# CRISPR-based Enhanced Molecular Chipper Technology for Identifying Functional Noncoding Elements in Cancer

> **NIH NIH R33** · YALE UNIVERSITY · 2020 · $395,674

## Abstract

PROJECT SUMMARY
 More than 98% of the human genome is composed of non-coding sequences. Noncoding
genomic elements, such as regulatory elements for gene expression and noncoding RNAs, are
increasingly being recognized to play critical roles in cancer biology. However, large-scale unbiased
functional characterization of noncoding genomic elements in cancer remains a major challenge. This
project proposes the development of a CRISPR-based Version2 Molecular Chipper technology to
transform the research of the noncoding genome in cancer. The CRISPR-technology allows the use
of programmable small RNAs, or single-guide RNAs (sgRNAs), to modify the genome at specific loci
on both alleles. Based on this principle, we recently published the Version1 Molecular Chipper
technology that uses standard molecular biology techniques to create dense-tiling sgRNA library for
functional mapping of noncoding genomic regions. Compared to the existing method of microarray-
based synthesis of sgRNAs, this Version1 technology has proven to be inexpensive, not limited in the
total number of sgRNAs, easily adoptable by regular cancer research laboratories, and importantly,
powerful for the identification of novel noncoding regulatory elements. However, this Version1
technology has a major weakness in that most of the sgRNAs in the library are not PAM (protospacer
adjacent motif)-specific. This weakness renders the library from the Version1 technology being
inefficient for functional mapping, and thus prevents this method to be truly transformative. Here we
propose a major improvement (Version2) to overcome this weakness, which is expected to increase
the efficiency by ~16 fold, to fully unleash the power of the Molecular Chipper technology. We will
achieve this through two complementary aims, with the first aim designed to develop the method and
the second aim designed to validate the technology through functional mapping of noncoding
regulatory elements controlling the expression of a key haploinsufficient tumor suppressor. This
proposed Version2 Molecular Chipper technology addresses the existing bottleneck on functional
mapping of the noncoding cancer genome. Successful development of this technology will allow its
use across wide areas of cancer research, and help the acceleration of research to understand the
functions of the noncoding genome in cancer.

## Key facts

- **NIH application ID:** 9924488
- **Project number:** 5R33CA225863-03
- **Recipient organization:** YALE UNIVERSITY
- **Principal Investigator:** Jun Lu
- **Activity code:** R33 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $395,674
- **Award type:** 5
- **Project period:** 2018-05-01 → 2022-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9924488

## Citation

> US National Institutes of Health, RePORTER application 9924488, CRISPR-based Enhanced Molecular Chipper Technology for Identifying Functional Noncoding Elements in Cancer (5R33CA225863-03). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9924488. Licensed CC0.

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