Publications

“Members of an array of zinc-finger proteins specify distinct Hox chromatin boundaries." Ortabozkoyun H, Huang PY, Gonzalez-Buendia E, Cho H, Kim SY, Tsirigos A, Mazzoni E.O., Reinberg D. Mol Cell. 2024 Sep 19;84(18):3406-3422.e6. doi: 10.1016/j.molcel.2024.08.007. Epub 2024 Aug 21. PubMed PMID: 39173638; PubMed Central PMCID: PMC11613955.

“Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation." Tiniakou I, Hsu PF, Lopez-Zepeda LS, Garipler G, Esteva E, Adams NM, Jang G, Soni C, Lau CM, Liu F, Khodadadi-Jamayran A, Rodrick TC, Jones D, Tsirigos A, Ohler U, Bedford MT, Nimer SD, Kaartinen V, Mazzoni E.O., Reizis B. Sci Immunol. 2024 Apr 12;9(94):eadi1023. doi: 10.1126/sciimmunol.adi1023. Epub 2024 Apr 12. PubMed PMID: 38608038; PubMed Central PMCID: PMC11182672.

“Essential transcription factors for induced neuron differentiation." Lu C, Garipler G, Dai C, Roush T, Salome-Correa J, Martin A, Liscovitch-Brauer N, Mazzoni E.O., Sanjana NE. Nat Commun. 2023 Dec 15;14(1):8362. doi: 10.1038/s41467-023-43602-7. PubMed PMID: 38102126; PubMed Central PMCID: PMC10724217.

“ISSCR Education Committee syllabus and learning guide for enhancing stem cell literacy." Perlin JR, Anderson WJ, Bartfeld S, Couturier A, de Soysa Y, Hawley RS, Hu P, Loh YH, Mandal L, Master Z, Muotri AR, Piddini E, Polo JM, Mazzoni E.O., Stem Cell Reports. 2023 Feb 14;18(2):417-419. doi: 10.1016/j.stemcr.2022.12.004. Epub 2023 Jan 12. PubMed PMID: 36638789; PubMed Central PMCID: PMC9968981.

“Synthetic regulatory reconstitution reveals principles of mammalian Hox cluster regulation.” Pinglay S, Bulajić M, Rahe DP, Huang E, Brosh R, Mamrak NE, King BR, German S, Cadley JA, Rieber L, Easo N, Lionnet T, Mahony S, Maurano MT, Holt LJ, Mazzoni EO, Boeke JD. Science. 2022 Jul;377(6601):eabk2820. doi: 10.1126/science.abk2820. Epub 2022 Jul 1. PubMed PMID: 35771912; PubMed Central PMCID: PMC9648154.

“Foxa2 and Pet1 Direct and Indirect Synergy Drive Serotonergic Neuronal Differentiation." Aydin B, Sierk M, Moreno-Estelles M, Tejavibulya L, Kumar N, Flames N, Mahony S, Mazzoni EO. Front Neurosci. 2022;16:903881. doi: 10.3389/fnins.2022.903881. eCollection 2022. PubMed PMID: 35801179; PubMed Central PMCID: PMC9254625.

“Capybara: A computational tool to measure cell identity and fate transitions." Kong W, Fu YC, Holloway EM, Garipler G, Yang X, Mazzoni EO, Morris SA. Cell Stem Cell. 2022 Apr 7;29(4):635-649.e11. doi: 10.1016/j.stem.2022.03.001. Epub 2022 Mar 29. PubMed PMID: 35354062; PubMed Central PMCID: PMC9040453.

“The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by repressing pro-differentiation genes." Garipler G, Lu C, Morrissey A, Lopez-Zepeda LS, Pei Y, Vidal SE, Zen Petisco Fiore AP, Aydin B, Stadtfeld M, Ohler U, Mahony S, Sanjana NE, Mazzoni EO. Cell Rep.2022 Mar 15;38(11):110524. doi: 10.1016/j.celrep.2022.110524. PubMed PMID: 35294876; PubMed Central PMCID: PMC8972945.

“An expansion of the non-coding genome and its regulatory potential underlies vertebrate neuronal diversity." Closser M, Guo Y, Wang P, Patel T, Jang S, Hammelman J, De Nooij JC, Kopunova R, Mazzoni EO, Ruan Y, Gifford DK, Wichterle H.  Neuron. 2022 Jan 5;110(1):70-85.e6. doi: 10.1016/j.neuron.2021.10.014. Epub 2021 Nov 1. PubMed PMID: 34727520; PubMed Central PMCID: PMC8738133.

