Yu, Chuanhe

Abstract Epigenetic inheritance relies on the precise recycling of parental histones during DNA replication. The N-terminal region of Pol1, the catalytic subunit of DNA polymerase α, has previously been implicated in chaperoning parental histone recycling. In this study, we identify a single amino acid mutation in the C-terminal region of Saccharomyces cerevisiae Pol1 (pol1-F1396S) that destabilizes the protein and disrupts the transfer of parental histones to the lagging strand during DNA replication. As a primary consequence, pol1-F1396S cells exhibit decreased chromatin stability. Furthermore, we demonstrate that the cellular abundance—or dosage—of all three DNA polymerases (Pol α, Pol δ, and Pol ε) influences the distribution of parental histones between the leading and lagging strands, revealing a dosage-sensitive mechanism of epigenetic regulation during DNA replication.

Abstract Bruton tyrosine kinase (BTK) is central to chronic lymphocytic leukemia (CLL) biology, yet the regulatory programs that depend on BTK remain poorly defined. Here, we used acute NX-5948 (Bexobrutideg)-mediated BTK degradation to define BTK-dependent regulatory circuitry in CLL. Integrating early transcriptional and chromatin responses with chromatin-state annotation, target-gene linkage, and transcription factor assignment, we resolved a chromatin-informed framework linking BTK loss to downstream gene-regulatory output. This framework is separated into two directional programs: a dominant BTK-maintained network that collapsed after BTK degradation and a smaller BTK-released network that emerged upon BTK loss. BTK-responsive elements were concentrated in promoter- and enhancer-linked chromatin compartments, consistent with a model in which BTK-dependent transcriptional output is mediated through specific active regulatory elements. Functional validation in a CLL-like cell model provided orthogonal support for the NFAT-linked component of the BTK-maintained regulatory circuitry. BTK-dependent regulon activity was associated with clinical outcome, and projection of bulk-derived programs into longitudinal single-cell RNA-seq resolved malignant CLL cells into distinct regulatory states with maintained-like and released-like features. Together, this work defines BTK-dependent regulatory programs in CLL through a chromatin-informed framework linking BTK activity to gene-regulatory output. These findings lay the foundation for understanding how BTK-dependent circuitry contributes to malignant cell-state diversity, clinical outcome, and remodeling during therapy.

Abstract Recycling of parental histones is an important step in epigenetic inheritance. During DNA replication, DNA polymerase epsilon subunit DPB3/DPB4 and DNA replication helicase subunit MCM2 are involved in the transfer of parental histones to the leading and lagging strands, respectively. Single Dpb3 deletion (dpb3Δ) or Mcm2 mutation (mcm2-3A), which each disrupts one parental histone transfer pathway, leads to the other's predominance. However, the biological impact of the two histone transfer pathways on chromatin structure and DNA repair remains elusive. In this study, we used budding yeast Saccharomyces cerevisiae to determine the genetic and epigenetic outcomes from disruption of parental histone H3–H4 tetramer transfer. We found that a dpb3Δ mcm2-3A double mutant did not exhibit the asymmetric parental histone patterns caused by a single dpb3Δ or mcm2-3A mutation, suggesting that the processes by which parental histones are transferred to the leading and lagging strands are independent. Surprisingly, the frequency of homologous recombination was significantly lower in dpb3Δ, mcm2-3A and dpb3Δ mcm2-3A mutants, likely due to the elevated levels of free histones detected in the mutant cells. Together, these findings indicate that proper transfer of parental histones during DNA replication is essential for maintaining chromatin structure and that lower homologous recombination activity due to parental histone transfer defects is detrimental to cells.

Abstract Extrachromosomal DNA (ecDNA) drives the evolution of cancer cells by conferring survival advantages over normal cells. However, the functional importance of ecDNA replication and maintenance is yet to be evaluated, and the molecular components that contributed to these processes remain largely unknown. Here, using CRISPR-C (circularization of genes and chromosomes by CRISPR) technology and synthetic circular DNA mimicking ecDNA identified in tumors, we generated ecDNA-positive (ecDNA+) cell models. Using these models, we identified the proteins involved in ecDNA replication and maintenance and found DNA damage response (DDR)-related pathways were significantly enriched. We further demonstrated that ecDNA replication led to increased DDR and genome instability and DDR was also essential for ecDNA maintenance, consistent with observations that ecDNA+ tumors exhibited higher DDR scores than ecDNA-negative (ecDNA–) tumors in patients. ATM, MDC1, and CHK2, but not ATR, were activated in ecDNA+ cells compared to ecDNA– cells. Moreover, ecDNA+ cells were more sensitive to ATM and CHK2 inhibition. We further found that type II topoisomerase TOP2B and DNA ligase III (LIG3) were critical regulators for ecDNA replication and maintenance and related DDR. In summary, our findings of the reciprocal interactions between ecDNA and DDR provide new insights into detection and therapy for ecDNA+ tumors.

How cells ensure symmetric inheritance Parental histones with modifications are recycled to newly replicated DNA strands during genome replication, but do the two sister chromatids inherit modified histones equally? Yu et al. and Petryk et al. found in mouse and yeast, respectively, that modified histones are segregated to both DNA daughter strands in a largely symmetric manner (see the Perspective by Ahmad and Henikoff). However, the mechanisms ensuring this symmetric inheritance in yeast and mouse were different. Yeasts use subunits of DNA polymerase to prevent the lagging-strand bias of parental histones, whereas in mouse cells, the replicative helicase MCM2 counters the leading-strand bias. Science , this issue p. 1386 , p. 1389 ; see also p. 1311