Our lab studies the mechanism of cell fate restriction. The approaches we take fall at the interface of several disciplines, including developmental biology, stem cell biology and epigenetics. Below is a brief summary of our work.
The hallmark of multicellular life is the presence of diverse cell types within a single organism, all bearing the same genome but disparate gene expression patterns. In mammals, as in many other taxa, this is accomplished via the progressive differentiation of pluripotent stem cells into a variety of specialized cell types. During this process, cells lose their potential for all but the lineage to which they have become committed. A longstanding but unresolved question in biology is: how is cell fate restricted during somatic differentiation? Furthermore, how is this restriction reversed during reproduction to reestablish pluripotency at the onset of development? Based on emerging data from the literature and our lab, we developed a conceptually simple model, dubbed the “gene occlusion” model, to account for cell fate restriction during somatic development and its reversal during reproduction.
The model makes three assertions: (1) A gene’s transcriptional potential can assume either the competent state wherein the gene is responsive to, and can be activated by, trans-acting factors in the cellular milieu, or the occluded state wherein the gene is blocked by cis-acting, chromatin-based mechanisms from responding to trans factors such that it remains silent irrespective of the presence of transcriptional activators. (2) As somatic differentiation proceeds, lineage-inappropriate genes shift progressively and irreversibly from competent to occluded state, thus restricting cell fate. (3) During reproduction, global deocclusion occurs in the germline and/or early zygotic cells to reset the genome to the competent state.
Monoallelic silencing such as X inactivation and imprinting is a clear example of occlusion. Here, the inactive state of the silent alleles can be causally attributed to cis (as opposed to trans) mechanisms given the presence of corresponding active alleles within the same trans environment of the cell. It was unclear, however, whether there are also many genes for which both alleles are occluded. We showed this to be the case using a cell fusion assay. Specifically, we fused two cell types and searched for genes with silent copies in one fusion partner but active copies in the other partner. The active copies served as a positive control for the presence of a transcriptionally supportive milieu, much like the active alleles of monoallelically silenced genes. With this control, the silent copies are identified as being occluded.
In the last few years, our lab has accumulated a substantial body of evidence supporting key predictions of the gene occlusion model in mammalian systems. We showed that occlusion is a prevalent phenomenon affecting a large number of genes in a variety of somatic cell types, including both terminally differentiated cells and somatic stem cells. We found that occluded genes in a given cell type include many master regulators of alternative lineages. We established a mechanistic link between DNA methylation and the maintenance of occlusion for at least some occluded genes, and showed that a variety of well-studied chromatin marks are likely not involved in occlusion. We uncovered functional evidence for a critical requirement of occlusion in cell fate restriction. Finally, we showed that embryonic stem cells are fundamentally distinct from somatic cells in that they have the capacity for genome-wide deocclusion. Collectively, these data establish the gene occlusion model as a simple and coherent conceptual framework for studying how the restriction of cell fate is brought about during development, erased during reproduction, and possibly subverted in disease.
Currently, we are continuing to study several aspects of the gene occlusion model. First, we are investigating the biochemical mechanism underlying the maintenance of occlusion in somatic cells. Second, we are probing the mechanism by which de novo occlusion is established during differentiation. Third, we are exploring the implications of gene occlusion in a variety of biological processes including stem cell differentiation, induction of iPS cells, cancer and aging.
Hydroxymethylation at gene regulatory regions directs stem/early progenitor cell commitment during erythropoiesis. Madzo J, Liu H, Rodriguez A, Vasanthakumar A, Sundaravel S, Caces DB, Looney TJ, Zhang L, Lepore JB, Macrae T, Duszynski R, Shih AH, Song CX, Yu M, Yu Y, Grossman R, Raumann B, Verma A, He C, Levine RL, Lavelle D, Lahn BT, Wickrema A, Godley LA. (2014 Jan) Cell Rep 2014 Jan 16;6(1):231-44. doi: 10.1016/j.celrep.2013.11.044. Epub 2013 Dec 27.24373966
Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells. Looney TJ, Zhang L, Chen CH, Lee JH, Chari S, Mao FF, Pelizzola M, Zhang L, Lister R, Baker SW, Fernandes CJ, Gaetz J, Foshay KM, Clift KL, Zhang Z, Li WQ, Vallender EJ, Wagner U, Qin JY, Michelini KJ, Bugarija B, Park D, Aryee E, Stricker T, Zhou J, White KP, Ren B, Schroth GP, Ecker JR, Xiang AP, Lahn BT. (2014 Feb) Genome Res. 2014 Feb;24(2):267-80. doi: 10.1101/gr.143891.112. Epub 2013 Dec 5.24310002 ( Full Text )
Evidence for a critical role of gene occlusion in cell fate restriction. Gaetz J, Clift KL, Fernandes CJ, Mao FF, Lee JH, Zhang L, Baker SW, Looney TJ, Foshay KM, Yu WH, Xiang AP, Lahn BT. (2012 May) Cell Res. 2012 May;22(5):848-58. doi: 10.1038/cr.2011.190. Epub 2011 Nov 29. 22124232( Full Text )
Embryonic stem cells induce pluripotency in somatic cell fusion through biphasic reprogramming. Foshay KM, Looney TJ, Chari S, Mao FF, Lee JH, Zhang L, Fernandes CJ, Baker SW, Clift KL, Gaetz J, Di CG, Xiang AP, Lahn BT.(2012 Apr) Mol Cell. 2012 Apr 27;46(2):159-70. doi: 10.1016/j.molcel.2012.02.013. Epub 2012 Mar 22.22445485
The "occlusis" model of cell fate restriction. Lahn BT. (2011 Jan) Bioessays. 2011 Jan;33(1):13-20. doi: 10.1002/bies.201000090. Epub 2010 Oct 15.20954221
Nestin is required for the proper self-renewal of neural stem cells. Park D, Xiang AP, Mao FF, Zhang L, Di CG, Liu XM, Shao Y, Ma BF, Lee JH, Ha KS, Walton N, Lahn BT. (2010 Dec) Stem Cells. 2010 Dec;28(12):2162-71. doi: 10.1002/stem.541. 20963821
Chromatin analysis of occluded genes. Lee JH, Gaetz J, Bugarija B, Fernandes CJ, Snyder GE, Bush EC, Lahn BT. (2009 Jul) Hum Mol Genet. 2009 Jul 15;18(14):2567-74. doi: 10.1093/hmg/ddp188. Epub 2009 Apr 20.19380460 ( Full Text )
Systematic identification of cis-silenced genes by trans complementation. Lee JH, Bugarija B, Millan EJ, Walton NM, Gaetz J, Fernandes CJ, Yu WH, Mekel-Bobrov N, Vallender TW, Snyder GE, Xiang AP, Lahn BT. (2009 Mar) Hum Mol Genet. 2009 Mar 1;18(5):835-46. doi: 10.1093/hmg/ddn409. Epub 2008 Dec 2.19050040 ( Full Text )
Genetic basis of human brain evolution. Vallender EJ, Mekel-Bobrov N, Lahn BT. (2008 Dec) Trends Neurosci. 2008 Dec;31(12):637-44. doi: 10.1016/j.tins.2008.08.010. Epub 2008 Oct 8. 18848363 ( Full Text )
Critical role of phosphoinositide 3-kinase cascade in adipogenesis of human mesenchymal stem cells. Yu W, Chen Z, Zhang J, Zhang L, Ke H, Huang L, Peng Y, Zhang X, Li S, Lahn BT, Xiang AP. (2008 Mar) Mol Cell Biochem. 2008 Mar;310(1-2):11-8. Epub 2007 Dec 2. 18060476
Extensive contribution of embryonic stem cells to the development of an evolutionarily divergent host. Xiang AP, Mao FF, Li WQ, Park D, Ma BF, Wang T, Vallender TW, Vallender EJ, Zhang L, Lee J, Waters JA, Zhang XM, Yu XB, Li SN, Lahn BT. (2008 Jan) Hum Mol Genet. 2008 Jan 1;17(1):27-37. Epub 2007 Oct 3. 17913699
Proteomic identification of differently expressed proteins responsible for osteoblast differentiation from human mesenchymal stem cells. Zhang AX, Yu WH, Ma BF, Yu XB, Mao FF, Liu W, Zhang JQ, Zhang XM, Li SN, Li MT, Lahn BT, Xiang AP. (2007 Oct) Mol Cell Biochem. 2007 Oct;304(1-2):167-79. Epub 2007 May 26. 17530189
Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage. Evans PD, Mekel-Bobrov N, Vallender EJ, Hudson RR, Lahn BT. (2006 Nov) Proc Natl Acad Sci U S A. 2006 Nov 28;103(48):18178-83. Epub 2006 Nov 7. 17090677 (Full Text )
Robust signals of coevolution of interacting residues in mammalian proteomes identified by phylogeny-aided structural analysis. Choi SS, Li W, Lahn BT. (2005 Dec) Nat Genet. 2005 Dec;37(12):1367-71. Epub 2005 Nov 13. 16282975
Trak1 mutation disrupts GABA(A) receptor homeostasis in hypertonic mice. Gilbert SL, Zhang L, Forster ML, Anderson JR, Iwase T, Soliven B, Donahue LR, Sweet HO, Bronson RT, Davisson MT, Wollmann RL, Lahn BT. (2006 Feb) Nat Genet. 2006 Feb;38(2):245-50. Epub 2005 Dec 25. 16380713
Microcephalin, a gene regulating brain size, continues to evolve adaptively in humans. Evans PD, Gilbert SL, Mekel-Bobrov N, Vallender EJ, Anderson JR, Vaez-Azizi LM, Tishkoff SA, Hudson RR, Lahn BT. (2005 Sep) Science. 2005 Sep 9;309(5741):1717-20. 16151009
Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens. Mekel-Bobrov N, Gilbert SL, Evans PD, Vallender EJ, Anderson JR, Hudson RR, Tishkoff SA, Lahn BT. (2005 Sep) Science. 2005 Sep 9;309(5741):1720-2. 16151010
Rate of molecular evolution of the seminal protein gene SEMG2 correlates with levels of female promiscuity. Dorus S, Evans PD, Wyckoff GJ, Choi SS, Lahn BT. (2004 Dec) Nat Genet. 2004 Dec;36(12):1326-9. Epub 2004 Nov 7. 15531881
Accelerated evolution of nervous system genes in the origin of Homo sapiens. Dorus S, Vallender EJ, Evans PD, Anderson JR, Gilbert SL, Mahowald M, Wyckoff GJ, Malcom CM, Lahn BT. (2004 Dec) Cell. 2004 Dec 29;119(7):1027-40. 15620360
Reconstructing the evolutionary history of microcephalin, a gene controlling human brain size. Evans PD, Anderson JR, Vallender EJ, Choi SS, Lahn BT. (2004 Jun) Hum Mol Genet. 2004 Jun 1;13(11):1139-45. Epub 2004 Mar 31. 15056607
Adaptive evolution of ASPM, a major determinant of cerebral cortical size in humans. Evans PD, Anderson JR, Vallender EJ, Gilbert SL, Malcom CM, Dorus S, Lahn BT. (2004 Mar) Hum Mol Genet. 2004 Mar 1;13(5):489-94. Epub 2004 Jan 13. 14722158