Figure 1.
KAT2A-containing ATAC and SAGA complexes have unique targets in hematopoietic cells. (A) Schematic representation of the human ATAC (left) and SAGA (right) multiprotein complexes. SAGA (right) is organized into distinct structural and functional modules, colored similarly. The KAT2A-containing histone acetyltransferase (HAT) module is depicted in orange and partially hared with ATAC (left), with exception of TADA2B, which is replaced by TADA2A in ATAC. The histone deubiquitination (DUB) module is shown in red; the core module, which includes SPT20, in blue. TF-binding module, TRRAP, is shown in yellow. TATA-binding protein (TBP), in purple, is not part of the complex architecture, but it associates with SUPT3H to recruit SAGA to TATA box and facilitate transcription. The ATAC complex does not have a modular organization. Its main structure is shown in green and includes DNA-binding subunit ZZZ3. Subunits tested in this study are delineated with a dashed line. (B) Venn diagram of consensus ZZZ3 and SPT20 ChIP-seq binding from 2 independent experiments. (C) Genomic location of ZZZ3 (left) and SPT20 (right) ChIP-seq binding in K562 cells. Summary of consensus peaks from 2 independent ChIP-seq experiments is shown. (D) Representative ChIP-seq peak for ZZZ3 target in K562 cells (RPS7) and representative ChIP-seq peak for SPT20 target in K562 cells (HBB). (E) Publicly available ChIP-seq tracks for H3K9ac (ENCFF257CLC) and ZZZ3 (ENCFF856KCV) in K562 cells at the RPS7 and HBB loci retrieved from the ENCODE project portal (www.encodeproject.org). The RPS7 and HBB loci in panel D are represented confirming the presence of H3K9ac peaks and reproducing the selective ZZZ3 binding at RPS7 also observed in our data. (F) H3K9ac ChIP-qPCR analysis of representative SPT20 and ZZZ3 targets upon knockdown in K562 cells. N ≥ 3 independent experiments. Mean ± SEM of enrichment relative to rabbit IgG, with normalization to control intergenic region with no significant H3K9ac enrichment. Two-tailed Student t test for significance *P < .05. (G) qRT-PCR analysis of expression of ATAC and SAGA complex targets in K562 cells. N ≥ 3 independent experiments, mean ± SEM of gene expression relative to CTRLsh, normalized to HPRT1 housekeeping gene. Two-tailed Student t test for significance *P < .05, **P < .01, ***P < .001.

KAT2A-containing ATAC and SAGA complexes have unique targets in hematopoietic cells. (A) Schematic representation of the human ATAC (left) and SAGA (right) multiprotein complexes. SAGA (right) is organized into distinct structural and functional modules, colored similarly. The KAT2A-containing histone acetyltransferase (HAT) module is depicted in orange and partially hared with ATAC (left), with exception of TADA2B, which is replaced by TADA2A in ATAC. The histone deubiquitination (DUB) module is shown in red; the core module, which includes SPT20, in blue. TF-binding module, TRRAP, is shown in yellow. TATA-binding protein (TBP), in purple, is not part of the complex architecture, but it associates with SUPT3H to recruit SAGA to TATA box and facilitate transcription. The ATAC complex does not have a modular organization. Its main structure is shown in green and includes DNA-binding subunit ZZZ3. Subunits tested in this study are delineated with a dashed line. (B) Venn diagram of consensus ZZZ3 and SPT20 ChIP-seq binding from 2 independent experiments. (C) Genomic location of ZZZ3 (left) and SPT20 (right) ChIP-seq binding in K562 cells. Summary of consensus peaks from 2 independent ChIP-seq experiments is shown. (D) Representative ChIP-seq peak for ZZZ3 target in K562 cells (RPS7) and representative ChIP-seq peak for SPT20 target in K562 cells (HBB). (E) Publicly available ChIP-seq tracks for H3K9ac (ENCFF257CLC) and ZZZ3 (ENCFF856KCV) in K562 cells at the RPS7 and HBB loci retrieved from the ENCODE project portal (www.encodeproject.org). The RPS7 and HBB loci in panel D are represented confirming the presence of H3K9ac peaks and reproducing the selective ZZZ3 binding at RPS7 also observed in our data. (F) H3K9ac ChIP-qPCR analysis of representative SPT20 and ZZZ3 targets upon knockdown in K562 cells. N ≥ 3 independent experiments. Mean ± SEM of enrichment relative to rabbit IgG, with normalization to control intergenic region with no significant H3K9ac enrichment. Two-tailed Student t test for significance *P < .05. (G) qRT-PCR analysis of expression of ATAC and SAGA complex targets in K562 cells. N ≥ 3 independent experiments, mean ± SEM of gene expression relative to CTRLsh, normalized to HPRT1 housekeeping gene. Two-tailed Student t test for significance *P < .05, **P < .01, ***P < .001.

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