Alternative titles; symbols
HGNC Approved Gene Symbol: KLF1
SNOMEDCT: 115824003, 719453009;
Cytogenetic location: 19p13.13 Genomic coordinates (GRCh38): 19:12,884,422-12,887,201 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 19p13.13 | [Hereditary persistence of fetal hemoglobin] | 613566 | 3 | |
| Blood group--Lutheran inhibitor | 111150 | 3 | ||
| Dyserythropoietic anemia, congenital, type IV | 613673 | Autosomal dominant | 3 |
The KLF1 gene encodes an essential transcriptional activator that directs high-level expression of the adult beta-globin promoter by binding to its CACCC element (Bieker, 1996). KLF1 also acts as a transcription factor for the BCAM protein (612773) as well as for other proteins expressed on erythroid cells (summary by Helias et al., 2013).
Bieker (1996) isolated KLF1, which is the human homolog of murine Eklf. The predicted KLF1 protein contains 3 zinc fingers that share more than 90% sequence similarity with, and are predicted to bind the same target sequence as, mouse Eklf. The rest of the protein is proline-rich and retains approximately 70% sequence similarity to the mouse gene. Human KLF1 is expressed in bone marrow and erythroleukemic cells lines but not in myeloid or lymphoid cell lines.
Van Ree et al. (1997) cloned KLF1 from a bone marrow cDNA library. The predicted 362-amino acid human protein is 69% identical to that of mouse Eklf. Northern blot analysis revealed expression exclusively in erythropoietic tissues (fetal liver and adult bone marrow).
Bieker (1996) determined that the KLF1 gene is contained within 3 kb of genomic DNA, and its coding region is interrupted by 2 introns whose locations are conserved with the murine gene.
Van Ree et al. (1997) mapped the KLF1 gene to chromosome 19p13.13-p13.12 by fluorescence in situ hybridization.
Nuez et al. (1995) and Perkins et al. (1995) used homologous recombination in embryonic stem cells to inactivate the mouse Eklf gene and demonstrated defective hematopoiesis. The Eklf gene was originally isolated from mouse erythroid cell RNA by differential screening and was shown to be erythroid-specific, although a lower level of Eklf was found in mast cell lines. Eklf contains 3 zinc fingers homologous to those found in the Kruppel family of transcription factors (see 165220). Because it binds to the sequence CCACACCCT, EKLF was suspected to affect erythroid development through its ability to bind to the CAC box in the promoter of the beta-globin gene (HBB; 141900). The mutation in this element leads to reduced beta-globin expression, and it appears to mediate the effect of the globin locus control region on the promoter. From study of transgenic mice heterozygous for a lacZ reporter sequence within the EKLF gene, Nuez et al. (1995) found that the reporter gene is expressed in a developmentally specific manner in all types of erythroblasts in the fetal liver and adult bone marrow. Homozygous EKLF-deficient mice appeared normal during the embryonic stage of hematopoiesis in the yolk sac, but developed a fatal anemia during early fetal life when hematopoiesis shifted to the fetal liver. Enucleated erythrocytes were formed, but these did not contain the proper amount of hemoglobin. Perkins et al. (1995) pointed out that the anemia developing during fetal liver erythropoiesis has the molecular and hematologic features of beta-globin deficiency found in beta-thalassemia. Although it is expressed at all stages, EKLF is not required for yolk sac erythropoiesis, erythroid commitment, or expression of other potential target genes. Its stage-specific and beta-globin gene-specific requirement suggests that EKLF may facilitate completion of the fetal-to-adult (hemoglobin gamma to beta) switch in humans.
EKLF is necessary for stage-specific expression of the human beta-globin gene. Armstrong et al. (1998) showed that EKLF requires a SWI/SNF-related chromatin remodeling complex, EKLF coactivator remodeling complex-1 (ERC1), to generate a DNase I hypersensitive, transcriptionally active beta-globin promoter on chromatin templates in vitro. ERC1 contains BRG1, BAF170 (601734), BAF155 (601732), and INI1 (601607) homologs of yeast SWI/SNF subunits, as well as a subunit unique to higher eukaryotes, BAF57 (603111), which is critical for chromatin remodeling and transcription with EKLF. Thus, a member of the SWI/SNF family acts directly in transcriptional activation and may regulate subsets of genes by selectively interacting with specific DNA-binding proteins.
