Biology subjects

Schaub, C.

Publications and source records attributed to Schaub, C..

6 recordsLinked to original sources

bioRxiv2025

Heterotypic directional motifs contribute to TAD boundary function in Drosophila

While convergent CTCF binding sites are essential for topologically associating domain (TAD) formation in mammals, how TADs are formed in other species remains unclear. In Drosophila, TAD boundaries lack convergent CTCF sites and are occupied by different insulator protein combinations with no obvious pairing rules. To identify sequence features required for boundary pairing, we inserted different endogenous boundaries into two Drosophila TADs in both orientations, creating 53 ectopic insertions and measured their ability to form interactions with the endogenous boundaries to their left and right. 70% of inserted boundaries had context- and/or orientation-dependent effects, indicating specificity and directionality encoded in their sequence. Known insulator motifs or promoters could not explain boundary specificity. Instead, we identified heterotypic pairs of directional motifs that predict compatible boundary pairs. Our results indicate that directional motif pairs are a conserved property of boundaries from flies to mammals, but gained complexity in Drosophila through heterotypic combinations.

genomics↗

bioRxiv2022

New enhancer-promoter interactions are gained during tissue differentiation and reflect changes in E/P activity

To regulate gene expression, enhancers must come into proximity with their target gene. At some loci the timing of enhancer-promoter proximity is uncoupled from gene activation, while at others it is tightly linked. Here, we assessed this more globally for 600 characterized enhancers or promoters (E/P) with tissue-specific activity in Drosophila embryos, by performing Capture-C and insulator ChIP in FACS-purified myogenic or neurogenic cells at different stages of embryogenesis. This high-resolution view enabled direct comparison between E/P interactions and activity across 5 developmental conditions. This revealed largely invariant E/P contacts between the blastoderm and cell fate specification stages, despite changes in activity. However, E/P interactions diverge during terminal tissue differentiation when many tissue-specific interactions are gained on top of a pre-existing topology. Changes in E/P proximity reflect changes in enhancer activity and gene activation, and are generally not accompanied by changes in insulator binding. Using transgenes and deletions, we show that many tissue-specific interactions represent functional E-P pairs. Our results reveal a shift in E-P landscapes as embryogenesis proceeds, from largely pre-formed topologies at early stages to more distal tissue-specific loops during differentiation, when E/P proximity appears coupled to activation.

developmental biology↗

bioRxiv2020

Twist regulates Yorkie to guide lineage reprogramming of syncytial alary muscles

The genesis of syncytial muscles is typically considered as a paradigm for an irreversible developmental process. Notably, transdifferentiation of syncytial muscles is naturally occurring during Drosophila development. The ventral longitudinal heart-associated musculature (VLM) arises by a unique mechanism that revokes the differentiated fate from the so-called alary muscles and comprises at least two distinct steps: syncytial muscle cell fragmentation into single myoblasts and direct reprogramming into founder cells of the VLM lineage. Here we provide evidence that the mesodermal master regulator twist plays a key role during this reprogramming process. Acting downstream of Drosophila Tbx1 (Org-1) in the alary muscle lineage, Twist is crucially required for the derepression of the Hippo pathway effector Yki and thus for the initiation of syncytial muscle dedifferentiation and fragmentation. Subsequently, cell-autonomous FGFR-Ras-MAPK signaling in the resulting mono-nucleated myoblasts is maintaining Twist expression, thereby stabilizing nuclear Yki activity and inducing their lineage switch into the founder cells of the VLM.

developmental biology↗

bioRxiv2020

The Hox transcription factor Ubx ensures somatic myogenesis by suppressing the mesodermal master regulator Twist

