Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Haploinsufficiency for the erythroid transcription factor KLF1 causes hereditary persistence of fetal hemoglobin


Hereditary persistence of fetal hemoglobin (HPFH) is characterized by persistent high levels of fetal hemoglobin (HbF) in adults. Several contributory factors, both genetic and environmental, have been identified1 but others remain elusive. HPFH was found in 10 of 27 members from a Maltese family. We used a genome-wide SNP scan followed by linkage analysis to identify a candidate region on chromosome 19p13.12–13. Sequencing revealed a nonsense mutation in the KLF1 gene, p.K288X, which ablated the DNA-binding domain of this key erythroid transcriptional regulator2. Only family members with HPFH were heterozygous carriers of this mutation. Expression profiling on primary erythroid progenitors showed that KLF1 target genes were downregulated in samples from individuals with HPFH. Functional assays suggested that, in addition to its established role in regulating adult globin expression, KLF1 is a key activator of the BCL11A gene, which encodes a suppressor of HbF expression3. These observations provide a rationale for the effects of KLF1 haploinsufficiency on HbF levels.

This is a preview of subscription content

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Chromosome 19 locus linked to HPFH in a Maltese family.
Figure 2: KLF1 target genes are downregulated in KLF1 p.K288X heterozygous HEPs.
Figure 3: Increased HBG1/HBG2 expression after knockdown of KLF1 in normal HEPs.
Figure 4: Expression of exogenous KLF1 in HEPs from donors with HPFH.
Figure 5: KLF1 binds to the promoter of the BCL11A gene in vivo.

Accession codes


Gene Expression Omnibus


  1. Serjeant, G. Geographic heterogeneity of sickle cell disease. in Disorders of Hemoglobin (eds. Steinberg, M.H., Forget, B.G., Higgs, D.R. & Nagel, R.L.) 895–906 (Cambridge Univ. Press, 2001).

  2. Bieker, J.J. Probing the onset and regulation of erythroid cell-specific gene expression. Mt. Sinai J. Med. 72, 333–338 (2005).

    PubMed  Google Scholar 

  3. Sankaran, V.G. et al. Human fetal hemoglobin expression is regulated by the developmental stage-specific repressor BCL11A. Science 322, 1839–1842 (2008).

    CAS  Article  Google Scholar 

  4. Stamatoyannopoulos, G. & Grosveld, F. Hemoglobin switching. in The Molecular Basis of Blood Diseases (eds. Stamatoyannopoulos, G., Majerus, P.W., Perlmutter, R.M. & Varmus, H.) 135–182 (WB Saunders Company, Philadelphia, 2001).

  5. Thein, S.L., Menzel, S., Lathrop, M. & Garner, C. Control of fetal hemoglobin: new insights emerging from genomics and clinical implications. Hum. Mol. Genet. 18, R216–R223 (2009).

    CAS  Article  Google Scholar 

  6. Craig, J.E. et al. Dissecting the loci controlling fetal haemoglobin production on chromosomes 11p and 6q by the regressive approach. Nat. Genet. 12, 58–64 (1996).

    CAS  Article  Google Scholar 

  7. Gilman, J.G. & Huisman, T.H. DNA sequence variation associated with elevated fetal G gamma globin production. Blood 66, 783–787 (1985).

    CAS  PubMed  Google Scholar 

  8. Close, J. et al. Genome annotation of a 1.5 Mb region of human chromosome 6q23 encompassing a quantitative trait locus for fetal hemoglobin expression in adults. BMC Genomics 5, 33 (2004).

    Article  Google Scholar 

  9. Garner, C. et al. Haplotype mapping of a major quantitative-trait locus for fetal hemoglobin production on chromosome 6q23. Am. J. Hum. Genet. 62, 1468–1474 (1998).

    CAS  Article  Google Scholar 

  10. Lettre, G. et al. DNA polymorphisms at the BCL11A, HBS1L-MYB, and β-globin loci associate with fetal hemoglobin levels and pain crises in sickle cell disease. Proc. Natl. Acad. Sci. USA 105, 11869–11874 (2008).

    CAS  Article  Google Scholar 

  11. Menzel, S. et al. A QTL influencing F cell production maps to a gene encoding a zinc-finger protein on chromosome 2p15. Nat. Genet. 39, 1197–1199 (2007).

    CAS  Article  Google Scholar 

  12. Abecasis, G.R., Cherny, S.S., Cookson, W.O. & Cardon, L.R. Merlin—rapid analysis of dense genetic maps using sparse gene flow trees. Nat. Genet. 30, 97–101 (2002).

