# Decoding chromosome structure with multiplexed super-resolution microscopy

> **NIH NIH R01** · HARVARD UNIVERSITY · 2020 · $546,650

## Abstract

Summary
Decades of study have revealed that genome organization is non-random and critically impacts many nuclear
processes including the regulation of transcription, DNA replication, and DNA repair, and increasing evidence
suggests that the three-dimensional structures adopted by chromosomes are critical for development and are
often perturbed in disease. Much of our current understanding comes from biochemical techniques performed
on large populations of cells, leading to many gaps in our understanding of the mechanisms that establish and
maintain organizational states, particularly in the context of individual cells. We propose to introduce a new set
of single-cell technologies based on the single-molecule super-resolution imaging method DNA-PAINT to
bridge this gap with a suite of tools possessing both high multiplexibility and spatial resolution. Specifically, in
Aim 1 we will develop a multiplexed (>20 color) super-resolution chromosomal imaging strategy to image
genomic targets ranging from kilobases to multiple megabases in Iength, which will enable us to investigate the
folding properties of the chromatin fiber in single cells over a range of length-scales. In Aim 2, we will develop
multiplexed assays to co-localize proteins, RNA molecules, and specific genomic sites in individual cells at the
nanoscale. We will then investigate organization of architectural proteins at a model hub of large chromatin
loops on the human inactive X-chromosome. In Aim 3, we will develop a proximity-dependent super-resolution
method to probe specific interactions between protein and DNA targets that will allow for the sensitive
detection of molecular interactions in crowded environments. We will deploy this technology to query the
composition and epigenetic states of the aforementioned chromatin looping hub in individual cells. Collectively,
our methods will make many questions about the positioning, composition, and epigenetic states of specific
genomic loci in individual cells accessible to researchers for the first time, and promise to impact diverse fields
beyond chromosome biology.

## Key facts

- **NIH application ID:** 9999613
- **Project number:** 5R01GM124401-03
- **Recipient organization:** HARVARD UNIVERSITY
- **Principal Investigator:** Peng Yin
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $546,650
- **Award type:** 5
- **Project period:** 2018-09-01 → 2022-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9999613

## Citation

> US National Institutes of Health, RePORTER application 9999613, Decoding chromosome structure with multiplexed super-resolution microscopy (5R01GM124401-03). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/9999613. Licensed CC0.

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