Vukic M, Chouaref J, Della Chiara V, Dogan S, Ratner F, Hogenboom JZM, Epp TA, Chawengsaksophak K, Vonk KKD, Breukel C, Ariyurek Y, San Leon Granado D, Kloet SL, Daxinger L. CDCA7-associated global aberrant DNA hypomethylation translates to localized, tissue-specific transcriptional responses. Sci Adv. 2024 Feb 9;10(6):eadk3384. doi:10.1126/sciadv.adk3384.

Liu Y, Sinke L, Jonkman TH, Slieker RC; BIOS Consortium; van Zwet EW, Daxinger L, Heijmans BT. The inactive X chromosome accumulates widespread epigenetic variability with age. Clin Epigenetics. 2023 Aug 25;15(1):135. doi:10.1186/s13148-023-01549-y.

Šikrová D, Testa AM, Willemsen I, van den Heuvel A, Tapscott SJ, Daxinger L, Balog J, van der Maarel SM. SMCHD1 and LRIF1 converge at the FSHD-associated D4Z4 repeat and LRIF1 promoter yet display different modes of action. CommunBiol. 2023 Jun 28;6(1):677. doi: 10.1038/s42003-023-05053-0.

Wang Z, Coban B, Wu H, Chouaref J, Daxinger L, Paulsen MT, Ljungman M, Smid M, Martens JWM, Danen EHJ. GRHL2-controlled gene expression networks in luminal breast cancer. Cell Commun Signal. 2023 Jan 23;21(1):15. doi:10.1186/s12964-022-01029-5.

*Desai VP, *Chouaref J, Wu H, Pastor WA, Kan RL, Oey HM, Li Z, Ho J, Vonk KKD, San Leon Granado D, Christopher MA, Clark AT, *Jacobsen SE, *Daxinger L. The role of MORC3 in silencing transposable elements in mouse embryonic stem cells. Epigenetics Chromatin. 2021 Oct 27;14(1):49. doi: 10.1186/s13072-021-00420-9.

*Saettini F, Poli C, Vengoechea J, Bonanomi S, Orellana JC, Fazio G, Rodriguez FH, Noguera LP, Booth C, Jarur-Chamy V, Shams M, Iascone M, Vukic M, Gasperini S, Quadri M, Barroeta Seijas A, Rivers E, Mauri M, Badolato R, Cazzaniga G, Bugarin C, Gaipa G, Kroes WGM, Moratto D, van Oostaijen-Ten Dam MM, Baas F, van der Maarel S, Piazza R, Coban-Akdemir ZH, Lupski JR, Yuan B, Chinn IK, *Daxinger L,*Biondi A. Absent B cells, agammaglobulinemia, and hypertrophic cardiomyopathy in folliculin-interacting protein 1 deficiency. Blood. 2021 Jan 28;137(4):493-499. doi: 10.1182/blood.2020006441.

Pagliaroli L, Porazzi P, Curtis AT, Scopa C, Mikkers HMM, Freund C, Daxinger L, Deliard S, Welsh SA, Offley S, Ott CA, Calabretta B, Brugmann SA, Santen GWE, Trizzino M. Inability to switch from ARID1A-BAF to ARID1B-BAF impairs exit from pluripotency and commitment towards neural crest formation in ARID1B-related neurodevelopmental disorders. Nat Commun. 2021 Nov 9;12(1):6469. doi: 10.1038/s41467-021-26810-x.

