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RNAi in Drosophila S2 Cells by dsRNA Soaking.

Li C, Zamore PD.

Cold Spring Harb Protoc. 2019 Mar 1;2019(3):pdb.prot097477. doi: 10.1101/pdb.prot097477.


Preparation of dsRNAs for RNAi by In Vitro Transcription.

Li C, Zamore PD.

Cold Spring Harb Protoc. 2019 Mar 1;2019(3):pdb.prot097469. doi: 10.1101/pdb.prot097469.


An automated Bayesian pipeline for rapid analysis of single-molecule binding data.

Smith CS, Jouravleva K, Huisman M, Jolly SM, Zamore PD, Grunwald D.

Nat Commun. 2019 Jan 17;10(1):272. doi: 10.1038/s41467-018-08045-5.


Maelstrom Represses Canonical Polymerase II Transcription within Bi-directional piRNA Clusters in Drosophila melanogaster.

Chang TH, Mattei E, Gainetdinov I, Colpan C, Weng Z, Zamore PD.

Mol Cell. 2019 Jan 17;73(2):291-303.e6. doi: 10.1016/j.molcel.2018.10.038. Epub 2018 Dec 6.


PIWI-interacting RNAs: small RNAs with big functions.

Ozata DM, Gainetdinov I, Zoch A, O'Carroll D, Zamore PD.

Nat Rev Genet. 2019 Feb;20(2):89-108. doi: 10.1038/s41576-018-0073-3. Review.


A Single Mechanism of Biogenesis, Initiated and Directed by PIWI Proteins, Explains piRNA Production in Most Animals.

Gainetdinov I, Colpan C, Arif A, Cecchini K, Zamore PD.

Mol Cell. 2018 Sep 6;71(5):775-790.e5. doi: 10.1016/j.molcel.2018.08.007.


Cas9-mediated allelic exchange repairs compound heterozygous recessive mutations in mice.

Wang D, Li J, Song CQ, Tran K, Mou H, Wu PH, Tai PWL, Mendonca CA, Ren L, Wang BY, Su Q, Gessler DJ, Zamore PD, Xue W, Gao G.

Nat Biotechnol. 2018 Oct;36(9):839-842. doi: 10.1038/nbt.4219. Epub 2018 Aug 13.


Analysis of Small RNAs by Northern Hybridization.

Li C, Zamore PD.

Cold Spring Harb Protoc. 2018 Aug 1;2018(8):pdb.prot097493. doi: 10.1101/pdb.prot097493.


Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers.

Fu Y, Wu PH, Beane T, Zamore PD, Weng Z.

BMC Genomics. 2018 Jul 13;19(1):531. doi: 10.1186/s12864-018-4933-1.


Transcriptome Profiling of Neovascularized Corneas Reveals miR-204 as a Multi-target Biotherapy Deliverable by rAAVs.

Lu Y, Tai PWL, Ai J, Gessler DJ, Su Q, Yao X, Zheng Q, Zamore PD, Xu X, Gao G.

Mol Ther Nucleic Acids. 2018 Mar 2;10:349-360. doi: 10.1016/j.omtn.2017.12.019. Epub 2017 Dec 30.


Inhibiting miRNA Function by Antisense Oligonucleotides in Drosophila S2 Cells.

Li C, Zamore PD.

Cold Spring Harb Protoc. 2018 Feb 1;2018(2):pdb.prot097543. doi: 10.1101/pdb.prot097543.


Inhibiting miRNA Function by Antisense Oligonucleotides in Cultured Mammalian Cells.

Li C, Zamore PD.

Cold Spring Harb Protoc. 2018 Feb 1;2018(2):pdb.prot097535. doi: 10.1101/pdb.prot097535.


Preparation of Antisense Oligonucleotides to Inhibit miRNA Function.

Li C, Zamore PD.

Cold Spring Harb Protoc. 2018 Feb 1;2018(2):pdb.prot097527. doi: 10.1101/pdb.prot097527.


Comparison of partially and fully chemically-modified siRNA in conjugate-mediated delivery in vivo.

