# Elucidating chromatin organization with molecular rulers

> **NIH NIH R21** · HARVARD UNIVERSITY · 2020 · $245,993

## Abstract

Summary
Higher order chromatin organization is perturbed in cancer cells. It is hypothesized that these perturbations are
closely linked to carcinogenesis and cancer phenotype. However, a fulsome picture of how chromatin
organization contributes to cancer phenotype still eludes us. This question is unlikely to be answered by
looking at just a handful of cells or cell types, since there is a tremendous variety in cancer phenotype. It is also
unlikely that looking at aggregate or population data will answer these questions, since there is heterogeneity
in chromosome organization from one cell to the next. Current tools to study chromatin organization have
proven unequal to this challenging ask, either because they can only look at a few cells at a time (microscopy
based techniques) or they only provide fragmented snapshots with no spatial context (chromosome
conformation capture based assays). We propose the development of a novel biochemical assay, a molecular
ruler, that combines the strength of microscopy techniques (multicolor labeling and spatial context) with the
high-throughput, scalable, single-molecule approach of new generation chromosome conformation capture
assays. Molecular rulers will label chromosomes with barcoded DNA probes and generate DNA records that
encode the absolute distance between labeled sites in their length. We will first develop and calibrate the
molecular ruler technology on a flat DNA origami substrate (Aim 1.1) and then test our ability to accurately
reconstruct the geometry of a 3D object with single-molecule resolution, in this case, an asymmetric wireframe
DNA origami tetrahedron (Aim 1.2). Next, we will develop the molecular technology on a population of fixed
K562 (human chronic myelogenous leukemia) cells to reconstruct aggregate chromosome geometry (Aim 2.1)
and then introduce single molecule barcodes to enable single molecule reconstruction of chromosome
geometry (Aim 2.2). This approach will give us the ability to assay chromosome geometry in a wide variety and
number of cell states and types, at single cell resolution, while also providing critical spatial context that will
help computer models reconstruct chromosome geometry in single cells. This ability is critical in answering
questions about the role played by chromosome architecture in carcinogenesis and the cancer phenotype.

## Key facts

- **NIH application ID:** 9851868
- **Project number:** 5R21CA235421-02
- **Recipient organization:** HARVARD UNIVERSITY
- **Principal Investigator:** Peng Yin
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $245,993
- **Award type:** 5
- **Project period:** 2019-02-01 → 2022-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9851868

## Citation

> US National Institutes of Health, RePORTER application 9851868, Elucidating chromatin organization with molecular rulers (5R21CA235421-02). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9851868. Licensed CC0.

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