Singleton et al. (2008) found that loss-of-function mutations in the KLF1 gene result in the dominantly inherited Lutheran-negative In(Lu) red blood cell phenotype (INLU; 111150). In(Lu) was originally postulated to result from inheritance of a gene that inhibited or suppressed the Lutheran antigen gene (BCAM; 612773) (Gibson, 1976). The findings of Singleton et al. (2008) indicated that the lack of expression of the Lu antigen in this phenotype results from decreased transcription of erythroid-specific genes associated with red blood cell maturation.
Schoenfelder et al. (2010) found that mouse Hbb and Hba (141800) associate with hundreds of active genes from nearly all chromosomes in nuclear foci that they called 'transcription factories.' The 2 globin genes preferentially associated with a specific and partially overlapping subset of active genes. Schoenfelder et al. (2010) also noted that expression of the Hbb locus is strongly dependent upon Klf1, while expression of the Hba locus is only partially dependent on Klf1. Immunofluorescence analysis of mouse erythroid cells showed that most Klf1 localized to the cytoplasm and that nuclear Klf1 was present in discrete sites that overlapped with RNAII foci. Klf1 knockout in mouse erythroid cells specifically disrupted the association of Klf1-regulated genes within the Hbb-associated network. Klf1 knockout more weakly disrupted interactions within the specific Hba network. Schoenfelder et al. (2010) showed that KLF1-regulated genes share KLF1-containing transcription factories and that KLF1 is required for the clustering of these coregulated genes. They concluded that transcriptional regulation involves a complex 3-dimensional network rather than factors acting on single genes in isolation.
Borg et al. (2010) demonstrated that KLF1 binds to and activates the promoter region of the BCL11A gene (606557), which is a repressor of the fetal hemoglobin genes HBG1 (142200) and HBG2 (142250). Chromatin immunoprecipitation (ChIP) assay of human erythroid progenitors from adult peripheral blood showed strong binding of KLF1 to the BCL11A promoter, whereas such binding was not observed in human fetal liver erythroid progenitors. These findings indicated that KLF1 acts as a dual regulator of fetal-to-adult globin switching in humans by acting as a preferential activator of the HBB gene and by activating expression of BCL11A, which in turn represses the HBG1x and HBG2 genes.
Arnaud et al. (2010) found that KLF1 plays a role in the expression of the water channel AQP1 (107776) and the adhesion molecule CD44 (107269) on erythroid cells.
Lutheran Red Blood Cell Group
Singleton et al. (2008) identified 9 different heterozygous loss-of-function mutations in the KLF1 gene (see, e.g., 600599.0001-600599.0004) in 21 of 24 persons with the dominant In(Lu) phenotype (INLU; 111150). The individuals had no reported pathology, indicating that 1 functional KLF1 allele is sufficient to sustain human erythropoiesis. KLF1 mutations were not identified in 37 controls.
In red blood cell samples from 10 probands with the dominant In(Lu) phenotype, Helias et al. (2013) identified 10 different heterozygous loss-of-function mutations in the KLF1 gene (see, e.g., 600599.0007-600599.0009). Flow cytometric analysis indicated that the red blood cells from these individuals had some weak expression of the Lu(b) antigen and low expression of CD44 (107269). In addition, these individuals had increased levels of fetal hemoglobin (HbF) (mean of 2.14%) compared to controls (mean less than 1.0%), and slightly increased levels of HbA2 (141850). Finally, 9 In(Lu) individuals who were heterozygous for the P1 allele (607922.0007) did not express the P1 antigen (see 111400), whereas 1 who was homozygous for the P1 allele expressed only weak P1. These findings suggested that the expression of P1 is suppressed in the In(Lu) blood type. Helias et al. (2013) concluded that the KLF1 haploinsufficiency has different effects on the expression of different erythroid proteins, likely reflecting the variable dependence of their respective genes on the KLF1 transcription factor.
Hereditary Persistence of Fetal Hemoglobin, KLF1-Related
In affected members of a Maltese family with hereditary persistence of fetal hemoglobin (613566), Borg et al. (2010) identified a heterozygous mutation in the KLF1 gene (K288X; 600599.0005). In vitro functional expression assays showed that loss of KLF1 function resulted in decreased BCL11A expression and increased expression of the fetal hemoglobin genes HBG1 and HBG2.
Congenital Dyserythropoietic Anemia IV
In 2 unrelated patients with congenital dyserythropoietic anemia IV (CDAN4; 613673), one of whom was reported by Wickramasinghe et al. (1991), Arnaud et al. (2010) identified a heterozygous de novo mutation in the KLF1 gene (E325K; 600599.0006). The findings indicated that the KLF1 gene plays a critical role in the regulation of several genes during erythropoiesis, and that dysregulation of certain gene targets can result in dyserythropoiesis.
