My Bibliography

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Verdejo-Torres O, Klein DC, Novoa-Aponte L, Carrazco-Carrillo J, Bonilla-Pinto D, Rivera A, Bakhshian A, Fitisemanu FM, Jiménez-González ML, Flinn L, Pezacki AT, Lanzirotti A, Ortiz Frade LA, Chang CJ, Navea JG, Blaby-Haas CE, Hainer SJ, Padilla-Benavides T. Cysteine Rich Intestinal Protein 2 is a copper-responsive regulator of skeletal muscle differentiation and metal homeostasis. PLoS Genet. 2024 Dec 5;20(12):e1011495. doi: 10.1371/journal.pgen.1011495. [Epub ahead of print] PubMed PMID: 39637238.

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Lynskey ML, Brown EE, Bhargava R, Wondisford AR, Ouriou JB, Freund O, Bowman RW 2nd, Smith BA, Lardo SM, Schamus-Hayes S, Hainer SJ, O'Sullivan RJ. HIRA protects telomeres against R-loop-induced instability in ALT cancer cells. Cell Rep. 2024 Nov 26;43(11):114964. doi: 10.1016/j.celrep.2024.114964. Epub 2024 Nov 6. PubMed PMID: 39509271.

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Patty BJ, Jordan C, Lardo SM, Troy K, Hainer SJ. H3.3K122A results in a neomorphic phenotype in mouse embryonic stem cells. Epigenetics Chromatin. 2024 Nov 1;17(1):32. doi: 10.1186/s13072-024-00557-3. PubMed PMID: 39487536; PubMed Central PMCID: PMC11531108.

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Verdejo-Torres O, Klein DC, Novoa-Aponte L, Carrazco-Carrillo J, Bonilla-Pinto D, Rivera A, Fitisemanu F, Jiménez-González ML, Flinn L, Pezacki AT, Lanzirotti A, Ortiz-Frade LA, Chang CJ, Navea JG, Blaby-Haas C, Hainer SJ, Padilla-Benavides T. Cysteine Rich Intestinal Protein 2 is a copper-responsive regulator of skeletal muscle differentiation. bioRxiv. 2024 May 5;. doi: 10.1101/2024.05.03.592485. PubMed PMID: 38746126; PubMed Central PMCID: PMC11092763.

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Patty BJ, Hainer SJ. Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements. bioRxiv. 2024 Apr 15;. doi: 10.1101/2024.04.12.589208. PubMed PMID: 38659863; PubMed Central PMCID: PMC11042195.

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Klein DC, Lardo SM, Hainer SJ. The ncBAF Complex Regulates Transcription in AML Through H3K27ac Sensing by BRD9. Cancer Res Commun. 2024 Jan 30;4(1):237-252. doi: 10.1158/2767-9764.CRC-23-0382. PubMed PMID: 38126767; PubMed Central PMCID: PMC10831031.

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Viner C, Ishak CA, Johnson J, Walker NJ, Shi H, Sjöberg-Herrera MK, Shen SY, Lardo SM, Adams DJ, Ferguson-Smith AC, De Carvalho DD, Hainer SJ, Bailey TL, Hoffman MM. Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet. Genome Biol. 2024 Jan 8;25(1):11. doi: 10.1186/s13059-023-03070-0. PubMed PMID: 38191487; PubMed Central PMCID: PMC10773111.

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Nmezi B, Bey GR, Oranburg TD, Dudnyk K, Lardo SM, Herdman N, Jacko A, Rubio S, Alcocer EL, Kofler J, Kim D, Rankin J, Kivuva E, Gutowski N, Schon K, van den Ameele J, Chinnery PF, Sousa SB, Palavra F, Toro C, Pinto E Vairo F, Saute J, Pan L, Alturkustani M, Hammond R, Gros-Louis F, Gold M, Park Y, Bernard G, Raininko R, Zhou J, Hainer SJ, Padiath QS. An oligodendrocyte silencer element underlies the pathogenic impact of lamin B1 structural variants. bioRxiv. 2023 Aug 9;. doi: 10.1101/2023.08.03.551473. PubMed PMID: 37609196; PubMed Central PMCID: PMC10441294.

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Klein DC, Lardo SM, McCannell KN, Hainer SJ. FACT regulates pluripotency through proximal and distal regulation of gene expression in murine embryonic stem cells. BMC Biol. 2023 Aug 4;21(1):167. doi: 10.1186/s12915-023-01669-0. PubMed PMID: 37542287; PubMed Central PMCID: PMC10403911.

