] [Accepted: 04/12/2023] [Indexed: 04/16/2023]
6
Shine M, Harris SE, Pellegrene KA, Kensinger AH, Mihailescu MR, Evanseck JD, Lackey PE. Uridylation of the histone mRNA stem-loop weakens binding interactions with SLBP while maintaining interactions with 3'hExo. RNA Biol 2023;20:469-481. [PMID: 37516934 PMCID: PMC10388802 DOI: 10.1080/15476286.2023.2171760] [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: 07/08/2022] [Revised: 12/03/2022] [Accepted: 01/19/2023] [Indexed: 07/31/2023]  Open
7
Design and Immunoinformatic Assessment of Candidate Multivariant mRNA Vaccine Construct against Immune Escape Variants of SARS-CoV-2. Polymers (Basel) 2022;14:polym14163263. [PMID: 36015519 PMCID: PMC9414445 DOI: 10.3390/polym14163263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/05/2022] [Accepted: 08/06/2022] [Indexed: 12/12/2022]  Open
8
Tucker MR, Piana S, Tan D, LeVine MV, Shaw DE. Development of Force Field Parameters for the Simulation of Single- and Double-Stranded DNA Molecules and DNA-Protein Complexes. J Phys Chem B 2022;126:4442-4457. [PMID: 35694853 PMCID: PMC9234960 DOI: 10.1021/acs.jpcb.1c10971] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
9
Ma J, Wang Y. Studies on Viroid Shed Light on the Role of RNA Three-Dimensional Structural Motifs in RNA Trafficking in Plants. FRONTIERS IN PLANT SCIENCE 2022;13:836267. [PMID: 35401640 PMCID: PMC8983868 DOI: 10.3389/fpls.2022.836267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/23/2022] [Indexed: 05/05/2023]
10
Bradford BR, Jin C. Stem-loop binding protein and metal carcinogenesis. Semin Cancer Biol 2021;76:38-44. [PMID: 34416372 PMCID: PMC8627438 DOI: 10.1016/j.semcancer.2021.08.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/06/2021] [Accepted: 08/16/2021] [Indexed: 11/21/2022]
11
Gutierrez PA, Baughman K, Sun Y, Tong L. A real-time fluorescence assay for CPSF73, the nuclease for pre-mRNA 3'-end processing. RNA (NEW YORK, N.Y.) 2021;27:1148-1154. [PMID: 34230059 PMCID: PMC8457007 DOI: 10.1261/rna.078764.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/17/2021] [Indexed: 05/09/2023]
12
U7 deciphered: the mechanism that forms the unusual 3' end of metazoan replication-dependent histone mRNAs. Biochem Soc Trans 2021;49:2229-2240. [PMID: 34351387 DOI: 10.1042/bst20210323] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 11/17/2022]
13
Machado de Amorim A, Chakrabarti S. Assembly of multicomponent machines in RNA metabolism: A common theme in mRNA decay pathways. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021;13:e1684. [PMID: 34351053 DOI: 10.1002/wrna.1684] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 11/05/2022]
14
Zaharias S, Zhang Z, Davis K, Fargason T, Cashman D, Yu T, Zhang J. Intrinsically disordered electronegative clusters improve stability and binding specificity of RNA-binding proteins. J Biol Chem 2021;297:100945. [PMID: 34246632 PMCID: PMC8348266 DOI: 10.1016/j.jbc.2021.100945] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/28/2021] [Accepted: 07/07/2021] [Indexed: 11/25/2022]  Open
15
Alvarez DR, Ospina A, Barwell T, Zheng B, Dey A, Li C, Basu S, Shi X, Kadri S, Chakrabarti K. The RNA structurome in the asexual blood stages of malaria pathogen plasmodium falciparum. RNA Biol 2021;18:2480-2497. [PMID: 33960872 DOI: 10.1080/15476286.2021.1926747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]  Open
16
Sun Y, Aik WS, Yang XC, Marzluff WF, Dominski Z, Tong L. Reconstitution and biochemical assays of an active human histone pre-mRNA 3'-end processing machinery. Methods Enzymol 2021;655:291-324. [PMID: 34183127 DOI: 10.1016/bs.mie.2021.03.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
17
Yang XC, Sun Y, Aik WS, Marzluff WF, Tong L, Dominski Z. Studies with recombinant U7 snRNP demonstrate that CPSF73 is both an endonuclease and a 5'-3' exonuclease. RNA (NEW YORK, N.Y.) 2020;26:1345-1359. [PMID: 32554553 PMCID: PMC7491329 DOI: 10.1261/rna.076273.120] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 05/26/2020] [Indexed: 05/24/2023]
