The dual role of LSD1 and HDAC3 in STAT5-dependent transcription is determined by protein interactions, binding affinities, motifs and genomic positions

Abstract

STAT5 interacts with other factors to control transcription, and the mechanism of regulation is of interest as constitutive active STAT5 has been reported in malignancies. Here, LSD1 and HDAC3 were identified as novel STAT5a interacting partners in pro-B cells. Characterization of STAT5a, LSD1 and HDAC3 target genes by ChIP-seq and RNA-seq revealed gene subsets regulated by independent or combined action of the factors and LSD1/HDAC3 to play dual role in their activation or repression. Genes bound by STAT5a alone or in combination with weakly associated LSD1 or HDAC3 were enriched for the canonical STAT5a GAS motif, and such binding induced activation or repression. Strong STAT5 binding was seen more frequently in intergenic regions, which might function as distal enhancer elements. Groups of genes bound weaker by STAT5a and stronger by LSD1/HDAC3 showed an absence of the GAS motif, and were differentially regulated based on their genomic binding localization and binding affinities. These genes exhibited increased binding frequency in promoters, and in conjunction with the absence of GAS sites, the data indicate a requirement for stabilization by additional factors, which might recruit LSD1/HDAC3. Our study describes an interaction network of STAT5a/LSD1/HDAC3 and a dual function of LSD1/HDAC3 on STAT5-dependent transcription, defined by protein–protein interactions, genomic binding localization/affinity and motifs.

STAT5-Interacting Proteins: A Synopsis of Proteins that Regulate STAT5 Activity

“…Recently, LSD1 and HDAC3 have been shown to interact with STAT5A. Immunoprecipitation experiments were conducted using nuclear extracts from IL-3 stimulated pro-B Ba/F3 cells with BirA biotinylated STAT5A [63]. The specific binding regions were determined using 35S-LSD1 and 35S-HDAC3 pull-downs with GST-STAT5A sub-fragments.…”

“…LSD1 was shown to interact with the DNA-binding linker and the SH2 domain. HDAC3 was shown to interact with the DNA-binding linker, SH2 domain, and the coiled coil domain [63] (refer to Figure 3). ChIP-seq experiments have shown that STAT5A, LSD1, and HDAC3 have many overlapping binding regions within the genome [63].…”

“…HDAC3 was shown to interact with the DNA-binding linker, SH2 domain, and the coiled coil domain [63] (refer to Figure 3). ChIP-seq experiments have shown that STAT5A, LSD1, and HDAC3 have many overlapping binding regions within the genome [63]. RNA-seq performed in Ba/F3 cells with either STAT5A or LSD1 knocked down has revealed co-regulation among 3 genes; Il4ra, Gfi1b, and Cnr2 [63].…”

“…ChIP-seq experiments have shown that STAT5A, LSD1, and HDAC3 have many overlapping binding regions within the genome [63]. RNA-seq performed in Ba/F3 cells with either STAT5A or LSD1 knocked down has revealed co-regulation among 3 genes; Il4ra, Gfi1b, and Cnr2 [63]. Based on the ChIP-seq and RNA-seq data, it appears that LSD1 and HDAC3 function to activate or repress STAT5A transcriptional activity [63] (refer to Figure 4).…”

“…RNA-seq performed in Ba/F3 cells with either STAT5A or LSD1 knocked down has revealed co-regulation among 3 genes; Il4ra, Gfi1b, and Cnr2 [63]. Based on the ChIP-seq and RNA-seq data, it appears that LSD1 and HDAC3 function to activate or repress STAT5A transcriptional activity [63] (refer to Figure 4). However, the direct effect of this interaction on STAT5A transcriptional activity has not been elucidated.…”