Help us understand the role of non-coding RNAs in stress and aging

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Chipman LB, Luc S, Nicastro IA, Hulahan JJ, Dann DC, Bodas DM, Pasquinelli AE. Expression, not sequence, distinguishes miR-238 from its miR-239ab sister miRNAs in promoting longevity in Caenorhabditis elegans. PLoS Genet. 2023 Nov 27;19(11):e1011055. doi: 10.1371/journal.pgen.1011055. eCollection 2023 Nov.PMID: 38011256. PMCID: 

Elder CR, Pasquinelli AE. New roles for microRNAs in old worms. Front Aging. 2022 Apr 12;3:871226. doi: 10.3389/fragi.2022.871226. eCollection 2022.PMID: 35821862. PMCID: PMC9261348

Nicholson-Shaw AL, Kofman ER, Yeo GW, Pasquinelli AE. Nuclear and Cytoplasmic poly(A) binding proteins (PABPs) favor distinct transcripts and isoforms. Nucleic Acids Res. 2022 May 6;50(8):4685-4702. doi: 10.1093/nar/gkac263.PMID: 35438785. PMCID: PMC9071453

Garrigues JM, Pasquinelli AE. Caenorhabditis elegans transposable elements harbor diverse transcription factor DNA-binding sites. G3. 2022 Mar 4;12(3):jkac009. doi: 10.1093/g3journal/jkac009. PMCID: PMC8896005

Pagliuso DC, Bodas DM, Pasquinelli AE. Recovery from Heat Shock Requires the MicroRNA Pathway in Caenorhabditis elegans. PLoS Genetics. 2021 Aug 5;17(8):e1009734. doi: 10.1371/journal.pgen.PMCID: PMC8370650

Schiksnis EC, Nicholson AL, Modena MS, Pule MN, Arribere JA, Pasquinelli, AE. Auxin-independent depletion of degron-tagged proteins by TIR1. Micropublication Biology. 2020 10.17912/micropub.biology.000213. PMCID: PMC7252403

Garrigues JM, Tsu BV, Daugherty MD, Pasquinelli AE. Diversification of the Caenorhabditis heat shock response by Helitron transposable elements. Elife. 2019 Dec 11;8. pii: e51139. doi: 10.7554/eLife.51139.PMCID: PMC6927752

Winkenbach LP, Doser R, Reed KJ, Pasquinelli AE, Phillips CM, Claycomb JM. Todos Santos Small RNA Symposium. RNA Biol. 2019 Nov;16(11):1526-1530. doi: 10.1080/15476286.2019.1649586. Epub 2019 Aug 9. PMCID: PMC6779373

Schreiner WP, Pagliuso DC, Garrigues JM, Chen JS, Aalto AP, Pasquinelli AE. Remodeling of the Caenorhabditis elegans non-coding RNA transcriptome by heat shock. Nucleic Acids Res. 2019 Oct 10;47(18):9829-9841. doi: 10.1093/nar/gkz693. PMCID: PMC6765114

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. RNA interference may result in unexpected phenotypes in Caenorhabditis elegans. Nucleic Acids Res. 2019 Mar 6. pii: gkz154. doi: 10.1093/nar/gkz154. PMCID: PMC6486631

Chipman LB, Pasquinelli AE. miRNA Targeting: Growing beyond the Seed. Trends Genet. 2019 Jan 9. pii: S0168-9525(18)30224-5. doi: 10.1016/j.tig.2018.12. 005 Review. PMCID: PMC7083087

Nicholson AL, Pasquinelli AE. Tales of Detailed Poly(A) Tails. Trends in Biol Chem. 2018 Nov 29. pii: S0962-8924(18)30188-0. doi: 10.1016/j.tcb.2018.11.002. Review. PMCID: PMC7083203

Broughton JP, Pasquinelli AE. Detection ofmicroRNA-Target Interactions by CimeraPCR (ChIMP). Methods Mol Biol. 2018;1823:153-165. DOI: 10.1007/978-1-4939-8624-8_12

Aalto AP, Nicastro IA, Broughton JP, Chipman LB, Schreiner WP, Chen JS, Pasquinelli AE. Opposing roles of microRNA Argonautes during Caenorhabditis elegans aging. PLoS Genet. 2018 Jun 21;14(6):e1007379. doi: 10.1371/journal.pgen.1007379. eCollection 2018 Jun. PMCID: PMC6013023

Pasquinelli AE. A rADAR defense against RNAi. Genes Dev, 2018 Feb 1;32(3-4):199-201. PMCID: PMC5859962

Azoubel Lima S, Chipman LB, Nicholson AL, Chen YH, Yee BA, Yeo GW, Coller J, Pasquinelli AE. Short Poly(A) Tails are a Conserved Feature of Highly Expressed Genes. Nat Struct Mol Biol, 2017 Dec;24(12):1057-1063. doi: 10.1038/nsmb.3499. Epub 2017 Nov 6. PMCID: PMC5877826

Schreiner WP and Pasquinelli AE. Making and Maintaining MicroRNAs in Animals, Chapter for “Essentials of microRNAs in neurogenesis: ontogenesis and plasticity of the mammalian neural system” 1st Ed. De Pietri Tonelli, Elsevier, 2017. p1-17.

