Publications

Here's what we've been up to! Check out our latest papers!

For a link to JM Claycomb in PubMed, click here.

For a link to Julie Claycomb's Google Scholar Profile, click here.

Small RNAs and C. elegans:

Analysis of C. elegans Germline Small RNA Pathways.

Renaud MS, Seroussi U, Claycomb JM.

Methods Mol Biol. 2023;2677:37-59. doi: 10.1007/978-1-0716-3259-8_2.

PMID: 37464234

A comprehensive survey of C. elegans argonaute proteins reveals organism-wide gene regulatory networks and functions.

Seroussi U, Lugowski A, Wadi L, Lao RX, Willis AR, Zhao W, Sundby AE, Charlesworth AG, Reinke AW, Claycomb JM.

Elife. 2023 Feb 15;12:e83853. doi: 10.7554/eLife.83853.

PMID: 36790166

Temperature-dependent Small RNA Expression Depends on Wild Genetic Backgrounds of Caenorhabditis briggsae.

Fusca DD, Sharma E, Weiss JG, Claycomb JM, Cutter AD.

Mol Biol Evol. 2022 Nov 3;39(11):msac218. doi: 10.1093/molbev/msac218.

PMID: 36223483

PIWI puts spermatogenesis in its place.

Charlesworth AG, Nitschko V, Renaud MS, Claycomb JM.

Dev Cell. 2022 Jan 24;57(2):149-151. doi: 10.1016/j.devcel.2022.01.001.

PMID: 35077678

Mechanisms of epigenetic regulation by C. elegans nuclear RNA interference pathways.

Seroussi U, Li C, Sundby AE, Lee TL, Claycomb JM, Saltzman AL.

Semin Cell Dev Biol. 2022 Jul;127:142-154. doi: 10.1016/j.semcdb.2021.11.018. Epub 2021 Dec 6.

PMID: 34876343

Two isoforms of the essential C. elegans Argonaute CSR-1 differentially regulate sperm and oocyte fertility.

Charlesworth AG, Seroussi U, Lehrbach NJ, Renaud MS, Sundby AE, Molnar RI, Lao RX, Willis AR, Woock JR, Aber MJ, Diao AJ, Reinke AW, Ruvkun G, Claycomb JM.

Nucleic Acids Res. 2021 Sep 7;49(15):8836-8865. doi: 10.1093/nar/gkab619.

PMID: 34329465

A parental transcriptional response to microsporidia infection induces inherited immunity in offspring.

Willis AR, Zhao W, Sukhdeo R, Wadi L, El Jarkass HT, Claycomb JM, Reinke AW.

Sci Adv. 2021 May 5;7(19):eabf3114. doi: 10.1126/sciadv.abf3114. Print 2021 May.

PMID: 33952520

Connecting the Dots: Linking Caenorhabditis elegans Small RNA Pathways and Germ Granules.

Sundby AE, Molnar RI, Claycomb JM.

Trends Cell Biol. 2021 May;31(5):387-401. doi: 10.1016/j.tcb.2020.12.012. Epub 2021 Jan 29.

PMID: 33526340

Anti-CRISPR AcrIIA5 Potently Inhibits All Cas9 Homologs Used for Genome Editing.

Garcia B, Lee J, Edraki A, Hidalgo-Reyes Y, Erwood S, Mir A, Trost CN, Seroussi U, Stanley SY, Cohn RD, Claycomb JM, Sontheimer EJ, Maxwell KL, Davidson AR.

Cell Rep. 2019 Nov 12;29(7):1739-1746.e5. doi: 10.1016/j.celrep.2019.10.017.

PMID: 31722192

P Granules Protect RNA Interference Genes from Silencing by piRNAs.

Ouyang JPT, Folkmann A, Bernard L, Lee CY, Seroussi U, Charlesworth AG, Claycomb JM, Seydoux G.

Dev Cell. 2019 Sep 23;50(6):716-728.e6. doi: 10.1016/j.devcel.2019.07.026. Epub 2019 Aug 8.

PMID: 31402283

Todos Santos small RNA symposium.

Winkenbach LP, Doser R, Reed KJ, Pasquinelli AE, Phillips CM, Claycomb JM.

RNA Biol. 2019 Nov;16(11):1526-1530. doi: 10.1080/15476286.2019.1649586. Epub 2019 Aug 9.

PMID: 31397621

Germ Granules Govern Small RNA Inheritance.

Lev I, Toker IA, Mor Y, Nitzan A, Weintraub G, Antonova O, Bhonkar O, Ben Shushan I, Seroussi U, Claycomb JM, Anava S, Gingold H, Zaidel-Bar R, Rechavi O.

Curr Biol. 2019 Sep 9;29(17):2880-2891.e4. doi: 10.1016/j.cub.2019.07.054. Epub 2019 Aug 1.

