The Insulator Protein SU(HW) Fine-Tunes Nuclear Lamina Interactions of the Drosophila Genome

Abstract

Specific interactions of the genome with the nuclear lamina (NL) are thought to assist chromosome folding inside the nucleus and to contribute to the regulation of gene expression. High-resolution mapping has recently identified hundreds of large, sharply defined lamina-associated domains (LADs) in the human genome, and suggested that the insulator protein CTCF may help to demarcate these domains. Here, we report the detailed structure of LADs in Drosophila cells, and investigate the putative roles of five insulator proteins in LAD organization. We found that the Drosophila genome is also organized in discrete LADs, which are about five times smaller than human LADs but contain on average a similar number of genes. Systematic comparison to new and published insulator binding maps shows that only SU(HW) binds preferentially at LAD borders and at specific positions inside LADs, while GAF, CTCF, BEAF-32 and DWG are mostly absent from these regions. By knockdown and overexpression studies we demonstrate that SU(HW) weakens genome – NL interactions through a local antagonistic effect, but we did not obtain evidence that it is essential for border formation. Our results provide insights into the evolution of LAD organization and identify SU(HW) as a fine-tuner of genome – NL interactions.

tDNA insulators and the emerging role of TFIIIC in genome organization

“…Supporting evidence comes from recent demonstration that insulators underlie long-range Pc interactions and are important for the maintenance of H3K27me3 levels within Pc domains in Drosophila. 6,9,58 Meanwhile, insulator proteins are distributed across the genome at thousands of sites, 32,[59][60][61][62][63] and are significantly enriched at the borders of laminaassociated domains, 64,65 consistent with microscopy-based staining of perinuclear insulator bodies. Numerous studies have also characterized the ability of CTCF and Drosophila insulator proteins to mediate locus specific interactions, [45][46][47][48] and recent genome-wide profiling of CTCF interactions in mouse ES cells suggests CTCF facilitates coregulation of related genes by establishing chromatin loops enriched for active or repressive epigenetic signatures, and by bridging interactions between enhancers and promoters.…”

Lamin B1 depletion in senescent cells triggers large-scale changes in gene expression and the chromatin landscape

“…LADs are generally gene-poor relative to their genomic occupancy (Pickersgill et al 2006;Guelen et al 2008;Peric-Hupkes et al 2010;van Bemmel et al 2010), suggesting that K27me3 canyons, often outside of LADs, may be enriched for genes and their regulatory regions. Strikingly, we found both inactive enhancers (as defined by regions enriched for H3K4me1) and active enhancers (as defined by regions enriched for both H3K4me1 and H3K27ac) strongly overlapping with K27me3 canyons (Fig.…”

Drosophila danyis essential for transcriptional control and nuclear architecture in spermatocytes

“…In cell types other than spermatocytes, most spermatocyte-specific genes appear to be packaged into a repressive type of heterochromatin designated 'BLACK' heterochromatin, which is associated with Lam at the nuclear envelope (El-Sharnouby et al, 2013;Filion et al, 2010;Shevelyov et al, 2009;van Bemmel et al, 2013). In case of two representative testis-specific gene clusters (at 60D1 and 22A1), loss of Lam was shown to result in their derepression in somatic larval and cultured cells, and the normal transcriptional activation was accompanied by cluster repositioning into the nuclear interior of late spermatocytes (Shevelyov et al, 2009).…”

“…Indeed, some important chromatin regulators and nuclear envelope proteins have been shown to undergo drastic changes in expression levels during normal spermatogenesis. Su(Hw), a multi-zinc finger DNA-binding protein that can function as a transcriptional insulator and modulator of chromatin association with the nuclear lamina (Soshnev et al, 2013;van Bemmel et al, 2010), and the PRC2 complex components E(z) and Su(z) (Chen et al, 2011) are strongly downregulated in early spermatocytes, whereas Lamin C (LamC) expression is induced (Chen et al, 2013). However, in these particular cases, we did not detect an abnormal expression program in dany mutant testis by immunolabeling (data not shown).…”