The Role of Topologically Associating Domains for Developmental Gene Regulation - ⁠ A Systematic Functional Analysis at the Sox9 and Shh Loci

Precise spatiotemporal gene expression during embryonic developmental is controlled by cis- regulatory elements (CREs) such as enhancers and promoters. Their physical chromatin proximity is correlated with active transcription and thought to be restricted to topologically associated domains (TADs) that help establish interactions between CREs and limit inappropriate contacts. Accordingly, TADs frequently overlap with gene regulatory landscapes, in which are contained diverse enhancers that transmit their activity across the domain towards their target promoter. Large structural variants reorganizing TADs were shown to cause gene misexpression and disease thereby linking gene regulation to chromatin structure. Recently, several studies revealed controversial results questioning the importance of TADs for transcriptional control. Acute depletion of CTCF and other architectural proteins in vitro led to loss of TAD structures with surprisingly modest effects on gene expression. However, the cytotoxicity of such depletion assays hindered analysis of more complex gene regulatory scenarios and their effect during development. This study specifically addresses the connection between TADs and developmental gene regulation through two projects using the murine limb as a model system. First, we took advantage of the Sox9/Kcnj2-locus that is subdivided into two adjacent TADs with distinct expression patterns of Sox9 and Kcnj2. The systematic deletion of individual CTCF binding sites at the TAD boundary and within the TAD resulted in gradual fusion of the neighboring domains without major effects on gene expression. TAD rearrangement by TAD-spanning inversions and repositioning of the boundary, however, redirected the regulatory activity and resulted in pathogenic gene misexpression. Thus, TAD structures may not be essential for developmental gene regulation, yet CTCF-dependent rearrangement of TADs can lead to the redirection of enhancer–promoter contacts and gene misexpression. In the second project, we studied how enhancer position relative to its TAD influences the function of an individual enhancer at the Shh-locus. Therefore, we repositioned the Shh-limb enhancer ZRS to five alternative locations inside and outside of its TAD. As expected, the enhancer lost all function in the positions outside of the Shh-TAD. Interestingly, the new positions inside the TAD also displayed decreased enhancer activity, albeit to varying degrees. Further analysis suggests that CTCF likely functions in some positions as a facilitator of enhancer-promoter contacts, while insulating short-range contacts in others. Ultimately, the ZRS is only able to ectopically activate some genes if repositioned to novel TADs, displaying strong enhancer-promoter selectivity. In summary, the results demonstrate that TADs provide robustness and precision to gene regulation, guiding enhancer-promoter interaction without being essential. The findings in this work build a basis for future studies aiming to understand enhancer-promoter interaction and can help in contextualizing potential disease-causing mutations disrupting TADs

Inhibitory effects on L- and N-type calcium channels by a novel Ca-V beta(1) variant identified in a patient with autism spectrum disorder

Voltage-gated calcium channel (VGCC) subunits have been genetically associated with autism spectrum disorders (ASD). The properties of the pore-forming VGCC subunit are modulated by auxiliary beta-subunits, which exist in four isoforms (Ca-V beta(1-4)). Our previous findings suggested that activation of L-type VGCCs is a common feature of Ca-V beta(2) subunit mutations found in ASD patients. In the current study, we functionally characterized a novel Ca-V beta(1b) variant (p.R296C) identified in an ASD patient. We used whole-cell and single-channel patch clamp to study the effect of Ca-V beta(1b_R296C) on the function of L- and N-type VGCCs. Furthermore, we used co-immunoprecipitation followed by Western blot to evaluate the interaction of the Ca-V beta(1b)-subunits with the RGK-protein Gem. Our data obtained at both, whole-cell and single-channel levels, show that compared to a wild-type Ca-V beta(1b), the Ca-V beta(1b_R296C) variant inhibits L- and N-type VGCCs. Interaction with and modulation by the RGK-protein Gem seems to be intact. Our findings indicate functional effects of the Ca-V beta(1b_R296C) variant differing from that attributed to Ca-V beta(2) variants found in ASD patients. Further studies have to detail the effects on different VGCC subtypes and on VGCC expression

Autism-associated mutations in the Ca-v beta(2) calcium-channel subunit increase Ba2+-currents and lead to differential modulation by the RGK-protein Gem

Voltage-gated calcium-channels (VGCCs) are heteromers consisting of several subunits. Mutations in the genes coding for VGCC subunits have been reported to be associated with autism spectrum disorder (ASD). In a previous study, we identified electrophysiologically relevant missense mutations of Ca-v beta(2) subunits of VGCCs. From this, we derived the hypothesis that several Ca-v beta(2)-mutations associated with ASD show common features sensitizing LTCCs and/or enhancing currents. Using a Ca-v beta(2d) backbone, we performed extensive whole-cell and single-channel patch-clamp analyses of Ba2+ currents carried by Ca(v)1.2 pore subunits co-transfected with the previously described Ca-v beta(2) mutations (G167S, S197F) as well as a recently identified point mutation (V2D). Furthermore, the interaction of the mutated Ca-v beta(2) subunits with the RGK protein Gem was analyzed by coimmunoprecipitation assays and electrophysiological studies. Patch-clamp analyses revealed that all mutations increase Ba2+ currents, e.g. by decreasing inactivation or increasing fraction of active sweeps. All Ca-v beta(2) mutations interact with Gem, but differ in the extent and characteristics of modulation by this RGK protein (e.g. decrease of fraction of active sweeps: Ca-v beta(2d_G167S) > Ca-v beta(2d_v2D) > Ca-v beta(2d_S197F). In conclusion, patch-clamp recordings of ASD-associated Ca-v beta(2d) mutations revealed differential modulation of Ba2+ currents carried by Ca(v)1.2 suggesting kind of an electrophysiological fingerprint each. The increase in current finally observed with all Ca-v beta(2d) mutations analyzed might contribute to the complex pathophysiology of ASD and by this indicate a possible underlying molecular mechanism

Jumping retroviruses nudge TADs apart

Far from being junk DNA, the pervasive retrotransposons that populate the genome have a powerful capacity to influence genes and chromatin. A new study demonstrates how the transcription of one such element, HERV-H, can modify the higher-order 3D structure of chromatin during early primate development

Single-cell, whole-embryo phenotyping of mammalian developmental disorders.

Mouse models are a critical tool for studying human diseases, particularly developmental disorders1. However, conventional approaches for phenotyping may fail to detect subtle defects throughout the developing mouse2. Here we set out to establish single-cell RNA sequencing of the whole embryo as a scalable platform for the systematic phenotyping of mouse genetic models. We applied combinatorial indexing-based single-cell RNA sequencing3 to profile 101 embryos of 22 mutant and 4 wild-type genotypes at embryonic day 13.5, altogether profiling more than 1.6 million nuclei. The 22 mutants represent a range of anticipated phenotypic severities, from established multisystem disorders to deletions of individual regulatory regions4,5. We developed and applied several analytical frameworks for detecting differences in composition and/or gene expression across 52 cell types or trajectories. Some mutants exhibit changes in dozens of trajectories whereas others exhibit changes in only a few cell types. We also identify differences between widely used wild-type strains, compare phenotyping of gain- versus loss-of-function mutants and characterize deletions of topological associating domain boundaries. Notably, some changes are shared among mutants, suggesting that developmental pleiotropy might be decomposable through further scaling of this approach. Overall, our findings show how single-cell profiling of whole embryos can enable the systematic molecular and cellular phenotypic characterization of mouse mutants with unprecedented breadth and resolution