Mouse Gene 2.0ST arrays (Affymetrix) were hybridized per the manufacturer’s protocols. In microarrays, ERCC RNA Spike-In Mix (Ambion) was added to TRIzol-homogenized samples in proportion to cell number. Reverse transcriptase (RT)–qPCR was performed with iScript (Bio-Rad) and Power SYBR Green (Invitrogen). Quantitative polymerase chain reaction (qPCR) was run on ViiA7 System (Life Technologies) using Power SYBR Green (Invitrogen). We characterized the relationship of BETs with GATA1 on a genome-wide scale and demonstrate that BETs facilitate GATA1-mediated transcriptional activation but are largely dispensable for repression.
Based on the results in the previous section, we tested whether BETs act in GATA1-activated transcription subsequent to the establishment of chromatin occupancy. The red line shows a Loess regression; the blue diagonal demarcates no change between control and JQ1 treatment. These results suggest that BETs are required for maximal GATA1 occupancy at numerous sites, but that the role of BETs in GATA1-mediated transcription is likely to extend beyond assisting GATA1 in chromatin binding. Sites at which GATA1 occupancy was JQ1-sensitive were more likely to be co-occupied by TAL1 (supplemental Table 1), consistent with TAL1 functioning predominantly at GATA1-activated genes.
Analysis of the expression patterns, subcellular localisations and interaction partners of Drosophila proteins using a pigP protein trap library. Yvonne Jones, Ilan Davis, Kay Grunewald & Rainer Kaufmann (2015) Correlative in-resin super-resolution and electron microscopy using standard fluorescent proteins.
(B) Confocal image of EGFP–RAB26-transfected (green) HGC-27 cells stained for LAMP1 (red). (A) Immunofluorescence of HGC-27 cells transfected with EGFP–RAB26 (green) and co-immunostained with LAMP1 (red). Interestingly, the JQ1 sensitivity of GATA1 occupancy is not predicted by the amounts of BRD2, BRD3, or BRD4 at GATA1 OS (supplemental Figure 8A). (C) Live confocal timelapse microscopy of EGFP–RAB26 (green), LysoTracker-labeled lysosomes (red) and MitoTracker-labeled mitochondria (purple) vesicle dynamics. (F–H) Panels of immunoelectron microscopy of EGFP–RAB26-transfected HGC-27 cells labeled with LAMP1 (18-nm gold particles, white arrowheads) and RAB26 (12-nm gold particles, yellow arrowheads) with mitochondria (‘M’) and lysosomes (‘L’) highlighted.
Together, these studies reveal that BETs have overlapping roles, and function at distinct steps of the transcription program controlled by GATA1, which are important considerations when interpreting the functions of chemical BET inhibitors. Unexpectedly, despite the presence of BRD3 at the great majority of GATA1-occupied sites, BRD3 is not required for normal GATA1-activated transcription.
To dissect the roles of individual BETs in GATA1-driven erythropoiesis, we used a loss-of-function approach combining CRISPR-Cas9-engineered gene disruption 61 Current knowledge of BET function is largely built on studies using inhibitors that do not distinguish between individual BETs. *P < .05="" comparing="" jq1="" treated="" and="" control="" samples="" (2-sample="" t="" test).="" (b)="" primary="" transcript="" rt-qpcr="" of="" indicated="" transcripts="" following="" jq1="" treatment="" in="" gata1-induced="">
To this end, we used shRNAs to deplete BRD3 in BRD2-replete and BRD2-deficient cells (Figure 6A, supplemental Figure 10A). These results suggest BRD2 and BRD4 are individually required for normal GATA1-mediated transcriptional activation. As BRD3 occupies nearly all GATA1 OSs, we had speculated that it was the most relevant BET in GATA1-mediated transcription. In contrast, transcription of other genes like Hba-a1 (α-globin) and Uros (involved in heme synthesis) were unperturbed by short-term JQ1 treatment despite their sensitivity to long-term JQ1 exposure and proximity to BET-bound regulatory elements. Indeed, JQ1 treatment of 1 hour removed BETs from all sites examined with relatively little effect on GATA1 occupancy (Figure 4A, supplemental Figure 9A).
Moreover, forced expression of BRD3 partially restores defects associated with BRD2 loss, suggesting redundant functions among these 2 BETs. We further found that BETs are required not only for initial GATA1 chromatin occupancy, but also for subsequent transcription activation. Exposure of erythroid cells to BET inhibitors diminishes GATA1 occupancy at a subset of target genes and prevents their activation. JQ1 does not distinguish between BET family members, and the development of additional BET inhibitors with distinct specificities remains an important goal.
Here the authors show that MMP12 expression is reduced in patients with SLE and that MMP12 post-translationally truncates IFN-y, inhibiting its function and affecting pathogenesis of mouse models of peritonitis, SLE and rheumatoid arthritis. RIPK3-mediated phosphorylation of the mixed lineage kinase domain-like (MLKL) pseudokinase is thought to be the trigger for MLKL activation during necroptotic signaling.