BackgroundSWI/SNF is a large heterogeneous multi-subunit chromatin remodeling complex. It consists of multiple sets of mutually exclusive components. Understanding how loss of one sibling of a mutually exclusive pair affects the occupancy and function of the remaining complex is needed to understand how mutations in a particular subunit might affect tumor formation. Recently, we showed that the members of the ARID family of SWI/SNF subunits (ARID1A, ARID1B and ARID2) had complex transcriptional relationships including both antagonism and cooperativity. However, it remains unknown how loss of the catalytic subunit(s) affects the binding and genome-wide occupancy of the remainder complex and how changes in occupancy affect transcriptional output.ResultsWe addressed this gap by depleting BRG1 and BRM, the two ATPase subunits in SWI/SNF, and characterizing the changes to chromatin occupancy of the remaining subunit and related this to transcription changes induced by loss of the ATPase subunits. We show that depletion of one subunit frequently leads to loss of the remaining subunit. This could cause either positive or negative changes in gene expression. At a subset of sites, the sibling subunit is either retained or gained. Additionally, we show genome-wide that BRG1 and BRM have both cooperative and antagonistic interactions with respect to transcription. Importantly, at genes where BRG1 and BRM antagonize one another we observe a nearly complete rescue of gene expression changes in the combined BRG/BRM double knockdown.ConclusionThis series of experiments demonstrate that mutually exclusive SWI/SNF complexes have heterogeneous functional relationships and highlight the importance of considering the role of the remaining SWI/SNF complexes following loss or depletion of a single subunit.Electronic supplementary materialThe online version of this article (10.1186/s13072-017-0167-8) contains supplementary material, which is available to authorized users.

SCHLAP1 is a long-noncoding RNA that is reported to function by depleting the SWI/SNF complex from the genome. We investigated the hypothesis that SCHLAP1 affects only specific compositions of SWI/SNF. Using several assays we found that SWI/SNF is not depleted from the genome by SCHLAP1, and that SWI/SNF is associated with many coding and non-coding RNAs, suggesting SCHLAP1 may function in a SWI/SNF independent manner.

Background

SCHLAP1 is a longnoncoding RNA that is prognostic for progression to metastatic prostate cancer and promotes an invasive phenotype. SCHLAP1 is reported to function by depleting the core SWI/SNF subunit, SMARCB1, from the genome. SWI/SNF is a large, multisubunit, chromatin remodeling complex that can be combinatorially assembled to yield hundreds to thousands of distinct complexes.Here, we investigated the hypothesis that SCHLAP1 affects only specific forms of SWI/SNF and that the remaining SWI/SNF complexes were important for the increased invasion in SCHLAP1 expressing prostate cells. Using several assays we found that SWI/SNF is not depleted from the genome by SCHLAP1 expression. We find that SCHLAP1 induces changes to chromatin openness but is not sufficient to drive changes in histone modifications. Additionally, we show that SWI/SNF binds many coding and noncoding RNAs. Together these results suggest that SCHLAP1 has roles independent of canonical SWI/SNF and that SWI/SNF broadly interacts with RNA.

The Slam/SAP (SLAM-associated protein) signaling pathway plays a central role in the host immune response to infections. Males that inherit an inactivated SAP gene develop X-linked lymphoproliferative syndrome (XLP), a serious immunodeficiency that often results in enhanced susceptibility to a variety of pathogens. SAP is a cytosolic adapter protein that transduces signals from Slam family receptors, a family of nine (SLAMf1 to SLAMf9) cell surface receptors that are expressed only on hematopoietic cells. Although the Slam/SAP axis is known to regulate the development and function of several lymphocyte subsets, their role in γδ T cell biology is less well understood. We analyzed simultaneously the expression of multiple Slam receptors on γδ T cells and observed significant heterogeneity among γδ T cell subsets. Interestingly, Slam expression patterns marked functional γδ T cell subsets in both naïve and influenza-infected mice. SLAMf6 expression on lung γδ T cells correlated with IFNγ-producing CD27+ cells while SLAMf1 expression characterized IL-17-producing CD27− RORγt+ γδ T cells. The heterogeneous Slam receptor expression patterns of γδ T cell subsets can already be seen during embryonic thymic development, suggesting a possible role in the developmental programming of γδ T cell effector function. Disruption of Slam signaling through deletion of SAP affected the development of RORγt+ CD44hi Vγ4 T cells in the embryonic thymus, and the frequency of RORγt+ Vγ4 T cells in the periphery was still diminished in the adult. These results suggest that the Slam/SAP signaling pathway is an important regulator of the functional programming γδ T cells undergo during thymic development which affects mucosal immune responses later in life.