Novel roles for KLF1 in erythropoiesis revealed by mRNA-seq

Abstract

KLF1 (formerly known as EKLF) regulates the development of erythroid cells from bi-potent progenitor cells via the transcriptional activation of a diverse set of genes. Mice lacking Klf1 die in utero prior to E15 from severe anemia due to the inadequate expression of genes controlling hemoglobin production, cell membrane and cytoskeletal integrity, and the cell cycle. We have recently described the full repertoire of KLF1 binding sites in vivo by performing KLF1 ChIP-seq in primary erythroid tissue (E14.5 fetal liver). Here we describe the KLF1-dependent erythroid transcriptome by comparing mRNA-seq from Klf1+/+ and Klf1−/− erythroid tissue. This has revealed novel target genes not previously obtainable by traditional microarray technology, and provided novel insights into the function of KLF1 as a transcriptional activator. We define a cis-regulatory module bound by KLF1, GATA1, TAL1, and EP300 that coordinates a core set of erythroid genes. We also describe a novel set of erythroid-specific promoters that drive high-level expression of otherwise ubiquitously expressed genes in erythroid cells. Our study has identified two novel lncRNAs that are dynamically expressed during erythroid differentiation, and discovered a role for KLF1 in directing apoptotic gene expression to drive the terminal stages of erythroid maturation.

Extrinsic and intrinsic control by EKLF (KLF1) within a specialized erythroid niche

“…Array and RNA-seq data demonstrate that ICAM4 levels are decreased in EKLF-null primitive and definitive erythroid cells (Hodge et al, 2006;Isern et al, 2010;Pilon et al, 2008;Tallack et al, 2012) and in a congenital dyserythropoietic anemia (CDA) patient harboring the EKLF-E325K mutation that exhibits a defect in red cell enucleation (Arnaud et al, 2010). ICAM4 levels also mirror EKLF levels during primitive and definitive erythroid differentiation ( Fig.…”

“…Comparative analysis of expression arrays between EKLF wildtype and EKLF-null fetal liver cells show that a number of genes involved in execution of the terminal erythroid differentiation program are downregulated in the absence of EKLF (Drissen et al, 2005;Hodge et al, 2006;Pilon et al, 2006Pilon et al, , 2011Tallack et al, 2012. Our studies, originating from observations of differentiating erythroid cells from embryoid bodies, have uncovered an erythroid-intrinsic role for EKLF in erythroblastic island biology.…”

“…4B). Although other molecules, such as EMP (MAEA) or α4β1 integrins (ITGA4/ITGB1) could also be contributory in the context of erythroblastic island formation (Chasis and Mohandas, 2008;Manwani and Bieker, 2008), these are not affected by changes in EKLF levels (Pilon et al, 2011(Pilon et al, , 2008Tallack et al, 2012).…”

Kruppel-like transcription factors KLF1 and KLF2 have unique and coordinate roles in regulating embryonic erythroid precursor maturation

“…2,13 In addition, KLF1 regulates cell cycle control, proliferation and apoptosis. [14][15][16] Pathogenic mutations in KLF1 can cause congenital dyserythropoietic anemia in humans. 17,18 To date, 17 mammalian KLFs have been identified, and they have diverse roles in development.…”

“…KLF2 ablation leads to increased apoptosis in E10.5 yolk sac erythroid cells, 19 and there is some evidence of a modest increase in apoptosis in KLF1-/-definitive erythroid cells. 16 Although it is not possible to study apoptosis directly in E8.5 erythroid progenitor cells, the stochastic event in KLF1-/-KLF2-/-cultures might logically involve apoptosis.…”