Jacob P Schwartz

All Publications

• Integrated analysis of multimodal long-read epigenetic assays. bioRxiv : the preprint server for biology Marcus, J., Dixon-Luinenburg, O., Gamarra, N., Schwartz, J. P., Rozenwald, M., Maslan, A., Urnov, F. D., Straight, A. F., Altemose, N., Ioannidis, N. M., Streets, A. 2025

  Abstract

  Long-read sequencing assays that detect base modifications are becoming increasingly important research tools for the study of epigenetic regulation, especially with the development of DiMeLo-seq and similar methods that deposit non-native base modifications to mark a range of epigenetic features such as protein-DNA interactions and chromatin accessibility. A main benefit of these methods is their inherent capacity for multimodality, enabling the encoding of multiple genomic signals onto single nucleic acid molecules. However, there are limited tools available for visualization and statistical analysis of this type of multimodal data. Here we introduce dimelo-toolkit, a python package built to enable flexible visualizations and easy integration into custom data processing workflows. We demonstrate the utility of dimelo-toolkit's preset visualizations of multiple base modifications in long-read single-molecule sequencing data with a novel extension of the DiMeLo-seq protocol that can capture three separate aspects of chromatin state on the same single reads: target protein binding, CpG methylation, and chromatin accessibility. We apply this multimodal method to simultaneously map chromatin accessibility, CpG methylation, and LMNB1 and CTCF binding patterns, respectively, in GM12878 cells. Additionally, we use dimelo-toolkit to investigate technical biases that arise when working with this type of multimodal data. This software tool will pave the way for developing well-optimized protocols and help unlock previously inaccessible biological insights.

  View details for DOI 10.1101/2025.11.09.687458

  View details for PubMedID 41279073

  View details for PubMedCentralID PMC12637566

• Regulation of X. laevis M18BP1 centromeric localization and CENP-A assembly. bioRxiv : the preprint server for biology Brown, R. R., Schwartz, J. P., Ghadri, L., Straight, A. F. 2025

  Abstract

  Eukaryotic chromosome segregation requires attachment of chromosomes to microtubules of the mitotic spindle through the kinetochore so that chromosomes can align and move in mitosis. Kinetochores are assembled on the centromere which is a unique chromatin domain that is epigenetically defined by the histone H3 variant CENtromere Protein A (CENP-A). During DNA replication CENP-A is equally divided between replicated chromatids and new CENP-A nucleosomes are re-assembled during the subsequent G1 phase of the cell cycle. How cells regulate the strict cell cycle timing of CENP-A assembly is a central question in the epigenetic maintenance of centromeres and kinetochores. One essential assembly factor for CENP-A nucleosomes is the Mis18 complex (Mis18α, Mis18β, and M18BP1) which is regulated in its localization to centromeres between metaphase and G1 when CENP-A assembly occurs. Here, we define a new regulatory mechanism that works through cell cycle dependent phosphorylation of Xenopus laevis M18BP1 between metaphase and interphase. This phosphoregulatory switch disrupts binding of M18BP1 to CENP-A nucleosomes in metaphase, and when relieved enables M18BP1 binding to CENP-A nucleosomes in interphase. We show that this phosphorylation dependent switching mechanism regulates CENP-A nucleosome assembly. We propose that the phospho-regulated binding of M18BP1 to CENP-A nucleosomes is an important control mechanism that restricts the timing of new CENP-A assembly.

  View details for DOI 10.1101/2025.07.15.664882

  View details for PubMedID 40791504

  View details for PubMedCentralID PMC12338635

• Histone H3 lysine methyltransferase activities control compartmentalization of human centromeres. bioRxiv : the preprint server for biology Sidhwani, P., Schwartz, J. P., Fryer, K. A., Straight, A. F. 2025

  Abstract

  Centromeres are essential chromosomal regions that ensure accurate genome segregation during cell division. They are organized into epigenetically discrete compartments: a Centromere Protein A (CENP-A)-rich core for microtubule attachment and surrounding heterochromatic pericentromeres that promote cohesion. Despite their importance, the mechanisms that define, enforce and partition these chromatin domains remain poorly understood. To address this, we disrupted key H3K9 methyltransferases- SUV39H1, SUV39H2, and SETDB1- that establish heterochromatin in humans. We find that SETDB1 is required for H3K9 dimethylation at core centromeres, while SUV39H1/2 complete trimethylation. Unexpectedly, depleting all three enzymes results in aberrantly high H3K9me3, driving CENP-A expansion into pericentromeres. This promiscuous deposition is mediated by G9a/GLP methyltransferases, which selectively reestablish H3K9me3 within the centromere core. SETDB1, regardless of its enzymatic activity, blocks G9a/GLP-mediated heterochromatin deposition and CENP-A expansion, revealing a novel, catalytic-independent function in safeguarding centromeres. Overall, our work defines the molecular logic governing centromeric repression, and uncovers foundational principles of epigenetic compartmentalization.