Hassler MR, Turanov AA, Alterman JF, Haraszti RA, Coles AH, Osborn MF, Echeverria D, Nikan M, Salomon WE, Roux L, Godinho BMDC, Davis SM, Morrissey DV, Zamore PD, Karumanchi SA, Moore MJ, Aronin N, Khvorova A.

Nucleic Acids Res. 2018 Mar 16;46(5):2185-2196. doi: 10.1093/nar/gky037.


The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology.

Fu Y, Yang Y, Zhang H, Farley G, Wang J, Quarles KA, Weng Z, Zamore PD.

Elife. 2018 Jan 29;7. pii: e31628. doi: 10.7554/eLife.31628.


Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements.

Lewis SH, Quarles KA, Yang Y, Tanguy M, Fr├ęzal L, Smith SA, Sharma PP, Cordaux R, Gilbert C, Giraud I, Collins DH, Zamore PD, Miska EA, Sarkies P, Jiggins FM.

Nat Ecol Evol. 2018 Jan;2(1):174-181. doi: 10.1038/s41559-017-0403-4. Epub 2017 Dec 4.


Molecular biology: Rhino gives voice to silent chromatin.

Zamore PD.

Nature. 2017 Sep 6;549(7670):38-39. doi: 10.1038/549038a. No abstract available.


Single-Molecule Imaging Reveals that Argonaute Reshapes the Binding Properties of Its Nucleic Acid Guides.

Salomon WE, Jolly SM, Moore MJ, Zamore PD, Serebrov V.

Cell. 2016 Jul 14;166(2):517-520. doi: 10.1016/j.cell.2016.06.048. Epub 2016 Jul 14. No abstract available.


Small methyltransferase RlmH assembles a composite active site to methylate a ribosomal pseudouridine.

Koh CS, Madireddy R, Beane TJ, Zamore PD, Korostelev AA.

Sci Rep. 2017 Apr 20;7(1):969. doi: 10.1038/s41598-017-01186-5.


Rapid Screening for CRISPR-Directed Editing of the Drosophila Genome Using white Coconversion.

Ge DT, Tipping C, Brodsky MH, Zamore PD.

G3 (Bethesda). 2016 Oct 13;6(10):3197-3206. doi: 10.1534/g3.116.032557.


Mycobacterium tuberculosis induces the miR-33 locus to reprogram autophagy and host lipid metabolism.

Ouimet M, Koster S, Sakowski E, Ramkhelawon B, van Solingen C, Oldebeken S, Karunakaran D, Portal-Celhay C, Sheedy FJ, Ray TD, Cecchini K, Zamore PD, Rayner KJ, Marcel YL, Philips JA, Moore KJ.

Nat Immunol. 2016 Jun;17(6):677-86. doi: 10.1038/ni.3434. Epub 2016 Apr 18.


MicroRNA-33-dependent regulation of macrophage metabolism directs immune cell polarization in atherosclerosis.

Ouimet M, Ediriweera HN, Gundra UM, Sheedy FJ, Ramkhelawon B, Hutchison SB, Rinehold K, van Solingen C, Fullerton MD, Cecchini K, Rayner KJ, Steinberg GR, Zamore PD, Fisher EA, Loke P, Moore KJ.

J Clin Invest. 2015 Oct 26;125(12):4334-48. doi: 10.1172/JCI81676.


Slicing and Binding by Ago3 or Aub Trigger Piwi-Bound piRNA Production by Distinct Mechanisms.

Wang W, Han BW, Tipping C, Ge DT, Zhang Z, Weng Z, Zamore PD.

Mol Cell. 2015 Sep 3;59(5):819-30. doi: 10.1016/j.molcel.2015.08.007.


Single-Molecule Imaging Reveals that Argonaute Reshapes the Binding Properties of Its Nucleic Acid Guides.

Salomon WE, Jolly SM, Moore MJ, Zamore PD, Serebrov V.

Cell. 2015 Jul 2;162(1):84-95. doi: 10.1016/j.cell.2015.06.029. Erratum in: Cell. 2016 Jul 14;166(2):517-520.


Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs.

Chou MT, Han BW, Hsiao CP, Zamore PD, Weng Z, Hung JH.

