Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression

Abstract

The transcription factor GATA1 regulates an extensive program of gene activation and repression during erythroid development. However, the associated mechanisms, including the contributions of distal versus proximal cis-regulatory modules, co-occupancy with other transcription factors, and the effects of histone modifications, are poorly understood. We studied these problems genome-wide in a Gata1 knockout erythroblast cell line that undergoes GATA1-dependent terminal maturation, identifying 2616 GATA1-responsive genes and 15,360 GATA1-occupied DNA segments after restoration of GATA1. Virtually all occupied DNA segments have high levels of H3K4 monomethylation and low levels of H3K27me3 around the canonical GATA binding motif, regardless of whether the nearby gene is induced or repressed. Induced genes tend to be bound by GATA1 close to the transcription start site (most frequently in the first intron), have multiple GATA1-occupied segments that are also bound by TAL1, and show evolutionary constraint on the GATA1-binding site motif. In contrast, repressed genes are further away from GATA1-occupied segments, and a subset shows reduced TAL1 occupancy and increased H3K27me3 at the transcription start site. Our data expand the repertoire of GATA1 action in erythropoiesis by defining a new cohort of target genes and determining the spatial distribution of cisregulatory modules throughout the genome. In addition, we begin to establish functional criteria and mechanisms that distinguish GATA1 activation from repression at specific target genes. More broadly, these studies illustrate how a ''master regulator'' transcription factor coordinates tissue differentiation through a panoply of DNA and protein interactions.

CDC6 expression is regulated by lineage-specific transcription factor GATA1

“…Also, the surrounding bases appear to follow a preference pattern, and C/G precedes the W, while a G preferentially follows the final A. [21][22][23] Second is that GATA1-regulated region is located at more than 3,000 bp upstream CDC6 promoter and functions as an enhancer when placed with a minimal promoter, in agreement with the observation that 90% of the sites occupied in vivo are located in were found in this 100 bp region, one of them being adjacent to GATA1 binding site (Fig. 3C), in a similar position as in other previously described regulatory regions of GATA1 controlled genes ( Fig.…”

“…In fact, only a small fraction of the in vitro characterized binding sites are actually occupied, according to various independent genome-wide occupancy analysis. [21][22][23] These reports have defined with further precision GATA1 preferred binding motif and unveiled a rich collection of targets that suggests a more global action of GATA 1 that would affect not only the lineage-specific program, but also cell processes such as signaling and cell cycle control.…”

Transcriptional divergence and conservation of human and mouse erythropoiesis

“…S3A) (28). We also compared the global expression data from adult murine bone marrow to that from the Gata1-null mouse cell line G1E-ER4, in which Gata1 activity was reactivated with estradiol treatment (29). After 14 and 21 h of estradiol induction, the G1E-ER4 cells differentiate into proerythroblast-like cells.…”

“…S4). We cross-compared the two human datasets to the three mouse datasets (15,16,(28)(29)(30). All intraspecies comparisons yielded mean Pearson correlations ranging from 0.832 to 0.993, whereas their interspecies equivalent yielded mean Pearson correlations of only 0.637-0.728 (Fig.…”

Genomics and transcriptomics of megakaryocytes and platelets: Implications for health and disease

“…These transcription factors have also been studied in the context of malignancy, where the skewing of megakaryocyte commitment may play a role in pre‐leukemic disorders and myeloproliferative neoplasms 18. There are several transcription factors that are shared by both the megakaryocyte and erythroid lineage (GATA1, GATA2, FOG, NF‐E2, and GFI1b),19 as well as lineage‐restricted transcription factors, such as KLF1 (erythroid) and ETS1/FLI1 (megakaryocyte) 18, 20. Additionally, MYB plays a key role in hematopoiesis by enhancing erythropoiesis through transactivation of KLF1 and LMO2 21.…”