RNA FISH to Study Zygotic Genome Activation in Early Mouse Embryos

Escape from X inactivation is directly modulated by levels of Xist non-coding RNA

In placental females, one copy of the two X chromosomes is largely silenced during a narrow developmental time window, in a process mediated by the non-coding RNA Xist1. Here, we demonstrate that Xist can initiate X-chromosome inactivation (XCI) well beyond early embryogenesis. By modifying its endogenous level, we show that Xist has the capacity to actively silence genes that escape XCI both in neuronal progenitor cells (NPCs) and in vivo, in mouse embryos. We also show that Xist plays a direct role in eliminating TAD-like structures associated with clusters of escapee genes on the inactive X chromosome, and that this is dependent on Xist's XCI initiation partner, SPEN2. We further demonstrate that Xist's function in suppressing gene expression of escapees and topological domain formation is reversible for up to seven days post-induction, but that sustained Xist up-regulation leads to progressively irreversible silencing and CpG island DNA methylation of facultative escapees. Thus, the distinctive transcriptional and regulatory topologies of the silenced X chromosome is actively, directly - and reversibly - controlled by Xist RNA throughout life.

Mapping of Chromosome Territories by 3D-Chromosome Painting During Early Mouse Development

Following fertilization in mammals, the chromatin landscape inherited from the two parental genomes and the nuclear organization are extensively reprogrammed. A tight regulation of nuclear organization is important for developmental success. One main nuclear feature is the organization of the chromosomes in discrete and individual nuclear spaces known as chromosome territories (CTs). In culture cells, their arrangements can be constrained depending on their genomic content (e.g., gene density or repeats) or by specific nuclear constrains such as the periphery or the nucleolus. However, during the early steps of mouse embryonic development, much less is known, specifically regarding how and when the two parental genomes intermingle. Here, we describe a three-dimensional fluorescence in situ hybridization (3D-FISH) for chromosome painting (3D-ChromoPaint) optimized to gain understanding in nuclear organization of specific CTs following fertilization. Our approach preserves the nuclear structure, and the acquired images allow full spatial analysis of interphase chromosome positioning and morphology across the cell cycle and during early development. This method will be useful in understanding the dynamics of chromosome repositioning during development as well as the alteration of chromosome territories upon changes in transcriptional status during key developmental steps. This protocol can be adapted to any other species or organoids in culture.

Imaging nascent transcription in wholemount vertebrate embryos to characterize zygotic genome activation

A major event in early embryo development is the awakening of the embryonic genome, a process of large-scale transcriptional induction termed zygotic genome activation (ZGA). To understand how ZGA is controlled temporally and spatially, tools are required to image and quantify nascent transcription in wholemount embryos. In this chapter, we describe a metabolic labeling approach that leverages 5-ethynyl uridine (5-EU) incorporation into newly transcribed RNAs. Subsequently, click chemistry is used to conjugate these nascent transcripts to fluorophores for wholemount confocal imaging or biotin for RNA sequencing. Such an approach facilitates direct visualization of the global transcriptional state of each cell during early embryogenesis and provides a spatial map of gene expression activity. We describe this procedure for imaging nascent transcription in a vertebrate embryo Xenopus laevis, and use it as our model the onset of large-scale ZGA. Unlike cell culture systems in which 5-EU can be added to the media, metabolic labeling in Xenopus embryos requires microinjection in one-cell or two-cell stage embryos. This method is a powerful tool to quantify the nascent transcriptome at a single-cell level and to dissect mechanisms that control ZGA. We propose that this methodology can be applied broadly in other embryonic systems, and demonstrate the feasibility using zebrafish cleavage stage embryos. Finally, we demonstrate how to sequence the nascent transcriptome via 5-EU incorporation and separation of zygotic vs maternal RNAs. Altogether, our generalizable methodology will facilitate new insights into gene regulation and spatial patterning of ZGA during early embryogenesis.

A Conserved Noncoding Locus Regulates Random Monoallelic Xist Expression across a Topological Boundary

cis-Regulatory communication is crucial in mammalian development and is thought to be restricted by the spatial partitioning of the genome in topologically associating domains (TADs). Here, we discovered that the Xist locus is regulated by sequences in the neighboring TAD. In particular, the promoter of the noncoding RNA Linx (LinxP) acts as a long-range silencer and influences the choice of X chromosome to be inactivated. This is independent of Linx transcription and independent of any effect on Tsix, the antisense regulator of Xist that shares the same TAD as Linx. Unlike Tsix, LinxP is well conserved across mammals, suggesting an ancestral mechanism for random monoallelic Xist regulation. When introduced in the same TAD as Xist, LinxP switches from a silencer to an enhancer. Our study uncovers an unsuspected regulatory axis for X chromosome inactivation and a class of cis-regulatory effects that may exploit TAD partitioning to modulate developmental decisions.