Fetal hemoglobin (HbF, αγ) level is genetically controlled and modifies severity of adult hemoglobin (HbA, αβ) disorders, sickle cell disease, and β-thalassemia. Common genetic variation affects expression of BCL11A, a regulator of HbF silencing. To uncover how BCL11A supports the developmental switch from γ- to β- globin, we use a functional assay and protein binding microarray to establish a requirement for a zinc-finger cluster in BCL11A in repression and identify a preferred DNA recognition sequence. This motif appears in embryonic and fetal-expressed globin promoters and is duplicated in γ-globin promoters. The more distal of the duplicated motifs is mutated in individuals with hereditary persistence of HbF. Using the CUT&RUN approach to map protein binding sites in erythroid cells, we demonstrate BCL11A occupancy preferentially at the distal motif, which can be disrupted by editing the promoter. Our findings reveal that direct γ-globin gene promoter repression by BCL11A underlies hemoglobin switching.

The evolution of transcriptional regulatory networks entails the expansion and diversification of transcription factor (TF) families. The forkhead family of TFs, defined by a highly conserved winged helix DNA-binding domain (DBD), has diverged into dozens of subfamilies in animals, fungi, and related protists. We have used a combination of maximum-likelihood phylogenetic inference and independent, comprehensive functional assays of DNA-binding capacity to explore the evolution of DNA-binding specificity within the forkhead family. We present converging evidence that similar alternative sequence preferences have arisen repeatedly and independently in the course of forkhead evolution. The vast majority of DNA-binding specificity changes we observed are not explained by alterations in the known DNA-contacting amino acid residues conferring specificity for canonical forkhead binding sites. Intriguingly, we have found forkhead DBDs that retain the ability to bind very specifically to two completely distinct DNA sequence motifs. We propose an alternate specificity-determining mechanism whereby conformational rearrangements of the DBD broaden the spectrum of sequence motifs that a TF can recognize. DNA-binding bispecificity suggests a previously undescribed source of modularity and flexibility in gene regulation and may play an important role in the evolution of transcriptional regulatory networks.transcription factor binding site motif | protein-DNA interactions T he regulation of gene expression by the interaction of sequence-specific transcription factors (TFs) with target sites (cis-regulatory elements) near their regulated genes is a central mechanism by which organisms interpret regulatory programs encoded in the genome to develop and interact with their environment. The emergence of new species has depended in part on the evolution of the network of interactions by which an organism's TFs control gene expression. Much attention has been paid to changes in cis-regulatory sequences over evolutionary time, because these changes can result in incremental modifications of organismal phenotypes without large-scale rewiring of transcriptional regulatory networks that would result from changes in TF DNA-binding specificity (1). Nevertheless, TFs and their DNA-binding specificities have changed over time (2). Gene duplication, followed by divergence of the resulting redundant TFs, has resulted in the emergence of families of paralogous TFs with diversified DNA-binding specificities and functions (3). Thus, identifying mechanisms by which related DNA-binding domains (DBDs) have acquired novel specificities is important for understanding TF evolution.The forkhead box (Fox) family of TFs spans a wide range of species and is one of the largest classes of TFs in humans. In metazoans, Fox proteins have vital roles in development of a variety of organ systems, metabolic homeostasis, and regulation of cell-cycle progression, and fungal Fox proteins are involved in cell-cycle progression and the expression of ribosomal proteins. ...

Sequencing of exomes and genomes has revealed abundant genetic variation affecting the coding sequences of human transcription factors (TFs), but the consequences of such variation remain largely unexplored. We developed a computational, structure-based approach to evaluate TF variants for their impact on DNA-binding activity and used universal protein binding microarrays to assay sequence-specific DNA-binding activity across 41 reference and 117 variant alleles found in individuals of diverse ancestries and families with Mendelian diseases. We found 77 variants in 28 genes that affect DNA-binding affinity or specificity and identified thousands of rare alleles likely to alter the DNA-binding activity of human sequence-specific TFs. Our results suggest that most individuals have unique repertoires of TF DNA-binding activities, which may contribute to phenotypic variation.