Chromosome compartments on the inactive X guide TAD formation independently of transcription during X-reactivation

Moritz Bauer,Enrique Vidal,Guillaume J Filion,Eduard Zorita,Nil Üresin,Bernhard Payer,Stefan F Pinter

doi:10.1038/s41467-021-23610-1

Abstract

A hallmark of chromosome organization is the partition into transcriptionally active A and repressed B compartments, and into topologically associating domains (TADs). Both structures were regarded to be absent from the inactive mouse X chromosome, but to be re-established with transcriptional reactivation and chromatin opening during X-reactivation. Here, we combine a tailor-made mouse iPSC reprogramming system and high-resolution Hi-C to produce a time course combining gene reactivation, chromatin opening and chromosome topology during X-reactivation. Contrary to previous observations, we observe A/B-like compartments on the inactive X harbouring multiple subcompartments. While partial X-reactivation initiates within a compartment rich in X-inactivation escapees, it then occurs rapidly along the chromosome, concomitant with downregulation of Xist. Importantly, we find that TAD formation precedes transcription and initiates from Xist-poor compartments. Here, we show that TAD formation and transcriptional reactivation are causally independent during X-reactivation while establishing Xist as a common denominator.

Highlights

A hallmark of chromosome organization is the partition into transcriptionally active A and repressed B compartments, and into topologically associating domains (TADs)
We investigate the temporal dynamics of transcriptional reactivation, chromatin opening, and reveal their relationship to the topological rearrangement of the inactive X in an optimized induced pluripotent stem cells (iPSCs) reprogramming system
Previous studies on X-chromosome reactivation during iPSC reprogramming were based on mouse embryonic fibroblast (MEF) reprogramming[25,31,32,33] and have been mitigated by several limitations inherent to these systems

Summary

Introduction

A hallmark of chromosome organization is the partition into transcriptionally active A and repressed B compartments, and into topologically associating domains (TADs). Xist coats the X from which it is expressed and silences the chromosome through the combined action of multiple interaction partners that set up a heterochromatic environment[11,15,16] During this process, Xist repels architectural proteins like CTCF and Cohesin[11], thereby actively contributing to the attenuation of TADs8 and leading to the distinct chromosome conformation[7,17,18] of the Xi. There has been intense research effort to understand the dynamics of transcriptional silencing, the mechanisms of transition to the unique structure of the Xi and the connection between the two processes[8,9,19,20], but how the process is reversed during the reactivation of the X chromosome has received attention only recently[1,21,22]. While mechanistically, both share common features like the downregulation of Xist and the erasure of silencing marks like H3K27me[3], their kinetics differ greatly, as

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