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Klein DC, Troy K, Tripplehorn SA, Hainer SJ. The esBAF and ISWI nucleosome remodeling complexes influence occupancy of overlapping dinucleosomes and fragile nucleosomes in murine embryonic stem cells. BMC Genomics. 2023 Apr 13;24(1):201. doi: 10.1186/s12864-023-09287-4. PubMed PMID: 37055726; PubMed Central PMCID: PMC10103515.

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Yong Joon Kim J, Sang Z, Xiang Y, Shen Z, Shi Y. Nanobodies: Robust miniprotein binders in biomedicine. Adv Drug Deliv Rev. 2023 Apr;195:114726. doi: 10.1016/j.addr.2023.114726. Epub 2023 Feb 7. Review. PubMed PMID: 36754285.

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Zou H, Poore B, Brown EE, Qian J, Xie B, Asimakidou E, Razskazovskiy V, Ayrapetian D, Sharma V, Xia S, Liu F, Chen A, Guan Y, Li Z, Wanggou S, Saulnier O, Ly M, Fellows-Mayle W, Xi G, Tomita T, Resnick AC, Mack SC, Raabe EH, Eberhart CG, Sun D, Stronach BE, Agnihotri S, Kohanbash G, Lu S, Herrup K, Rich JN, Gittes GK, Broniscer A, Hu Z, Li X, Pollack IF, Friedlander RM, Hainer SJ, Taylor MD, Hu B. A neurodevelopmental epigenetic programme mediated by SMARCD3-DAB1-Reelin signalling is hijacked to promote medulloblastoma metastasis. Nat Cell Biol. 2023 Mar;25(3):493-507. doi: 10.1038/s41556-023-01093-0. Epub 2023 Feb 27. PubMed PMID: 36849558; PubMed Central PMCID: PMC10014585.

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McCann C, Quinteros M, Adelugba I, Morgada MN, Castelblanco AR, Davis EJ, Lanzirotti A, Hainer SJ, Vila AJ, Navea JG, Padilla-Benavides T. The mitochondrial Cu(+) transporter PiC2 (SLC25A3) is a target of MTF1 and contributes to the development of skeletal muscle in vitro. Front Mol Biosci. 2022;9:1037941. doi: 10.3389/fmolb.2022.1037941. eCollection 2022. PubMed PMID: 36438658; PubMed Central PMCID: PMC9682256.

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Shen Z, Sang Z, Shi Y. Nanobodies as a powerful platform for biomedicine. Trends Mol Med. 2022 Nov;28(11):1006-1007. doi: 10.1016/j.molmed.2022.08.007. Epub 2022 Sep 6. PubMed PMID: 36075813.

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Sang Z, Xiang Y, Bahar I, Shi Y. Llamanade: An open-source computational pipeline for robust nanobody humanization. Structure. 2022 Mar 3;30(3):418-429.e3. doi: 10.1016/j.str.2021.11.006. Epub 2021 Dec 10. PubMed PMID: 34895471.

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Sarabipour S, Hainer SJ, Arslan FN, de Winde CM, Furlong E, Bielczyk N, Jadavji NM, Shah AP, Davla S. Building and sustaining mentor interactions as a mentee. FEBS J. 2022 Mar;289(6):1374-1384. doi: 10.1111/febs.15823. Epub 2021 Apr 5. PubMed PMID: 33818917; PubMed Central PMCID: PMC8490489.

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Lardo SM, Hainer SJ. Single-Cell Factor Localization on Chromatin using Ultra-Low Input Cleavage Under Targets and Release using Nuclease. J Vis Exp. 2022 Feb 1;(180). doi: 10.3791/63536. PubMed PMID: 35188122; PubMed Central PMCID: PMC9306226.

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Sarabipour S, Hainer SJ, Furlong E, Jadavji NM, de Winde CM, Bielczyk N, Shah AP. Writing an effective and supportive recommendation letter. FEBS J. 2022 Jan;289(2):298-307. doi: 10.1111/febs.15757. Epub 2021 Mar 5. Review. PubMed PMID: 33665964; PubMed Central PMCID: PMC8418620.

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Klein D, Lardo S, McCannell K, Hainer S. FACT maintains pluripotency factor expression through gene-distal regulation in embryonic stem cells. [preprint]. 2021 July. doi: 10.1101/2021.07.30.454509.

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Patty BJ, Hainer SJ. Transcription factor chromatin profiling genome-wide using uliCUT&RUN in single cells and individual blastocysts. Nat Protoc. 2021 May;16(5):2633-2666. doi: 10.1038/s41596-021-00516-2. Epub 2021 Apr 28. PubMed PMID: 33911257; PubMed Central PMCID: PMC8177051.