Pasquinelli AE. A sense-able microRNA. Genes Dev, 2016 Sep 15;30(18):2019-2020. PMCID: PMC5066609

Broughton JP, Lovci MT, Huang JL, Yeo GW, Pasquinelli AE. Pairing Beyond the Seed Supports MicroRNA Targeting Specificity. Mol Cell, 2016 Oct 20:64:1-14. PMCID: PMC5074850

Broughton JP, Pasquinelli AE. A tale of two sequences: microRNA-target chimeric reads. Genet Sel Evol. 2016 Apr 4;48:31. doi: 10.1186/s12711-016-0209-x. Review. PMCID: PMC4819279

Mondol V, Ahn BC, Pasquinelli AE. Splicing remodels the let-7 primary microRNA to facilitate Drosha processing in Caenorhabditis elegans. RNA, 2015 21(8):1396-1403. PMCID: PMC4509930

Pasquinelli AE. MicroRNAs: heralds of the non-coding RNA revolution. RNA, 2015. 21(4):709-710. PMCID: PMC4371344

Van Wynsberghe PM, Pasquinelli AE. Period Homolog LIN-42 regulates miRNA transcription to impact developmental timing. Worm, 2014 3(4)e974453. PMCID: PMC4589994

Lima SA, Pasquinelli AE. Identification of miRNAs and their targets in C. elegans. Adv Exp Med Biol. 2014; 825:431-50. DOI: 10.1007/978-1-4939-1221-6_12

Fonslow BR, Moresco JJ, Tu PG, Aalto AP, Pasquinelli AE, Dillin AG, Yates Iii JR. Mass spectrometry-based shotgun proteomic analysis of C. elegans protein complexes. WormBook. 2014 Jun 24:1-18. doi: 10.1895/wormbook.1.171.1. PMCID: PMC4716738

Van Wynsberghe PM, Finnegan EF, Stark T, Angelus EP, Homan KE, Yeo GW, Pasquinelli AE. The Period protein homolog LIN-42 negatively regulates microRNA biogenesis in C. elegans. Dev Biol. 2014 Mar 31. pii: S0012-1606(14)00173-0. doi: 10.1016/j.ydbio.2014.03.017. PMCID: PMC4077587

Pasquinelli AE. The primary target of let-7 miRNA. Biochem. Soc. Trans. 2013 Aug 1;41(4):821-4. DOI: 10.1042/BST20130020

Broughton JP, Pasquinelli AE.  Identifying Argonaute binding sites in Caenorhabditis elegans using iCLIP. Methods, 2013 Apr 10. S1046-2023(13)00102-3. PMCID: PMC3749250

Hunter SE, Finnegan EF, Zisoulis DG, Lovci MT, Melnik-Martinez KV, Yeo GW, Pasquinelli AE. Functional genomic analysis of the let-7 regulatory network in Caenorhabditis elegans. PLoS Genetics, 2013 Mar;9(3)e1003353. PMCID: PMC3597506

Massirer KB, Pasquinelli AE.  MicroRNAs that interfere with RNAi. Worm, 2013 Jan/Feb/Mar;2(1):e1-6. PMCID: PMC3670461

Kai, ZS, Finnegan EF, Huang S, Pasquinelli AE. Multiple cis-elements and trans-acting factors regulate dynamic spatio-temporal transcription of let-7 in Caenorhabditis elegans. Dev Biology, 2013 Feb 1;374(1):223-33. PMCID: PMC3548979

Finnegan EF, Pasquinelli AE.  MicroRNA biogenesis: Regulating the regulators. Critical Reviews In Biochemistry & Molecular Biology, 2013 Jan-Feb;48(1):51-68. PMCID: PMC3557704

Pasquinelli AE.  Birthing histone mRNAs by CSR-1-section. Embo J, 2012 Oct 3;31(19):3790-1. PMCID: PMC3463852

Zisoulis DG, Kai ZS, Chang RC, Pasquinelli AE. Auto-regulation of miRNA biogenesis by let-7 and Argonaute. Nature, 2012 Jun 28;486(7404):541-4. PMCID: PMC3387326

Aalto AP, Pasquinelli AE. Small non-coding RNAs mount a silent revolution in gene expression. Current Opinion in Cell Biology, 2012 Jun;24(3):333-40. PMCID: PMC3372702

Pasquinelli AE. MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship.Nat Rev Genet. 2012 Mar 13;13(4):271-82. DOI: 10.1038/nrg3162

