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Full-length direct RNA sequencing reveals extensive remodeling of RNA expression, processing and modification in aging Caenorhabditis elegans. Nucleic Acids Res. 2024 Dec 11; 52(22):13896-13913. Schiksnis EC, Nicastro IA, Pasquinelli AE. PMID: 39558169; PMCID: PMC11662692.
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Full-length direct RNA sequencing reveals extensive remodeling of RNA expression, processing and modification in aging Caenorhabditis elegans. bioRxiv. 2024 Jun 22. Schiksnis EC, Nicastro IA, Pasquinelli AE. PMID: 38948813; PMCID: PMC11213008.
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Expression, not sequence, distinguishes miR-238 from its miR-239ab sister miRNAs in promoting longevity in Caenorhabditis elegans. PLoS Genet. 2023 11; 19(11):e1011055. Chipman LB, Luc S, Nicastro IA, Hulahan JJ, Dann DC, Bodas DM, Pasquinelli AE. PMID: 38011256; PMCID: PMC10703411.
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Nuclear and cytoplasmic poly(A) binding proteins (PABPs) favor distinct transcripts and isoforms. Nucleic Acids Res. 2022 05 06; 50(8):4685-4702. Nicholson-Shaw AL, Kofman ER, Yeo GW, Pasquinelli AE. PMID: 35438785; PMCID: PMC9071453.
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New Roles for MicroRNAs in Old Worms. Front Aging. 2022; 3:871226. Elder CR, Pasquinelli AE. PMID: 35821862; PMCID: PMC9261348.
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Caenorhabditis elegans transposable elements harbor diverse transcription factor DNA-binding sites. G3 (Bethesda). 2022 03 04; 12(3). Garrigues JM, Pasquinelli AE. PMID: 35088854; PMCID: PMC8896005.
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Recovery from heat shock requires the microRNA pathway in Caenorhabditis elegans. PLoS Genet. 2021 08; 17(8):e1009734. Pagliuso DC, Bodas DM, Pasquinelli AE. PMID: 34351906; PMCID: PMC8370650.
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Auxin-independent depletion of degron-tagged proteins by TIR1. MicroPubl Biol. 2020 Jan 28; 2020. Schiksnis E, Nicholson A, Modena M, Pule M, Arribere J, Pasquinelli A. PMID: 32550513; PMCID: PMC7252403.
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Diversification of the Caenorhabditis heat shock response by Helitron transposable elements. Elife. 2019 12 11; 8. Garrigues JM, Tsu BV, Daugherty MD, Pasquinelli AE. PMID: 31825311; PMCID: PMC6927752.
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Remodeling of the Caenorhabditis elegans non-coding RNA transcriptome by heat shock. Nucleic Acids Res. 2019 10 10; 47(18):9829-9841. Schreiner WP, Pagliuso DC, Garrigues JM, Chen JS, Aalto AP, Pasquinelli AE. PMID: 31396626; PMCID: PMC6765114.
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Todos Santos small RNA symposium. RNA Biol. 2019 11; 16(11):1526-1530. Winkenbach LP, Doser R, Reed KJ, Pasquinelli AE, Phillips CM, Claycomb JM. PMID: 31397621; PMCID: PMC6779373.
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RNA interference may result in unexpected phenotypes in Caenorhabditis elegans. Nucleic Acids Res. 2019 05 07; 47(8):3957-3969. De-Souza EA, Camara H, Salgueiro WG, Moro RP, Knittel TL, Tonon G, Pinto S, Pinca APF, Antebi A, Pasquinelli AE, Massirer KB, Mori MA. PMID: 30838421; PMCID: PMC6486631.
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miRNA Targeting: Growing beyond the Seed. Trends Genet. 2019 03; 35(3):215-222. Chipman LB, Pasquinelli AE. PMID: 30638669; PMCID: PMC7083087.
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Tales of Detailed Poly(A) Tails. Trends Cell Biol. 2019 03; 29(3):191-200. Nicholson AL, Pasquinelli AE. PMID: 30503240; PMCID: PMC7083203.
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Opposing roles of microRNA Argonautes during Caenorhabditis elegans aging. PLoS Genet. 2018 06; 14(6):e1007379. Aalto AP, Nicastro IA, Broughton JP, Chipman LB, Schreiner WP, Chen JS, Pasquinelli AE. PMID: 29927939; PMCID: PMC6013023.
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A rADAR defense against RNAi. Genes Dev. 2018 02 01; 32(3-4):199-201. Pasquinelli AE. PMID: 29491134; PMCID: PMC5859962.