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de Winde C, Sarabipour S, Carignano H, davla S, eccles D, Hainer S, haidar M, Ilangovan V, Jadavji N, Kritsiligkou P, Lee T, Ólafsdóttir F. Towards inclusive funding practices for early career researchers. [preprint]. 2020 September. doi: 10.31219/osf.io/9sfm8.

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Patty BJ, Hainer SJ. Non-Coding RNAs and Nucleosome Remodeling Complexes: An Intricate Regulatory Relationship. Biology (Basel). 2020 Aug 7;9(8). doi: 10.3390/biology9080213. Review. PubMed PMID: 32784701; PubMed Central PMCID: PMC7465399.

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Hainer SJ, Kaplan CD. Specialized RSC: Substrate Specificities for a Conserved Chromatin Remodeler. Bioessays. 2020 Jul;42(7):e2000002. doi: 10.1002/bies.202000002. Epub 2020 Jun 3. PubMed PMID: 32490565; PubMed Central PMCID: PMC7329613.

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Troy K, Liu Y, Hainer SJ. PathSTORM: a road to early cancer detection. Mol Cell Oncol. 2020;7(5):1776086. doi: 10.1080/23723556.2020.1776086. eCollection 2020. PubMed PMID: 32944634; PubMed Central PMCID: PMC7469673.

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Florentino RM, Fraunhoffer NA, Morita K, Takeishi K, Ostrowska A, Achreja A, Animasahun O, Haep N, Arazov S, Agarwal N, Collin de l'Hortet A, Guzman-Lepe J, Tafaleng EN, Mukherjee A, Troy K, Banerjee S, Paranjpe S, Michalopoulos GK, Bell A, Nagrath D, Hainer SJ, Fox IJ, Soto-Gutierrez A. Cellular Location of HNF4α is Linked With Terminal Liver Failure in Humans. Hepatol Commun. 2020 Jun;4(6):859-875. doi: 10.1002/hep4.1505. eCollection 2020 Jun. PubMed PMID: 32490322; PubMed Central PMCID: PMC7262291.

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Xu J, Ma H, Ma H, Jiang W, Mela CA, Duan M, Zhao S, Gao C, Hahm ER, Lardo SM, Troy K, Sun M, Pai R, Stolz DB, Zhang L, Singh S, Brand RE, Hartman DJ, Hu J, Hainer SJ, Liu Y. Super-resolution imaging reveals the evolution of higher-order chromatin folding in early carcinogenesis. Nat Commun. 2020 Apr 20;11(1):1899. doi: 10.1038/s41467-020-15718-7. PubMed PMID: 32313005; PubMed Central PMCID: PMC7171144.

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Klein DC, Hainer SJ. Genomic methods in profiling DNA accessibility and factor localization. Chromosome Res. 2020 Mar;28(1):69-85. doi: 10.1007/s10577-019-09619-9. Epub 2019 Nov 27. PubMed PMID: 31776829; PubMed Central PMCID: PMC7125251.

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Klein DC, Hainer SJ. Chromatin regulation and dynamics in stem cells. Curr Top Dev Biol. 2020;138:1-71. doi: 10.1016/bs.ctdb.2019.11.002. Epub 2019 Dec 30. Review. PubMed PMID: 32220294; PubMed Central PMCID: PMC7333739.

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Klein D, Hainer S. Chromatin regulation and dynamics in stem cells. In: Current Topics in Developmental Biology [Internet] Elsevier; 2020. 1-71p. Available from: https://linkinghub.elsevier.com/retrieve/pii/S0070215319300894.

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Tavera-Montañez C, Hainer SJ, Cangussu D, Gordon SJV, Xiao Y, Reyes-Gutierrez P, Imbalzano AN, Navea JG, Fazzio TG, Padilla-Benavides T. The classic metal-sensing transcription factor MTF1 promotes myogenesis in response to copper. FASEB J. 2019 Dec;33(12):14556-14574. doi: 10.1096/fj.201901606R. Epub 2019 Nov 5. PubMed PMID: 31690123; PubMed Central PMCID: PMC6894080.

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Hainer SJ, Bošković A, McCannell KN, Rando OJ, Fazzio TG. Profiling of Pluripotency Factors in Single Cells and Early Embryos. Cell. 2019 May 16;177(5):1319-1329.e11. doi: 10.1016/j.cell.2019.03.014. Epub 2019 Apr 4. PubMed PMID: 30955888; PubMed Central PMCID: PMC6525046.

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Hainer SJ, Fazzio TG. High-Resolution Chromatin Profiling Using CUT&RUN. Curr Protoc Mol Biol. 2019 Apr;126(1):e85. doi: 10.1002/cpmb.85. Epub 2019 Jan 28. PubMed PMID: 30688406; PubMed Central PMCID: PMC6422702.