Nucleic Acids Res. 2015 Sep 30;43(17):e109. doi: 10.1093/nar/gkv537. Epub 2015 May 24.


Noncoding RNA. piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production.

Han BW, Wang W, Li C, Weng Z, Zamore PD.

Science. 2015 May 15;348(6236):817-21. doi: 10.1126/science.aaa1264.


Assessing long-distance RNA sequence connectivity via RNA-templated DNA-DNA ligation.

Roy CK, Olson S, Graveley BR, Zamore PD, Moore MJ.

Elife. 2015 Apr 13;4. doi: 10.7554/eLife.03700.


Pitfalls of mapping high-throughput sequencing data to repetitive sequences: Piwi's genomic targets still not identified.

Marinov GK, Wang J, Handler D, Wold BJ, Weng Z, Hannon GJ, Aravin AA, Zamore PD, Brennecke J, Toth KF.

Dev Cell. 2015 Mar 23;32(6):765-71. doi: 10.1016/j.devcel.2015.01.013.


The initial uridine of primary piRNAs does not create the tenth adenine that Is the hallmark of secondary piRNAs.

Wang W, Yoshikawa M, Han BW, Izumi N, Tomari Y, Weng Z, Zamore PD.

Mol Cell. 2014 Dec 4;56(5):708-16. doi: 10.1016/j.molcel.2014.10.016. Epub 2014 Nov 20.


piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing.

Han BW, Wang W, Zamore PD, Weng Z.

Bioinformatics. 2015 Feb 15;31(4):593-5. doi: 10.1093/bioinformatics/btu647. Epub 2014 Oct 17.



Han BW, Zamore PD.

Curr Biol. 2014 Aug 18;24(16):R730-3. doi: 10.1016/j.cub.2014.07.037. No abstract available.


High-throughput sequencing analysis of post-liver transplantation HCV E2 glycoprotein evolution in the presence and absence of neutralizing monoclonal antibody.

Babcock GJ, Iyer S, Smith HL, Wang Y, Rowley K, Ambrosino DM, Zamore PD, Pierce BG, Molrine DC, Weng Z.

PLoS One. 2014 Jun 23;9(6):e100325. doi: 10.1371/journal.pone.0100325. eCollection 2014.


The HP1 homolog rhino anchors a nuclear complex that suppresses piRNA precursor splicing.

Zhang Z, Wang J, Schultz N, Zhang F, Parhad SS, Tu S, Vreven T, Zamore PD, Weng Z, Theurkauf WE.

Cell. 2014 Jun 5;157(6):1353-63. doi: 10.1016/j.cell.2014.04.030.


Competitive endogenous RNAs cannot alter microRNA function in vivo.

Broderick JA, Zamore PD.

Mol Cell. 2014 Jun 5;54(5):711-3. doi: 10.1016/j.molcel.2014.05.023.


A universal small molecule, inorganic phosphate, restricts the substrate specificity of Dicer-2 in small RNA biogenesis.

Fukunaga R, Zamore PD.

Cell Cycle. 2014;13(11):1671-6. doi: 10.4161/cc.29066. Epub 2014 Apr 30.


Antisense piRNA amplification, but not piRNA production or nuage assembly, requires the Tudor-domain protein Qin.

Zhang Z, Koppetsch BS, Wang J, Tipping C, Weng Z, Theurkauf WE, Zamore PD.

EMBO J. 2014 Mar 18;33(6):536-9. doi: 10.1002/embj.201384895. No abstract available.


Cnidarian microRNAs frequently regulate targets by cleavage.

Moran Y, Fredman D, Praher D, Li XZ, Wee LM, Rentzsch F, Zamore PD, Technau U, Seitz H.

Genome Res. 2014 Apr;24(4):651-63. doi: 10.1101/gr.162503.113. Epub 2014 Mar 18.


Inorganic phosphate blocks binding of pre-miRNA to Dicer-2 via its PAZ domain.

Fukunaga R, Colpan C, Han BW, Zamore PD.

EMBO J. 2014 Feb 18;33(4):371-84. doi: 10.1002/embj.201387176. Epub 2014 Jan 31.


Diversifying microRNA sequence and function.

