The histone demethylase dKDM5/LID interacts with the SIN3 histone deacetylase complex and shares functional similarities with SIN3

Abstract

BackgroundRegulation of gene expression by histone-modifying enzymes is essential to control cell fate decisions and developmental processes. Two histone-modifying enzymes, RPD3, a deacetylase, and dKDM5/LID, a demethylase, are present in a single complex, coordinated through the SIN3 scaffold protein. While the SIN3 complex has been demonstrated to have functional histone deacetylase activity, the role of the demethylase dKDM5/LID as part of the complex has not been investigated.ResultsHere, we analyzed the developmental and transcriptional activities of dKDM5/LID in relation to SIN3. Knockdown of either Sin3A or lid resulted in decreased cell proliferation in S2 cells and wing imaginal discs. Conditional knockdown of either Sin3A or lid resulted in flies that displayed wing developmental defects. Interestingly, overexpression of dKDM5/LID rescued the wing developmental defect due to reduced levels of SIN3 in female flies, indicating a major role for dKDM5/LID in cooperation with SIN3 during development. Together, these observed phenotypes strongly suggest that dKDM5/LID as part of the SIN3 complex can impact previously uncharacterized transcriptional networks. Transcriptome analysis revealed that SIN3 and dKDM5/LID regulate many common genes. While several genes implicated in cell cycle and wing developmental pathways were affected upon altering the level of these chromatin factors, a significant affect was also observed on genes required to mount an effective stress response. Further, under conditions of induced oxidative stress, reduction of SIN3 and/or dKDM5/LID altered the expression of a greater number of genes involved in cell cycle-related processes relative to normal conditions. This highlights an important role for SIN3 and dKDM5/LID proteins to maintain proper progression through the cell cycle in environments of cellular stress. Further, we find that target genes are bound by both SIN3 and dKDM5/LID, however, histone acetylation, not methylation, plays a predominant role in gene regulation by the SIN3 complex.ConclusionsWe have provided genetic evidence to demonstrate functional cooperation between the histone demethylase dKDM5/LID and SIN3. Biochemical and transcriptome data further support functional links between these proteins. Together, the data provide a solid framework for analyzing the gene regulatory pathways through which SIN3 and dKDM5/LID control diverse biological processes in the organism.Electronic supplementary materialThe online version of this article (doi:10.1186/s13072-016-0053-9) contains supplementary material, which is available to authorized users.

Sin3a regulates epithelial progenitor cell fate during lung development

“…Furthermore, our data suggest that Sin3a LOF cannot be functionally compensated for by presence of the related Sin3 family member Sin3b. These findings are consistent with previous publications suggesting that Sin3a also serves as scaffold protein for other histone modification complexes such as those involved in histone demethylation (Gajan et al, 2016) and that Sin3b has functions that only partially overlap with those of Sin3a, but are not redundant (Das et al, 2013;McDonel et al, 2012;van Oevelen et al, 2010).…”

“…This core complex also transiently associates with other regulatory proteins including Rb1 and chromatin regulatory enzymes to control gene expression (Kadamb et al, 2013;Silverstein and Ekwall, 2005). In addition to the transcriptional repression activity of the Sin3-Hdac complex, growing evidence suggests that Sin3 might also function to activate transcription of certain target genes in different organisms, including yeast and Drosophila, as well as mammalian systems such as mouse muscle development, mouse embryonic fibroblast and mouse embryonic stem cells (Baltus et al, 2009;Dannenberg et al, 2005;Das et al, 2013;Lin et al, 2005;Ruiz-Roig et al, 2010;van Oevelen et al, 2010;Yoshimoto et al, 1992), which would be consistent with the observation that Sin3 could also serve as a scaffold protein for the histone demethylase dKDM5/LID (Gajan et al, 2016). Thus, these studies suggest that Sin3 modulates transcriptional activity by serving as a scaffold protein able to coordinate multiple histone modification activities, including deacetylation and demethylation in a context-dependent manner.…”

Inter-isoform-dependent Regulation of the Drosophila Master Transcriptional Regulator SIN3

“…Protein concentrations were determined using the Bio-Rad DC protein assay reagent in accordance with the manufacturer's protocol. Western blotting analysis was performed according to standard protocols (14) and as described previously (15). Primary antibodies used were as follows: HA-HRP (1:6000; Sigma), pan-SIN3 (1:2000 (16)), RPD3 (1:3000 (16)), and SIN3 220 (1:2000 (11)).…”

The Lid/KDM5 histone demethylase complex activates a critical effector of the oocyte-to-zygote transition

“…The conserved Sin3A protein scaffold interacts with the histone lysine deacetylase HDAC1 to form the core SIN3 histone deacetylase complex, which is generally considered as a transcriptional repressor [14]. The SIN3 complex regulates the expression of genes involved in a number of metabolic and developmental processes [15][16][17][18]. Interestingly, Lid and the largest Sin3A isoform were previously shown to physically and functionally interact [15,16,19,20], thus opening the possibility that these histone modifiers could control the same pathway leading to the formation of a diploid zygote.…”