Massirer KB, Perez SG, Mondol V, Pasquinelli AE. The miR-35-41 family of microRNAs regulates RNAi sensitivity in Caenorhabditis elegans. PLoS Genetics. 2012 Mar;8(3):e1002536. PMCID: PMC3297572

Mondol V, Pasquinelli AE. Let’s make it happen:  The role of let-7 microRNA in development. In Eran Hornstein, editors: MicroRNAs in Development, CTDB, UK: Academic Press, 2012, 99:1-30. DOI: 10.1016/B978-0-12-387038-4.00001-X

Pasquinelli AE.  A team effort blocks the ribosome in its tracks. Nat Struct Mol Biol. 2012 19(2):133-4. DOI: 10.1038/nsmb.2236

Van Wynsberghe PM, Chan S-P, Slack FJ, Pasquinelli AE. Analysis of microRNA Expression and Function.Methods Cell Biol. 2011;106:219-52. PMID: 22118279 PMCID: PMC4314212

Zisoulis DG, Yeo GW, Pasquinelli AE. Comprehensive identification of miRNA target sites in live animals. Methods Mol Biol. 2011 732:169-85. DOI: 10.1007/978-1-61779-083-6_13

Van Wynsberghe PM, Kai ZS, Massirer KB, Burton VH, Yeo GW, Pasquinelli AE. 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. PMCID: PMC3077891

Bracht JR, Van Wynsberghe PM, Mondol V, Pasquinelli AE. 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):201-21. PMCID: PMC2982876

Pasquinelli AE. Molecular biology. Paring miRNAs through pairing. Science. 2010 Jun 18;328(5985):1494-5. DOI: 10.1126/science.1191531

Godshalk SE, Melnik-Martinez KV, Pasquinelli AE, Slack F. MicroRNAs and cancer: a meeting summary of the eponymous Keystone Conference. Epigenetics. 2010 Feb;5(2):164-8. DOI: 10.4161/epi.5.2.11162

Kai Z, Pasquinelli AE. A genome wide view of hunchback-like-1 targets. Cell Cycle. 2010 Jan 15;9(2):230-1. PMID: 20061795

Kai ZS, Pasquinelli AE. MicroRNA assassins: factors that regulate the disappearance of miRNAs. Nat Struct Mol Biol. 2010 Jan;17(1):5-10. Review. PMCID: PMC6417416

Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo GW. Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans. Nat Struct Mol Biol. 2010 17:173-9. PMCID: PMC2834287

Hinton A, Afrikanova I, Wilson M, King C, Maurer B, Yeo G, Hayek A, Pasquinelli A. A Distinct MicroRNA Signature for Definitive Endoderm Derived From Human Embryonic Stem Cells. Stem Cells Dev. 2010 19:797-807. DOI: 10.1089/scd.2009.0224

Holtz J, Pasquinelli AE. Uncoupling of lin-14 mRNA and protein repression by nutrient deprivation in Caenorhabditis elegans. RNA. 2009 15:400-5. PMCID: PMC2657013

Norden-Krichmar TM, Holtz J, Pasquinelli AE, Gaasterland T. Computational prediction and experimental validation of Ciona intestinalis microRNA genes. BMC Genomics 2007 8:445. PMCID: PMC2243180

Chendrimada TP, Finn KJ, Ji X, Baillant D, Gregory RI, Liebhaber SA, Pasquinelli AE, Shiekhattar R. MicroRNA silencing through RISC recruitment of eIF6.  Nature 2007 447:823-828. DOI: 10.1038/nature05841

Massirer K, Pasquinelli AE. The evolving role of microRNAs in animal gene expression. BioEssays 2006 28:449-452. DOI: 10.1002/bies.20406

Pasquinelli AE. Demystifying Small RNA Pathways – A Meeting Review.  Dev Cell 2006 10:419-424. DOI: 10.1016/j.devcel.2006.03.005

Bagga S, Pasquinelli AE. Identification and analysis of microRNAs. Genet Eng (N Y) 2006 27:1-20. DOI: 10.1007/0-387-25856-6_1

Bagga S, Bracht J, Hunter S, Massirer K, Holtz J, Eachus R, Pasquinelli AE. Regulation by let-7 and lin-4miRNAs results in target mRNA degradation.  Cell. 2005 122:553-563. DOI: 10.1016/j.cell.2005.07.031

Lancman JJ, Caruccio NC, Harfe BD, Pasquinelli AE, Schageman JJ, Pertsemlidis A, Fallon JF.  Analysis of the regulation of lin-41 during chick and mouse limb development.  Dev Dyn. 2005 234:948-60. DOI: 10.1002/dvdy.20591

Kim JK, Gabel HW, Kamath RS, Tewari M, Pasquinelli AE, Rual JF, Kennedy S, Dybbs M, Bertin N, KaplanJM, Vidal M, Ruvkun G. Functional genomic analysis of RNA interference in C. elegans. Science. 2005 308:1164-1167.  DOI: 10.1126/science.1109267

Pasquinelli AE, Hunter SE, Bracht J. MicroRNAs:  A Developing Story. Curr. Opinion in Cell and Devel. Biol. 2005 15:200-205. DOI: 10.1016/j.gde.2005.01.002

Pasquinelli AE. MicroRNAs:  a Small Contribution from Worms.  In RNA Interference Technology: From Basic Science to Drug Development, ed. K Appasani. Cambridge, UK: Cambridge University Press. 2005. p69-83.