  View details for DOI 10.1101/2025.07.01.662447

  View details for PubMedID 40631212

• DiMeLo-cito: a one-tube protocol for mapping protein-DNA interactions reveals CTCF bookmarking in mitosis. bioRxiv : the preprint server for biology Gamarra, N., Chittenden, C., Sundararajan, K., Schwartz, J. P., Lundqvist, S., Robles, D., Dixon-Luinenburg, O., Marcus, J., Maslan, A., Franklin, J. M., Streets, A., Straight, A. F., Altemose, N. 2025

  Abstract

  Genome regulation relies on complex and dynamic interactions between DNA and proteins. Recently, powerful methods have emerged that leverage third-generation sequencing to map protein-DNA interactions genome-wide. For example, Directed Methylation with Long-read sequencing (DiMeLo-seq) enables mapping of protein-DNA interactions along long, single chromatin fibers, including in highly repetitive genomic regions. However, DiMeLo-seq involves lossy centrifugation-based wash steps that limit its applicability to many sample types. To address this, we developed DiMeLo-cito, a single-tube, wash-free protocol that maximizes the yield and quality of genomic DNA obtained for long-read sequencing. This protocol enables the interrogation of genome-wide protein binding with as few as 100,000 cells and without the requirement of a nuclear envelope, enabling confident measurement of protein-DNA interactions during mitosis. Using this protocol, we detected strong binding of CTCF to mitotic chromosomes in diploid human cells, in contrast with earlier studies in karyotypically unstable cancer cell lines, suggesting that CTCF "bookmarks" specific sites critical for maintaining genome architecture across cell divisions. By expanding the capabilities of DiMeLo-seq to a broader range of sample types, DiMeLo-cito can provide new insights into genome regulation and organization.

  View details for DOI 10.1101/2025.03.11.642717

  View details for PubMedID 40161611

  View details for PubMedCentralID PMC11952428

• Structure of phosphorylated-like RssB, the adaptor delivering σs to the ClpXP proteolytic machinery, reveals an interface switch for activation. The Journal of biological chemistry Brugger, C., Schwartz, J., Novick, S., Tong, S., Hoskins, J. R., Majdalani, N., Kim, R., Filipovski, M., Wickner, S., Gottesman, S., Griffin, P. R., Deaconescu, A. M. 2023; 299 (12): 105440

  Abstract

  In enterobacteria such as Escherichia coli, the general stress response is mediated by σs, the stationary phase dissociable promoter specificity subunit of RNA polymerase. σs is degraded by ClpXP during active growth in a process dependent on the RssB adaptor, which is thought to be stimulated by the phosphorylation of a conserved aspartate in its N-terminal receiver domain. Here we present the crystal structure of full-length RssB bound to a beryllofluoride phosphomimic. Compared to the structure of RssB bound to the IraD anti-adaptor, our new RssB structure with bound beryllofluoride reveals conformational differences and coil-to-helix transitions in the C-terminal region of the RssB receiver domain and in the interdomain segmented helical linker. These are accompanied by masking of the α4-β5-α5 (4-5-5) "signaling" face of the RssB receiver domain by its C-terminal domain. Critically, using hydrogen-deuterium exchange mass spectrometry, we identify σs-binding determinants on the 4-5-5 face, implying that this surface needs to be unmasked to effect an interdomain interface switch and enable full σs engagement and hand-off to ClpXP. In activated receiver domains, the 4-5-5 face is often the locus of intermolecular interactions, but its masking by intramolecular contacts upon phosphorylation is unusual, emphasizing that RssB is a response regulator that undergoes atypical regulation.

  View details for DOI 10.1016/j.jbc.2023.105440

  View details for PubMedID 37949227

  View details for PubMedCentralID PMC10755785

• Phospho-dependent signaling during the general stress response by the atypical response regulator and ClpXP adaptor RssB PROTEIN SCIENCE Schwartz, J., Son, J., Brugger, C., Deaconescu, A. M. 2021; 30 (4): 899-907

  Abstract

  In the model organism Escherichia coli and related species, the general stress response relies on tight regulation of the intracellular levels of the promoter specificity subunit RpoS. RpoS turnover is exclusively dependent on RssB, a two-domain response regulator that functions as an adaptor that delivers RpoS to ClpXP for proteolysis. Here, we report crystal structures of the receiver domain of RssB both in its unphosphorylated form and bound to the phosphomimic BeF3 - . Surprisingly, we find only modest differences between these two structures, suggesting that truncating RssB may partially activate the receiver domain to a "meta-active" state. Our structural and sequence analysis points to RssB proteins not conforming to either the Y-T coupling scheme for signaling seen in prototypical response regulators, such as CheY, or to the signaling model of the less understood FATGUY proteins.

  View details for DOI 10.1002/pro.4047

  View details for Web of Science ID 000623310600001

  View details for PubMedID 33599047

  View details for PubMedCentralID PMC7980512

• Sexually experienced, but not naive, female rats show a conditioned object preference (COP) for mating after a single training trial PHYSIOLOGY & BEHAVIOR Piergies, A. M. H., Hicks, M. E., Schwartz, J. P., Meerts, S. H. 2019; 198: 42-47

  Abstract

  Female rats with mating experience spend more time with the male rat, exhibit shorter contact-return latency to intromission, and display more proceptive behaviors in the male rat's compartment than during the first mating experience. The present study tested 1) whether mating induced conditioned object preference (COP) is possible with a single conditioning trial and 2) whether a preference is induced for an object associated with the first mating encounter or the fifth mating encounter in female rats. Ovariectomized, Long-Evans female rats were primed with estradiol benzoate + progesterone and either exposed to an empty paced mating chamber for 15 min (Naïve) or received a 15 intromission test of paced mating behavior (Experienced) on four separate occasions before undergoing the COP procedure. Experienced, but not Naïve, female rats developed a COP for a single mating bout, indicating that mating is highly rewarding for sexually experienced female rats. The findings raise questions about the effect of sexual experience on reward regions in the brain, the responsiveness of genital tissue, and learning mechanisms.

  View details for DOI 10.1016/j.physbeh.2018.09.017

  View details for Web of Science ID 000452563000005

  View details for PubMedID 30290181