Biology subjects

Schwartz, Y. B.

Publications and source records attributed to Schwartz, Y. B..

10 recordsLinked to original sources

bioRxiv2026

Hybrid Drosophila cell lines show selective genome instabilities

Background: Post-zygotic reproductive isolation is thought to be caused by genomic conflict. However, the exact nature of these detrimental incompatibilities is largely unknown. To identify genomic regions that became incompatible during the formation of species and are therefore prone to get lost in hybrids, we established hybrid cell lines derived from an authentic interspecies cross between Drosophila melanogaster and Drosophila simulans. Results: All four independently derived lines selectively lost the D. melanogaster allele of the hybrid incompatibility gene Hmr, confirming its incompatibility with cellular viability. Moreover, each line underwent distinct but directionally biased erosion of additional D. melanogaster chromosomal regions, preferentially affecting the X chromosome, chromosome 4, and chromosome 3R. Loss of the D. melanogaster X was dosage compensated by upregulation of genes on the hemizygous D. simulans X, while D. melanogaster rDNA was paradoxically amplified across all lines. Nucleolar dominance was driven by relative rDNA copy number rather than species identity, overturning the prevailing view of fixed species-based dominance. Finally, the measurements of the species-specific proteome revealed species specific differences in the RNA to protein coefficient K_p as novel and yet undescribed sources of molecular conflict in hybrids. Conclusions: These findings reveal a hierarchical, constraint-driven mechanism of hybrid genome resolution.

evolutionary biology↗

bioRxiv2025

Polycomb repression works without Siesta

Polycomb group proteins mediate epigenetic repression via multi-subunit complexes, including canonical Polycomb Repressive Complex 1 (PRC1), which monoubiquitylates histone H2A and binds histone H3 tri-methylated at lysine 27 (H3K27me3). The RING1 subunit of PRC1, critical for H2A ubiquitylation, forms other complexes. These variant RING1 complexes also ubiquitylate H2A but cannot bind H3K27me3, and their evolutionary origins and functions are debated. Using Drosophila genetics, we discovered that canonical PRC1 and variant RING1 complexes ubiquitylate H2A at distinct genomic regions. We established that the sole Drosophila PCGF protein specific for variant RING1 complexes, which we named Siesta, is not required for epigenetic repression of developmental genes, but controls larval locomotion independently of H2A ubiquitylation. Leveraging a massively parallel transgenic approach, we demonstrated that H2A ubiquitylation has minimal impact on transcriptional repression. Our findings imply that variant RING1 complexes operate outside the Polycomb regulatory system and that the popular PRC1 nomenclature needs revision.

genetics↗

bioRxiv2023

Forecasting histone methylation by Polycomb complexes with minute-scale precision

All animals use the Polycomb system to epigenetically repress developmental genes. The repression requires tri-methylation of Lysine 27 of histone H3 (H3K27me3) by Polycomb Repressive Complex 2 (PRC2), but the dynamics of this process is poorly understood. To bridge the gap, we developed a computational model that forecasts H3K27 methylation in Drosophila with high temporal resolution and spatial accuracy of contemporary experimental techniques. Using this model, we show that pools of methylated H3K27 in dividing cells are defined by the effective concentration of PRC2 and the replication frequency. We find that the allosteric stimulation by pre-existing H3K27me3 makes PRC2 better in methylating developmental genes as opposed to indiscriminate methylation throughout the genome. Applied to Drosophila development, our model argues that, in this organism, the intergenerationally inherited H3K27me3 does not "survive" rapid cycles of embryonic chromatin replication and is unlikely to transmit the memory of epigenetic repression to the offspring. We foresee that our model is adaptable to other organisms, including mice and humans.

developmental biology↗

bioRxiv2023

DNA elements tether canonical Polycomb Repressive Complex 1 to human genes

Development of multicellular animals requires epigenetic repression by Polycomb group proteins. The latter assemble in multi-subunit complexes, of which two kinds, Polycomb Repressive Complex 1 (PRC1) and Polycomb Repressive Complex 2 (PRC2), act together to effect the repression of key developmental genes. How PRC1 and PRC2 recognize specific genes remains an open question. Here we report systematic identification of DNA elements that tether canonical PRC1 to human developmental genes. Their analysis indicates that sequence features associated with PRC1 tethering differ from those that favour PRC2 binding. Throughout the genome, the two kinds of sequence features mix in different proportions to yield a gamut of DNA elements that range from those tethering predominantly PRC1 to ones capable of tethering both PRC1 and PRC2. The emerging picture is similar to paradigmatic targeting of Polycomb complexes by Polycomb Response Elements (PREs) of Drosophila but providing for greater plasticity.

developmental biology↗

bioRxiv2022

Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements

Drosophila insulators were the first DNA elements discovered to regulate gene expression by delimiting chromatin contacts. Remarkably, it is still unclear how many of them exist in the Drosophila genome and whether they have a pervasive impact on the genome folding. Contrary to vertebrates, there is no evidence that fly insulators block cohesin-mediated chromatin loop extrusion. Therefore, their mechanism of action remains an open question. To bridge these gaps, we mapped genomic contacts, transcriptomes and binding landscapes of insulator associated proteins in Drosophila cells deficient for CTCF and Cp190. With this approach, we discovered hundreds of chromatin insulator elements. Their study indicates that Drosophila insulators play a minor role in shaping the overall chromosome folding patterns but impact chromatin contacts locally at many individual loci. Our observations argue that Cp190 promotes co-binding of other insulator proteins and that the model, where Drosophila insulators block chromatin contacts by forming loops, needs revision. The extended catalogue of insulator elements presented here provides a significant new resource to study mechanisms that shape the folding of eukaryotic genomes.

