Brian Dynlacht, PhD
Professor, Dept of Pathology; Scientific Director, Genomics Facility
PhD, 1992, UC Berkeley
We are attempting to understand the epigenetic and transcriptional landscapes underlying skeletal muscle satellite (stem) cell identity.
skeletal muscle differentiation, satellite cell, muscle stem cell, genome-wide epigenetic approaches, ChIP-seq, chromatin regulation
We have used genome-wide methods (ChIP-seq and ChIP-on-chip) to begin deciphering the regulatory networks that control myogenic differentiation. Myogenesis is orchestrated through a series of transcriptional controls governed by myogenic regulatory factors (MRFs). MyoD, a basic helix-loop-helix (bHLH) transcription factor that binds sequence elements termed E-boxes, is the founding member of the MRF family which includes the closely related Myf5, myogenin, and MRF4 proteins. MRFs are key in the activation of the expression of genes that specify muscle. The first steps in the myogenic transcriptional regulatory cascade involve expression of MyoD and Myf5, which subsequently leads to expression of myogenin and MEF2, promoting conversion of myoblasts to myotubes. MyoD collaborates with myogenin to regulate the expression of genes necessary for terminal differentiation. Myogenic differentiation proceeds through irreversible cell cycle arrest of precursor cells (myoblasts), followed by a gradual increase in expression of muscle function genes, leading to fusion of myoblasts into multinucleate myofibers in the animal. This process can be recapitulated in vitro, wherein myoblasts can be converted to myotubes with high efficiency in well-established models. In adult skeletal muscle, a pool of self-renewing stem cells (satellite cells) proliferate and differentiate in response to specific stimuli, such as injury or exercise.
Given the similarities between regeneration and the muscle differentiation program and the observation that deficiency of certain muscle regulatory factors (MRFs) leads to defects in muscle regeneration, we sought to identify the critical downstream targets of two MRFs, MyoD and the related MRF, myogenin, which is known to play a critical role in the later stages of muscle development. We used a combination of genome-wide approaches to identify physiological targets of MyoD1. In addition, by combining chromatin immunoprecipitation and high throughput sequencing (ChIP-seq) and computational strategies in myoblasts and terminally differentiated myotubes, we identified the compendium of activating and repressive histone modifications that are deposited during myogenic differentiation.
We have further identified the compendium of promoters and enhancers and found that MyoD1 is recruited to distal regulatory elements, where it helps to assemble transcriptional enhancers. More recently, we have examined the recruitment of sequence-specific transcription factors, elongation factors, histone-modifying enzymes, and chromatin readers. By examining >30 histone modifications and transcriptional regulatory proteins, we have assembled one of the largest genome-wide datasets extant for a single tissue. These data have allowed us to begin dissecting a comprehensive network of key factors governing skeletal muscle differentiation.
By investigating muscle stem (satellite) cells, we hope to understand the epigenetic mechanisms that confer "steminess" on these muscle precursors and act as regulatory switches to determine mesodermal fates by silencing genes in certain lineages (fat and bone) while activating those in muscle. We hope that these studies will shed important new light on the myogenic transcriptional network and reveal novel insights into mesoderm development, muscle function and regeneration, as well as disease.
- Fu W, Asp P, Canter B, Dynlacht BD (2014) Primary cilia control hedgehog signaling during muscle differentiation and are deregulated in rhabdomyosarcoma. Proceedings of the National Academy of Sciences 111(25): 9151-9156.
- Cheng J, Blum R, Bowman, C, Hu D, Shilatifard A, Shen S, Dynlacht BD (2014) A Role for H3K4 Monomethylation in Gene Repression and Partitioning of Chromatin Readers. Molecular Cell, Vol 53 No. 6, pg 979-992.
- Kobayashi T, Kim S, Lin YC, Inoue T, Dynlacht BD. (2014) The CP110 interacting proteins Talpid3 and Cep290 play overlapping and distinct roles in cilia assembly. Journal of Cell Biology 204(2):215-229.
- Li J, D'Angiolella V, Seeley ES, Kim S, Kobayashi T, Fu W, Campos EI, Pagano M, Dynlacht BD (2013) USP33 regulates centrosome biogenesis via deubiquitination of the centriolar protein CP110 Nature 45(7740) : 255-9.
- Blum R, Vethantham V, Bowman C, Rudnicki M, and Dynlacht BD (2012) Genome-wide identification of enhancers in skeletal muscle: the role of MyoD1. Genes and Development 26: 2763-2779.
- Li J, Kim S, Kobayashi T, Liang FX, Korzeniewski N, Duensing S, Dynlacht BD (2012) Neurl4, a novel daughter centriole protein, prevents formation of ectopic microtubule organizing centres. EMBO Reports 13(6):547-53
- Vethantham V, Yang Y, Bowman C, Asp P, Lee JH, Skalnik DG, Dynlacht BD (2012). Dynamic loss of H2B ubiquitylation without corresponding changes in H3K4 tri-methylation during myogenic differentiation.? Mol. Cell. Biol. 32(6):1044-55.