Chiara VD, Daxinger L, Staal FJT. The Route of Early T Cell Development: Crosstalk between Epigenetic and Transcription Factors. Cells. 2021 Apr30;10(5):1074. doi: 10.3390/cells10051074.

van Dongen J, Gordon SD, McRae AF, Odintsova VV, Mbarek H, Breeze CE, Sugden K, Lundgren S, Castillo-Fernandez JE, Hannon E, Moffitt TE, Hagenbeek FA, van Beijsterveldt CEM, Jan Hottenga J, Tsai PC; BIOS Consortium; Genetics of DNA Methylation Consortium; Min JL, Hemani G, Ehli EA, Paul F, Stern CD, Heijmans BT, Slagboom PE, Daxinger L, van der Maarel SM, de Geus EJC, Willemsen G, Montgomery GW, Reversade B, Ollikainen M, Kaprio J, Spector TD, Bell JT, Mill J, Caspi A, Martin NG, Boomsma DI. Identical twins carry a persistent epigenetic signature of early genome programming. Nat Commun. 2021 Sep 28;12(1):5618. doi: 10.1038/s41467-021-25583-7.

van den Heuvel D, Spruijt CG, González-Prieto R, Kragten A, Paulsen MT, Zhou D, Wu H, Apelt K, van der Weegen Y, Yang K, Dijk M, Daxinger L, Marteijn JA, Vertegaal ACO, Ljungman M, Vermeulen M, Luijsterburg MS. A CSB-PAF1C axis restores processive transcription elongation after DNA damage repair. NatCommun. 2021 Feb 26;12(1):1342. doi: 10.1038/s41467-021-21520-w.

Garcia-Perez L, Famili F, Cordes M, Brugman M, van Eggermond M, Wu H, Chouaref J, Granado DSL, Tiemessen MM, Pike-Overzet K, Daxinger L, Staal FJT. Functional definition of a transcription factor hierarchy regulating T cell lineage commitment. Sci Adv. 2020 Jul 31;6(31):eaaw7313. doi:10.1126/sciadv.aaw7313.

Hop PJ, Luijk R, Daxinger L, van Iterson M, Dekkers KF, Jansen R; BIOS Consortium, van Meurs JBJ, 't Hoen PAC, Ikram MA, van Greevenbroek MMJ, Boomsma DI, Slagboom PE, Veldink JH, van Zwet EW, Heijmans BT. Genome-wide identification of genes regulating DNA methylation using genetic anchors for causal inference. Genome Biol. 2020 Aug 28;21(1):220. doi: 10.1186/s13059-020-02114-z.

Vukic M, Daxinger L. DNA methylation in disease: Immunodeficiency, Centromeric instability, Facial anomalies syndrome. Essays Biochem. 2019 Dec20;63(6):773-783. doi: 10.1042/EBC20190035.

Wu H, Vonk KKD, van der Maarel SM, Santen GWE, Daxinger L. A functional assay to classify ZBTB24 missense variants of unknown significance. Hum Mutat. 2019 May 8. doi: 10.1002/humu.23786

Vukic M, Wu H, Daxinger L. Making headway towards understanding how epigenetic mechanisms contribute to early-life effects. Philos Trans R Soc Lond B Biol Sci. 2019 Apr 15;374(1770):20180126. doi: 10.1098/rstb.2018.0126.

Luijk R, Wu H, Ward-Caviness CK, Hannon E, Carnero-Montoro E, Min JL, Mandaviya P, Müller-Nurasyid M, Mei H, van der Maarel SM; BIOS Consortium; Relton C, Mill J, Waldenberger M, Bell JT, Jansen R, Zhernakova A, Franke L, 't Hoen PAC, Boomsma DI, van Duijn CM, van Greevenbroek MMJ, Veldink JH, Wijmenga C, van Meurs J, Daxinger L, Slagboom PE, van Zwet EW, Heijmans BT. Autosomal genetic variation is associated with DNA methylation in regions variably escaping X-chromosome inactivation. Nat Commun. 2018 Sep 14;9(1):3738. doi:10.1038/s41467-018-05714-3.

