1. In Vivo Analysis of Protein-DNA Interactions in the β-Globin Gene Locus Karen F. Vieira, Padraic P. Levings & Jörg Bungert Biochemistry and Molecular Biology, University of Florida, Gainesville, FL Abstract Erythroid-specific, high-level expression of the β-globin genes is regulated by the locus control region, located far upstream of the genes. Recent studies show that locus control region core elements recruit RNA polymerase II. Here, we analyzed the interaction of transcription factors and RNA polymerase II with the β-globin locus in erythroleukemia cell lines using chromatin immunoprecipitation. The data show that transcription initiation complexes are recruited to the LCR and to the genes. Moreover, RNA polymerase II dissociates and re-associates during early S-phase in synchronized erythroid cells suggesting that replication disrupts the association of transcription complexes with the globin locus. The interaction of NF- E2 and USF2 precedes the re-association of RNA polymerase II implicating these proteins in a process regulating the recruitment of RNA polymerase to the globin locus during replication. Introduction The five genes of the human β-globin locus are expressed in erythroid cells in a tissue- and developmental-stage specific manner (1). Appropriate expression of the globin genes is regulated by many DNA elements that are located proximal or distal to the genes. The human β-globin locus control region (LCR) is a powerful regulatory DNA element located far upstream of the genes and required for high-level expression of all the globin genes throughout development (2,3). There is currently no consensus on how the LCR acts to stimulate globin gene transcription but it is generally believed that it involves some form of communication between the LCR and the globin genes (4, 5). Some models view the LCR as a holocomplex in which the individual HS sites interact via extensive protein/DNA and protein/protein interactions. The LCR holocomplex may provide a highly accessible region for the efficient recruitment of macromolecular complexes involved in chromatin modification and transcription (6). Indeed, it has been shown that RNA polymerase II (Pol II) transcription complexes are recruited to the LCR in vitro and in vivo (7, 8, 9, 10), suggesting that transcription complexes are first recruited to the LCR and subsequently transferred to the globin genes (6). Activation of at least some gene loci depends on replication, and it is possible that replication could provide a window of opportunity for transcription factors to gain access to regulatory sequences before repressive chromatin is formed. Accordingly, the globin locus replicates late in non-erythroid cells and early in cells expressing the globin genes. It is not known how or if replication affects the association of transcription factors and Pol II with the globin locus. In this study we analyzed the interaction of transcription complexes with the human and murine β-globin loci in erythroid cells expressing either the human embryonic/fetal ε- and γ-globin (K562 cells) or the murine adult β-globin genes (MEL cells). This was done by chromatin immunoprecipitation (ChIP) in unsynchronized cells and during the DNA synthesis phase of synchronized cells. LCR HS 5 4 3 2 1  G  A   human  -globin gene locus LCR HS 5 4 3 2 1  maj  min hHS2hHS2 5’flankh5’HS5 hh hh hh hh mHS2mHS2 5’flankm5’HS5 m  m  maj murine  -globin gene locus  Diagrammatic representation of the human and murine β-globin gene locus. The human β-globin gene locus is located on chromosome 11 and consists of five developmentally regulated genes: the embryonic ε-globin gene, the two fetal γ-globin genes, and the adult δ- and β-globin genes. The LCR is located upstream of the ε-globin gene and composed of at least 5 HS sites. The murine β-globin locus is located on chromosome 7 and contains 4 developmentally regulated genes: the εγ-and βH1 globin genes, which are co-expressed in the embryonic yolk sac and the βmaj and βmin globin genes, which are expressed during the fetal and adult stages of erythropoiesis. The overall organization of the LCR is highly conserved between the murine and the human β-globin locus. PCR fragments analyzed in the ChIP experiments or used as probes in the NRO assays are indicated as lines (horizontal bars) below the respective loci. Figure 1 References 1.Stamatoyannopoulos, G., and Nienhuis, A. (1994) p 107-155. In G. Stamatoyannopoulos, A. Nienhuis, P. Majerus, and H. Varmus (ed.), W. B. Saunders, Philadelphia, PA. 2.Higgs, D. (1998) Cell 95, 299-302. 