Nathan Gamarra

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

• 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

• Gene expression and cell identity controlled by anaphase-promoting complex NATURE Oh, E., Mark, K. G., Mocciaro, A., Watson, E. R., Prabu, J., Cha, D. D., Kampmann, M., Gamarra, N., Zhou, C. Y., Rape, M. 2020; 579 (7797): 136-+

  Abstract

  Metazoan development requires the robust proliferation of progenitor cells, the identities of which are established by tightly controlled transcriptional networks1. As gene expression is globally inhibited during mitosis, the transcriptional programs that define cell identity must be restarted in each cell cycle2-5 but how this is accomplished is poorly understood. Here we identify a ubiquitin-dependent mechanism that integrates gene expression with cell division to preserve cell identity. We found that WDR5 and TBP, which bind active interphase promoters6,7, recruit the anaphase-promoting complex (APC/C) to specific transcription start sites during mitosis. This allows APC/C to decorate histones with ubiquitin chains branched at Lys11 and Lys48 (K11/K48-branched ubiquitin chains) that recruit p97 (also known as VCP) and the proteasome, which ensures the rapid expression of pluripotency genes in the next cell cycle. Mitotic exit and the re-initiation of transcription are thus controlled by a single regulator (APC/C), which provides a robust mechanism for maintaining cell identity throughout cell division.

  View details for DOI 10.1038/s41586-020-2034-1

  View details for Web of Science ID 000517050000002

  View details for PubMedID 32076268

  View details for PubMedCentralID PMC7402266

• Cryo-EM structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome ELIFE Armache, J., Gamarra, N., Johnson, S. L., Leonard, J. D., Wu, S., Narlikar, G. J., Cheng, Y. 2019; 8

  Abstract

  The SNF2h remodeler slides nucleosomes most efficiently as a dimer, yet how the two protomers avoid a tug-of-war is unclear. Furthermore, SNF2h couples histone octamer deformation to nucleosome sliding, but the underlying structural basis remains unknown. Here we present cryo-EM structures of SNF2h-nucleosome complexes with ADP-BeFx that capture two potential reaction intermediates. In one structure, histone residues near the dyad and in the H2A-H2B acidic patch, distal to the active SNF2h protomer, appear disordered. The disordered acidic patch is expected to inhibit the second SNF2h protomer, while disorder near the dyad is expected to promote DNA translocation. The other structure doesn't show octamer deformation, but surprisingly shows a 2 bp translocation. FRET studies indicate that ADP-BeFx predisposes SNF2h-nucleosome complexes for an elemental translocation step. We propose a model for allosteric control through the nucleosome, where one SNF2h protomer promotes asymmetric octamer deformation to inhibit the second protomer, while stimulating directional DNA translocation.

  View details for DOI 10.7554/eLife.46057

  View details for Web of Science ID 000474234700001

  View details for PubMedID 31210637

  View details for PubMedCentralID PMC6611695