18
Chen D, Chen QY, Wang Z, Zhu Y, Kluz T, Tan W, Li J, Wu F, Fang L, Zhang X, He R, Shen S, Sun H, Zang C, Jin C, Costa M. Polyadenylation of Histone H3.1 mRNA Promotes Cell Transformation by Displacing H3.3 from Gene Regulatory Elements. iScience 2020;23:101518. [PMID: 32920490 PMCID: PMC7492993 DOI: 10.1016/j.isci.2020.101518] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 07/17/2020] [Accepted: 08/26/2020] [Indexed: 12/17/2022]  Open
19
Sun Y, Zhang Y, Aik WS, Yang XC, Marzluff WF, Walz T, Dominski Z, Tong L. Structure of an active human histone pre-mRNA 3'-end processing machinery. Science 2020;367:700-703. [PMID: 32029631 DOI: 10.1126/science.aaz7758] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/31/2019] [Indexed: 01/10/2023]
20
Bucholc K, Aik WS, Yang XC, Wang K, Zhou ZH, Dadlez M, Marzluff WF, Tong L, Dominski Z. Composition and processing activity of a semi-recombinant holo U7 snRNP. Nucleic Acids Res 2020;48:1508-1530. [PMID: 31819999 PMCID: PMC7026596 DOI: 10.1093/nar/gkz1148] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 10/29/2019] [Accepted: 11/25/2019] [Indexed: 11/14/2022]  Open
21
Wu X, Qu L, Li S, Guo Y, He J, Liu M, Liu X, Lin H. Molecular characterization and expression patterns of stem-loop binding protein (SLBP) genes in protogynous hermaphroditic grouper, Epinephelus coioides. Gene 2019;700:120-130. [PMID: 30910559 DOI: 10.1016/j.gene.2019.02.092] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/21/2019] [Accepted: 02/01/2019] [Indexed: 12/31/2022]
22
Application of tyrosine-tryptophan fluorescence resonance energy transfer in monitoring protein size changes. Anal Biochem 2018;557:142-150. [DOI: 10.1016/j.ab.2018.07.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 07/19/2018] [Accepted: 07/23/2018] [Indexed: 11/19/2022]
23
Marzluff WF, Koreski KP. Birth and Death of Histone mRNAs. Trends Genet 2017;33:745-759. [PMID: 28867047 DOI: 10.1016/j.tig.2017.07.014] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 07/24/2017] [Accepted: 07/28/2017] [Indexed: 12/22/2022]
24
Cook KB, Vembu S, Ha KCH, Zheng H, Laverty KU, Hughes TR, Ray D, Morris QD. RNAcompete-S: Combined RNA sequence/structure preferences for RNA binding proteins derived from a single-step in vitro selection. Methods 2017;126:18-28. [PMID: 28651966 DOI: 10.1016/j.ymeth.2017.06.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/16/2017] [Accepted: 06/21/2017] [Indexed: 12/15/2022]  Open
25
Skrajna A, Yang XC, Bucholc K, Zhang J, Hall TMT, Dadlez M, Marzluff WF, Dominski Z. U7 snRNP is recruited to histone pre-mRNA in a FLASH-dependent manner by two separate regions of the stem-loop binding protein. RNA (NEW YORK, N.Y.) 2017;23:938-951. [PMID: 28289156 PMCID: PMC5435866 DOI: 10.1261/rna.060806.117] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 03/09/2017] [Indexed: 05/07/2023]
26
Lampert F, Brodersen MML, Peter M. Guard the guardian: A CRL4 ligase stands watch over histone production. Nucleus 2017;8:134-143. [PMID: 28072566 DOI: 10.1080/19491034.2016.1276143] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]  Open
27
Bernat V, Disney MD. RNA Structures as Mediators of Neurological Diseases and as Drug Targets. Neuron 2015;87:28-46. [PMID: 26139368 PMCID: PMC4508199 DOI: 10.1016/j.neuron.2015.06.012] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
28
Stefanovic L, Longo L, Zhang Y, Stefanovic B. Characterization of binding of LARP6 to the 5' stem-loop of collagen mRNAs: implications for synthesis of type I collagen. RNA Biol 2014;11:1386-401. [PMID: 25692237 PMCID: PMC4615758 DOI: 10.1080/15476286.2014.996467] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 10/31/2014] [Indexed: 01/11/2023]  Open
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