PMID: 31378614

Genome structure predicts modular transcriptome responses to genetic and environmental conditions.

Mark S, Weiss J, Sharma E, Liu T, Wang W, Claycomb JM, Cutter AD.

Mol Ecol. 2019 Aug;28(16):3681-3697. doi: 10.1111/mec.15185. Epub 2019 Aug 5.

PMID: 31325381

Next-Gen Learning: The C. elegans Approach.

Charlesworth AG, Seroussi U, Claycomb JM.

Cell. 2019 Jun 13;177(7):1674-1676. doi: 10.1016/j.cell.2019.05.039.

PMID: 31199913

Secretion of an Argonaute protein by a parasitic nematode and the evolution of its siRNA guides.

Chow FW, Koutsovoulos G, Ovando-Vázquez C, Neophytou K, Bermúdez-Barrientos JR, Laetsch DR, Robertson E, Kumar S, Claycomb JM, Blaxter M, Abreu-Goodger C, Buck AH.

Nucleic Acids Res. 2019 Apr 23;47(7):3594-3606. doi: 10.1093/nar/gkz142.

PMID: 30820541

The TRIM-NHL protein NHL-2 is a co-factor in the nuclear and somatic RNAi pathways in C. elegans.

Davis GM, Tu S, Anderson JW, Colson RN, Gunzburg MJ, Francisco MA, Ray D, Shrubsole SP, Sobotka JA, Seroussi U, Lao RX, Maity T, Wu MZ, McJunkin K, Morris QD, Hughes TR, Wilce JA, Claycomb JM, Weng Z, Boag PR.

Elife. 2018 Dec 21;7:e35478. doi: 10.7554/eLife.35478.

PMID: 30575518

Post-transcriptional regulation of gene expression.

Lipshitz HD, Claycomb JM, Smibert CA.

Methods. 2017 Aug 15;126:1-2. doi: 10.1016/j.ymeth.2017.08.007.

PMID: 28867174

The Conserved Intron Binding Protein EMB-4 Plays Differential Roles in Germline Small RNA Pathways of C. elegans.

Tyc KM, Nabih A, Wu MZ, Wedeles CJ, Sobotka JA, Claycomb JM.

Dev Cell. 2017 Aug 7;42(3):256-270.e6. doi: 10.1016/j.devcel.2017.07.003.

PMID: 28787592

The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription.

Akay A, Di Domenico T, Suen KM, Nabih A, Parada GE, Larance M, Medhi R, Berkyurek AC, Zhang X, Wedeles CJ, Rudolph KLM, Engelhardt J, Hemberg M, Ma P, Lamond AI, Claycomb JM, Miska EA.

Dev Cell. 2017 Aug 7;42(3):241-255.e6. doi: 10.1016/j.devcel.2017.07.002.

PMID: 28787591

Examining the intersection between splicing, nuclear export and small RNA pathways.

Nabih A, Sobotka JA, Wu MZ, Wedeles CJ, Claycomb JM.

Biochim Biophys Acta. 2017 Nov;1861(11 Pt B):2948-2955. doi: 10.1016/j.bbagen.2017.05.027. Epub 2017 May 31. Review.

PMID: 28578161

RNA-mediated communication between helminths and their hosts: The missing links.

Claycomb J, Abreu-Goodger C, Buck AH.

RNA Biol. 2017 Apr 3;14(4):436-441. doi: 10.1080/15476286.2016.1274852. Epub 2017 Jan 26. Review.

PMID: 28125361

The Smaug RNA-Binding Protein Is Essential for microRNA Synthesis During the Drosophila Maternal-to-zygotic Transition.

Luo H, Li X, Claycomb JM, Lipshitz HD.

G3 (Bethesda). 2016 Sep 2. pii: g3.116.034199. doi: 10.1534/g3.116.034199. [Epub ahead of print]

PMID: 27591754

Comparative genomic analysis of upstream miRNA regulatory motifs in Caenorhabditis.

Jovelin R, Krizus A, Taghizada B, Gray JC, Phillips PC, Claycomb JM, Cutter AD.

RNA. 2016 Jul;22(7):968-78. doi: 10.1261/rna.055392.115. Epub 2016 May 2.

PMID: 27140965

Comparative functional characterization of the CSR-1 22G-RNA pathway in Caenorhabditis nematodes.

Tu S, Wu MZ, Wang J, Cutter AD, Weng Z, Claycomb JM.

Nucleic Acids Res. 2015 Jan;43(1):208-24. doi: 10.1093/nar/gku1308. Epub 2014 Dec 15.

PMID: 25510497

From early lessons to new frontiers: the worm as a treasure trove of small RNA biology.

Youngman EM, Claycomb JM.

Front Genet. 2014 Nov 27;5:416. doi: 10.3389/fgene.2014.00416. eCollection 2014. Review.

PMID: 25505902

Silent no more: Endogenous small RNA pathways promote gene expression.

