Identification of Biologically Relevant Enhancers in Human Erythroid Cells

Su, Mack Y.; Steiner, Laurie A.; Bogardus, Hannah H; Mishra, Tejaswini; Schulz, Vincent P.; Hardison, Ross C.; Gallagher, Patrick G.

doi:10.1074/jbc.m112.413260

Cited by 50 publications

(59 citation statements)

References 128 publications

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“…29 We also found a KLF1 ChIP-seq peak within the promoter, introns, or within 20 kb of the transcriptional start site for many genes in Clusters 1 and 2. 37 In some cases, we confirmed Klf1 occupancy at an equivalent position within the murine gene homolog. 26 Thus, it is likely that many of the genes in Clusters 1 and 2 are direct human KLF1 target genes.…”

Section: The Klf1-dependent Erythroid Transcriptomesupporting

confidence: 53%

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KLF1-null neonates display hydrops fetalis and a deranged erythroid transcriptome

Magor

Tallack

Gillinder

et al. 2015

Blood

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Key Points• Complete loss of KLF1 function is compatible with life but results in severe nonspherocytic hemolytic anemia and kernicterus.• Human KLF1 regulates most aspects of red cell biology.We describe a case of severe neonatal anemia with kernicterus caused by compound heterozygosity for null mutations in KLF1, each inherited from asymptomatic parents. One of the mutations is novel. This is the first described case of a KLF1-null human. The phenotype of severe nonspherocytic hemolytic anemia, jaundice, hepatosplenomegaly, and marked erythroblastosis is more severe than that present in congenital dyserythropoietic anemia type IV as a result of dominant mutations in the second zinc-finger of KLF1. There was a very high level of HbF expression into childhood (>70%), consistent with a key role for KLF1 in human hemoglobin switching. We performed RNA-seq on circulating erythroblasts and found that human KLF1 acts like mouse Klf1 to coordinate expression of many genes required to build a red cell including those encoding globins, cytoskeletal components, AHSP, heme synthesis enzymes, cell-cycle regulators, and blood group antigens. We identify novel KLF1 target genes including KIF23 and KIF11 which are required for proper cytokinesis. We also identify new roles for KLF1 in autophagy, global transcriptional control, and RNA splicing. We suggest loss of KLF1 should be considered in otherwise unexplained cases of severe neonatal NSHA or hydrops fetalis. (Blood. 2015;125(15):2405-2417

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Section: The Klf1-dependent Erythroid Transcriptomesupporting

confidence: 53%

“…Many are well-known murine Klf1 target genes, 28,29,45 but some are novel. For each gene, we examined the UCSC Browser (hg19) after generation of wiggle tracks for RNA-seq data, ChIP-seq data, 37 and DNase1 HS-seq data for K562 cells generated by ENCODE (see Methods).…”

Section: 19mentioning

confidence: 99%

KLF1-null neonates display hydrops fetalis and a deranged erythroid transcriptome

Magor

Tallack

Gillinder

et al. 2015

Blood

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“…4C). This overlaps with GATA1, TAL1 and p300 binding, consistent with the 'core' transcription factor observations that have been noted at a subset of EKLF binding sites (Li et al, 2013;Su et al, 2013;Tallack et al, 2012;Wontakal et al, 2012). Inspection of the EKLF DNA binding cognate sequence shows that it falls into the 'class I' site category within 5 0 -CCMCRCCCN, and thus should bind the neonatal anemia (Nan) EKLF variant based on our analysis of Nan-EKLF biochemical properties (Siatecka and Bieker, 2011;Siatecka et al, 2010).…”