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. MicroRNA-responsive ‘sensor’ transgenes uncover Hox-like and other developmentally regulated patterns of vertebrate microRNA expression. Nat Genet. 2004 36:1079-1083. DOI: 10.1038/ng1421

Bracht J, Hunter S, Eachus R, Weeks P, Pasquinelli AE.  Trans-splicing and polyadenylation of let-7microRNA primary transcripts. RNA. 2004 10:1586-1594. PMCID: PMC1370645

Pasquinelli AE, McCoy A, Jimenez E, Salo E, Ruvkun G, Martindale MQ, Baguna J. Expression of the 22 nucleotide let-7 heterochronic RNA throughout the Metazoa: A role in life history evolution? Evol Dev. 2003 5:372-378. DOI: 10.1046/j.1525-142x.2003.03044.x

Bashirullah A, Pasquinelli AE, Kiger, AA, Perrimon N, Ruvkun G, Thummel C. Coordinate regulation of small temporal RNAs at the onset of Drosophila metamorphosis. Dev Biol. 2003 259:1-8. DOI: 10.1016/s0012-1606(03)00063-0

Lin S, Johnson SM, Abraham M, Vella MC, Pasquinelli AE, Gamberi C, Gottlieb E, Slack F. The C. elegans hunchback homologue hbl-1, controls temporal patterning and is a probable microRNA target. Dev Cell2003 4:639-650. DOI: 10.1016/s1534-5807(03)00124-2

Pasquinelli AE. MicroRNAs:  Deviants No Longer. Trends in Genetics.  2002 18:171-173.DOI: 10.1016/s0168-9525(01)02624-5

Pasquinelli AE, Ruvkun G. Control of Developmental Timing by MicroRNAs and Their Targets. Annu Rev Cell and Dev Biol. 2002 18:495-513. DOI: 10.1146/annurev.cellbio.18.012502.105832

Hutvagner G, McLachlan J, Pasquinelli AE, Balint E, Tuschl T, Zamore PD. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science. 2001 293:834-838. DOI: 10.1126/science.1062961

Grishok A, Pasquinelli AE, Conte D, Li N, Parrish S, Ha I, Baillie DL, Fire A, Ruvkun G, Mello CC. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell. 2001 106:23-34. DOI: 10.1016/s0092-8674(01)00431-7

Pierce SB, Costa M, Wisotzkey R, Devadhar S, Homburger SA, Buchman AR, Ferguson KC, Heller J, Platt DM, Pasquinelli AE, Liu LX, Doberstein SK, Ruvkun G. Regulation of DAF-2 receptor signaling by human insulin and ins-1, a member of the unusually large and diverse C. elegans insulin gene family. Genes Dev. 2001 15:672-686.  PMCID: PMC312654

Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, Hayward DC, Ball EE, Degnan B, Muller P, Spring J, Srinivasan A, Fishman M, Finnerty J, Corbo J, Levine M, Leahy P, Davidson E, Ruvkun G. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature. 2000 408:86-89. DOI: 10.1038/35040556

Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR, Ruvkun G. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature. 2000 403:901-906. DOI: 10.1038/35002607

Pasquinelli AE, Ernst RK, Lund E, Grimm C, Zapp ML, Rekosh D, Hammarskjöld ML, Dahlberg JE. The constitutive transport element (CTE) of Mason-Pfizer monkey virus (MPMV) accesses a cellular mRNA export pathway. EMBO J. 1997 16:7500-7510. PMCID: PMC1170349

Pasquinelli AE, Powers MA, Lund E, Forbes D, Dahlberg JE. Inhibition of mRNA export in vertebrate cells by nuclear export signal conjugates. Proc Natl Acad Sci USA. 1997 94:14394-14399. PMCID: PMC24994

Pasquinelli AE, Dahlberg JE, Lund E. Reverse 5′ caps in RNAs made in vitro by phage RNA polymerases. RNA. 1995 1:957-967. PMCID: PMC1369344

Greenspan DS, Pasquinelli AE. BstUI and DpnII RFLPs at the COL5A1 gene. Hum Mol Genet. 1994 3:385. DOI: 10.1093/hmg/3.2.385-a