Wijgerde et al. (1996) produced a strain of Eklf-knockout mice, embryos of which expressed the epsilon- and gamma-globin genes normally. Gamma- and beta-globins were expressed with altered ratios in heterozygous knockout mouse fetal liver. Homozygous knockout mouse fetuses had no beta-globin transcription and had coincident changes in chromatin structure at the beta promoter. Wijgerde et al. (1996) proposed that EKLF stabilizes the interaction between the globin locus control region and the beta-globin gene. In addition, they considered these findings to provide further evidence that developmental modulation of globin gene expression within individual cells is accomplished by alteration of the frequency and/or duration of transcriptional periods of a gene, rather than by a change in the rate of transcription.
Zhou et al. (2010) found that transgenic mice homozygous for a deletion of the 50-bp HS1 enhancer (EHS1) in the Klf1 gene had greatly increased gene expression ratios of mouse epsilon-y2-globin/beta-globin and BAC-derived human gamma-globin/beta-globin in the liver at embryonic day 14.5. Adult erythroid progenitors isolated from the mutant mice showed markedly reduced Bcl11a expression, suggesting that Klf1 regulates Bcl11a expression. ChIP analysis showed that wildtype Klf1 binds to a CACCC box in the promoter region of Bcl11a. Studies in adult human progenitor blood cells showed that knockdown of KLF1 resulted in decreased BCL11A expression and upregulation of gamma-globin genes, similar to the mouse studies. The findings indicated that developmental stage-specific changes in KLF1 abundance mediate the competitive interactions of globin gene expression.
Lyon (1983, 1986) described an ethylnitrosourea-induced mouse mutation, neonatal anemia (Nan), resulting in a semidominant hemolytic anemia that shares several features of hereditary spherocytosis (see 182900). Nan was mapped to mouse chromosome 8. Siatecka et al. (2010) identified the Nan mutation as a glu339-to-asp (E339D) substitution in the second C2H2 zinc finger motif of Eklf. E339 is absolutely conserved across the entire mouse and human KLF family and across EKLF proteins from different species. The substitution, which is conservative, did not affect Eklf protein expression, but it abrogated binding of mutant Eklf to a subset of Eklf target promoters containing a thymidine in the middle position of the Eklf-binding motif. This altered binding specificity of mutant Eklf resulted in distorted Eklf-dependent gene expression and abnormal residual embryonic beta-h1 globin expression in Nan heterozygous mice. The Nan mutation was more severe than Eklf deletion, as homozygous Nan mutant mice died at an earlier embryonic time point than Eklf -/- embryos. Furthermore, heterozygous Nan mice showed severe anemia, whereas Eklf +/- mice were indistinguishable from wildtype.
In 8 individuals of English descent with the dominant In(Lu) blood phenotype (INLU; 111150), Singleton et al. (2008) identified a heterozygous 1-bp duplication (954dupG) in exon 3 of the KLF1 gene, resulting in a frameshift and premature termination. The substitution was predicted to render the transcription factor nonfunctional. The individuals had no reported pathology, indicating that 1 functional KLF1 allele is sufficient to sustain human erythropoiesis.
In 6 individuals of Spanish descent with the dominant In(Lu) blood phenotype (INLU; 111150), Singleton et al. (2008) identified a heterozygous 1-bp deletion (569delC) in exon 2 of the KLF1 gene, resulting in a frameshift and premature termination. The substitution was predicted to render the transcription factor nonfunctional. The individuals had no reported pathology, indicating that 1 functional KLF1 allele is sufficient to sustain human erythropoiesis.
In an individual with the dominant In(Lu) blood phenotype (INLU; 111150), Singleton et al. (2008) identified a heterozygous 874A-T transversion in the KLF1 gene, resulting in a lys292-to-ter (K292X) substitution. The substitution was predicted to result in premature termination and a lack of all zinc finger domains.
In an individual with the dominant In(Lu) blood phenotype (INLU; 111150), Singleton et al. (2008) identified a heterozygous 895C-T transition in the KLF1 gene, resulting in a his299-to-tyr (H299Y) substitution. The substitution was predicted to result in diminished zinc binding.
