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.
Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. Dekker J, Alber F, Aufmkolk S, Beliveau BJ, Bruneau BG, Belmont AS, Bintu L, Boettiger A, Calandrelli R, Disteche CM, Gilbert DM, Gregor T, Hansen AS, Huang B, Huangfu D, Kalhor R, Leslie CS, Li W, Li Y, Ma J, Noble WS, Park PJ, Phillips-Cremins JE, Pollard KS, Rafelski SM, Ren B, Ruan Y, Shav-Tal Y, Shen Y, Shendure J, Shu X, Strambio-De-Castillia C, Vertii A, Zhang H, Zhong S. Mol Cell. 2023 Aug 3;83(15):2624-2640. doi: 10.1016/j.molcel.2023.06.018. Epub 2023 Jul 6.
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.
Smarcd3 is an epigenetic modulator of the metabolic landscape in pancreatic ductal adenocarcinoma. Ferguson LP, Gatchalian J, McDermott ML, Nakamura M, Chambers K, Rajbhandari N, Lytle NK, Rosenthal SB, Hamilton M, Albini S, Wartenberg M, Zlobec I, Galván JA, Karamitopoulou E, Vavinskaya V, Wascher A, Lowy AM, Schürch CM, Puri PL, Bruneau BG, Hargreaves DC, Reya T. Nat Commun. 2023 Jan 18;14(1):292.
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.
Transcription Factor GATA4 Regulates Cell Type-Specific Splicing Through Direct Interaction With RNA in Human Induced Pluripotent Stem Cell-Derived Cardiac Progenitors. Zhu L, Choudhary K, Gonzalez-Teran B, Ang YS, Thomas R, Stone NR, Liu L, Zhou P, Zhu C, Ruan H, Huang Y, Jin S, Pelonero A, Koback F, Padmanabhan A, Sadagopan N, Hsu A, Costa MW, Gifford CA, van Bemmel JG, Hüttenhain R, Vedantham V, Conklin BR, Black BL, Bruneau BG, Steinmetz L, Krogan NJ, Pollard KS, Srivastava D. Circulation. 2022 Sep 6;146(10):770-787.
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.
Transcription factor protein interactomes reveal genetic determinants in heart disease. Gonzalez-Teran B, Pittman M, Felix F, Thomas R, Richmond-Buccola D, Hüttenhain R, Choudhary K, Moroni E, Costa MW, Huang Y, Padmanabhan A, Alexanian M, Lee CY, Maven BEJ, Samse-Knapp K, Morton SU, McGregor M, Gifford CA, Seidman JG, Seidman CE, Gelb BD, Colombo G, Conklin BR, Black BL, Bruneau BG, Krogan NJ, Pollard KS, Srivastava D. Cell. 2022 Mar 3;185(5):794-814.e30. Epub 2022 Feb 18.
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.
Co-emergence of cardiac and gut tissues promotes cardiomyocyte maturation within human iPSC-derived organoids. Silva AC, Matthys OB, Joy DA, Kauss MA, Natarajan V, Lai MH, Turaga D, Blair AP, Alexanian M, Bruneau BG, McDevitt TC. Cell Stem Cell. 2021 Dec 2;28(12):2137-2152.
Mechanisms of Congenital Heart Disease caused by NAA15 Haplionsufficiency. Ward T, Tai W, Morton S, Impens F, Van Damme P, Van Haver D, Timmerman E, Venturini G, Zhang K, Jang MY, Willcox JAL, Haghighi A, Gelb BD, Chung WK, Goldmuntz E, Porter GA Jr, Lifton RP, Brueckner M, Yost HJ, Bruneau B.G., Gorham J, Kim Y, Pereira A, Homsy J, Benson CC, DePalma SR, Varland S, Chen CS, Arnesen T, Gevaert K, Seidman C, Seidman JG.Circ Res. 2021 Apr 16;128(8):1156-1169.
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.
WAPL maintains a cohesin loading cycle to preserve cell-type specific distal gene regulation. Liu N.Q., Maresca M., van den Brand T., Braccioli L., Schinjs M.G.A., Teunissen H., Bruneau B.G., Nora E.P., & de Wit E. Nature Genetics 2020 in press
Regulation of single-cell genome organization into TADs and chromatin nanodomains. Szabo Q., Donjon A., Jerkovic I., Papadopoulos G.L., Cheutin T., Bonev B., Nora E.P., Bruneau B.G., Bantingnies F., & Cavalli G. Nature Genetics 2020 in press
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
Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation. Nishana M., Ha C., Rodriguez-Hernaez J., Ranjbaran A., Chio E., Nora E.P., Badri S.B., Kloetgen A., Bruneau B.G., Tsirigos A., Skok J.A. Genome Biology 2020 21(1):108.
