Chromatin Modifications in Hematopoietic Multipotent and Committed Progenitors Are Independent of Gene Subnuclear Positioning Relative to Repressive Compartments CLAIRE GUILLEMIN, a,b MARTA MALESZEWSKA, c,d ADELINE GUAIS, a,b J ´ ER ˆ OME MA ¨ ES, c,d MARIE-CHRISTINE ROUYEZ, a,b AZZEDINE YACIA, a,b SERGE FICHELSON, a,b MICHELE GOODHARDT, c,d CLAIRE FRANCASTEL a,b a Institut Cochin, Universite ´ Paris Descartes, Centre National de la Recherche Scientifique (Unite ´ Mixte de Recherche [UMR] 8104), Paris, France; b Institut National de la Sante ´ et de la Recherche Me ´dicale, U567, Paris, France; c Institut Universitaire d’He ´matologie, Ho ˆpital Saint-Louis, Paris, France; d Institut National de la Sante ´ et de la Recherche Me ´dicale, U662, Paris, France Key Words. Epigenetic processes • Regulation of gene expression • Cell differentiation • Hematopoietic stem cells • Hematopoietic progenitor cells ABSTRACT To further clarify the contribution of nuclear architecture in the regulation of gene expression patterns during differentia- tion of human multipotent cells, we analyzed expression status, histone modifications, and subnuclear positioning relative to repressive compartments, of hematopoietic loci in multipotent and lineage-committed primary human hematopoietic progen- itors. We report here that positioning of lineage-affiliated loci relative to pericentromeric heterochromatin compartments (PCH) is identical in multipotent cells from various origins and is unchanged between multipotent and lineage-committed he- matopoietic progenitors. However, during differentiation of multipotent hematopoietic progenitors, changes in gene expres- sion and histone modifications at these loci occur in committed progenitors, prior to changes in gene positioning relative to pericentromeric heterochromatin compartments, detected at later stages in precursor and mature cells. Therefore, during normal human hematopoietic differentiation, changes in gene subnuclear location relative to pericentromeric heterochroma- tin appear to be dictated by whether the gene will be perma- nently silenced or activated, rather than being predictive of commitment toward a given lineage. STEM CELLS 2009;27: 108 –115 Disclosure of potential conflicts of interest is found at the end of this article. INTRODUCTION The multilineage potential of human hematopoietic stem cells (HSC) is gradually lost as these multipotential progenitors make commitment choices to differentiate to non-self-renewing and then lineage-committed progenitors along the different blood lineages (reviewed in [1, 2]). When a stem cell is committed to differentiating toward a given lineage, global genome repro- gramming involves both repression of nonaffiliated genes and selective activation of genes involved in the establishment of this lineage. Accumulating evidence indicates that lineage-spe- cific gene expression is determined not only by the availability of specific transcription factors but also by epigenetic modifi- cations, including both local modifications of DNA and chro- matin and global topological changes in chromosome and gene positioning in the nucleus (reviewed in [3– 6]). Combined, these different levels of gene regulation allow for fine control that integrates environmental and intracellular signals to establish appropriate gene expression programs, and hence ultimately determine the identity of the cell. Specific histone amino-terminal modifications can generate synergistic or antagonistic interaction affinities for chromatin- associated proteins, which in turn dictate dynamic transitions between transcriptionally active and transcriptionally silent chromatin states [7]. For example, acetylation of certain N- terminal lysine residues in histones H3 and H4 (H3ac and H4ac) is generally associated with a transcriptionally active chromatin configuration, whereas methylation of lysine 9 of histone H3 (H3K9me3) appears to be a hallmark of condensed chromatin at silent loci. These modifications play an important role in prim- ing of gene activity and in maintenance of gene expression over several cell divisions (reviewed in [8, 9]). Chromatin accessi- bility might therefore be the key to regulating the activity of transcription factors and hence ultimately determine cell fate. Accumulating evidence indicates that the subnuclear loca- tion of a gene also influences its activity. This has been shown for a number of genes expressed in hematopoietic cells (recently Author contributions: C.G.: performance of research, data analysis and interpretation; M.M., A.G., and J.M.: performance of research; M.-C.R.: contributions to real-time PCR; A.Y.: contributions to expansion of erythroid progenitors; S.F.: provision of study material; M.G.: data analysis and interpretation, manuscript drafting; C.F.: conception and design, financial support, data analysis and interpretation, manuscript writing, final approval of manuscript. C.G. and M.M. contributed equally to this work. Correspondence: Claire Francastel, Ph.D., Institut Cochin, De ´partement d’He ´matologie, INSERM U567–CNRS UMR 8104, Maternite ´ Port-Royal, 5e `me e ´tage, 123, Boulevard Port-Royal, 75014 Paris, France. Telephone: 33-1-53-10-43-84; Fax: 33-1-43-25-11-67; e-mail: claire.francastel@inserm.fr Received August 5, 2008; accepted for publication October 16, 2008; first published online in STEM CELLS EXPRESS October 30, 2008. ©AlphaMed Press 1066-5099/2008/$30.00/0 doi: 10.1634/stemcells.2008-0755 STEM CELL EPIGENETICS,GENOMICS, AND PROTEOMICS S TEM CELLS 2009;27:108 –115 www.StemCells.com