Effie Apostolou

Mitotic bookmarking enables transmission of regulatory information across cell division, yet how active chromatin states are molecularly preserved during mitosis and how they contribute to postmitotic cell fate decisions remain unresolved. Here, we demonstrate that the acetyltransferases KAT6 and KAT7 remain chromatin-bound and catalytically active throughout mitosis in mouse and human pluripotent stem cells. Acute KAT6/7 depletion disrupts mitotic histone acetylation and the retention of multiple chromatin regulators with minimal effects on chromatin accessibility. Mechanistically, KAT6/7 bookmark both self renewal and developmental gene loci, where they are required for post-mitotic transcriptional reactivation and priming of lineage-specific programs. Consistently, genes impaired during postmitotic reactivation also fail to activate during neuronal differentiation upon continuous KAT6/7 perturbation, compromising the establishment of the neuronal program and identity. Altogether, our findings identify KAT6 and KAT7 as a cooperative mitotic chromatin maintenance system that couples active histone acetylation to preservation of chromatin composition, transcriptional memory, and developmental competence across cell division, extending the bookmarking function beyond transcriptional memory. These findings also provide a new framework for understanding KAT6/7 function in neurodevelopmental disorders and cancer.

The BAF (also known as mammalian SWI/SNF) chromatin remodelling complexes are essential regulators of nucleosome positioning and transcription factor binding ^1,2 . Loss-of-function (LOF) mutations in genes encoding components of the BAF complexes are among the most frequent across cancer types ³ . However, a unifying mechanism that explains their widespread disruption remains unclear. Here we disrupted BAF function through pharmacological inhibition and ARID1A deletion across various mammalian cell types and tissues and observed a conserved chromatin response: increased accessibility at CTCF-binding sites. ARID1A LOF alone was sufficient to drive these changes, which demonstrates that canonical BAF (cBAF) disruption is the key driver of CTCF gain. Genomic profiling showed increased CTCF and SMC3 occupancy, which reveals an antagonistic relationship between cBAF and CTCF–cohesin complexes. Furthermore, cBAF loss restructured 3D genome organization, which led to a strengthening of topologically associating domain boundaries and subdivision of large domains into smaller insulated structures. Long-range enhancer–promoter loops were replaced by shorter, promoter-proximal loops anchored at CTCF-enriched sites. To determine how CTCF function is enabled following cBAF loss, we profiled CTCF-interacting cofactors and found that CTCF binds directly to fully assembled PBAF. After cBAF depletion, PBAF was recruited to sites of increased CTCF occupancy, which demonstrates that there is an antagonistic switch between SWI/SNF subcomplexes. In vivo, conditional Arid1a deletion in primary mouse cells resulted in the expansion of a highly proliferative population marked by elevated accessibility at CTCF sites. This phenotype was fully reversed by either Ctcf or Pbrm1 deletion, which establishes that cBAF and the activity of CTCF and PBAF have contrasting roles.

Summary: Ubiquitously expressed chromatin regulators orchestrate cell-type-specific gene expression programs, yet how they acquire distinct regulatory functions during development remains fundamentally unresolved ^1,2 . Using temporally controlled protein depletion during human cortical neurogenesis in vitro , we show that the autism-associated histone methyltransferase EHMT1 ^3,4 is developmentally repurposed from epiblast to cortical neurons. Broadly expressed zinc finger proteins recruit EHMT1 to distinct cis-regulatory elements within changing chromatin landscapes associated with lineage-specific transcription factor activity, with extensive remodeling of EHMT1 enhancer occupancy during neural induction dependent on ZNF462. This genomic rewiring is accompanied by a fundamental shift from restraining premature developmental gene expression in pluripotent cells to supporting neuronal programs, with distinct transcriptional consequences of EHMT1 loss across neural progenitors and excitatory and inhibitory neuronal subtypes. Timed depletion and recovery experiments identify the neural progenitor stage as the onset of a developmental period during which EHMT1 is required for faithful neuronal maturation. Remarkably, EHMT1 can re-engage stage-specific targets after prolonged deficiency, allowing extensive transcriptional recovery with only limited molecular scarring. These findings reveal how ubiquitous epigenetic machinery acquires developmental specificity while demonstrating the resilience of developmental gene regulatory programs to prolonged disruption, with implications for neurodevelopmental disorders.

Acute cohesin loss causes widespread reorganization of three-dimensional (3D) chromatin architecture but has relatively minor effects on steady-state transcription. It remains unclear whether its role in gene regulation becomes more critical during mitotic exit, when 3D chromatin architecture and transcription are globally re-established. To address this, we acutely depleted RAD21 in mouse embryonic stem cells during mitotic exit under self-renewal or differentiation conditions. Here we show that, although most loops failed to reform without cohesin, the few cohesin-independent loops were linked to active promoters, strong enhancers and H3K27ac mitotic bookmarking. Transcriptional changes were only modest, indicating that gene reactivation largely bypasses cohesin. Sensitive genes showed RAD21 promoter binding, a higher number of structural loops and positioning within well-insulated, gene-poor topologically associating domains. During differentiation, cohesin loss impaired activation of a broader set of developmental genes, partly due to defective de novo regulatory interactions. Together, these findings demonstrate context-specific requirements for cohesin in gene activation.

