Recent and representative publications from our lab.

For a full list: http://www.ncbi.nlm.nih.gov/pubmed/?term=bruneau+bg{C}

• TBXT dose sensitivity and the decoupling of nascent mesoderm specification from EMT progression in 2D human gastruloids. Bulger EA, Muncie-Vasic I, Libby ARG, McDevitt TC, Bruneau BG. Development. 2024 Feb 26:dev.202516.

• CDX2 dose-dependently influences the gene regulatory network underlying human extraembryonic mesoderm development. Bulger EA, McDevitt TC, Bruneau BG. bioRxiv [Preprint]. 2024 Jan 26:2024.01.25.577277.

• A disrupted compartment boundary underlies abnormal cardiac patterning and congenital heart defects. Kathiriya IS, Dominguez MH, Rao KS, Muncie-Vasic JM, Devine WP, Hu KM, Hota SK, Garay BI, Quintero D, Goyal P, Matthews MN, Thomas R, Sukonnik T, Miguel-Perez D, Winchester S, Brower EF, Forjaz A, Wu PH, Wirtz D, Kiemen AL, Bruneau BG. bioRxiv [Preprint]. 2024 Mar 4:2024.02.05.578995. doi: 10.1101/2024.02.05.578995.

• A Mesp1-dependent developmental breakpoint in transcriptional and epigenomic specification of early cardiac precursors. Krup AL, Winchester SAB, Ranade SS, Agrawal A, Devine WP, Sinha T, Choudhary K, Dominguez MH, Thomas R, Black BL, Srivastava D, Bruneau BG. Development. 2023 Mar 30:dev.201229.

• Graded mesoderm assembly governs cell fate and morphogenesis of the early mammalian heart. Dominguez MH, Krup AL, Muncie JM, Bruneau BG. Cell. 2023 Feb 2;186(3):479-496.e23.

• Cell Layers: uncovering clustering structure in unsupervised single-cell transcriptomic analysis. Blair AP, Hu RK, Farah EN, Chi NC, Pollard KS, Przytycki PF, Kathiriya IS, Bruneau BG. Bioinform Adv. 2022 Aug 4;2(1):vbac051.

• Targeting transcription in heart failure via CDK7/12/13 inhibition. Hsu A, Duan Q, Day DS, Luo X, McMahon S, Huang Y, Feldman ZB, Jiang Z, Zhang T, Liang Y, Alexanian M, Padmanabhan A, Brown JD, Lin CY, Gray NS, Young RA, Bruneau BG, Haldar SM. Nat Commun. 2022 Jul 27;13(1):4345.

• Modeling congenital heart disease: lessons from mice, hPSC-based models, and organoids. Rao KS, Kameswaran V, Bruneau BG. Genes Dev. 2022 Jun 1;36(11-12):652-663.

• Brahma safeguards canalization of cardiac mesoderm differentiation. Hota SK, Rao KS, Blair AP, Khalilimeybodi A, Hu KM, Thomas R, So K, Kameswaran V, Xu J, Polacco BJ, Desai RV, Chatterjee N, Hsu A, Muncie JM, Blotnick AM, Winchester SAB, Weinberger LS, Hüttenhain R, Kathiriya IS, Krogan NJ, Saucerman JJ, Bruneau BG. Nature. 2022 Feb;602(7895):129-134. Epub 2022 Jan 26.

• Molecular basis of CTCF binding polarity in genome finding. Nora EP, Caccianini L, Fudenberg G, So K, Kameswaran V, Nagle A, Uebersohn A, Hajj B, Saux AL, Coulon A, Mirny LA, Pollard KS, Dahan M, Bruneau B.G..Nat Commun. 2020 Nov 5;11(1):5612.

• Modeling human TBX5 haploinsufficiency predicts regulatory networks for congenital heart disease. Kathiriya I.K., Rao K.S., Iacono G., Devine W.P., Blair A.P., Hota S.K., Lai M.H., Garay B.I., Thomas R., Gong H.Z., Wasson L.K., Goyal P., Sukonnik T., Hu K.M., Akgun G.A., Bernard L.D., Akerberg B.N., Gu F., Li K., Speir M.L, Haeussler M., Pu W.T., Stuart, J.M., Seidman C.E., Seidman J.G., Heyn H., & Bruneau B.G.

