Publications

Preprints from the Meers Lab

• Intermediately Methylated Regions in Normal Cells Are Epimutation Hotspots in Cancer. Mahgoub M, Abel HJ, Davarapalli N, Struthers H, Kotnik E, Markovic C, Fronick C, Fulton RS, Meers MP, Spencer DH. bioRxiv. 2025 Sep 20. doi: https://doi.org/10.1101/2025.09.18.677221

• A protocol for high-throughput microplate-based CUT&Tag. Johnson BB, Boyle GE, Federico AJ, Ma J, Hemani H, Spencer DH, Sarthy JF, Meers MP. bioRxiv. 2025 Sep 20. doi: https://doi.org/10.1101/2025.09.18.676951

• Chromatin Profiling of CBFA2T3-GLIS2 AMLs Identifies Key Transcription Factor Dependencies and BRG1 Inhibition as a Novel Therapeutic Strategy. Kaonis S, Smith JL, Katiyar N, Merrill M, Hyelkma T, Namciu , Le Q, Babaeva E, Ishida T, Morris SM, Girard E, Furuyama S, Ries R, Bernstein I, Meshinchi S, Henikoff S, Meers MP, Hadland, Sarthy JF. bioRxiv. 2023 Sep 1. doi: https://doi.org/10.1101/2023.08.30.555598

Publications from Mike’s Graduate and Postdoctoral Work

• Multifactorial profiling of epigenetic landscapes at single-cell resolution using MulTI-Tag. Meers MP, Llagas G, Janssens DH, Codomo CA, Henikoff S. Nat Biotechnol. 2023 May;41(5):708-716. doi: 10.1038/s41587-022-01522-9. Epub 2022 Oct 31. PMID: 36316484

• Distinct roles for canonical and variant histone H3 lysine-36 in Polycomb silencing. Salzler HR, Vandadi V, McMichael BD, Brown JC, Boerma SA, Leatham-Jensen MP, Adams KM, Meers MP, Simon JM, Duronio RJ, McKay DJ, Matera AG. Sci Adv. 2023 Mar;9(9):eadf2451. doi: 10.1126/sciadv.adf2451. Epub 2023 Mar 1. PMID: 36857457

• Nucleosome Patterns in Circulating Tumor DNA Reveal Transcriptional Regulation of Advanced Prostate Cancer Phenotypes. De Sarkar N, Patton RD, Doebley AL, Hanratty B, Adil M, Kreitzman AJ, Sarthy JF, Ko M, Brahma S, Meers MP, Janssens DH, Ang LS, Coleman IM, Bose A, Dumpit RF, Lucas JM, Nunez TA, Nguyen HM, McClure HM, Pritchard CC, Schweizer MT, Morrissey C, Choudhury AD, Baca SC, Berchuck JE, Freedman ML, Ahmad K, Haffner MC, Montgomery RB, Corey E, Henikoff S, Nelson PS, Ha G. Cancer Discov. 2023 Mar 1;13(3):632-653. doi: 10.1158/2159-8290.CD-22-0692. PMID: 36399432

• CUT&Tag2for1: a modified method for simultaneous profiling of the accessible and silenced regulome in single cells. Janssens DH, Otto DJ, Meers MP, Setty M, Ahmad K, Henikoff S. Genome Biol. 2022 Mar 17;23(1):81. doi: 10.1186/s13059-022-02642-w. PMID: 35300717

• Automated CUT&Tag profiling of chromatin heterogeneity in mixed-lineage leukemia. Janssens DH, Meers MP, Wu SJ, Babaeva E, Meshinchi S, Sarthy JF, Ahmad K, Henikoff S. Nat Genet. 2021 Nov;53(11):1586-1596. doi: 10.1038/s41588-021-00941-9. Epub 2021 Oct 18. PMID: 34663924

• Selective androgen receptor modulators activate the canonical prostate cancer androgen receptor program and repress cancer growth. Nyquist MD, Ang LS, Corella A, Coleman IM, Meers MP, Christiani AJ, Pierce C, Janssens DH, Meade HE, Bose A, Brady L, Howard T, De Sarkar N, Frank SB, Dumpit RF, Dalton JT, Corey E, Plymate SR, Haffner MC, Mostaghel EA, Nelson PS. J Clin Invest. 2021 May 17;131(10):e146777. doi: 10.1172/JCI146777. PMID: 33998604

• Histone deposition pathways determine the chromatin landscapes of H3.1 and H3.3 K27M oncohistones. Sarthy JF, Meers MP, Janssens DH, Henikoff JG, Feldman H, Paddison PJ, Lockwood CM, Vitanza NA, Olson JM, Ahmad K, Henikoff S.Elife. 2020 Sep 9;9:e61090. doi: 10.7554/eLife.61090. PMID: 32902381