“Differential abilities to engage inaccessible chromatin diversify vertebrate Hox binding patterns”, Milica Bulajić, Divyanshi Srivastava, Jeremy S Dasen, Hynek Wichterle, Shaun Mahony, Esteban O Mazzoni. Development. 2020 Nov 23;147(22):dev194761. doi: 10.1242/dev.194761.

“Simple Method to Quantify Protein Abundances from 1000 Cells." Vitrinel B, Iannitelli DE, Mazzoni EO, Christiaen L, Vogel C. ACS Omega. 2020 Jun 30;5(25):15537-15546. doi: 10.1021/acsomega.0c01191. eCollection 2020 Jun 30. PubMed PMID: 32637829; PubMed Central PMCID: PMC7331059.

"Cell Reprogramming: The Many Roads to Success", Aydin B., Mazzoni, E.O., Annual Review of Cell and Developmental Biology (2019) 35:1; 433-452 doi: https://doi.org/10.1146/annurev-cellbio-100818-125127

“Stem cell-derived cranial and spinal motor neurons reveal proteostatic differences between ALS resistant and sensitive motor neurons.” An, D., Fujiki, R., Iannitelli, D. E., Smerdon, J. W., Maity, S., Rose, M. F., Gelber A., Wanaselja E. K., Yagudayeva I., Lee J. Y., Vogel C., Wichterle H., Engle E. C., Mazzoni, E. O. (2019). ELife, 8. https://doi.org/10.7554/eLife.44423

“Proneural factors Ascl1 and Neurog2 contribute to neuronal subtype identities by establishing distinct chromatin landscape.” Begüm Aydin, Akshay Kakumanu, Mary Rosillo, Mireia Moreno-Estelles, Niels Ringstad, Nuria Flames, Shaun Mahony, Esteban O. Mazzoni. Nature Neuroscience (2019) doi: 10.1038/s41593-019-0399-y PMID: 31086315

“cAMPr: A single-wavelength fluorescent sensor for cyclic AMP." Hackley CR, Mazzoni EO, Blau J. Sci Signal. 2018 Mar 6;11(520). doi: 10.1126/scisignal.aah3738. PubMed PMID: 29511120; PubMed Central PMCID: PMC5863242.

“Deconvolving sequence features that discriminate between overlapping regulatory annotations." Kakumanu A, Velasco S, Mazzoni E, Mahony S.  PLoS Comput Biol. 2017 Oct;13(10):e1005795. doi: 10.1371/journal.pcbi.1005795. eCollection 2017 Oct. PubMed PMID: 29049320; PubMed Central PMCID: PMC5663517.

“RNA localization is a key determinant of neurite-enriched proteome." Zappulo A, van den Bruck D, Ciolli Mattioli C, Franke V, Imami K, McShane E, Moreno-Estelles M, Calviello L, Filipchyk A, Peguero-Sanchez E, Müller T, Woehler A, Birchmeier C, Merino E, Rajewsky N, Ohler U, Mazzoni EO, Selbach M, Akalin A, Chekulaeva M. Nat Commun. 2017 Sep 19;8(1):583. doi: 10.1038/s41467-017-00690-6. PubMed PMID: 28928394; PubMed Central PMCID: PMC5605627.

"A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells."
Velasco S, Ibrahim MM, Kakumanu A, Garipler G, Aydin B, Al-Sayegh MA, Hirsekorn A, Abdul-Rahman F, Satija R, Ohler U, Mahony S, Mazzoni EO.
Cell Stem Cell. 2017 Feb 2;20(2):205-217.e8. doi: 10.1016/j.stem.2016.11.006. Epub 2016 Dec 8. PMID:27939218

"CTCF-mediated topological boundaries during development foster appropriate gene regulation."
Narendra V, Bulajić M, Dekker J, Mazzoni EO, Reinberg D.
Genes Dev. 2016 Dec 15;30(24):2657-2662. doi: 10.1101/gad.288324.116. PMID: 28087711

"Iterative Role of Notch Signaling in Spinal Motor Neuron Diversification."
Tan C., Mazzoni EO, Wichterle H.
Cell Rep. 2016 Jul 26;16(4):907-16. doi: 10.1016/j.celrep.2016.06.067. Epub 2016 Jul 14. PMID: 27425621

"CRISPR-dCas9 and sgRNA scaffolds enable dual-color live imaging of satellite sequences and repeat-enriched individual loci."
Yi Fu, Pedro Rocha, Vincent Luo, Ramya Raviram, Yan Deng, Esteban O Mazzoni, and Jane Skok.
Nature Communications. (2016) May 25;7:11707. PMID: 27222091.