3.Grosveld, F. (1999) Curr. Opin. Genet. Dev. 9, 152-57. 4.Bulger, M. and Groudine, M. (1999) Genes & Dev. 13, 2465-2477. 5.Engel, J.D., and Tanimoto, K. (2000) Cell 100, 499-502. 6.Levings, P.P., and Bungert, J. (2002) Eur. J. Biochem. 269, 1589-1599. 7.Tuan, D., Kong, S., and Hu, K. (1992) Proc. Natl. Acad. Sci. 89, 11219-11223. 8.Leach, K.M., Nightingale, K., Igarashi, K., Levings, P.P., Engel, J.D., Becker, P.B., and Bungert J. (2001) Mol. Cell. Biol. 21, 2629-2640. 9.Johnson, K., Christensen, H., Zhao, B., and Bresnick, E.H. (2001) Mol. Cell 8, 465-471. 10.Routledge S.J., and Proudfoot, N.J. (2002) J. Mol. Biol. 323, 601-11. Results Unsynchronized K562: The interaction of Pol II with the globin genes is consistent with gene expression Pol II is detectable at the embryonic ε- but not at the adult β-globin gene Pol II and other basal transcription factors, which are part of transcription initiation complexes, are associated with HS2 Unsynchronized MEL: Pol II, TBP, and TFIIB can be crosslinked to both HS2 and the β-globin gene promoter NF-E2 (p45) can be crosslinked to HS2 and to the β-globin gene promoter Synchronized K562: At time 0, Pol II interacts with HS2, the ε-, and γ-globin genes, but not with the β-globin gene After 45 min, Pol II is no longer detectable at the ε-globin gene but remains associated with HS2 and the γ-globin genes After 2 hrs, Pol II no longer interacts with the LCR or the ε- and γ-globin genes At this time there is a clear interaction of NF-E2 and USF2 with HS2 and the ε- and γ-globin genes After 6 hrs, Pol II re-associates with HS2 and the γ-globin genes, but not with the ε-globin gene Accompanied with the reappearance of Pol II is the dissociation of USF2 from the genes and HS2 Synchronized MEL: Pol II dissociates and re-associates with the globin locus during early S-phase NF-E2 appears to remain associated with the globin locus at all the time points analyzed here Interaction of transcription factors with and transcription in the murine β-globin locus in MEL cells. A) Interaction of transcription factors and RNA polymerase II with the β-globin locus. MEL cells were incubated in formaldehyde and the crosslinked chromatin fragmented, isolated, and precipitated with antibodies specific for RNA polymerase II (αPol II), RNA polymerase II phosphorylated at the C-terminal domain (αPol II Phosph.), TBP, TFIIB, NF-E2 p45, and acetylated histone H3 (αH3 acet.). DNA purified from the precipitate was analyzed by PCR with primers corresponding to regions in the murine β-globin locus as indicated (see Fig.1). The no antibody and input controls were processed as described in the legend to Fig. 2. B) Nuclear run-on analysis of transcription in specific regions of the β-globin locus. Nuclei were isolated from MEL cells and incubated in the presence of radioactive aP32GTP. The RNA was then isolated and hybridized to specific DNA fragments blotted onto nylon membranes. The position of these fragments is indicated in Fig. 1. The lane labeled unspecific shows hybridization to the negative control plasmid pK0916. Figure 3 B m5’HS5 mHS2  maj unspecific  Pol II phosph. Marker No Ab Input  Pol II  P  FII B  NF-E2 p45  H3 acet. A mHS2  maj  mHS2 5’flank mNecdin Interaction of transcription factors with and transcription in the human β-globin locus in K562 cells. A) Interaction of transcription factors and RNA polymerase II with the β-globin locus. K562 cells were incubated in formaldehyde, the