• MYCN amplification and ATRX mutations are incompatible in neuroblastoma. Zeineldin M, Federico S, Chen X, Fan Y, Xu B, Stewart E, Zhou X, Jeon J, Griffiths L, Nguyen R, Norrie J, Easton J, Mulder H, Yergeau D, Liu Y, Wu J, Van Ryn C, Naranjo A, Hogarty MD, Kamiński MM, Valentine M, Pruett-Miller SM, Pappo A, Zhang J, Clay MR, Bahrami A, Vogel P, Lee S, Shelat A, Sarthy JF, Meers MP, George RE, Mardis ER, Wilson RK, Henikoff S, Downing JR, Dyer MA. Nat Commun. 2020 Feb 14;11(1):913. doi: 10.1038/s41467-020-14682-6. PMID: 32060267

• Pioneer Factor-Nucleosome Binding Events during Differentiation Are Motif Encoded. Meers MP, Janssens DH, Henikoff S.Mol Cell. 2019 Aug 8;75(3):562-575.e5. doi: 10.1016/j.molcel.2019.05.025. Epub 2019 Jun 25. PMID: 31253573

• Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling. Meers MP, Tenenbaum D, Henikoff S. Epigenetics Chromatin. 2019 Jul 12;12(1):42. doi: 10.1186/s13072-019-0287-4. PMID: 31300027

• Improved CUT&RUN chromatin profiling tools. Meers MP, Bryson TD, Henikoff JG, Henikoff S. Elife. 2019 Jun 24;8:e46314. doi: 10.7554/eLife.46314. PMID: 31232687

• Old cogs, new tricks: the evolution of gene expression in a chromatin context. Talbert PB, Meers MP, Henikoff S. Nat Rev Genet. 2019 May;20(5):283-297. doi: 10.1038/s41576-019-0105-7. PMID: 30886348

• Automated in situ chromatin profiling efficiently resolves cell types and gene regulatory programs. Janssens DH, Wu SJ, Sarthy JF,
  Meers MP, Myers CH, Olson JM, Ahmad K, Henikoff S. Epigenetics Chromatin. 2018 Dec 21;11(1):74. doi: 10.1186/s13072-018-0243-8.
  PMID: 30577869

• Transcription start site profiling uncovers divergent transcription and enhancer-associated RNAs in Drosophila melanogaster. Meers MP, Adelman K, Duronio RJ, Strahl BD, McKay DJ, Matera AG. BMC Genomics. 2018 Feb 21;19(1):157. doi: 10.1186/s12864-018-4510-7. PMID: 29466941

• An Animal Model for Genetic Analysis of Multi-Gene Families: Cloning and Transgenesis of Large Tandemly Repeated Histone Gene Clusters. Meers MP, Leatham-Jensen M, Penke TJR, McKay DJ, Duronio RJ, Matera AG. Methods Mol Biol. 2018;1832:309-325. doi: 10.1007/978-1-4939-8663-7_17. PMID: 30073535

• Histone gene replacement reveals a post-transcriptional role for H3K36 in maintaining metazoan transcriptome fidelity. Meers MP, Henriques T, Lavender CA, McKay DJ, Strahl BD, Duronio RJ, Adelman K, Matera AG. Elife. 2017 Mar 27;6:e23249. doi: 10.7554/eLife.23249. PMID: 28346137

• Interrogating the function of metazoan histones using engineered gene clusters. McKay DJ, Klusza S, Penke TJ, Meers MP, Curry KP, McDaniel SL, Malek PY, Cooper SW, Tatomer DC, Lieb JD, Strahl BD, Duronio RJ, Matera AG. Dev Cell. 2015 Feb 9;32(3):373-86. doi: 10.1016/j.devcel.2014.12.025. PMID: 25669886

• Poly(A) RNA-binding proteins and polyadenosine RNA: new members and novel functions. Wigington CP, Williams KR, Meers MP, Bassell GJ, Corbett AH. Wiley Interdiscip Rev RNA. 2014 Sep-Oct;5(5):601-22. doi: 10.1002/wrna.1233. Epub 2014 Apr 30. PMID: 24789627

• Developmental arrest of Drosophila survival motor neuron (Smn) mutants accounts for differences in expression of minor intron-containing genes. Garcia EL, Lu Z, Meers MP, Praveen K, Matera AG. RNA. 2013 Nov;19(11):1510-6. doi: 10.1261/rna.038919.113. Epub 2013 Sep 4.
  PMID: 24006466