Fransen MF, Benonisson H, van Maren WW, Sow HS, Breukel C, Linssen MM, Claassens JWC, Brouwers C, van der Kaa J, Camps M, Kleinovink JW, Vonk KK, van Heiningen S, Klar N, van Beek L, van Harmelen V, Daxinger L, Nandakumar KS, Holmdahl R, Coward C, Lin Q, Hirose S, Salvatori D, van Hall T, van Kooten C, Mastroeni P, Ossendorp F, Verbeek JS. A Restricted Role for FcγR in the Regulation of Adaptive Immunity. J Immunol. 2018 Apr 15;200(8):2615-2626. doi:10.4049/jimmunol.1700429.

van den Boogaard ML, Thijssen PE, Aytekin C, Licciardi F, Kıykım AA, Spossito L, Dalm VASH, Driessen GJ, Kersseboom R, de Vries F, van Ostaijen-Ten Dam MM, Ikinciogullari A, Dogu F, Oleastro M, Bailardo E, Daxinger L, Nain E, Baris S, van Tol MJD, Weemaes C, van der Maarel SM. Expanding the mutation spectrum in ICF syndrome: Evidence for a gender bias in ICF2. Clin Genet. 2017 Oct;92(4):380-387. doi: 10.1111/cge.12979.

Li S, Yen L, Pastor WA, Johnston JB, Shew C, Du J, Liu W, Ho J, Stender B, Clark AT, Burlingame A, *Daxinger L, *Patel DJ, *Jacobsen SE. Mouse MORC3 is an ATP dependent dimer involved in gene silencing that localizes to H3K4me3-marked chromatin. ProcNatlAcadSci USA.2016 Aug 30;113(35):E5108-16. doi: 10.1073/pnas.1609709113.

Wu H, Thijssen PE, de Klerk E, Vonk KK, Wang J, den Hamer B, Aytekin C, van der Maarel SM, Daxinger L. Converging disease genes in ICF syndrome: ZBTB24 controls expression of CDCA7 in mammals. Hum Mol Genet. 2016 Sep 15;25(18):4041-4051. doi: 10.1093/hmg/ddw243.

Isbel L, Prokopuk L, Wu H, Daxinger L, Oey H, Spurling A, Lawther AJ, Hale MW, Whitelaw E. Wiz binds active promoters and CTCF-binding sites and is required for normal behaviour in the mouse. Elife. 2016 Jul 13;5:e15082. doi: 10.7554/eLife.15082.

Daxinger L, Oey H, Isbel L, Whitelaw NC, Youngson NA, Spurling A, Vonk KK, Whitelaw E. Hypomethylation of ERVs in the sperm of mice haploinsufficient for the histone methyltransferase Setdb1 correlates with a paternal effect on phenotype. Sci Rep. 2016 Apr 26;6:25004. doi: 10.1038/srep25004.

Isbel L, Srivastava R, Oey H, Spurling A, Daxinger L, Puthalakath H, Whitelaw E. Trim33 Binds and Silences a Class of Young Endogenous Retroviruses in the Mouse Testis; a Novel Component of the Arms Race between Retrotransposons and the Host Genome. PLoS Genet. 2015 Dec 1;11(12):e1005693. doi:10.1371/journal.pgen.1005693.

Daxinger L, Tapscott SJ, van der Maarel SM. Genetic and epigenetic contributors to FSHD. Curr Opin Genet Dev. 2015 Aug;33:56-61. doi:10.1016/j.gde.2015.08.007.

Harten SK, Oey H, Bourke LM, Bharti V, Isbel L, Daxinger L, Faou P,Robertson N, Matthews JM, Whitelaw E. The recently identified modifier of murine metastable epialleles, Rearranged L-Myc Fusion, is involved in maintaining epigenetic marks at CpG island shores and enhancers. BMC Biol. 2015 Mar26;13:21. doi: 10.1186/s12915-015-0128-2.

Sorolla A, Tallack MR, Oey H, Harten SK, Daxinger LC, Magor GW, Combes AN, Ilsley M, Whitelaw E, Perkins AC. Identification of novel hypomorphic and null mutations in Klf1 derived from a genetic screen for modifiers of α-globin transgene variegation. Genomics. 2015 Feb;105(2):116-22. doi:10.1016/j.ygeno.2014.09.013.