genomics↗

bioRxiv2022

Variant Polycomb complexes in Drosophila consistent with ancient functional diversity

Polycomb group (PcG) mutants were first identified in Drosophila based on their failure to maintain proper Hox gene repression during development. The proteins encoded by the corresponding fly genes mainly assemble into one of two discrete Polycomb Repressive Complexes: PRC1 or PRC2. However, biochemical analyses in mammals have revealed alternative forms of PRC2, and multiple distinct types of non-canonical or variant PRC1. Through a series of proteomic analyses, we identify analogous PRC2 and variant PRC1 complexes in Drosophila, as well as a broader repertoire of interactions implicated in early development. Our data provide strong support for the ancient diversity of PcG complexes, and a framework for future analysis in a longstanding and versatile genetic system.

developmental biology↗

bioRxiv2021

The role of H3K36 methylation and associated methyltransferases in chromosome-specific gene regulation

In Drosophila, two chromosomes require special mechanisms to balance their transcriptional output to the rest of the genome. These are the male-specific lethal complex targeting the male X-chromosome, and Painting of fourth targeting chromosome 4. The two systems are evolutionarily linked to dosage compensation of the X-chromosome and the chromosomes involved display specific chromatin structures. Here we explore the role of histone H3 tri-methylated at lysine 36 (H3K36me3) and the associated methyltransferases in these two chromosome-specific systems. We show that the loss of Set2 impairs the MSL complex mediated dosage compensation; however, the effect is not recapitulated by H3K36 replacement and indicates an alternative target of Set2. Unexpectedly, balanced transcriptional output from the 4th chromosome requires intact H3K36 and depends on the additive functions of NSD and the Trithorax group protein Ash1. We conclude that H3K36 methylation and the associated methyltransferases are important factors to balance transcriptional output of the male X-chromosome and the 4th chromosome. Furthermore, our study highlights the pleiotropic effects of these enzymes.

genetics↗

bioRxiv2019

Genetic dissection reveals the role of Ash1 domains in counteracting Polycomb repression

Antagonistic functions of Polycomb and Trithorax proteins are essential for proper development of all metazoans. While the Polycomb proteins maintain the repressed state of key developmental genes, the Trithorax proteins ensure that these genes stay active in cells where they have to be expressed. Ash1 is the Trithorax protein that was proposed to counteract Polycomb repression by methylating lysine 36 of histone H3. However, recently it was shown that genetic replacement of Drosophila histone H3 with the variant that carried Arginine instead of Lysine at position 36 did not impair the ability of Ash1 to counteract Polycomb repression. This argues that Ash1 counteracts Polycomb repression by methylating, yet unknown, non-histone proteins. To find these substrates, one may need to look beyond the function of the Ash1 histone methyltransferase SET domain at other evolutionary conserved parts of the protein that received little attention. Here we used Drosophila genetics to demonstrate that Ash1 requires each of the BAH, PHD and SET domains to counteract Polycomb repression, while AT hooks are dispensable. Our findings argue that, in vivo, Ash1 acts as a multimer. Thereby, it can combine the input of the SET domain and PHD-BAH cassette residing in different peptides. Finally, using new loss of function alleles, we show that zygotic Ash1 is required to prevent erroneous repression of homeotic genes.

genetics↗

bioRxiv2019

Pervasive head-to-tail insertions of DNA templates mask desired CRISPR/Cas9-mediated genome editing events

CRISPR/Cas9 mediated homology-directed DNA repair is the method of choice for precise gene editing in a wide range of model organisms, including mouse and human. Broad use by the biomedical community refined the method, making it more efficient and sequence specific. Nevertheless, the rapidly evolving technique still contains pitfalls. During the generation of six different conditional knock-out mouse models, we discovered that frequently (sometimes solely) homology-directed repair and/or non-homologous end-joining mechanisms caused multiple unwanted head-to-tail insertions of donor DNA templates. Disturbingly, conventionally applied PCR analysis--in most cases--failed to identify such multiple integration events, which led to a high rate of falsely claimed precisely edited alleles. We caution that comprehensive analysis of modified alleles is essential, and offer practical solutions to correctly identify precisely edited chromosomes.

genetics↗

bioRxiv2017

PTE, a novel module of mammalian Polycomb Response Elements

Polycomb Group proteins are essential epigenetic repressors. They form multiple protein complexes of which two kinds, PRC1 and PRC2, are indispensable for repression. Although much is known about their biochemical properties, how PRC1 and PRC2 are targeted to specific genes is poorly understood. Here we establish the Cyclin D2 (CCND2) oncogene as a simple model to address this question. We provide the evidence that coordinated recruitment of PRC1 and PRC2 complexes to CCND2 involves a combination of a specialized PRC1 targeting element (PTE) and an adjacent CpG-island, which together act as a human Polycomb Response Element. Chromatin immunoprecipitation analysis of CCND2 in different transcriptional states indicates that histone modifications produced by PRC1 and PRC2 are not sufficient to recruit either of the complexes. However, catalytic activity of PRC2 helps to anchor PRC1 at the PTE. Our analyses suggest that coordinated targeting of PRC1 and PRC2 complexes by juxtaposed AT-rich PTEs and CpG-islands may be a general feature of Polycomb repression in mammals.

molecular biology↗