Early determination factors and lineage-specific master regulators are essential for the specification of cell and tissue types. However, once a cell has committed to a specific fate, it is equally critical to restrict the activity of such factors to enable proper differentiation. In many studies the functional network for master regulators are under constant investigations. Yet, how these factors are silenced remains unclear. Using the Drosophila mesoderm as a model and a comparative genomic approach, we identified the Hox transcription factor (TF) Ultrabithorax (Ubx) to be critical for the repression of the mesodermal master regulator Twist (Twi). Mesoderm-specific Ubx loss-of-function experiments using CRISPR/Cas9 as well as overexpression experiments demonstrated that Ubx majorly impacts twi transcription. A detailed mechanistic analysis revealed that Ubx requires the function of the NK-homeodomain protein Tinman (Tin) but not the muscle differentiation factor Myocyte enhancer factor 2 (Mef2) to bind to the twi promoter. Furthermore, we found these TF interactions to be critical for silencing of the twi promoter region by recruiting the Polycomb DNA binding protein Pleiohomeotic (Pho). In sum, our study demonstrates that the Hox TF Ubx is a critical player in mediating the silencing of the mesodermal master regulator Twi, which is crucial for coordinated muscle differentiation.

developmental biology↗

bioRxiv2019

Yorkie and JNK revert syncytial muscles into myoblasts during Org-1 dependent lineage reprogramming

Lineage reprogramming has become a prominent focus in research since it was demonstrated that lineage restricted transcription factors can be used in vitro for direct reprogramming [1]. Recently, we reported that the ventral longitudinal musculature (VLM) of the adult Drosophila heart arises in vivo by direct lineage reprogramming from alary muscles (AM), a process which starts with dedifferentiation and fragmentation of syncytial alary muscles into mononucleate myoblasts. Central upstream activators of the genetic program regulating the development of VLMs from alary muscles are the T-box factor Org-1 (Drosophila Tbx1) and the LIM homeodomain factor Tup (Drosophila Islet1) [2]. However, the events downstream of Org-1 and Tup that exert dedifferentiation and fragmentation of alary muscles have been unknown. In the present report, we shed light on the initiation of this first step of transdifferentiation and show that AM lineage specific activation of Yorkie (Yki), the transcriptional co-activator of the transcription factor Scalloped (Sd), has a key role in initiating AM lineage reprogramming. An additional necessary input comes from active dJNK signaling, which contributes to the inactivation of the Hippo kinase cascade upstream of Yki and furthermore activates dJun. The synergistic activities of the Yki/Sd and dJun/dFos (AP-1) transcriptional activator complexes in the absence of Hippo activity initiate AM dedifferentiation and lead to the expression of Myc and piwi, which are crucial for different aspects of AM transdifferentiation. Our results provide new insights into the mechanisms that mediate muscle lineage plasticity during a cellular reprogramming process occurring in vivo.\n\nHighlightsO_LIDirect lineage reprogramming of alary muscles depends on Yorkie and JNK\nC_LIO_LIYorkie and JNK mediate reversal of syncytial muscle cell fate\nC_LIO_LIYki/Sd and AP-1 induce alary muscle dedifferentiation synergistically\nC_LIO_LIYki dependent Myc induces and Piwi mediates reprogramming of alary muscles\nC_LI

developmental biology↗

bioRxiv2018

A large-scale systemic RNAi screen in the red flour beetle Tribolium castaneum identifies novel genes involved in arthropod muscle development

Although muscle development has been widely studied in Drosophila melanogaster there are still many gaps in our knowledge, and it is not known to which extent this knowledge can be transferred to other insects. To help in closing these gaps we participated in a large-scale RNAi screen that used the red flour beetle, Tribolium castaneum, as a screening platform. The effects of systemic RNAi were screened upon double-stranded RNA injections into appropriate muscle-EGFP tester strains. Injections into pupae were followed by the analysis of the late embryonic/early larval muscle patterns, and injections into larvae by the analysis of the adult thoracic muscle patterns. Herein we describe the results of the first-pass screens with pupal and larval injections, which covered ~8,500 and ~5,000 genes, respectively, of a total of ~16,500 genes of the Tribolium genome. Apart from many genes known from Drosophila as regulators of muscle development, a collection of genes previously unconnected to muscle development yielded phenotypes in larval body wall and leg muscles as well as in indirect flight muscles. We then present the main candidates from the pupal injection screen that remained after being processed through a series of verification and selection steps. Further, we discuss why distinct though overlapping sets of genes are revealed by the Drosophila and Tribolium screening approaches.

developmental biology↗