crosslinked chromatin fragmented, isolated, and precipitated with antibodies specific for RNA polymerase II (αPol II), RNA polymerase II phosphorylated at the C-terminal domain (αPol II Phosph.), TBP, TFIIB, NF-E2 p45, and acetylated histone H3 (αH3 acet.). DNA purified from the precipitate was analyzed by PCR with primers corresponding to regions in the β- globin locus as indicated (see Fig.1). The no antibody lanes represent negative controls; the samples were subjected to the same procedure except that no specific antibody was added during the precipitation step. The lane labeled input represents the positive PCR control and was taken from the crosslinked no antibody sample. B) Nuclear run-on analysis of transcription in specific regions of the β-globin locus. Nuclei were isolated from K562 cells and incubated in the presence of radioactive αP32UTP. The RNA was then isolated and hybridized to specific DNA fragments blotted onto nylon membranes. The position of these fragments is indicated in Fig. 1. The lane labeled as unspecific shows hybridization to the negative control plasmid pK0916. Figure 2 B h5’HS5 hHS25’flank hHS2 hh unspecific  Pol II phosph. Marker No Ab Input  Pol II  P  FII B  NF-E2 p45  H3 acet. A hHS2 hh hh hHS2 5’flank hNecdin Interactions of transcription factors and RNA polymerase II with the human β-globin locus during early S-phase in synchronized K562 cells. K562 cells were grown in RPMI and arrested at the G1/S-phase border using the double thymidine block method. Aliquots of cells were harvested at specific time points and analyzed for DNA content by flow cytometry (shown on top). The remaining cells were harvested at time 0 or at specific time points after release from cell cycle arrest (as indicated), crosslinked with formaldehyde, and subjected to ChIP using antibodies specific for RNA polymerase II (αPol II), the p45 subunit of NF-E2 (αNF-E2), and USF2 (αUSF2); time 0 represents the status of the blocked cells at the G1/S-phase boundary. After reversal of the crosslinks, the DNA was purified and subjected to PCR using primers specific for HS2, the ε-globin gene, the γ-globin gene, and the β-globin gene as indicated (see Fig. 1). The no antibody and input controls were processed as described in the legend to Fig. 2. Figure 4 0 min 15 min 2hrs 6 hrs Time 45 min HS2  -globin  -globin Marker No Ab Input  Pol II  USF2  NF-E2 p45 Marker No Ab Input  Pol II  USF2  NF-E2 p45 Marker No Ab Input  Pol II  USF2  NF-E2 p45 Marker No Ab Input  Pol II  USF2  NF-E2 p45  -globin Interactions of transcription factors and RNA polymerase II with the β-globin locus during early S-phase in synchronized MEL cells. MEL cells were grown in RPMI and arrested using the double thymidine block. At specific time points after release from cell cycle arrest (as indicated) cells were harvested, crosslinked with formaldehyde, and subjected to ChIP analysis. Antibodies against RNA polymerase II (αPol II), TFIIB (αTFIIB), TBP (αTBP), the p45 subunit of NF-E2 (αNF-E2), and acetylated histone H3 (αact.H3) were used in these experiments. The no antibody and input controls were processed as described in the legend to Fig. 4. After the reversal of the crosslinks, the DNA was purified and subjected to PCR analysis using primers specific for HS2 and the β maj -globin gene. Figure 5 LCR  maj -globin gene No Antibody Marker Input PolIITFIIBNF-E2 H3acetylated Time No Antibody Marker Input PolII TFIIB NF-E2 H3acetylated 0 7min 45min 2hrs Conclusions The data show that transcription initiation complexes are recruited to the LCR and to the genes. Moreover, RNA polymerase II dissociates and re-associates during early S-phase in synchronized erythroid cells suggesting that replication disrupts the association of transcription complexes with the globin locus. The interaction of NF-E2 and USF2 precedes the re- association of RNA polymerase II implicating these proteins in a process regulating the recruitment of RNA polymerase to the globin locus during replication.