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Detection of microRNA-Target Interactions by Chimera PCR (ChimP). Methods Mol Biol. 2018; 1823:153-165. Broughton JP, Pasquinelli AE. PMID: 29959680.
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Short poly(A) tails are a conserved feature of highly expressed genes. Nat Struct Mol Biol. 2017 Dec; 24(12):1057-1063. Lima SA, Chipman LB, Nicholson AL, Chen YH, Yee BA, Yeo GW, Coller J, Pasquinelli AE. PMID: 29106412; PMCID: PMC5877826.
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Pairing beyond the Seed Supports MicroRNA Targeting Specificity. Mol Cell. 2016 10 20; 64(2):320-333. Broughton JP, Lovci MT, Huang JL, Yeo GW, Pasquinelli AE. PMID: 27720646; PMCID: PMC5074850.
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A sense-able microRNA. Genes Dev. 2016 09 15; 30(18):2019-2020. Pasquinelli AE. PMID: 27798846; PMCID: PMC5066609.
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A tale of two sequences: microRNA-target chimeric reads. Genet Sel Evol. 2016 Apr 04; 48:31. Broughton JP, Pasquinelli AE. PMID: 27044644; PMCID: PMC4819279.
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Splicing remodels the let-7 primary microRNA to facilitate Drosha processing in Caenorhabditis elegans. RNA. 2015 Aug; 21(8):1396-403. Mondol V, Ahn BC, Pasquinelli AE. PMID: 26081559; PMCID: PMC4509930.
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MicroRNAs: heralds of the noncoding RNA revolution. RNA. 2015 Apr; 21(4):709-10. Pasquinelli AE. PMID: 25780202; PMCID: PMC4371344.
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Period homolog LIN-42 regulates miRNA transcription to impact developmental timing. Worm. 2014 Oct-Dec; 3(4):e974453. Van Wynsberghe PM, Pasquinelli AE. PMID: 26435883; PMCID: PMC4589994.
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The Period protein homolog LIN-42 negatively regulates microRNA biogenesis in C. elegans. Dev Biol. 2014 Jun 15; 390(2):126-35. Van Wynsberghe PM, Finnegan EF, Stark T, Angelus EP, Homan KE, Yeo GW, Pasquinelli AE. PMID: 24699545; PMCID: PMC4077587.
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Identification of miRNAs and their targets in C. elegans. Adv Exp Med Biol. 2014; 825:431-50. Lima SA, Pasquinelli AE. PMID: 25201113.
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The primary target of let-7 microRNA. Biochem Soc Trans. 2013 Aug; 41(4):821-4. Pasquinelli AE. PMID: 23863138.
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Identifying Argonaute binding sites in Caenorhabditis elegans using iCLIP. Methods. 2013 Sep 15; 63(2):119-25. Broughton JP, Pasquinelli AE. PMID: 23583680; PMCID: PMC3749250.
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Functional genomic analysis of the let-7 regulatory network in Caenorhabditis elegans. PLoS Genet. 2013; 9(3):e1003353. Hunter SE, Finnegan EF, Zisoulis DG, Lovci MT, Melnik-Martinez KV, Yeo GW, Pasquinelli AE. PMID: 23516374; PMCID: PMC3597506.
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MicroRNAs that interfere with RNAi. Worm. 2013 Jan 01; 2(1):e21835. Massirer KB, Pasquinelli AE. PMID: 24058860; PMCID: PMC3670461.
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Multiple cis-elements and trans-acting factors regulate dynamic spatio-temporal transcription of let-7 in Caenorhabditis elegans. Dev Biol. 2013 Feb 01; 374(1):223-33. Kai ZS, Finnegan EF, Huang S, Pasquinelli AE. PMID: 23201578; PMCID: PMC3548979.
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MicroRNA biogenesis: regulating the regulators. Crit Rev Biochem Mol Biol. 2013 Jan-Feb; 48(1):51-68. Finnegan EF, Pasquinelli AE. PMID: 23163351; PMCID: PMC3557704.
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Birthing histone mRNAs by CSR-1 section. EMBO J. 2012 Oct 03; 31(19):3790-1. Pasquinelli AE. PMID: 22960639; PMCID: PMC3463852.
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Autoregulation of microRNA biogenesis by let-7 and Argonaute. Nature. 2012 Jun 28; 486(7404):541-4. Zisoulis DG, Kai ZS, Chang RK, Pasquinelli AE. PMID: 22722835; PMCID: PMC3387326.
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Small non-coding RNAs mount a silent revolution in gene expression. Curr Opin Cell Biol. 2012 Jun; 24(3):333-40. Aalto AP, Pasquinelli AE. PMID: 22464106; PMCID: PMC3372702.
