Abstract
Krûppel-like factor-1 (KLF1) is a C2H2 zinc finger transcription factor which is essential for broad erythroid gene expression and erythropoiesis in vivo. A number of studies have shown ∼700 genes are poorly expressed when KLF1 is absent [1-8]. This global loss of expression is responsible for failure of effective red blood cell production in KLF1 knockout mice [9,10], and partly responsible for congenital anemia in humans and mice with dominant mutations in KLF1 [11,12]. To determine whether KLF1-dependent genes are direct or indirect targets of KLF1, we have previously performed global ChIP-seq experiments identifying 945-1350 regions of KLF1 occupancy in the mouse genome [7]. About 15% of these regions fall within the promoters of KLF1 target genes but surprisingly, most are thousands of kilobases distant from any known gene. Many of these distant sites exhibit co-occupancy with other transcriptional regulators involved in erythropoiesis, including GATA1. Approximately half of the KLF1 occupied sites are found within regions of mono-methylation of lysine 4 on histone 3 (H3K4me1). These regions are devoid of histones tri-methylated at the same residue (H3K4me3). This methylation signature is commonly associated with regions of the genome that act as transcriptional enhancers [13,14] and many are also bound by the co-activator, p300. The nature and function of these distant sites, particularly those without enhancer marks, is interesting as they may shed light on novel mechanisms of action of KLF1 and associated transcription factors. The transcriptional machinery of the cell, including many transcription factors is found in large sub-nuclear compartments called transcriptional factories [15]. KLF1 has been found localized to a subset of these in erythroid cells. KLF1 is also required for long-range looping of the β-globin gene into these transcription factories [16]. Other erythroid genes involved in the production of a functional haemoglobin molecule such as α-globin and haem synthesis enzymes are often found in the same transcription factory. This strongly suggests KLF1 can employ this sub-nuclear machine to co-ordinate the transcriptional output from many genes and thereby direct erythroid cell differentiation. To explore the function of KLF1-bound loci, we have performed multiplexed chromosome conformation capture (3C) coupled with sequencing (Capture-seq) using a tamoxifen responsive, KLF1 inducible cell line to investigate the role of KLF1 in chromosomal looping. In addition, we have analysed primary transcriptional output of KLF1 target genes by nascent RNA-seq. As expected β-globin and a-globin transcription is rapidly induced, becoming detectable within 5 minutes. However, the transcriptional response of dematin and a set direct KLF1 target genes is much slower. Thus, the mechanism of KLF1 transcriptional activation differs between target gene loci. We find a dynamic role of KLF1-dependent chromosomal looping and transcriptional co-factor recruitment required to effect gene transcription during erythropoiesis. We will discuss models of differentiation transcription regulation by KLF1.
References:
1. Drissen R, et al. (2005). Molecular and Cellular Biology 25: 5205–5214.
2. Funnell APW, et al. (2007). Molecular and Cellular Biology 27: 2777–2790.
3. Hodge D, et al. (2006). Blood 107: 3359–3370.
4. Pilon AM, et al. (2008). Molecular and Cellular Biology 28: 7394–7401.
5. Siatecka M, et al. (2010). PNAS 107: 15151–15156.
6. Siatecka M, Bieker JJ (2011). Blood 118: 2044–2054.
7. Tallack MR, et al. (2010). Genome Res 20: 1052–1063.
8. Tallack MR, Perkins AC (2010). IUBMB Life 62: 886–890.
9. Perkins AC, Sharpe AH, Orkin SH (1995). Nature 375: 318–322.
10. Nuez B, et al. (1995). Nature 375: 316–318.
11. Arnaud L, S et al. (2010). Am J Hum Genet 87: 721–727.
12. Borg J, et al. (2011). Haematologica 96: 635–638.
13. Zentner GE, et al. (2011). Genome Res 21: 1273–1283.
14. Pekowska A, et al. (2011). EMBO J 30: 4198–4210.
15. Osborne CS, et al. (2004). Nat Genet 36: 1065–1071.
16. Schoenfelder S, et al. (2010). Nat Genet 42: 53–61.
Disclosures:
Perkins: Novartis Oncology: Consultancy, Honoraria, Membership on an entity’s Board of Directors or advisory committees.
Principles of transcription factor traffic on folded chromatin