Section: Eklf Regulation Of Relevant Targets In Erythroblastic Islandsmentioning

confidence: 49%

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

et al. 2014

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The erythroblastic island provides an important nutritional and survival support niche for efficient erythropoietic differentiation. Island integrity is reliant on adhesive interactions between erythroid and macrophage cells. We show that erythroblastic islands can be formed from single progenitor cells present in differentiating embryoid bodies, and that these correspond to erythro-myeloid progenitors (EMPs) that first appear in the yolk sac of the early developing embryo. Erythroid Krüppel-like factor (EKLF; KLF1), a crucial zinc finger transcription factor, is expressed in the EMPs, and plays an extrinsic role in erythroid maturation by being expressed in the supportive macrophage of the erythroblastic island and regulating relevant genes important for island integrity within these cells. Together with its well-established intrinsic contributions to erythropoiesis, EKLF thus plays a coordinating role between two different cell types whose interaction provides the optimal environment to generate a mature red blood cell.

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“…number of multimeric complexes involving other TFs and can activate or repress target gene expression (29)(30)(31)(32)(33)(34)(35)(36)(37).…”

Section: Significancementioning

confidence: 99%

Insight into GATA1 transcriptional activity through interrogation ofciselements disrupted in human erythroid disorders

Wakabayashi

Ulirsch

Ludwig

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Whole-exome sequencing has been incredibly successful in identifying causal genetic variants and has revealed a number of novel genes associated with blood and other diseases. One limitation of this approach is that it overlooks mutations in noncoding regulatory elements. Furthermore, the mechanisms by which mutations in transcriptional cis-regulatory elements result in disease remain poorly understood. Here we used CRISPR/Cas9 genome editing to interrogate three such elements harboring mutations in human erythroid disorders, which in all cases are predicted to disrupt a canonical binding motif for the hematopoietic transcription factor GATA1. Deletions of as few as two to four nucleotides resulted in a substantial decrease (>80%) in target gene expression. Isolated deletions of the canonical GATA1 binding motif completely abrogated binding of the cofactor TAL1, which binds to a separate motif. Having verified the functionality of these three GATA1 motifs, we demonstrate strong evolutionary conservation of GATA1 motifs in regulatory elements proximal to other genes implicated in erythroid disorders, and show that targeted disruption of such elements results in altered gene expression. By modeling transcription factor binding patterns, we show that multiple transcription factors are associated with erythroid gene expression, and have created predictive maps modeling putative disruptions of their binding sites at key regulatory elements. Our study provides insight into GATA1 transcriptional activity and may prove a useful resource for investigating the pathogenicity of noncoding variants in human erythroid disorders.GATA1 | cis-regulatory elements | noncoding mutations | Mendelian erythroid disorders W hole-exome sequencing (WES) and targeted sequencing approaches have greatly accelerated our ability to identify causal genetic lesions in both previously implicated and novel genes underlying monogenic disorders (1, 2). In hematology, WES has been extremely useful for identifying unknown genetic etiologies for various disorders, such as those affecting red blood cell (RBC) production, including Diamond-Blackfan anemia and congenital dyserythropoietic anemia (3-5), disorders of RBC structure and function (6, 7), and disorders affecting other aspects of hematologic function (2, 8). Despite this considerable success, however, more than 50% of cases of presumed monogenic diseases are refractory to current WES approaches (9). Although resolving these remaining cases will benefit from improvements in exome capture (10), read alignment (11), and variant annotation methodologies (11), the importance of genetic variation occurring within regulatory elements (REs) outside of the traditionally investigated coding sequences in hematologic and other diseases is being increasingly appreciated (12).Whole-genome sequencing (WGS) approaches are becoming progressively more available and affordable, but separating pathogenic genetic variation from benign or unrelated mutations remains especially difficult outside of protein-coding gen...

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Identification of Biologically Relevant Enhancers in Human Erythroid Cells

Cited by 50 publications

References 128 publications

KLF1-null neonates display hydrops fetalis and a deranged erythroid transcriptome

KLF1-null neonates display hydrops fetalis and a deranged erythroid transcriptome

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

Insight into GATA1 transcriptional activity through interrogation ofciselements disrupted in human erythroid disorders

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