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MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship. Nat Rev Genet. 2012 Mar 13; 13(4):271-82. Pasquinelli AE. PMID: 22411466.
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The miR-35-41 family of microRNAs regulates RNAi sensitivity in Caenorhabditis elegans. PLoS Genet. 2012; 8(3):e1002536. Massirer KB, Perez SG, Mondol V, Pasquinelli AE. PMID: 22412382; PMCID: PMC3297572.
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A team effort blocks the ribosome in its tracks. Nat Struct Mol Biol. 2012 Feb 03; 19(2):133-4. Pasquinelli AE. PMID: 22301874.
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Let's make it happen: the role of let-7 microRNA in development. Curr Top Dev Biol. 2012; 99:1-30. Mondol V, Pasquinelli AE. PMID: 22365733.
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LIN-28 co-transcriptionally binds primary let-7 to regulate miRNA maturation in Caenorhabditis elegans. Nat Struct Mol Biol. 2011 Mar; 18(3):302-8. Van Wynsberghe PM, Kai ZS, Massirer KB, Burton VH, Yeo GW, Pasquinelli AE. PMID: 21297634; PMCID: PMC3077891.
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Analysis of microRNA expression and function. Methods Cell Biol. 2011; 106:219-252. Van Wynsberghe PM, Chan SP, Slack FJ, Pasquinelli AE. PMID: 22118279; PMCID: PMC4314212.
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Comprehensive identification of miRNA target sites in live animals. Methods Mol Biol. 2011; 732:169-85. Zisoulis DG, Yeo GW, Pasquinelli AE. PMID: 21431713.
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Regulation of lin-4 miRNA expression, organismal growth and development by a conserved RNA binding protein in C. elegans. Dev Biol. 2010 Dec 15; 348(2):210-21. Bracht JR, Van Wynsberghe PM, Mondol V, Pasquinelli AE. PMID: 20937268; PMCID: PMC2982876.
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Molecular biology. Paring miRNAs through pairing. Science. 2010 Jun 18; 328(5985):1494-5. Pasquinelli AE. PMID: 20558697.
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A distinct microRNA signature for definitive endoderm derived from human embryonic stem cells. Stem Cells Dev. 2010 Jun; 19(6):797-807. Hinton A, Afrikanova I, Wilson M, King CC, Maurer B, Yeo GW, Hayek A, Pasquinelli AE. PMID: 19807270.
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MicroRNAs and cancer: a meeting summary of the eponymous Keystone Conference. Epigenetics. 2010 Feb 16; 5(2):164-8. Godshalk SE, Melnik-Martinez KV, Pasquinelli AE, Slack FJ. PMID: 20168081.
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A genome wide view of hunchback-like-1 targets. Cell Cycle. 2010 Jan 15; 9(2):230-1. Kai Z, Pasquinelli AE. PMID: 20061795.
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Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans. Nat Struct Mol Biol. 2010 Feb; 17(2):173-9. Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo GW. PMID: 20062054; PMCID: PMC2834287.
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MicroRNA assassins: factors that regulate the disappearance of miRNAs. Nat Struct Mol Biol. 2010 Jan; 17(1):5-10. Kai ZS, Pasquinelli AE. PMID: 20051982; PMCID: PMC6417416.
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Uncoupling of lin-14 mRNA and protein repression by nutrient deprivation in Caenorhabditis elegans. RNA. 2009 Mar; 15(3):400-5. Holtz J, Pasquinelli AE. PMID: 19155321; PMCID: PMC2657013.
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Computational prediction and experimental validation of Ciona intestinalis microRNA genes. BMC Genomics. 2007 Nov 29; 8:445. Norden-Krichmar TM, Holtz J, Pasquinelli AE, Gaasterland T. PMID: 18047675; PMCID: PMC2243180.
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MicroRNA silencing through RISC recruitment of eIF6. Nature. 2007 Jun 14; 447(7146):823-8. Chendrimada TP, Finn KJ, Ji X, Baillat D, Gregory RI, Liebhaber SA, Pasquinelli AE, Shiekhattar R. PMID: 17507929.
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The evolving role of microRNAs in animal gene expression. Bioessays. 2006 May; 28(5):449-52. Massirer KB, Pasquinelli AE. PMID: 16615087.
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Demystifying small RNA pathways. Dev Cell. 2006 Apr; 10(4):419-24. Pasquinelli AE. PMID: 16625708.
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Identification and analysis of microRNAs. Genet Eng (N Y). 2006; 27:1-20. Bagga S, Pasquinelli AE. PMID: 16382868.
