Rnf12—A Jack of All Trades in X Inactivation?

International audiencePlacental mammals compensate the dosage imbalance of X-linked genes between males (XY) and females (XX) by silencing one randomly chosen X chromosome in females. This process is initiated during early embryonic development and can be recapitulated during differentiation of murine embryonic stem cells (mESCs). X chromosome inactivation (XCI) is initiated by up-regulation of a non-coding RNA on the future inactive X chromosome, named Xist, which lies within a large complex locus, called the X inactivation center (Xic). Subsequently, Xist RNA induces silencing of the entire chromosome in cis. Although central to the XCI process, the molecular mechanisms underlying Xist's regulation still remain to be deciphered. In particular, it is unclear (1) how the up-regulation of Xist is triggered at the onset of differentiation, (2) why this is restricted to female cells, and (3) why one allele and not the other is affected? Although each aspect could in principle be controlled by distinct factors and sequence elements, one protein has recently been proposed to regulate Xist at all three levels: the E3 ubiquitin ligase Rnf12/Rlim. The X-linked Rnf12 gene acts as a dose-dependent activator of Xist, which is expressed at elevated levels in female relative to male cells and is up-regulated during differentiation. Two recent studies shed further light on the precise role of Rnf12 in XCI

The bipartite TAD organization of the X-inactivation center ensures opposing developmental regulation of Tsix and Xist

The mouse X-inactivation center (Xic) locus represents a powerful model for understanding the links between genome architecture and gene regulation, with the non-coding genes Xist and Tsix showing opposite developmental expression patterns while being organized as an overlapping sense/antisense unit. The Xic is organized into two topologically associating domains (TADs) but the role of this architecture in orchestrating cis-regulatory information remains elusive. To explore this, we generated genomic inversions that swap the Xist/Tsix transcriptional unit and place their promoters in each other’s TAD. We found that this led to a switch in their expression dynamics: Xist became precociously and ectopically upregulated, both in male and female pluripotent cells, while Tsix expression aberrantly persisted during differentiation. The topological partitioning of the Xic is thus critical to ensure proper developmental timing of X inactivation. Our study illustrates how the genomic architecture of cis-regulatory landscapes can affect the regulation of mammalian developmental processes

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.Galupa et al. uncover elements important for Xist regulation in its neighboring TAD and reveal that these elements can influence gene regulation both within and between topological domains. These findings, in a context where dynamic, developmental expression is necessary, challenge current models for TAD-based gene-regulatory landscapes

The bipartite TAD organization of the X-inactivation center ensures opposing developmental regulation of Tsix and Xist

The mouse X-inactivation center (Xic) locus represents a powerful model for understanding the links between genome architecture and gene regulation, with the non-coding genes Xist and Tsix showing opposite developmental expression patterns while being organized as an overlapping sense/antisense unit. The Xic is organized into two topologically associating domains (TADs) but the role of this architecture in orchestrating cis-regulatory information remains elusive. To explore this, we generated genomic inversions that swap the Xist/Tsix transcriptional unit and place their promoters in each other’s TAD. We found that this led to a switch in their expression dynamics: Xist became precociously and ectopically upregulated, both in male and female pluripotent cells, while Tsix expression aberrantly persisted during differentiation. The topological partitioning of the Xic is thus critical to ensure proper developmental timing of X inactivation. Our study illustrates how the genomic architecture of cis-regulatory landscapes can affect the regulation of mammalian developmental processes

Établissement de l’inactivation transcriptionnelle du chromosome X pendant le développement embryonnaire

L’inactivation du chromosome X est un modèle de choix pour étudier les mécanismes épigénétiques de contrôle de l’expression génique. Il est particulièrement remarquable que ce processus implique la mise en place et la maintenance d’un traitement différent entre les deux chromosomes X, pourtant présents au sein du même noyau cellulaire. L’acquisition du destin inactif du X repose sur l’expression du gène Xist, qui une fois activé produit un ARN non-codant capable de recouvrir le chromosome à partir duquel il est produit. L’activation monoallélique de Xist est finement contrôlée par une série de mécanismes régulateurs impliquant à la fois des facteurs protéiques et la réorganisation physique, dynamique, des séquences géniques entourant le locus Xist au sein du noyau. Une fois Xist exprimé sur l’un des deux X, celui-ci entraîne l’exclusion de la machinerie de transcription du territoire du chromosome qu’il recouvre et l’acquisition de marques hétérochromatiques. La répression transcriptionnelle progresse ensuite et s’accompagne de l’internalisation des séquences inactivées au sein du domaine nucléaire défini par l’accumulation de l’ARN Xist. Enfin, l’hétérogénéité dans la cinétique d’inactivation des différents gènes du chromosome X révèle l’existence de plusieurs voies amenant à la répression transcriptionnelle, et le rôle particulier des répétitions de type LINE-1 dans la propagation de l’inactivation le long du chromosome

Investigating the transcriptional control of cardiovascular development.

Transcriptional regulation of thousands of genes instructs complex morphogenetic and molecular events for heart development. Cardiac transcription factors choreograph gene expression at each stage of differentiation by interacting with cofactors, including chromatin-modifying enzymes, and by binding to a constellation of regulatory DNA elements. Here, we present salient examples relevant to cardiovascular development and heart disease, and review techniques that can sharpen our understanding of cardiovascular biology. We discuss the interplay between cardiac transcription factors, cis-regulatory elements, and chromatin as dynamic regulatory networks, to orchestrate sequential deployment of the cardiac gene expression program

Investigating the transcriptional control of cardiovascular development.

Transcriptional regulation of thousands of genes instructs complex morphogenetic and molecular events for heart development. Cardiac transcription factors choreograph gene expression at each stage of differentiation by interacting with cofactors, including chromatin-modifying enzymes, and by binding to a constellation of regulatory DNA elements. Here, we present salient examples relevant to cardiovascular development and heart disease, and review techniques that can sharpen our understanding of cardiovascular biology. We discuss the interplay between cardiac transcription factors, cis-regulatory elements, and chromatin as dynamic regulatory networks, to orchestrate sequential deployment of the cardiac gene expression program

The X chromosome inactivation network.

<p>(A) <i>Xist</i> expression is controlled by counteracting activators (red) and repressors (blue). Stem cell factors (blue ovals) might repress <i>Xist</i> directly or indirectly via activating the repressive transcript Tsix or repressing the activator Rnf12. Rnf12 is the only known activator, and may function by targeting the <i>Xist</i> promoter directly and/or by inducing degradation of an unknown <i>Xist</i> repressor (blue squares). The existence of additional X-linked activators (red triangles) and long-range control elements such as <i>Xpr</i>, <i>Xce</i>, <i>Xite</i>, and others (red box) has been suggested <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002002#pgen.1002002-Nora1" target="_blank">[10]</a>. (B) The time window when XCI can be initiated (grey) could be controlled by the down-regulation of <i>Xist</i> repressors such as stem cell factors (blue) and up-regulation of <i>Xist</i> activators like Rnf12 (red). (C) Different cell lines might require Rnf12 (ESC line B) or not (ESC line A), depending on the expression kinetics of other X-linked activators (dotted red line).</p