Transcriptional profiling and therapeutic targeting of oxidative stress in neuroinflammation.
Mendiola AS, Ryu JK, Bardehle S, Meyer-Franke A, Ang KK, Wilson C, Baeten KM, Hanspers K, Merlini M, Thomas S, Petersen MA, Williams A, Thomas R, Rafalski VA, Meza-Acevedo R, Tognatta R, Yan Z, Pfaff SJ, Machado MR, Bedard C, Rios Coronado PE, Jiang X, Wang J, Pleiss MA, Green AJ, Zamvil SS, Pico AR, Bruneau B.G., Arkin MR, Akassoglou K. Nature Immunology 2020 21(5):513-524.
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.
CTCF confers local nucleosome resiliency after DNA replication and during mitosis. Owens N., Papadopoulou T., Festuccia N., Tachtsidi A., Gonzalez I., Dubois A., Vandormael-Pournin S., Nora E.P., Bruneau B.G., Cohen-Tannoudji M., Navarro P. Elife 2019 8. pii: e47898.
RNA Interactions Are Essential for CTCF-Mediated Genome Organization. Saldaña-Meyer R., Rodriguez-Hernaez J., Escobar T., Nishana M., Jácome-López K., Nora E.P., Bruneau B.G., Tsirigos A., Furlan-Magaril M., Skok J., Reinberg D.Molecular Cell 2019 76(3):412-422
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.
A de novo shape-motif discovery algorithm reveals structural preferences of transcription factors beyond sequence motifs. Samee Mb.A.H., Bruneau B.G., & Pollard K.S. Cell Systems 2019 8:27-42
Identification of cis elements for spatio-temporal control of mammalian DNA replication. Sima J., Chakraborty A., Dileep V., Michalski M., Klein K.N., Holcomb N.P., Turner J.L.,Paulsen M.T., Rivera-Mulia J.C., Trevilla-Garcia C., Bartlett D.A., Zhao P.A., Washburn B.K., Nora E.P., Kraft K., Mundlos S., Bruneau B.G., Ljungman M., Fraser P., Ay F., & Gilbert D.M.Cell 2019 176:816-830
Heart enhancers with deeply conserved regulatory activity are established early in zebrafish development. Yuan X., Song M., Devine P., Bruneau B.G., Scott I.C., Wilson M.D. Nature Communications. 2018 9(1):4977
A novel reporter allele for monitoring Dll4 expression within the embryonic and adult mouse. Herman A.M., Rhyner A.M., Devine W.P., Marrelli S.P., Bruneau B.G., Wythe J.D. Biol Open. 2018 7(3). pii: bio026799.
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
Cooperative activation of cardiac transcription through myocardin bridging of paired MEF2 sites. Anderson C.M., Hu J., Thomas R., Gainous T.B., Celona B., Sinha T., Dickel D.E., Heidt A.B., Xu S.M., Bruneau B.G., Pollard K.S., Pennacchio L.A., Black B.L. Development 2017 144:1235-1241
Single-Cell Resolution of Temporal Gene Expression during Heart Development. DeLaughter D.M., Bick A.G., Wakimoto H., McKean D., Gorham J.M., Kathiriya I.S., Hinson J.T., Homsy J., Gray J., Pu W., Bruneau B.G., Seidman J.G., Seidman C.E. Developmental Cell 2016 39:480-490
Loss of Iroquois homeobox transcription factors 3 and 5 in osteoblasts disrupts cranial mineralization. Cain C.J., Gaborit N., Lwin W., Barruet E., Ho S., Bonnard C., Hamamy H., Shboul M., Reversade B., Kayserili H., Bruneau B.G., & Hsiao E.C. Bone Reports 2016 5:86-95
Expandable Cardiovascular Progenitor Cells Reprogrammed from Fibroblasts. Zhang Y., Cao N., Huang Y., Spencer C.I., Fu J.-D., Yu C., Liu K., Nie B., Xu T., Li K., Xu S., Bruneau B.G., Srivastava D., & Ding S. Cell Stem Cell 2016 18:368-381
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