- Kobayashi T, Tsang WY, Li J, Lane W, Dynlacht BD (2011) Centriolar Kinesin Kif24 Interacts with CP110 to Remodel Microtubules and Regulate Ciliogenesis. Cell 145(6): 914-25.
- Asp P, Blum R, Vethantham V, Parisi F, Micsinai M, Cheng J, Bowman C, Kluger Y, Dynlacht BD (2011) Genome-wide remodeling of the epigenetic landscape during myogenic differentiation. Proceedings of the National Academy of Sciences 108 (22) : 149-158.
- Kobayashi T, Dynlacht BD (2011) Regulating the transition from centriole to basal body. J Cell Biol. 193(3):435-44.
- van Oevelen C, Bowman C, Pellegrino J, Asp P, Cheng J, Parisi F, Micsinai M, Kluger Y, Chu A, Blais A, David G, Dynlacht BD (2010) The mammalian Sin3 proteins are required for muscle development and sarcomere specification. Mol Cell Biol. 30(24):5686-97.
- Tsikitis M, Acosta-Alvear D, Blais A, Campos EI, Lane WS, Sánchez I, Dynlacht BD (2010) Traf7, a MyoD1 transcriptional target, regulates nuclear factor-?B activity during myogenesis. EMBO Reports 11(12):969-76.
- Tsang, WY, Spekor, A, Vijayakumar S, Bista BR, Li J, Sánchez I, Duensing S, Dynlacht BD (2009) Cep76, a Centrosomal Protein that Specifically Restrains Centriole Reduplication, Developmental Cell 16, 640-60
- Asp P, Acosta-Alvear D, Tsikitis M, van Oevelen C, Dynlacht BD (2009) E2f3b plays an essential role in myogenic differentiation through isoform-specific gene regulation. Genes Dev 23,37-53
- Van Oevelen C, Wang J, Asp P, Yan Q, Kaelin, WG Jr, Kluger Y, Dynlacht BD (2008) A role for mammalian Sin3 in permanent gene silencing Mol Cell 32, 359-70.
- Tsang WY, Bossard C, Khanna H, Peränen J, Swaroop A, Malhotra V, Dynlacht BD. (2008) CP110 suppresses primary cilia formation through its interaction with CEP290, a protein deficient in human ciliary disease. Dev Cell 15, 187-97.
- A. Blais, A., C. van Oevelen, D. Acosta, and B.D. Dynlacht. (2007). RB-specific methylation of histone H3 lysine 27 enforces irreversible cell cycle exit. J. Cell Biology 179, 1399-1412.
- D.Acosta-Alvear, Y. Zhou, A. Blais, M. Tsikitis, N. H. Lents, C. Arias, C. J. Lennon, Y. Kluger, and B.D. Dynlacht. (2007). XBP1 controls diverse cell type- and condition-specific transcriptional regulatory networks. Molecular Cell 27, 53-66.
- A. Spektor, W. Y. Tsang, D. Khoo, and B.D.Dynlacht. (2007). Cep97 and CP110 suppress a cilia assembly program. Cell 130, 678-690.
- W.Y.Tsang, L. Wang, Z. Chen, I. Sánchez, and B.D. Dynlacht. (2007). SCAPER, a novel cyclin A interacting protein that regulates cell cycle progression. J. Cell Biology 178, 621-633.
- W. Tsang, A. Spektor, V. Indjeian, J. Salisbury, Z. Chen, D. Luciano, I. Sanchez, and B. D. Dynlacht. (2006). CP110 cooperates with two calcium-binding proteins to regulate cytokinesis and genome stability. Molecular Biology of the Cell 17, 3423-34.
- A. Blais, M. Tsikitis, D. Acosta, R. Sharan, Y. Kluger, and B.D. Dynlacht (2005). An initial blueprint for myogenic differentiation. Genes and Development 19, 553-569.
- A. Blais and B.D. Dynlacht. (2005). Constructing regulatory networks governing growth and differentiation. Genes and Development 19, 1499-1511.
- E. Balciunaite, A. Spektor, N. H. Lents, H. Cam, H. te Riele, R.A. Young, and B. D. Dynlacht. (2005). Genome-wide analysis reveals distinct roles for E2F4 and pocket proteins in cell proliferation. Mol. Cell. Biol. 25, 8166-8178.
- H. Cam, E. Balciunaite, A. Blais, A. Spektor, R. Scarpulla, R. Young, Yuval Kluger, and B. D. Dynlacht (2004). A common set of gene regulatory networks links metabolism and growth inhibition. Molecular Cell 16, 399-411.