Wedeles CJ, Wu MZ, Claycomb JM.

Worm. 2014 Apr 2;3:e28641. doi: 10.4161/worm.28641. eCollection 2014.

PMID: 25254148

Ancient endo-siRNA pathways reveal new tricks.

Claycomb JM.

Curr Biol. 2014 Aug 4;24(15):R703-15. doi: 10.1016/j.cub.2014.06.009. Review.

PMID: 25093565

Epstein-Barr virus EBNA1 protein regulates viral latency through effects on let-7 microRNA and dicer.

Mansouri S, Pan Q, Blencowe BJ, Claycomb JM, Frappier L.

J Virol. 2014 Oct;88(19):11166-77. doi: 10.1128/JVI.01785-14. Epub 2014 Jul 16.

PMID: 25031339

Emerging from the clouds: Vasa helicase sheds light on piRNA amplification.

Claycomb JM.

Dev Cell. 2014 Jun 23;29(6):632-4. doi: 10.1016/j.devcel.2014.06.009.

PMID: 24960691

Protection of germline gene expression by the C. elegans Argonaute CSR-1.

Wedeles CJ, Wu MZ, Claycomb JM.

Dev Cell. 2013 Dec 23;27(6):664-71.

PMID: 24360783

A multitasking Argonaute: exploring the many facets of C. elegans CSR-1.

Wedeles CJ, Wu MZ, Claycomb JM.

Chromosome Res. 2013 Dec;21(6-7):573-86. doi: 10.1007/s10577-013-9383-7. Review.

PMID: 24178449

Caenorhabditis elegans small RNA pathways make their mark on chromatin.

Claycomb JM.

DNA Cell Biol. 2012 Oct;31 Suppl 1:S17-33. doi: 10.1089/dna.2012.1611. Review.

PMID: 23046453

Cloning Argonaute-associated small RNAs from Caenorhabditis elegans.

Gu W, Claycomb JM, Batista PJ, Mello CC, Conte D.

Methods Mol Biol. 2011;725:251-80. doi: 10.1007/978-1-61779-046-1_17.

PMID: 21528459

Argonautes ALG-3 and ALG-4 are required for spermatogenesis-specific 26G-RNAs and thermotolerant sperm in Caenorhabditis elegans.

Conine CC, Batista PJ, Gu W, Claycomb JM, Chaves DA, Shirayama M, Mello CC.

Proc Natl Acad Sci U S A. 2010 Feb 23;107(8):3588-93. doi: 10.1073/pnas.0911685107. Epub 2010 Feb 4.

PMID: 20133686

Sequential rounds of RNA-dependent RNA transcription drive endogenous small-RNA biogenesis in the ERGO-1/Argonaute pathway.

Vasale JJ, Gu W, Thivierge C, Batista PJ, Claycomb JM, Youngman EM, Duchaine TF, Mello CC, Conte D Jr.

Proc Natl Acad Sci U S A. 2010 Feb 23;107(8):3582-7. doi: 10.1073/pnas.0911908107. Epub 2010 Feb 2.

PMID: 20133583

CDE-1 affects chromosome segregation through uridylation of CSR-1-bound siRNAs.

van Wolfswinkel JC, Claycomb JM, Batista PJ, Mello CC, Berezikov E, Ketting RF.

Cell. 2009 Oct 2;139(1):135-48. doi: 10.1016/j.cell.2009.09.012.

PMID: 19804759

The Argonaute CSR-1 and its 22G-RNA cofactors are required for holocentric chromosome segregation.

Claycomb JM, Batista PJ, Pang KM, Gu W, Vasale JJ, van Wolfswinkel JC, Chaves DA, Shirayama M, Mitani S, Ketting RF, Conte D Jr, Mello CC.

Cell. 2009 Oct 2;139(1):123-34. doi: 10.1016/j.cell.2009.09.014.

PMID: 19804758

Distinct argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline.

Gu W, Shirayama M, Conte D Jr, Vasale J, Batista PJ, Claycomb JM, Moresco JJ, Youngman EM, Keys J, Stoltz MJ, Chen CC, Chaves DA, Duan S, Kasschau KD, Fahlgren N, Yates JR 3rd, Mitani S, Carrington JC, Mello CC.

Mol Cell. 2009 Oct 23;36(2):231-44. doi: 10.1016/j.molcel.2009.09.020. Epub 2009 Oct 1.

PMID: 19800275

PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegans.

Batista PJ, Ruby JG, Claycomb JM, Chiang R, Fahlgren N, Kasschau KD, Chaves DA, Gu W, Vasale JJ, Duan S, Conte D Jr, Luo S, Schroth GP, Carrington JC, Bartel DP, Mello CC.

Mol Cell. 2008 Jul 11;31(1):67-78. doi: 10.1016/j.molcel.2008.06.002. Epub 2008 Jun 19.

PMID: 18571452