Ameres SL, Zamore PD.

Nat Rev Mol Cell Biol. 2013 Aug;14(8):475-88. doi: 10.1038/nrm3611. Epub 2013 Jun 26. Review.


Defining piRNA primary transcripts.

Li XZ, Roy CK, Moore MJ, Zamore PD.

Cell Cycle. 2013 Jun 1;12(11):1657-8. doi: 10.4161/cc.24989. Epub 2013 May 10. No abstract available.


Small RNA-directed silencing: the fly finds its inner fission yeast?

Ge DT, Zamore PD.

Curr Biol. 2013 Apr 22;23(8):R318-20. doi: 10.1016/j.cub.2013.03.033.


An ancient transcription factor initiates the burst of piRNA production during early meiosis in mouse testes.

Li XZ, Roy CK, Dong X, Bolcun-Filas E, Wang J, Han BW, Xu J, Moore MJ, Schimenti JC, Weng Z, Zamore PD.

Mol Cell. 2013 Apr 11;50(1):67-81. doi: 10.1016/j.molcel.2013.02.016. Epub 2013 Mar 21.


Human monoclonal antibody MBL-HCV1 delays HCV viral rebound following liver transplantation: a randomized controlled study.

Chung RT, Gordon FD, Curry MP, Schiano TD, Emre S, Corey K, Markmann JF, Hertl M, Pomposelli JJ, Pomfret EA, Florman S, Schilsky M, Broering TJ, Finberg RW, Szabo G, Zamore PD, Khettry U, Babcock GJ, Ambrosino DM, Leav B, Leney M, Smith HL, Molrine DC.

Am J Transplant. 2013 Apr;13(4):1047-1054. doi: 10.1111/ajt.12083. Epub 2013 Jan 28.


Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection.

Zhang Z, Theurkauf WE, Weng Z, Zamore PD.

Silence. 2012 Dec 28;3(1):9. doi: 10.1186/1758-907X-3-9.


Increased Steady-State Mutant Huntingtin mRNA in Huntington's Disease Brain.

Liu W, Chaurette J, Pfister EL, Kennington LA, Chase KO, Bullock J, Vonsattel JP, Faull RL, Macdonald D, DiFiglia M, Zamore PD, Aronin N.

J Huntingtons Dis. 2013;2(4):491-500. doi: 10.3233/JHD-130079.


Rapid and specific purification of Argonaute-small RNA complexes from crude cell lysates.

Flores-Jasso CF, Salomon WE, Zamore PD.

RNA. 2013 Feb;19(2):271-9. doi: 10.1261/rna.036921.112. Epub 2012 Dec 18.


Argonaute divides its RNA guide into domains with distinct functions and RNA-binding properties.

Wee LM, Flores-Jasso CF, Salomon WE, Zamore PD.

Cell. 2012 Nov 21;151(5):1055-67. doi: 10.1016/j.cell.2012.10.036. Erratum in: Cell. 2013 Jan 17;152(1-2):366.


UAP56 couples piRNA clusters to the perinuclear transposon silencing machinery.

Zhang F, Wang J, Xu J, Zhang Z, Koppetsch BS, Schultz N, Vreven T, Meignin C, Davis I, Zamore PD, Weng Z, Theurkauf WE.

Cell. 2012 Nov 9;151(4):871-884. doi: 10.1016/j.cell.2012.09.040.


Dicer Partner Proteins Tune the Length of Mature miRNAs in Flies and Mammals.

Fukunaga R, Han BW, Hung JH, Xu J, Weng Z, Zamore PD.

Cell. 2012 Nov 9;151(4):912. doi: 10.1016/j.cell.2012.10.029. Epub 2012 Nov 8. No abstract available.


Dicer partner proteins tune the length of mature miRNAs in flies and mammals.

Fukunaga R, Han BW, Hung JH, Xu J, Weng Z, Zamore PD.

Cell. 2012 Oct 26;151(3):533-46. doi: 10.1016/j.cell.2012.09.027. Epub 2012 Oct 11. Erratum in: Cell. 2012 Nov 9;151(4):912. Cell. 2012 Nov 9;151(4):912.

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