“CTCF establishes discrete functional chromatin domains at the Hox clusters during Differentiation.”
Varun Narendra, Pedro P. Rocha, Disi An, Ramya Raviram, Jane A. Skok, Esteban O. Mazzoni, Danny Reinberg.
Science. (2015) Feb 27;347(6225):1017-21. PMID: 25722416. Co-corresponding author.

“Evolving Hox Activity Profiles Govern Diversity in Locomotor Systems”.
Heekyung Jung, Esteban O. Mazzoni, Natalia Soshnikova, Olivia Hanley, Byrappa Venkatesh, Denis Duboule, Jeremy S. Dasen. (2014). 
Dev. Cell. Apr 28;29(2):171-87..

“An integrated model of multiple-condition ChIP-Seq data reveals predeterminants of Cdx2 binding”.
Shaun Mahony, Matthew D. Edwards,  Esteban O. Mazzoni, Richard I. Sherwood, Akshay Kakumanu, Carolyn A. Morrison, Hynek Wichterle and David K. Gifford.
Plos Comput. Bio. (2014) Mar 27;10(3):e1003501.

“Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals.”
Esteban O. Mazzoni, Shaun Mahony, Scott McCuine, Timothy W Danford, Christopher Reeder, P Alexander Rolfe, Robin D. Dowell, Seraphim Thornton, Laurie A Boyer, Thomas M. Jessell, Richard A Young, David K Gifford and Hynek Wichterle­.
Nat Neurosci. 2013 Sep;16(9):1191-8. doi: 10.1038/nn.3490. (PMID: 23955559).  Co-corresponding author.

“Synergistic Recruitment of Transcription Factors to Cell Type Specific Enhancers Programs Motor Neuron Identity”. Esteban O. Mazzoni, Shaun Mahony, Michael Closser, Carolyn A. Morrison, Disi An, Stephane Nedelec, David K. Gifford and Hynek Wichterle.
Nat Neurosci. 2013 Sep;16(9):1219-27. (PMID: 23872598). Co-corresponding author.

“Mapping Neuronal Diversity One Cell at a Time”.
Hynek Wichterle, David. K. Gifford and Esteban O. Mazzoni.  
Science. 2013 Aug 16;341(6147):726-7. (PMID: 23955559)

“Lineage-based identification of cellular states and expression programs”.
Hashimoto T, Jaakkola T, Sherwood R, Mazzoni EO, Wichterle H, Gifford D.
Bioinformatics. 2012 Jun 15;28(12):i250-7.

“Embryonic Stem cell system to study transcription factor binding during development.” Esteban O. Mazzoni, Shaun Mahony, Michelina Iacovino, Carolyn A. Morrison, George Mountoufaris, Michael Closser, Warren A. Whyte, Richard A. Young,  Michael Kyba, David K. Gifford and Hynek Wichterle.
Nat Methods. 2011 Nov 13;8(12):1056-8.

"Feedback from Rhodopsin protein controls rhodopsin exclusion in Drosophila R8 photoreceptors”. Daniel Vasiliauskas, Esteban O. Mazzoni, Simon G. Sprecher, Robert J. Johnston Jr., Preetmoninder Lidder, Nina Vogt, and Claude Desplan. Nature. 2011 Oct 9;479(7371):108-12.

“An alternative splicing switch regulates embryonic stem cell pluripotency and reprogramming.” Gabut M, Samavarchi-Tehrani P, Wang X, Slobodeniuc V, O'Hanlon D, Sung HK, Alvarez M, Talukder S, Pan Q, Mazzoni EO, Nedelec S, Wichterle H, Woltjen K, Hughes TR, Zandstra PW, Nagy A, Wrana JL, Blencowe BJ. Cell. 2011 Sep 30;147(1):132-46.

“Wnt Signaling Specifies and Patterns Intestinal Endoderm”. Richard I Sherwood, Rene Maehr, Esteban O. Mazzoni, and Douglas A Melton. Mech Dev. 2011 Aug 10.  Sep-Dec;128(7-10):387-400. 