  Developmental Cell 2020 accepted

• Molecular basis of CTCF binding polarity in genome folding. Nora E.P., Caccianini L., Fudenberg G., Kameswaran V., Nagle A., Uebersohn A.,

  So K., Hajj B., Le Saux A., Coulon A., Mirny L.A., Pollard K.S., Dahan M., & Bruneau B.G. Nature Communications 2020 in press

• Salt-inducible kinase 1 maintains HDAC7 stability to promote pathologic cardiac remodeling. Hsu A, Duan Q, McMahon S, Huang Y, Wood SA, Gray NS, Wang B, Bruneau B.G.*, Haldar SM*. Journal of Clinical Investigation 2020.130(6):2966-2977 *co-corresponding authors

• Minimal in vivo requirements for developmentally regulated cardiac long intergenic non-coding RNAs. George M.R., Duan Q., Nagle A., Kathiriya I.S., Huang Y., Rao K., Haldar S.M., Bruneau B.G. Development 2019 146(23). pii: dev185314.

• Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards.

  Lind A.L., Lai Y.Y.Y., Mostovoy Y., Holloway A.K., Iannucci A., Mak A.C.Y., Fondi M., Orlandini V., Eckalbar W.L., Milan M., Rovatsos M., Kichigin I.G., Makunin A.I., Johnson Pokorná M., Altmanová M, Trifonov V.A., Schijlen E., Kratochvíl L., Fani R., Velenský P., Rehák I, Patarnello T., Jessop T.S., Hicks J.W., Ryder O.A., Mendelson J.R. III, Ciofi C., Kwok P.-Y., Pollard K.S., & Bruneau B.G. Nature Ecology and Evolution 2019 3(8):1241-1252

• Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis.

  Hota S.K., Johnson J.R., Verschueren E., Thomas R., Blotnick A.M., Zhu Y., Sun X.,Pennacchio L.A., Krogan N.J., & Bruneau B.G.

  Development 2019 146(19) pii: dev.174086.

• Cardiac-enriched BAF chromatin-remodeling complex subunit Baf60c regulates gene expression programs essential for heart development and function. Sun X., Hota S.K., Zhou Y.Q., Novak S., Miguel-Perez D., Christodoulou D., Seidman C.E., Seidman J.G., Gregorio C.C., Henkelman R.M., Rossant J., Bruneau B.G. Biol Open. 2018 7(1). pii: bio029512.

• Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization Nora E.P., Goloborodko A., Valton A.-L., Gibcus J.H., Uebersohn A., Abdennur N., Dekker J., Mirny L.A., Bruneau B.G Cell 2017 169:930-944

• KMT2D regulates specific programs in heart development via histone H3 lysine 4 dimethylation. Ang S.-Y., Uebersohn A., Spencer C.I., Huang Y., Lee J.-E., Ge K., & Bruneau B.G. Development 2016 143:810-821

• Complex interdependence regulates heterotypic transcription factor distribution and coordinates cardiogenesis. Luna-Zurita L., Stirnimann C.U., Glatt S., Kaynak B.L., Thomas S., Baudin F., Samee Md.A.H., He D., Small E.M., Mileikovsky M., Nagy A., Holloway A.K., Pollard K.S., Muller C.W., & Bruneau B.G. (2016) Cell 164:999-1014

• KMT2D regulates specific programs in heart development via histone H3 lysine 4 dimethylation. Ang S.-Y., Uebersohn A., Spencer C.I., Huang Y., Lee J.-E., Ge K., & Bruneau B.G. (2016) Development 143:810-821

• Brg1 modulates enhancer activation in mesoderm linege commitment. Alexander J.A., Hota S.K., He D., Thomas S., Ho L., Pennacchio L.P., Bruneau B.G. (2015) Development 142:1418-1430

• Human disease modeling reveals integrated transcriptional and epigenetic mechanisms of NOTCH1 haploinsufficiency. Theodoris C.V., Li M., White M.P., Liu L., He D., Pollard K.S.*, Bruneau B.G.*, Srivastava D.* (2015) Cell 160:1072-1086 (*co-senior authors)

• Ezh2-mediated repression of a transcriptional pathway upstream of Mmp9 maintains integrity of the developing vasculature. Delgado-Olguin P.D.*, Dang L.T., He D., Thomas S., Chi L., Sukonnik T., Khyzha N., Dobenecker M.-W., Fish J.E., & Bruneau B.G.* (2014) Development 141:4610-4617 (* Corresponding authors)