In affected members of a Maltese family with hereditary persistence of fetal hemoglobin (613566), Borg et al. (2010) identified a heterozygous A-to-T transversion in the KLF1 gene, resulting in a lys288-to-ter (K288X) substitution, which was not found in 400 controls. The mutation was predicted to ablate the complete zinc finger domain and abrogate DNA binding. The truncated protein was not detected in patient cells, suggesting nonsense-mediated mRNA decay. The proband was ascertained because of mild hypochromatic microcytic indices, but no other phenotypic abnormalities were described. Gene expression profiles showed that mutation carriers had decreased expression of the fetal globin repressor BCL11A (606557), and upregulation of the fetal hemoglobin genes HBG1 (142200) and HBG2 (142250). Knockdown of KLF1 in control cells caused similar changes in gene expression, and further expression studies excluded a dominant-negative effect of the K288X mutant protein. Borg et al. (2010) concluded that haploinsufficiency for KLF1 is a cause of HPFH.
In 2 unrelated patients with congenital dyserythropoietic anemia type IV (CDAN4; 613673), Arnaud et al. (2010) identified a heterozygous de novo 973G-A transition in exon 3 of the KLF1 gene, resulting in a glu325-to-lys (E325K) substitution. One of the patients had previously been reported by Wickramasinghe et al. (1991). The phenotype was characterized by hydrops and severe anemia at birth, ineffective erythropoiesis, nucleated peripheral red blood cells, and absence of expression of CD44 (107269) and AQP1 (107776) on erythrocytes. Both patients also showed increased fetal hemoglobin. The E325K mutation occurred in a conserved residue in the second zinc finger domain, and structural modeling predicted that the mutation would stabilize the bond between KLF1 and DNA target sequences. Expression studies in human erythroid cells showed that the mutant E325K protein had similar expression and nuclear localization as the wildtype protein. However, the mutant protein showed markedly decreased transcriptional activity toward CD44 and AQP1 compared to wildtype, consistent with the clinical findings. The mutant KLF1 protein also showed a dominant-negative effect. The findings indicated that the KLF1 gene plays a critical role in the regulation of several genes during erythropoiesis, and that dysregulation of certain gene targets can result in dyserythropoiesis.
By in vitro functional expression studies, Helias et al. (2013) demonstrated that the E325K mutant KLF1 protein retained transactivation activity for the BCAM (612773) promoter as well as, or ever better than, wildtype KLF1. The findings were consistent with the fact that CDAN4 is not associated with reduced levels of BCAM on red blood cells.
In a blood sample derived from a patient with the dominant In(Lu) blood phenotype (111150), Helias et al. (2013) identified a heterozygous 977T-G transversion in the KLF1 gene, resulting in a leu326-to-arg (L326R) substitution in the zinc finger domain. In vitro functional expression studies indicated that the mutant protein resulted in reduced transcriptional activity of BCAM (612773) compared to wildtype KLF1, consistent with a loss of function.
In a blood sample derived from a patient with the dominant In(Lu) blood phenotype (111150), Helias et al. (2013) identified a heterozygous 1071C-A transversion in the KLF1 gene, resulting in a his357-to-gln (H357Q) substitution in the zinc finger domain. In vitro functional expression studies indicated that the mutant protein resulted in reduced transcriptional activity of BCAM (612773) compared to wildtype KLF1, consistent with a loss of function.
In a mother and son with the dominant In(Lu) blood phenotype (111150), Helias et al. (2013) identified a heterozygous 591C-G transversion in the KLF1 gene, resulting in a tyr197-to-ter (Y197X) substitution. Flow cytometric analysis of patient blood cells showed weak expression of the Lu(b) antigen and low expression of CD44 (107269). Both individuals also had increased levels of fetal hemoglobin (HbF) (3.5% and 3.7%, respectively) compared to non-KLF1 mutation family members (0.9-1.1% HbF).