"Distinct visual pathways mediate Drosophila larval light avoidance and circadian clock entrainment". Alex Keene, Esteban O. Mazzoni, Jamie Zhen, Meg Younger, Satoko Yamaguchi, Justin Blau, Claude Desplan, and Simon Sprecher. J Neurosci. 2011 Apr 27;31(17):6527-34. 

“Mir-17-3p Controls Spinal Neural Progenitor Patterning by Regulating Olig2/Irx3 Cross-repressive Loop.” Jun-An Chen, Yuan-Ping Huang, Esteban O. Mazzoni, G. Christopher Tan, Jiri Zavadil, and Hynek Wichterle. Neuron. 2011 Feb 24;69(4):721-35.

“Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis.” Shaun Mahony, Esteban O. Mazzoni, Scott McCuine, Richard A. Young , Hynek Wichterle, and David K. Gifford. Genome Biology. 2011 Jan 13;12(1) & Equal contribution.

“Global control of motor neuron topography mediated by the repressive actions of a single hox gene.” Heekyung Jung, Julie Lacombe, Esteban O. Mazzoni, Karel F. Liem Jr.&, Jonathan Grinstein, Shaun Mahony, Debnath Mukhopadhyay, David K. Gifford, Richard A. Young, Kathryn V. Anderson, Hynek Wichterle and Jeremy S. Dasen. Neuron. 2010 Sep 9;67(5):781-96. & Equal contribution.

“Functional diversity of ESC-derived motor neuron subtypes revealed through intraspinal transplantation.” Mirza Peljto, Jeremy S.  Dasen, Esteban O.  Mazzoni, Thomas M.  Jessell, and Hynek Wichterle. Cell Stem Cell. 2010 Sep 3;7(3):355-66.

“Iroquois complex genes induce co-expression of rhodopsins in Drosophila.” Mazzoni EO, Celik A, Wernet MF, Vasiliauskas D, Johnston RJ, Cook TA, Pichaud F, Desplan C. PLoS Biol. (2008) 6(4):e97.

“Stochastic expression of the Drosophila Dioxin receptor homolog Spineless creates the retina mosaic for color vision”. Wernet MF, Mazzoni EO, Celik A, Duncan DM, Duncan I and Desplan C. Nature (2006) 440(7081):174:80. Equal contribution.

“Drosophila cryptochrome is a tissue specific circadian repressor”. Collins B, Mazzoni EO, Stanewsky R and Blau J. Curr Biol (2006) 16(5):441-9. &Equal contribution.

“The growth regulators warts/lats and melted interact in a bistable loop to specify opposite fates in Drosophila R8 photoreceptors”. Mikeladze-Dvali T, Wernet M, Pistillo D, Mazzoni EO, Teleman A, Chen Y and Desplan C. B. Cell (2005)122(5):775-87.

“Circadian pacemaker neurons transmit and modulate visual information to control a rapid behavioral response”. Mazzoni EO, Desplan C and Blau J. Neuron (2005) 45(2):293-300.

“'One receptor' rules in sensory neurons”. Mazzoni EO, Desplan C and Celik A. Dev. Neuroscience. (2004) 26(5-6):388-95.

“Homothorax Switches Function of Drosophila Photoreceptors from Color to Polarized Light Sensors”. Wernet MF, Labhart T, Baumann F, Mazzoni EO, Pichaud P and Desplan C. Cell (2003) 115: 267-279.

“Immortalized mammary epithelial cells overexpressing protein kinase C gamma acquire a malignant phenotype and become tumorigenic in vivo”. Mazzoni E, Adam A, Bal de Kier Joffe E, Aguirre-Ghiso JA. Mol Cancer Res. (2003) 1(10):776-87.

“Nitric oxide synthase, arginase and cyclooxygenase are involved in muscarinic receptor activation in different murine mammary adenocarcinoma cell lines”. Espanol A, Eijan AM, Mazzoni E, Davel L, Jasnis MA, Sacerdote De Lustig E, Sales ME. Int J Mol Med. (2002)  9(6):651-7.

“Signaling pathways regulating the expression of proteases during tumor progression.” de Kier Joffe EB, Mazzoni E, Aguirre Ghiso JA. (2000). Medicina. 60 Suppl 2:34-40.

“The time of tumor cell division and death depends on the site of growth.” Colombo LL, Mazzoni EO, Meiss RP.  Oncol Rep. (2000) 7(6):1363-6.