Daxinger L, Harten SK, Oey H, Epp T, Isbel L, Huang E, Whitelaw N, Apedaile A, Sorolla A, Yong J, Bharti V, Sutton J, Ashe A, Pang Z, Wallace N, Gerhardt DJ, Blewitt ME, Jeddeloh JA, Whitelaw E. An ENU mutagenesis screen identifies novel and known genes involved in epigenetic processes in the mouse. Genome Biol. 2013;14(9):R96. doi: 10.1186/gb-2013-14-9-r96.

Roberts AR, Huang E, Jones L, Daxinger L, Chong S, Whitelaw E. Non-telomeric epigenetic and genetic changes are associated with the inheritance of shorter telomeres in mice. Chromosoma. 2013 Dec;122(6):541-54. doi:10.1007/s00412-013-0427-8

Youngson NA, Epp T, Roberts AR, Daxinger L, Ashe A, Huang E, Lester KL, Harten SK, Kay GF, Cox T, Matthews JM, Chong S, Whitelaw E. No evidence for cumulative effects in a Dnmt3b hypomorph across multiple generations. MammGenome. 2013 Jun;24(5-6):206-17.

You W, Tyczewska A, Spencer M, Daxinger L, Schmid MW, Grossniklaus U, Simon SA, Meyers BC, Matzke AJ, Matzke M. Atypical DNA methylation of genes encoding cysteine-rich peptides in Arabidopsis thaliana. BMC Plant Biol. 2012 Apr 19;12:51. doi: 10.1186/1471-2229-12-51.

Daxinger L, Whitelaw E. Understanding transgenerational epigenetic inheritance via the gametes in mammals. Nat Rev Genet. 2012 Jan 31;13(3):153-62. doi: 10.1038/nrg3188.

Naumann U, Daxinger L, Kanno T, Eun C, Long Q, Lorkovic ZJ, Matzke M, Matzke AJ. Genetic evidence that DNA methyltransferase DRM2 has a direct catalytic role in RNA-directed DNA methylation in Arabidopsis thaliana. Genetics. 2011 Mar;187(3):977-9. doi: 10.1534/genetics.110.125401. Epub 2011 Jan 6.

Daxinger L, Whitelaw E. Transgenerational epigenetic inheritance: more questions than answers. Genome Res. 2010 Dec;20(12):1623-8. doi:10.1101/gr.106138.110. Epub 2010 Nov 1.

Vrbsky J, Akimcheva S, Watson JM, Turner TL, Daxinger L, Vyskot B, Aufsatz W, Riha K. siRNA-mediated methylation of Arabidopsis telomeres. PLoS Genet. 2010 Jun 10;6(6):e1000986. doi: 10.1371/journal.pgen.1000986.

Gao Z, Liu HL, Daxinger L, Pontes O, He X, Qian W, Lin H, Xie M, Lorkovic ZJ, Zhang S, Miki D, Zhan X, Pontier D, Lagrange T, Jin H, Matzke AJ, Matzke M, Pikaard CS, Zhu JK. An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation. Nature. 2010 May 6;465(7294):106-9. doi:10.1038/nature09025. Epub 2010 Apr 21.

Kanno T, Bucher E, Daxinger L, Huettel B, Kreil DP, Breinig F, Lind M, Schmitt MJ, Simon SA, Gurazada SG, Meyers BC, Lorkovic ZJ, Matzke AJ, Matzke M. RNA-directed DNA methylation and plant development require an IWR1-type transcription factor. EMBO Rep. 2010 Jan;11(1):65-71. doi:10.1038/embor.2009.246. Epub 2009 Dec 11.

Matzke M, Kanno T, Daxinger L, Huettel B, Matzke AJ. RNA-mediated chromatin-based silencing in plants. Curr Opin Cell Biol. 2009 Jun;21(3):367-76. doi:

10.1016/j.ceb.2009.01.025. Epub 2009 Feb 23.

