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Related Experiment Video

Updated: May 26, 2026

Dissection of Enhancer Function Using Multiplex CRISPR-based Enhancer Interference in Cell Lines

Dissection of Enhancer Function Using Multiplex CRISPR-based Enhancer Interference in Cell Lines

Published on: June 2, 2018

An InDel Genomic Variant within a Bifunctional Super-Enhancer for LINC00636 and CD47 Regulation in Breast Cancer.

Carolina Dibenedetto¹, Amelia Tsark¹, Daniza Acenas¹

¹Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA.

Research Square

|May 25, 2026

Summary

A common genetic variant in breast cancer super-enhancers influences gene expression and tumor progression. This insertion-deletion variant affects chromatin accessibility, impacting cancer-promoting genes and immune cell interactions.

Keywords:

CD47 LINC00636 Super-enhancer breast cancer genomic variation

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Last Updated: May 26, 2026

Dissection of Enhancer Function Using Multiplex CRISPR-based Enhancer Interference in Cell Lines

Dissection of Enhancer Function Using Multiplex CRISPR-based Enhancer Interference in Cell Lines

Published on: June 2, 2018

Area of Science:

Genomics
Cancer Biology
Epigenetics

Background:

Super-enhancers are crucial regulatory elements in cancer.
The role of genomic variation within super-enhancers is not well understood.
Cancer-promoting genes like LINC00636 and CD47 are implicated in breast cancer.

Purpose of the Study:

To investigate the impact of genomic variation in a breast cancer super-enhancer.
To identify the regulatory function of a specific super-enhancer and its associated genes.
To understand how genetic variants affect chromatin accessibility and gene expression in breast cancer.

Main Methods:

Identification of a bifunctional super-enhancer regulating LINC00636 and CD47.
Analysis of a common germline insertion-deletion variant within the super-enhancer.
Assessment of chromatin accessibility changes upon variant deletion.
Evaluation of gene expression (LINC00636, CD47) and cellular phenotypes (apoptosis resistance, senescence, macrophage infiltration).

Main Results:

A common germline insertion variant reduces chromatin accessibility at the super-enhancer.
Deletion of the insertion increases accessibility, upregulating LINC00636 and CD47.
Upregulation of CD47 enhances resistance to nutrient-deprivation-induced apoptosis.
Elevated LINC00636 activates senescence and delays cell death.
Reduced infiltration of CD80+ pro-inflammatory macrophages was observed.

Conclusions:

A common insertion-deletion variant fine-tunes the regulatory activity of a bifunctional super-enhancer.
The insertion allele may play a protective role in breast cancer.
LINC00636 has a previously unrecognized role in senescence and breast cancer biology.
This variant impacts tumor-promoting features and immune interactions.