• Early patterning and specification of cardiac progenitors in gastrulating mesoderm. Devine W.P.*, Wythe J.D., George M., Koshiba-Takeuchi K., & Bruneau B.G.* (2014) eLife published online 10/08/14; DOI: http://dx.doi.org/10.7554/eLife.03848 (* Corresponding authors)

• ETS factors regulate Vegf-dependent arterial specification. Wythe J.D.*, Dang L.T.H., Devine W.P., Boudreau E., Artap S.T., He D., Schacterle W., Stainier D.Y.R., Oettgen P., Black B.L., Bruneau B.G.*, Fish J.E.* (2013) Developmental Cell 15:45-58 (* Corresponding authors)

• Cooperative and antagonistic roles for Irx3 and Irx5 in cardiac morphogenesis and postnatal physiology. Gaborit N., Sakuma R., Wylie J.N., Kin K.-H., Zhang S.-S., Hui C.c., & Bruneau B.G. (2012) Development 139:4007-4019

• Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Wamstad J.A., Alexander J.M., Truty R.M., Shrikumar A., Li F., Eilertson K.E., Ding H., Wylie J.N., Pico A.R., Capra J.A., Erwin G., Kattman S.J., Keller G.M., Srivastava D., Levine S.S., Pollard K.S., Holloway A.K., Boyer L.A.*, & Bruneau B.G.* (2012) Cell 151:206-220 (* Corresponding authors)

• Epigenetic repression of cardiac progenitor gene expression by Ezh2 is required for postnatal cardiac homeostasis. Delgado-Olguín P., Huang Y., Li X., Christodoulou D., Seidman C.E., Seidman J.G., Tarakhovsky A., & Bruneau B.G. (2012) Nature Genetics 44(3):343-7

• Iroquois homeobox gene 3 establishes fast conduction in the cardiac His-Purkinje network. Zhang S.-S., Kim K.-H., Rosen A., Smyth J., Sakuma R., Delgado-Olguin P., Davis M., Chi N.C., Puviindran V., Gaborit N., Sukonnik T., Wylie J.N., Brand-Armzamendi K., Farman G., Kim J., Rose R.A., Marsden P.A., Zhu Y., Zhou Y., Miquerol L., Henkelman R.M., Stainier D.Y., Shaw R.M., Hui C.c.*, Bruneau B.G.*, & Backx P.H. (2011) Proc Natl Acad Sci U S A. 108:13576-81 (*corresponding authors)

• Chromatin remodeling complex dosage modulates transcription factor function in heart development. Takeuchi J.K., Lou X., Alexander J.M., Sugizaki H., Delgado-Olguin P., Holloway A.K., Mori A.D., Wylie J.N., Munson C., Zhu Y., Zhou Y.Q., Yeh R.F., Henkelman R.M., Harvey R.P., Metzger D., Chambon P., Stainier D.Y., Pollard K.S., Scott I.C., & Bruneau B.G. (2011) Nature Communications 2011,2:187 (PMC: Open; PMC3096875)

• Reptilian heart development and the molecular basis of cardiac chamber evolution. Koshiba-Takeuchi K.T., Mori A.D., Kaynak B.L., Cebra-Thomas J., Sukonnik T., Georges R.O., Latham S., Beck L., Henkelman R.M., Black B.L., Olson E.N., Wade J., Takeuchi J.K., Nemer M., Gilbert S.F. & Bruneau B.G. (2009) Nature 461:95-98 (PMC2753965).

• Directed transdifferentiation of mouse mesoderm to heart tissue by defined factors. Takeuchi J.K., & Bruneau B.G. (2009) Nature 459:708-711 (PMC2728356).

• The homeodomain transcription factor Irx5 establishes the mouse cardiac ventricular repolarization gradient. Costantini D.L., Arruda E.P., Agarwal P., Kim K.-H., Zhu Y., Zhu W., Lebel M., Cheng C.W., Park C.Y., Pierce S., Guerchicoff A., Pollevick G., Chan T.Y., Kabir M.G., Cheng S.H., Husain M., Antzelevitch C., Srivastava D.,Gross G.J., Hui C.-c., Backx P.H., & Bruneau B.G. (2005) Cell 123:347–358

• Baf60c is essential for function of BAF chromatin remodelling complexes in heart development. Lickert H., Takeuchi J.K., von Both I., Walls J., McAuliffe F., Adamson S.L., Henkelman R.M., Wrana J.L., Rossant J., & Bruneau B.G. (2004) Nature 432:107–112