    CAS  Article  Google Scholar 

  13. Hoffmann, K. & Lindner, T.H. easyLINKAGE-Plus—automated linkage analyses using large-scale SNP data. Bioinformatics 21, 3565–3567 (2005).

    CAS  Article  Google Scholar 

  14. Leykin, I. et al. Comparative linkage analysis and visualization of high-density oligonucleotide SNP array data. BMC Genet. 6, 7 (2005).

    Article  Google Scholar 

  15. Singleton, B.K., Burton, N.M., Green, C., Brady, R.L. & Anstee, D.J. Mutations in EKLF/KLF1 form the molecular basis of the rare blood group In(Lu) phenotype. Blood 112, 2081–2088 (2008).

    CAS  Article  Google Scholar 

  16. Miller, I.J. & Bieker, J.J. A novel, erythroid cell-specific murine transcription factor that binds to the CACCC element and is related to the Kruppel family of nuclear proteins. Mol. Cell. Biol. 13, 2776–2786 (1993).

    CAS  Article  Google Scholar 

  17. Feng, W.C., Southwood, C.M. & Bieker, J.J. Analyses of β-thalassemia mutant DNA interactions with erythroid Kruppel-like factor (EKLF), an erythroid cell-specific transcription factor. J. Biol. Chem. 269, 1493–1500 (1994).

    CAS  PubMed  Google Scholar 

  18. Leberbauer, C. et al. Different steroids co-regulate long-term expansion versus terminal differentiation in primary human erythroid progenitors. Blood 105, 85–94 (2005).

    CAS  Article  Google Scholar 

  19. Pilon, A.M. et al. Failure of terminal erythroid differentiation in EKLF-deficient mice is associated with cell cycle perturbation and reduced expression of E2F2. Mol. Cell. Biol. 28, 7394–7401 (2008).

    CAS  Article  Google Scholar 

  20. Moffat, J. et al. A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell 124, 1283–1298 (2006).

    CAS  Article  Google Scholar 

  21. Antoniou, M. Induction of erythroid-specific expression in murine erythroleukemia (MEL) cell lines. Methods Mol. Biol. 7, 421–434 (1991).

    CAS  PubMed  Google Scholar 

  22. Mühlemann, O., Eberle, A.B., Stalder, L. & Zamudio Orozco, R. Recognition and elimination of nonsense mRNA. Biochim. Biophys. Acta 1779, 538–549 (2008).

    Article  Google Scholar 

  23. Donze, D., Townes, T.M. & Bieker, J.J. Role of erythroid Kruppel-like factor in human γ- to β-globin gene switching. J. Biol. Chem. 270, 1955–1959 (1995).

    CAS  Article  Google Scholar 

  24. Drissen, R. et al. The active spatial organization of the β-globin locus requires the transcription factor EKLF. Genes Dev. 18, 2485–2490 (2004).

    CAS  Article  Google Scholar 

  25. Zhou, D., Pawlik, K.M., Ren, J., Sun, C.W. & Townes, T.M. Differential binding of erythroid Krupple-like factor to embryonic/fetal globin gene promoters during development. J. Biol. Chem. 281, 16052–16057 (2006).

    CAS  Article  Google Scholar 

  26. Bottardi, S., Ross, J., Pierre-Charles, N., Blank, V. & Milot, E. Lineage-specific activators affect beta-globin locus chromatin in multipotent hematopoietic progenitors. EMBO J. 25, 3586–3595 (2006).

    CAS  Article  Google Scholar 

  27. Wijgerde, M. et al. The role of EKLF in human β-globin gene competition. Genes Dev. 10, 2894–2902 (1996).

    CAS  Article  Google Scholar 

  28. Drissen, R. et al. The erythroid phenotype of EKLF-null mice: defects in hemoglobin metabolism and membrane stability. Mol. Cell. Biol. 25, 5205–5214 (2005).

    CAS  Article  Google Scholar 

  29. Miller, S.A., Dykes, D.D. & Polesky, H.F. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. 16, 1215 (1988).

    CAS  Article  Google Scholar 

  30. Trifillis, P., Ioannou, P., Schwartz, E. & Surrey, S. Identification of four novel δ-globin gene mutations in Greek Cypriots using polymerase chain reaction and automated fluorescence-based DNA sequence analysis. Blood 78, 3298–3305 (1991).