Daxinger L, Kanno T, Bucher E, van der Winden J, Naumann U, Matzke AJ, Matzke M. A stepwise pathway for biogenesis of 24-nt secondary siRNAs and spreading of DNA methylation. EMBO J. 2009 Jan 7;28(1):48-57. doi:10.1038/emboj.2008.260. Epub 2008 Dec 11.

Daxinger L, Kanno T, Matzke M. Pol V transcribes to silence. Cell. 2008 Nov14;135(4):592-4. doi: 10.1016/j.cell.2008.10.027.

Kanno T, Bucher E, Daxinger L, Huettel B, Böhmdorfer G, Gregor W, Kreil DP, Matzke M, Matzke AJ. A structural-maintenance-of-chromosomes hinge domain-containing protein is required for RNA-directed DNA methylation. Nat Genet. 2008 May;40(5):670-5. doi: 10.1038/ng.119. Epub 2008 Apr 20.

Daxinger L, Hunter B, Sheikh M, Jauvion V, Gasciolli V, Vaucheret H, Matzke M, Furner I. Unexpected silencing effects from T-DNA tags in Arabidopsis. Trends Plant Sci. 2008 Jan;13(1):4-6. doi: 10.1016/j.tplants.2007.10.007.

Matzke M, Kanno T, Huettel B, Daxinger L, Matzke AJ. Targets of RNA-directed DNA methylation. Curr Opin Plant Biol. 2007 Oct;10(5):512-9. doi:10.1016/j.pbi.2007.06.007. Epub 2007 Aug 16.

Huettel B, Kanno T, Daxinger L, Bucher E, van der Winden J, Matzke AJ, Matzke M. RNA-directed DNA methylation mediated by DRD1 and Pol IVb: a versatile pathway for transcriptional gene silencing in plants. Biochim Biophys Acta. 2007 May-Jun;1769(5-6):358-74. doi: 10.1016/j.bbaexp.2007.03.001. Epub 2007 Mar 12.

Matzke M, Kanno T, Huettel B, Daxinger L, Matzke AJ. RNA-directed DNA methylation and Pol IVb in Arabidopsis. Cold Spring Harb Symp Quant Biol. 2006;71:449-59. doi:10.1101/sqb.2006.71.028.

Huettel B, Kanno T, Daxinger L, Aufsatz W, Matzke AJ, Matzke M. Endogenous targets of RNA-directed DNA methylation and Pol IV in Arabidopsis. EMBO J. 2006 Jun 21;25(12):2828-36. doi: 10.1038/sj.emboj.7601150. Epub 2006 May 25.

Mette MF, Aufsatz W, Kanno T, Daxinger L, Rovina P, Matzke M, Matzke AJ. Analysis of double-stranded RNA and small RNAs involved in RNA-mediated transcriptional gene silencing. Methods Mol Biol. 2005;309:61-82. doi:10.1385/1-59259-935-4:061.

Kanno T, Huettel B, Mette MF, Aufsatz W, Jaligot E, Daxinger L, Kreil DP, Matzke M, Matzke AJ. Atypical RNA polymerase subunits required for RNA-directed DNA methylation. Nat Genet. 2005 Jul;37(7):761-5. doi: 10.1038/ng1580. Epub 2005May 29.

Matzke M, Aufsatz W, Kanno T, Daxinger L, Papp I, Mette MF, Matzke AJ. Genetic analysis of RNA-mediated transcriptional gene silencing. Biochim BiophysActa. 2004 Mar 15;1677(1-3):129-41. doi: 10.1016/j.bbaexp.2003.10.015.

Papp I, Mette MF, Aufsatz W, Daxinger L, Schauer SE, Ray A, van der Winden J, Matzke M, Matzke AJ. Evidence for nuclear processing of plant micro RNA and short interfering RNA precursors. Plant Physiol. 2003 Jul;132(3):1382-90. doi:10.1104/pp.103.021980.

Lrif1 modulates Trim28-mediated repression of the Dux locus in mouse embryonic stem cells. Darina Šikrová, Román González-Prieto, Alfred C. O. Vertegaal, Judit Balog, Lucia Daxinger, Silvère M. van der Maarel bioRxiv 2024.11.18.624083; doi: https://doi.org/10.1101/2024.11.18.624083

The inactive X chromosome accumulates widespread epigenetic variability with age Yunfeng Liu, Lucy Sinke, Thomas H. Jonkman, Roderick C. Slieker, BIOS Consortium, Erik W. van Zwet, Lucia Daxinger, Bastiaan T. Heijmans bioRxiv 2023.03.10.532039; doi: https://doi.org/10.1101/2023.03.10.532039

Genome-wide identification of binding sites of GRHL2 in luminal-like and basal A subtypes of breast cancer Zi Wang, Haoyu Wu, Lucia Daxinger, Erik HJ Danen bioRxiv 2020.02.13.946947; doi: https://doi.org/10.1101/2020.02.13.946947

Inability to switch from ARID1A-BAF to ARID1B-BAF impairs exit from pluripotency and commitment towards neural crest formation in ARID1B-related neurodevelopmental disorders Luca Pagliaroli, Patrizia Porazzi, Alyxandra T. Curtis, Chiara Scopa, Harald M.M. Mikkers, Christian Freund, Lucia Daxinger, Sandra Deliard, Sarah A. Welsh, Sarah Offley, Connor A. Ott, Bruno Calabretta, Samantha A. Brugmann, Gijs W.E. Santen, Marco Trizzino bioRxiv 2021.04.02.438227; doi: https://doi.org/10.1101/2021.04.02.438227

Zbtb24 binding protects promoter activity by antagonizing DNA methylation in mESCs Haoyu Wu, David San Leon Granado, Maja Vukic, Kelly K.D. Vonk, Cor Breukel, Jihed Chouaref, Jeroen F.J. Laros, Lucia Daxinger bioRxiv 858662; doi: https://doi.org/10.1101/858662

A CSB-PAF1C axis restores processive transcription elongation after DNA damage repair Diana van den Heuvel, Cornelia G. Spruijt, Román González-Prieto, Angela Kragten, Michelle T. Paulsen, Di Zhou, Haoyu Wu, Katja Apelt, Yana van der Weegen, Kevin Yang, Madelon Dijk, Lucia Daxinger, Jurgen A. Marteijn, Alfred C.O. Vertegaal, Mats Ljungman, Michiel Vermeulen, Martijn S. Luijsterburg bioRxiv 2020.01.04.894808; doi: https://doi.org/10.1101/2020.01.04.894808

SMCHD1 has separable roles in chromatin architecture and gene silencing that could be targeted in disease Andres Tapia del Fierro, Bianca den Hamer, Natasha Jansz, Kelan Chen, Tamara Beck, Hannah Vanyai, Natalia Benetti, Alexandra D Gurzau, Lucia Daxinger, Shifeng Xue, Thanh Thao Nguyen Ly, Iromi Wanigasuriya, Kelsey Breslin, Harald Oey, Yvonne Krom, Dinja van der Hoorn, Linde F Bouwman, Matthew E. Ritchie, Bruno Reversade, Fabrice Prin, Timothy Mohun, Silvère M van der Maarel, Edwina McGlinn, James M Murphy, Andrew Keniry, Jessica C de Greef, Marnie E Blewitt bioRxiv 2021.05.12.443934; doi: https://doi.org/10.1101/2021.05.12.443934

Genome-wide identification of genes regulating DNA methylation using genetic anchors for causal inference Paul J. Hop, René Luijk, Lucia Daxinger, Maarten van Iterson, Koen F. Dekkers, Rick Jansen, BIOS Consortium, Joyce B.J. van Meurs, Peter A.C. ’t Hoen, M. Arfan Ikram, Marleen M.J. van Greevenbroek, Dorret I. Boomsma, P. Eline Slagboom, Jan H. Veldink, Erik W. van Zwet, Bastiaan T. Heijmans bioRxiv 823807; doi:https://doi.org/10.1101/823807