1724–1740 Nucleic Acids Research, 2018, Vol. 46, No. 4 Published online 4 December 2017 doi: 10.1093/nar/gkx1214 Endothelial cell differentiation is encompassed by changes in long range interactions between inactive chromatin regions Henri Niskanen1, Irina Tuszynska2,†, Rafal Zaborowski2,†, Merja Heinaniemi¨ 3, Seppo Yla-Herttuala¨ 1,4,*, Bartek Wilczynski2,* and Minna U. Kaikkonen1,*
1A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland, 2Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw 02-097, Poland, 3School of Medicine, University of Eastern Finland, FI-70211 Kuopio, Finland and 4Heart Center and Gene Therapy Unit, Kuopio University Hospital, FI-70211 Kuopio, Finland
Received August 18, 2017; Revised October 21, 2017; Editorial Decision November 21, 2017; Accepted November 27, 2017
ABSTRACT results show that large structural rearrangements es- tablish chromatin architecture required for functional Endothelial cells (ECs) differentiate from mesoder- endothelium and this architecture remains largely mal progenitors during vasculogenesis. By compar- unchanged in response to hypoxia. ing changes in chromatin interactions between hu- man umbilical vein ECs, embryonic stem cells and mesendoderm cells, we identified regions exhibit- INTRODUCTION ing EC-specific compartmentalization and changes The circulatory system is the first organ system to develop in the degree of connectivity within topologically in the growing embryo as it is needed for the rapid delivery associated domains (TADs). These regions were of oxygen and nutrients to tissues. Endothelial cells (ECs), characterized by EC-specific transcription, binding which constitute the luminal layer of blood vessels, differ- of lineage-determining transcription factors and co- entiate from their mesodermal progenitors during a pro- hesin. In addition, we identified 1200 EC-specific cess called vasculogenesis. ECs act as functional local oxy- gen sensors within the vascular system and during hypoxia long-range interactions (LRIs) between TADs. Most they modulate vascular tone and induce vascular remod- of the LRIs were connected between regions en- eling and angiogenesis. Recent studies have uncovered ex- riched for H3K9me3 involving pericentromeric re- tensive chromatin reorganization during cellular differenti- gions, suggesting their involvement in establishing ation (1). We and others have shown that different cell types compartmentalization of heterochromatin during dif- are characterized by differences in the location of active ferentiation. Second, we provide evidence that EC- and inactive chromatin compartments (1–3). These com- specific LRIs correlate with changes in the hierarchy partments are further divided into single or series of topo- of chromatin aggregation. Despite these rearrange- logically associating domains (TADs) (4), large fraction of ments, the majority of chromatin domains fall within a which are conserved between cell types and in response to pre-established hierarchy conserved throughout dif- extracellular signals (5). However, the chromatin interac- ferentiation. Finally, we investigated the effect of hy- tions within and between TADs have been shown to ex- hibit extensive changes between cell types and in response poxia on chromatin organization. Although hypoxia to senescence and hormone induced gene regulation (1,6– altered the expression of hundreds of genes, mini- 8). The most extensive changes have been documented dur- mal effect on chromatin organization was seen. Nev- ing the heat shock response in Drosophila, where a dramatic ertheless, 70% of hypoxia-inducible genes situated increase in inter-TAD interactions correlated with genome- within a TAD bound by HIF1␣ suggesting that tran- wide repression of transcription (9). scriptional responses to hypoxia largely depend on Despite recent advances in describing local changes in the pre-existing chromatin organization. Collectively our units of chromosome organization, our understanding of the long range interactions between these units and their
*To whom correspondence should be addressed. Tel: +358 40 355 2413; Email: [email protected] Correspondence may also be addressed to Seppo Yla-Herttuala.¨ Tel: +358 40 355 2075; Email: [email protected] Correspondence may also be addressed to Bartek Wilczynski. Tel: +48 22 5544 577; Email: [email protected] †These authors contributed equally to the paper as second authors.