# Multiscale exploration of the functional non-coding genome

> **NIH NIH R35** · MASSACHUSETTS GENERAL HOSPITAL · 2021 · $507,642

## Abstract

PROJECT SUMMARY
Most disease- or trait-associated genetic variants lie within non-coding sequences of the genome such as
enhancers, promoters and insulators. Those sequences regulate gene expression, play critical roles in
determining disease severity and may serve as targets for novel rational therapeutic interventions.
However, we still lack insights on the exact mechanisms by which non-coding sequences are translated
into function and on the impact of genetic variation within them. CRISPR perturbations of non-coding
elements, offer unprecedented opportunities for assessing their function in a myriad of developmental and
disease settings. We hypothesize that an improved understanding of non-coding sequences by direct
perturbation in their endogenous context, and with a direct readout of the genetic perturbations, will offer
new opportunities to therapeutically intervene in human disease. The long-term goal of our work is to
overcome the limitations of the current strategies to study the non-coding genome. Our overall vision is to
push our understanding of the mechanisms of action of non-coding sequences on gene expression at
nucleotide resolution and single-cell level. The main objective of this proposal is a multi-scale discovery and
dissection of regulatory elements by combining CRISPR targeted perturbations and single cell assays with
two key goals: (1) Uncover functional non-coding elements with unbiased and generalizable approaches for
different cell types and elucidate their regulatory grammar and mechanisms of action on gene expression.
(2) Study how endogenous or perturbation induced mutations in non-coding sequences are reflected in
gene expression programs at a single-cell level. To pilot our conceptual framework, we will study the non-
coding regulatory elements within the BCL11A gene, a master regulator of the hemoglobin switch and a
therapeutic target for sickle cell disease (SCD) and β-thalassemia. In fact, several clinical trials (e.g.
NCT03432364) are underway aiming to disrupt regulatory sequences at BCL11A as a therapy for these β-
hemoglobin disorders. This is one of the most well-studied loci identified by GWAS and is a system in
which we have extensive experience and expertise. However, our approaches will also be generally
applicable to other loci linked to traits or diseases. At the end of this project we will provide a general
framework and user-friendly computational tools to study the function and the structure of non-coding
regulatory sequences generalizable to different perturbation screens, regulatory regions, cell types and
phenotypes. Importantly, all the computational tools developed in this proposal will be shared with NHGRI
funded consortia with similar goals such as ENCODE, and with the broader scientific community. We
anticipate that the proposed research could have a positive translational impact providing the foundation to
develop strategies involving non-coding sequence perturbations with direct therapeuti...

## Key facts

- **NIH application ID:** 10170407
- **Project number:** 5R35HG010717-03
- **Recipient organization:** MASSACHUSETTS GENERAL HOSPITAL
- **Principal Investigator:** Luca Pinello
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $507,642
- **Award type:** 5
- **Project period:** 2019-09-01 → 2024-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10170407

## Citation

> US National Institutes of Health, RePORTER application 10170407, Multiscale exploration of the functional non-coding genome (5R35HG010717-03). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10170407. Licensed CC0.

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