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Analysis of the regulation of lin-41 during chick and mouse limb development. Dev Dyn. 2005 Dec; 234(4):948-60. Lancman JJ, Caruccio NC, Harfe BD, Pasquinelli AE, Schageman JJ, Pertsemlidis A, Fallon JF. PMID: 16245339.
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Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell. 2005 Aug 26; 122(4):553-63. Bagga S, Bracht J, Hunter S, Massirer K, Holtz J, Eachus R, Pasquinelli AE. PMID: 16122423.
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MicroRNAs: a developing story. Curr Opin Genet Dev. 2005 Apr; 15(2):200-5. Pasquinelli AE, Hunter S, Bracht J. PMID: 15797203.
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Functional genomic analysis of RNA interference in C. elegans. Science. 2005 May 20; 308(5725):1164-7. Kim JK, Gabel HW, Kamath RS, Tewari M, Pasquinelli A, Rual JF, Kennedy S, Dybbs M, Bertin N, Kaplan JM, Vidal M, Ruvkun G. PMID: 15790806.
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MicroRNA-responsive 'sensor' transgenes uncover Hox-like and other developmentally regulated patterns of vertebrate microRNA expression. Nat Genet. 2004 Oct; 36(10):1079-83. Mansfield JH, Harfe BD, Nissen R, Obenauer J, Srineel J, Chaudhuri A, Farzan-Kashani R, Zuker M, Pasquinelli AE, Ruvkun G, Sharp PA, Tabin CJ, McManus MT. PMID: 15361871.
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Trans-splicing and polyadenylation of let-7 microRNA primary transcripts. RNA. 2004 Oct; 10(10):1586-94. Bracht J, Hunter S, Eachus R, Weeks P, Pasquinelli AE. PMID: 15337850; PMCID: PMC1370645.
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Coordinate regulation of small temporal RNAs at the onset of Drosophila metamorphosis. Dev Biol. 2003 Jul 01; 259(1):1-8. Bashirullah A, Pasquinelli AE, Kiger AA, Perrimon N, Ruvkun G, Thummel CS. PMID: 12812783.
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Expression of the 22 nucleotide let-7 heterochronic RNA throughout the Metazoa: a role in life history evolution? Evol Dev. 2003 Jul-Aug; 5(4):372-8. Pasquinelli AE, McCoy A, Jiménez E, Saló E, Ruvkun G, Martindale MQ, Baguñà J. PMID: 12823453.
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The C elegans hunchback homolog, hbl-1, controls temporal patterning and is a probable microRNA target. Dev Cell. 2003 May; 4(5):639-50. Lin SY, Johnson SM, Abraham M, Vella MC, Pasquinelli A, Gamberi C, Gottlieb E, Slack FJ. PMID: 12737800.
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Control of developmental timing by micrornas and their targets. Annu Rev Cell Dev Biol. 2002; 18:495-513. Pasquinelli AE, Ruvkun G. PMID: 12142272.
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MicroRNAs: deviants no longer. Trends Genet. 2002 Apr; 18(4):171-3. Pasquinelli AE. PMID: 11932009.
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Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell. 2001 Jul 13; 106(1):23-34. Grishok A, Pasquinelli AE, Conte D, Li N, Parrish S, Ha I, Baillie DL, Fire A, Ruvkun G, Mello CC. PMID: 11461699.
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A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science. 2001 Aug 03; 293(5531):834-8. Hutvágner G, McLachlan J, Pasquinelli AE, Bálint E, Tuschl T, Zamore PD. PMID: 11452083.
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Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature. 2000 Nov 02; 408(6808):86-9. Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, Hayward DC, Ball EE, Degnan B, Müller P, Spring J, Srinivasan A, Fishman M, Finnerty J, Corbo J, Levine M, Leahy P, Davidson E, Ruvkun G. PMID: 11081512.
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The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature. 2000 Feb 24; 403(6772):901-6. Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR, Ruvkun G. PMID: 10706289.
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The constitutive transport element (CTE) of Mason-Pfizer monkey virus (MPMV) accesses a cellular mRNA export pathway. EMBO J. 1997 Dec 15; 16(24):7500-10. Pasquinelli AE, Ernst RK, Lund E, Grimm C, Zapp ML, Rekosh D, Hammarskjöld ML, Dahlberg JE. PMID: 9405378; PMCID: PMC1170349.
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Reverse 5' caps in RNAs made in vitro by phage RNA polymerases. RNA. 1995 Nov; 1(9):957-67. Pasquinelli AE, Dahlberg JE, Lund E. PMID: 8548660; PMCID: PMC1369344.
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