# Elucidating the role of chromatin architecture in the pathophysiology of Cornelia de Lange Syndrome

> **NIH NIH F31** · UNIVERSITY OF PENNSYLVANIA · 2022 · $7,823

## Abstract

PROJECT SUMMARY
Cornelia de Lange Syndrome (CdLS) is a multi-system genetic disorder caused by mutations in the regulatory
or structural components of the cohesin complex. Cohesin mediates sister chromatid cohesion during mitosis
and is theorized to extrude DNA throughout interphase to form enhancer-promoter chromatin loops and
maintain self-interacting clusters of DNA called topologically associating domains (TADs). Chromosome
instability is rarely observed in patients. Rather, widespread transcriptional changes have been identified
across CdLS patient samples, implicating the structural role of cohesin in the pathogenesis of the disorder. I
hypothesize that in the absence of cohesin, chromatin loops that mediate enhancer-promoter interactions are
disrupted and instead contacts form between genes and proximal regulatory elements. I further expect that this
enhancer reorganization will affect gene expression at the level of transcriptional bursting. To visualize
chromatin organization in single cells, I have designed Oligopaints to probe neighboring TADs in the human
genome by fluorescence in situ hybridization (FISH). My preliminary data indicate this assay is sensitive to
detect changes in local chromosome topology following acute cohesin depletion by both conventional and
super resolution microscopy. Therefore, I will apply this and other assays to answer questions regarding the
mechanisms by which cohesin folds chromatin to facilitate transcription at the single cell level. In aim 1, I will
determine the effect of cohesin loss on promoter topology and transcriptional regulation. To study the role of
cohesin in these processes, I will perform these experiments in a cell culture model that facilitates acute
cohesin degradation. I will apply a high-throughput RNA FISH technique, seq-FISH, to assess changes in
bursting frequencies genome-wide. Then, I will map differences in enhancer-promoter contacts in effort to
explain the altered gene expression using a high-resolution Capture-C method. In aim 2, I will detect
signatures of chromatin disorganization and transcriptional bursting changes in CdLS. I will probe TAD
organization and nascent gene expression in cells derived from CdLS patients. I will then relate phenotypes to
the mutation type, clinical severity, and cohesin abundance in each patient. Together, these aims will illuminate
the relationship between transcriptional regulation and local genomic architecture while providing new
mechanisms to explain how chromosome misfolding may lead to developmental disorders such as CdLS.

## Key facts

- **NIH application ID:** 10441509
- **Project number:** 5F31HD102084-03
- **Recipient organization:** UNIVERSITY OF PENNSYLVANIA
- **Principal Investigator:** Jennifer Mary Luppino
- **Activity code:** F31 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $7,823
- **Award type:** 5
- **Project period:** 2020-07-01 → 2022-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10441509

## Citation

> US National Institutes of Health, RePORTER application 10441509, Elucidating the role of chromatin architecture in the pathophysiology of Cornelia de Lange Syndrome (5F31HD102084-03). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10441509. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*