During the germinal centre (GC) reaction, mature B cells undergo rapid and reversible phenotypic shifts that are essential for adaptive immunity. Here we report that GC B cells, unlike other mature B cells, transiently acquire a unique epigenetic plasticity, demonstrated by their enhanced capacity to reprogram to induced pluripotent stem cells. This plasticity depends on T follicular helper (T_FH) cells and is not due to increased proliferation or MYC activation. Instead, it involves weakening of B-cell identity and derepression of stem and progenitor programs driven by NF-κB and other T_FH-derived signals. Thus, physiological GC plasticity is tightly constrained by the affinity maturation process of positive selection. Loss of histone 1, a chromatin compaction regulator restricting the accessibility of embryonic stem cell programs, further enhances GC plasticity by bypassing this gatekeeping mechanism. Importantly, patients with B-cell lymphoma enriched for GC plasticity signatures had worse outcomes, suggesting that this mechanism may also contribute to lymphomagenesis.

Mouse embryonic stem cells (mESCs), in addition to differentiating into the three germ layers, can reverse typical developmental trajectories, as exemplified by their ability to de-differentiate into 2-cell-like cells (2CLCs) that resemble the mammalian embryo during zygotic genome activation (ZGA). This unique property offers the opportunity to elucidate the molecular principles that govern the pre-implantation stages of mammalian development. Here, we dissect the functions of the chromatin repressor EHMT2, a candidate antagonist of the mESC-to-2CLC transition, by leveraging a multipurpose allele for acute protein depletion and efficient immunoprecipitation. Our experiments revealed distinct principles of EHMT2-mediated gene repression in mESCs based on specific chromatin binding patterns and protein co-factors. Most notably, EHMT2 directly represses large clusters of co-regulated gene loci that comprise a significant fraction of the 2CLC-specific transcriptome by initiating H3K9me2 spreading from distal LINE-1 elements. EHMT2 counteracts the recruitment of the activator DPPA2/4 to promoter-proximal endogenous retroviral elements (ERVs) at 2CLC genes. EHMT2 depletion enhances the expression of ZGA-associated transcripts in 2CLCs and synergizes with spliceosome inhibition and retinoic acid signaling to facilitate the mESC-to-2CLC transition. In contrast to ZGA-associated genes, the repression of germ layer-associated transcripts by EHMT2 occurs outside of gene clusters, in collaboration with ZFP462, and involves binding to non-repetitive candidate enhancers. Our observations provide novel mechanistic insight into how pluripotent cells achieve attenuation of their bidirectional differentiation potential and reveal unique transcriptional features of murine totipotent cells.

Cells fine-tune gene expression in response to cellular stress, a process critical for tumorigenesis. However, mechanisms governing stress-responsive transcription remain incompletely understood. This study shows that the MED1 subunit of the Mediator coactivator complex is acetylated in its intrinsically disordered region (IDR). Under stress, SIRT1 associates with the super elongation complex to deacetylate MED1 in promoter-proximal regions. The deacetylated (or acetylation-defective mutant) MED1 amplified stress-activated cytoprotective genes and rescued stress-suppressed growth-supportive genes in estrogen-receptor-positive breast cancer (ER⁺ BC) cells. Mechanistically, deacetylated MED1 promotes chromatin incorporation of RNA polymerase II (Pol II) through IDR-mediated interactions. Functionally, ER⁺ BC cells with deacetylated MED1 exhibit faster growth and enhanced stress resistance in culture and in an orthotopic mouse model. These findings advance our understanding of Pol II regulation under cellular stress and potentially suggest therapeutic strategies targeting oncogenic transcription driven by MED1 and Mediator.

Transposable elements (TEs) are abundant in the human genome, and they provide the source for genetic and functional diversity. Previous studies have suggested that TEs are repressed by DNA methylation and chromatin modifications. Here through integrating transcriptome and 3D genome architecture studies, we showed that haploinsufficient loss of NIPBL selectively activates alternative promoters (altPs) at the long terminal repeats (LTRs) of the TE subclasses. This activation occurs through the reorganization of topologically associating domain (TAD) hierarchical structures and the recruitment of proximal enhancers. These observations indicate that TAD hierarchy restricts transcriptional activation of LTRs that already possess open chromatin features. Perturbation of hierarchical chromatin topology can lead to co-option of LTRs as functional altPs, driving aberrant transcriptional activation of oncogenes. These data uncovered a new layer of regulatory mechanisms of TE expression and posit TAD hierarchy dysregulation as a new mechanism for altP-mediated oncogene activation and transcriptional diversity in cancer.