# A low-input microfluidic ChIRP-seq technology for studying endogenous lncRNA binding

> **NIH NIH R01** · VIRGINIA POLYTECHNIC INST AND ST UNIV · 2021 · $278,523

## Abstract

Project Summary
Long non-coding RNAs (lncRNAs) are >200 bp in length and bear no protein-coding potential. About 27,000
lncRNAs have been identified so far, most of which have versatile or unknown biological functions. LncRNAs
have cell-type-specific expression that responds to environmental stimuli and developmental cues. lncRNAs
may serve as molecular signals, decoys, guides, and scaffolds during their regulatory processes. Some
lncRNAs are known to play important roles in development and diseases. Thus there is clear potential that they
participate widely in the regulation of chromatin states and gene expression. Mapping of lncRNA binding sites
in the genome is particularly important for understanding their regulatory roles. Over the years, a number of
methods were developed to study genome-wide lncRNA-chromatin binding. ChIRP-seq (Chromatin Isolation
by RNA purification) uses antisense DNA oligonucleotide probes to capture crosslinked and fragmented
chromatin-lncRNA complexes before the purified genomic DNA is sequenced for lncRNA binding locations.
Although ChIRP-seq has been gaining popularity, the method is plagued by several major issues including
requirements of a huge number of starting cells, lncRNA overexpression, and tedious manual operation. In this
project, we will develop a low-input version of ChIRP-seq that allows testing using 10K-100K starting cells,
compared to tens of millions of cells required by current ChIRP-seq assay. This microfluidic ChIRP-seq
technology will pave the way for studies in primary cells and tissues with endogenous lncRNA level and native
lncRNA-chromatin interactions that bear direct biomedical relevance. Furthermore, the dramatic decrease in
the required input will also allow cell-type-specific profiling of lncRNA binding which is critical for understanding
cell-type-specific regulatory mechanisms. Our microfluidic technology offers much more reproducible, precise
and effective manipulation of magnetic beads during pulldown of lncRNA-chromatin complexes than manual
operation. The platform also offers fully automated and high-throughput processing, which will be important for
the eventual processing of a large number of patient samples in clinical setting.

## Key facts

- **NIH application ID:** 10180461
- **Project number:** 1R01GM141096-01
- **Recipient organization:** VIRGINIA POLYTECHNIC INST AND ST UNIV
- **Principal Investigator:** Chang Lu
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $278,523
- **Award type:** 1
- **Project period:** 2021-05-01 → 2025-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10180461

## Citation

> US National Institutes of Health, RePORTER application 10180461, A low-input microfluidic ChIRP-seq technology for studying endogenous lncRNA binding (1R01GM141096-01). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10180461. Licensed CC0.

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