    CAS  PubMed  Google Scholar 

  31. Craig, J.E., Barnetson, R.A., Prior, J., Raven, J.L. & Thein, S.L. Rapid detection of deletions causing δβ-thalassemia and hereditary persistence of fetal hemoglobin by enzymatic amplification. Blood 83, 1673–1682 (1994).

    CAS  PubMed  Google Scholar 

  32. Higgs, D.R. & Wood, W.G. Genetic complexity in sickle cell disease. Proc. Natl. Acad. Sci. USA 105, 11595–11596 (2008).

    CAS  Article  Google Scholar 

  33. O'Connell, J.R. & Weeks, D.E. PedCheck: a program for identification of genotype incompatibilities in linkage analysis. Am. J. Hum. Genet. 63, 259–266 (1998).

    CAS  Article  Google Scholar 

  34. Schmittgen, T.D. & Livak, K.J. Analyzing real-time PCR data by the comparative C(T) method. Nat. Protoc. 3, 1101–1108 (2008).

    CAS  Article  Google Scholar 

  35. Follenzi, A., Sabatino, G., Lombardo, A., Boccaccio, C. & Naldini, L. Efficient gene delivery and targeted expression to hepatocytes in vivo by improved lentiviral vectors. Hum. Gene Ther. 13, 243–260 (2002).

    CAS  Article  Google Scholar 

  36. Zufferey, R., Nagy, D., Mandel, R.J., Naldini, L. & Trono, D. Multiply attenuated lentiviral vector achieves efficient gene delivery in vivo. Nat. Biotechnol. 15, 871–875 (1997).

    CAS  Article  Google Scholar 

  37. Andrews, N.C. & Faller, D.V. A rapid micropreparation technique for extraction of DNA-binding proteins from limiting numbers of mammalian cells. Nucleic Acids Res. 19, 2499 (1991).

    CAS  Article  Google Scholar 

  38. Follows, G.A. et al. Epigenetic consequences of AML1-ETO action at the human c-FMS locus. EMBO J. 22, 2798–2809 (2003).

    CAS  Article  Google Scholar 

Download references


We thank the family members for their cooperation; T. van Gent for help with statistical analysis; T. van Dijk for expertise in lentiviral technology; N. Papazian for preparation of human fetal liver samples; and M. Pizzuto for administrative support. The population samples from Malta were obtained from the Malta BioBank (EuroBioBank). Recombinant human erythropoietin (Epo) was a kind gift from Ortho-Biotech, and recombinant human Stem Cell Factor (SCF) was a kind gift from Amgen. Supported by the University of Malta and Mater Dei Hospital (A.E.F.); the Malta Government (J.B.); the European Molecular Biology Organization (J.B., P.P.); the Netherlands Scientific Organization (VENI 863.09.012 to L.G. and DN 82-294 and 912-07-019 to S.P.); the Netherlands Genomics Initiative, Erasmus MC (MRace; 296088 to S.P.); the Landsteiner Foundation for Blood Transfusion Research (0615 to S.P.); the Centre for Biomedical Genetics (F.G.G.); the European Commission FP6 EuTRACC consortium (037445 to F.G.G.); the US National Institutes of Health (NIH) (R01-HL073455 to F.G.G.); the Research Promotion Foundation of Cyprus (ΠΔE046_02 to G.P.P.); and the European Commission FP7 GEN2PHEN (200754 to G.P.P).

Author information

Authors and Affiliations



F.G.G., A.E.F., G.P.P. and S.P. designed experiments. J.B., P.P., M.G., L.G., G.G., P.F., M.P., C.A.S., W.C., R.G., Z.Ö., N.G. and M.v.L. performed experiments. J.B., P.P., M.G., L.G. and G.G. analyzed results. P.J.v.d.S., F.G.G., A.E.F., G.P.P. and S.P. supervised data analysis. P.J.v.d.S., W.v.IJ. and M.B. provided expertise, analysis tools and infrastructure. A.J.M.H.V., J.H. and M.B. analyzed data. J.B., P.P., M.G., F.G.G., M.v.L., A.E.F., G.P.P. and S.P. wrote the paper.

Corresponding authors

Correspondence to Alex E Felice, George P Patrinos or Sjaak Philipsen.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–5, Supplementary Tables 1–3 and Supplementary Note (PDF 810 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Borg, J., Papadopoulos, P., Georgitsi, M. et al. Haploinsufficiency for the erythroid transcription factor KLF1 causes hereditary persistence of fetal hemoglobin. Nat Genet 42, 801–805 (2010).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

Further reading


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing