Molecular Hallmarks of Endogenous Chromatin Complexes Containing Master Regulators of Hematopoiesis

Abstract

Combinatorial interactions among trans-acting factors establish transcriptional circuits that orchestrate cellular differentiation, survival, and development. Unlike circuits instigated by individual factors, efforts to identify gene ensembles controlled by multiple factors simultaneously are in their infancy. A paradigm has emerged in which the important regulators of hematopoiesis GATA-1 and GATA-2 function combinatorially with Scl/TAL1, another key regulator of hematopoiesis. The underlying mechanism appears to involve preferential assembly of a multimeric complex on a composite DNA element containing WGATAR and E-box motifs. Based on this paradigm, one would predict that GATA-2 and Scl/TAL1 would commonly co-occupy such composite elements in cells. However, chromosome-wide analyses indicated that the vast majority of conserved composite elements were occupied by neither GATA-2 nor Scl/TAL1. Intriguingly, the highly restricted set of GATA-2-occupied composite elements had characteristic molecular hallmarks, specifically Scl/TAL1 occupancy, a specific epigenetic signature, specific neighboring cis elements, and preferential enhancer activity in GATA-2-expressing cells. Genes near the GATA-2-Scl/TAL1-occupied composite elements were regulated by GATA-2 or GATA-1, and therefore these fundamental studies on combinatorial transcriptional mechanisms were also leveraged to discover novel GATA factor-mediated cell regulatory pathways.

SUPPLEMENTAL MATERIAL

Supplemental material for this article may be found at http://mcb.asm.org/ .

ACKNOWLEDGMENTS

We thank Stuart Orkin for providing Gata2^−/− ES cells. We appreciate critical comments from the Bresnick group.

This work was funded by NIH grants DK06834 (E.H.B.), HG003747 (S.K.), and HL55337 (K.C.); National Research Service Award T32 HL 07936 from the NHLBI to the University of Wisconsin—Madison Cardiovascular Research Center (R.J.W.); Ruth L. Kirschstein fellowship F32HL092736 from the National Heart, Lung, and Blood Institute (R.J.W.); and the PhRMA Foundation Research Starter Grant in Informatics (S.K.).

The content of this article does not necessarily represent the official views of the National Heart, Lung, and Blood Institute or the National Institutes of Health.