# Determining the influence of 3D chromatin structure on human evolution

> **NIH NIH F31** · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · 2022 · $23,910

## Abstract

PROJECT SUMMARY/ABSTRACT
The importance of 3D genome structure on the evolution of human specific gene regulation,
phenotypes, and speciation remains largely unknown. Here, I plan to characterize in a high-
throughput manner the impact of topologically associated domains (TADs), which are genomic
neighborhoods of self-interacting DNA, and CCCTC binding factor (CTCF) binding motifs, which
help facilitate DNA looping, on cell viability and evolution. I hypothesize that a subset of TAD
boundaries are critical for maintaining important gene regulation throughout evolution
and that derived CTCF binding sites in the human lineage may have led to gene
expression changes. I will interrogate this hypothesis by first performing a high-throughput
CRISPR-deletion screen in which I will delete a set of over 300 evolutionarily conserved and
human specific TAD boundaries in a human haploid cell line to determine if any of these
boundaries are essential for cell viability (Aim 1). Second, I will identify human specific CTCF
binding motifs that are gained or lost in humans or have orientation changes by comparing
genome sequences from human, chimpanzee, and two extinct archaic hominids: Neanderthal
and Denisovan. I will further interrogate the importance of a subset of these novel CTCF sites
by CRISPR/Cas9 editing human cells to mimic that of an extinct genome and phenotype them
for changes in gene expression changes and chromatin conformation. It will then be possible to
determine if these changes caused differences in gene regulation and genome looping (Aim 2).
Combined, this proposal will take a crucial step in further understanding how 3D chromatin
structure can affect phenotypes especially as it relates to human evolution.

## Key facts

- **NIH application ID:** 10473729
- **Project number:** 5F31HG011568-03
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
- **Principal Investigator:** Lana Harshman
- **Activity code:** F31 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $23,910
- **Award type:** 5
- **Project period:** 2020-09-16 → 2022-11-18

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10473729

## Citation

> US National Institutes of Health, RePORTER application 10473729, Determining the influence of 3D chromatin structure on human evolution (5F31HG011568-03). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10473729. Licensed CC0.

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