Armstrong, J. A., Bieker, J. J., Emerson, B. M. A SWI/SNF-related chromatin remodeling complex, E-RC1, is required for tissue-specific transcriptional regulation by EKLF in vitro. Cell 95: 93-104, 1998. [PubMed: 9778250] [Full Text: https://doi.org/10.1016/s0092-8674(00)81785-7]
Arnaud, L., Saison, C., Helias, V., Lucien, N., Steschenko, D., Giarratana, M.-C., Prehu, C., Foliguet, B., Montout, L., de Brevern, A. G., Francina, A., Ripoche, P., and 11 others. A dominant mutation in the gene encoding the erythroid transcription factor KLF1 causes a congenital dyserythropoietic anemia. Am. J. Hum. Genet. 87: 721-727, 2010. [PubMed: 21055716] [Full Text: https://doi.org/10.1016/j.ajhg.2010.10.010]
Bieker, J. J. Isolation, genomic structure, and expression of human erythroid Kruppel-like factor (EKLF). DNA Cell Biol. 15: 347-352, 1996. [PubMed: 8924208] [Full Text: https://doi.org/10.1089/dna.1996.15.347]
Borg, J., Papadopoulos, P., Georgitsi, M., Gutierrez, L., Grech, G., Fanis, P., Phylactides, M., Verkerk, A. J. M. H., van der Spek, P. J., Scerri, C. A., Cassar, W., Galdies, R., and 10 others. Haploinsufficiency for the erythroid transcription factor KLF1 causes hereditary persistence of fetal hemoglobin. Nature Genet. 42: 801-805, 2010. [PubMed: 20676099] [Full Text: https://doi.org/10.1038/ng.630]
Gibson, T. Two kindred with the rare dominant inhibitor of the Lutheran and P1 red cell antigens. Hum. Hered. 26: 171-174, 1976. [PubMed: 955641] [Full Text: https://doi.org/10.1159/000152801]
Helias, V., Saison, C., Peyrard, T., Vera, E., Prehu, C., Cartron, J.-P., Arnaud, L. Molecular analysis of the rare In(Lu) blood type: toward decoding the phenotypic outcome of haploinsufficiency for the transcription factor KLF1. Hum. Mutat. 34: 221-228, 2013. [PubMed: 23125034] [Full Text: https://doi.org/10.1002/humu.22218]
Lyon, M. F. Position of neonatal anaemia (Nan) on chromosome 8. Mouse News Lett. 74: 95 only, 1986.
Lyon, M. F. Dominant haemolytic anaemia. Mouse News Lett. 68: 68 only, 1983.
Nuez, B., Michalovich, D., Bygrave, A., Ploemacher, R., Grosveld, F. Defective haematopoiesis in fetal liver resulting from inactivation of the EKLF gene. Nature 375: 316-318, 1995. [PubMed: 7753194] [Full Text: https://doi.org/10.1038/375316a0]
Perkins, A. C., Sharpe, A. H., Orkin, S. H. Lethal beta-thalassaemia in mice lacking the erythroid CACCC-transcription factor EKLF. Nature 375: 318-322, 1995. [PubMed: 7753195] [Full Text: https://doi.org/10.1038/375318a0]
Schoenfelder, S., Sexton, T., Chakalova, L., Cope, N. F., Horton, A., Andrews, S., Kurukuti, S., Mitchell, J. A., Umlauf, D., Dimitrova, D. S., Eskiw, C. H., Luo, Y., Wei, C.-L., Ruan, Y., Bieker, J. J., Fraser, P. Preferential associations between co-regulated genes reveal a transcription interactome in erythroid cells. Nature Genet. 42: 53-61, 2010. [PubMed: 20010836] [Full Text: https://doi.org/10.1038/ng.496]
Siatecka, M., Sahr, K. E., Andersen, S. G., Mezei, M., Bieker, J. J., Peters, L. L. Severe anemia in the Nan mutant mouse caused by sequence-selective disruption of erythroid Kruppel-like factor. Proc. Nat. Acad. Sci. 107: 15151-15156, 2010. [PubMed: 20696915] [Full Text: https://doi.org/10.1073/pnas.1004996107]
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. [PubMed: 18487511] [Full Text: https://doi.org/10.1182/blood-2008-03-145672]
van Ree, J. H., Roskrow, M. A., Becher, A. M., McNall, R., Valentine, V. A., Jane, S. M., Cunningham, J. M. The human erythroid-specific transcription factor EKLF localizes to chromosome 19p13.12-p13.13. Genomics 39: 393-395, 1997. [PubMed: 9119377] [Full Text: https://doi.org/10.1006/geno.1996.4472]
Wickramasinghe, S. N., Illum, N., Wimberley, P. D. Congenital dyserythropoietic anaemia with novel intra-erythroblastic and intra-erythrocytic inclusions. Brit. J. Haemat. 79: 322-330, 1991. [PubMed: 1659863] [Full Text: https://doi.org/10.1111/j.1365-2141.1991.tb04541.x]
Wijgerde, M., Gribnau, J., Trimborn, T., Nuez, B., Philipsen, S., Grosveld, F., Fraser, P. The role of EKLF in human beta-globin gene competition. Genes Dev. 10: 2894-2902, 1996. [PubMed: 8918890] [Full Text: https://doi.org/10.1101/gad.10.22.2894]
Zhou, D., Liu, K., Sun, C.-W., Pawlik, K. M., Townes, T. M. KLF1 regulates BCL11A expression and gamma- to beta-globin gene switching. Nature Genet. 42: 742-744, 2010. [PubMed: 20676097] [Full Text: https://doi.org/10.1038/ng.637]