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Acharya D, Hainer SJ, Yoon Y, Wang F, Bach I, Rivera-Pérez JA, Fazzio TG. KAT-Independent Gene Regulation by Tip60 Promotes ESC Self-Renewal but Not Pluripotency. Cell Rep. 2017 Apr 25;19(4):671-679. doi: 10.1016/j.celrep.2017.04.001. PubMed PMID: 28445719; PubMed Central PMCID: PMC5484067.

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Hainer SJ, McCannell KN, Yu J, Ee LS, Zhu LJ, Rando OJ, Fazzio TG. DNA methylation directs genomic localization of Mbd2 and Mbd3 in embryonic stem cells. Elife. 2016 Nov 16;5. doi: 10.7554/eLife.21964. PubMed PMID: 27849519; PubMed Central PMCID: PMC5111885.

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Hainer SJ, Martens JA. Regulation of chaperone binding and nucleosome dynamics by key residues within the globular domain of histone H3. Epigenetics Chromatin. 2016;9:17. doi: 10.1186/s13072-016-0066-4. eCollection 2016. PubMed PMID: 27134679; PubMed Central PMCID: PMC4851828.

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Hainer SJ, Fazzio TG. Regulation of Nucleosome Architecture and Factor Binding Revealed by Nuclease Footprinting of the ESC Genome. Cell Rep. 2015 Oct 6;13(1):61-69. doi: 10.1016/j.celrep.2015.08.071. Epub 2015 Sep 24. PubMed PMID: 26411677; PubMed Central PMCID: PMC4598306.

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Hainer SJ, Gu W, Carone BR, Landry BD, Rando OJ, Mello CC, Fazzio TG. Suppression of pervasive noncoding transcription in embryonic stem cells by esBAF. Genes Dev. 2015 Feb 15;29(4):362-78. doi: 10.1101/gad.253534.114. PubMed PMID: 25691467; PubMed Central PMCID: PMC4335293.

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Chen PB, Zhu LJ, Hainer SJ, McCannell KN, Fazzio TG. Unbiased chromatin accessibility profiling by RED-seq uncovers unique features of nucleosome variants in vivo. BMC Genomics. 2014 Dec 15;15(1):1104. doi: 10.1186/1471-2164-15-1104. PubMed PMID: 25494698; PubMed Central PMCID: PMC4378318.

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Carone BR, Hung JH, Hainer SJ, Chou MT, Carone DM, Weng Z, Fazzio TG, Rando OJ. High-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm. Dev Cell. 2014 Jul 14;30(1):11-22. doi: 10.1016/j.devcel.2014.05.024. Epub 2014 Jul 3. PubMed PMID: 24998598; PubMed Central PMCID: PMC4184102.

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Hainer SJ, Charsar BA, Cohen SB, Martens JA. Identification of Mutant Versions of the Spt16 Histone Chaperone That Are Defective for Transcription-Coupled Nucleosome Occupancy in Saccharomyces cerevisiae. G3 (Bethesda). 2012 May;2(5):555-67. doi: 10.1534/g3.112.002451. Epub 2012 May 1. PubMed PMID: 22670226; PubMed Central PMCID: PMC3362939.

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Pruneski JA, Hainer SJ, Petrov KO, Martens JA. The Paf1 complex represses SER3 transcription in Saccharomyces cerevisiae by facilitating intergenic transcription-dependent nucleosome occupancy of the SER3 promoter. Eukaryot Cell. 2011 Oct;10(10):1283-94. doi: 10.1128/EC.05141-11. Epub 2011 Aug 26. PubMed PMID: 21873510; PubMed Central PMCID: PMC3187070.

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Hainer SJ, Martens JA. Identification of histone mutants that are defective for transcription-coupled nucleosome occupancy. Mol Cell Biol. 2011 Sep;31(17):3557-68. doi: 10.1128/MCB.05195-11. Epub 2011 Jul 5. PubMed PMID: 21730290; PubMed Central PMCID: PMC3165560.

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Hainer SJ, Martens JA. Transcription of ncDNA: Many roads lead to local gene regulation. Transcription. 2011 May;2(3):120-123. doi: 10.4161/trns.2.3.15684. PubMed PMID: 21826282; PubMed Central PMCID: PMC3149688.

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Hainer SJ, Pruneski JA, Mitchell RD, Monteverde RM, Martens JA. Intergenic transcription causes repression by directing nucleosome assembly. Genes Dev. 2011 Jan 1;25(1):29-40. doi: 10.1101/gad.1975011. Epub 2010 Dec 14. PubMed PMID: 21156811; PubMed Central PMCID: PMC3012934.