Inactivation of one of the two female X chromosomes involves condensing it into a repressive subnuclear territory, which is depleted of transcriptional components and undergoes late-stage DNA replication. Two new studies unravel how compartmentalization of the inactive mammalian X chromosome affects transcription and DNA replication.

Unlike autosomal genes, X-linked genes are expressed from only one copy in both male and female mammals. How cells increase X-linked gene expression to match autosomal levels is unclear. New evidence suggests that lower levels of RNA modifications on X chromosome-derived transcripts critically regulate mRNA stability and help to balance X-to-autosome gene expression levels.

Pioneer transcription factors access gene regulatory sites embedded within chromatin. They drive gene expression programs vital for cell fate decisions and cellular reprogramming, but how they engage nucleosomal sites at the molecular level is unclear. New results show that they engage histones and collaborate to overcome the nucleosome barrier.

NuA4 is a highly conserved histone acetyltransferase complex that functions in transcription and DNA repair. Four groups have recently determined the structure of NuA4 from two different yeasts using cryo-EM, revealing important mechanistic details of its function and allowing a detailed comparison to the related SAGA complex.

Here, the authors show that PDHE1α accumulates at DNA double-strand breaks, in a PARylation-dependent manner, where it locally supplies acetyl-CoA for histone acetylation. These events facilitate remodeling of the chromatin landscape and efficient repair.

Here, using cryogenic electron microscopy and cryoDRGN, the authors delineate how the anaphase-promoting complex/cyclosome is reconfigurated to interact with its cognate E2s and thus polyubiquitinate its target. Unexpectedly, multiple ubiquitin moieties are shown to interact with the anaphase-promoting complex/cyclosome machinery, including its activator Cdh1.

Here, the authors unveil the intrinsic ability of the C terminus of SSX, as part of different oncogenic fusions, to determine fusion occupancy independent of the BAF complex by both recognizing and stimulating histone H2AK119 monoubiquitylation by PRC1.1.

Here the authors show that the m⁶A modification on mRNAs mediates their length-dependent enrichment in stress granules, and that mRNAs with longer exons—which usually harbor more m⁶A sites—are preferentially enriched in the granules.

By obtaining structural snapshots of the catalytic cycle of NADH:quinone oxidoreductase from Vibrio cholerae, the authors uncover its mechanism. They show how electrons are shuttled and determine the importance of the [2Fe-2S] cluster in the movement of the electron transfer switch.

Here, using cryo-EM, the authors show how Cas1–Cas2/3 and integration host factor, by means of a U-shaped bend that traps the invading DNA and a loop that positions it for the integrase, regulate integration of foreign DNA into the first repeat of the CRISPR array.

In January 2024, Nature Structural & Molecular Biology (NSMB) will celebrate the 30^th anniversary of publishing its first issue. Though initially launched as Nature Structural Biology in 1994, the journal has since expanded its scope to include all research into the molecular underpinnings of life, with the vision that the broadest insight can be gleaned through a suite of complementary approaches.

Understanding the underlying molecular mechanisms of dosage compensation and how cells equalize gene expression from the sex chromosomes has interested scientists for more than six decades. However, with so many questions still unanswered, the field continues to capture the attention of researchers.