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HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries

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TSCRE: a comprehensive database for tumor-specific cis-regulatory elements.

Guanjie Peng^1,2,3, Bingyuan Liu^1,2,3, Mohan Zheng²

¹Clinical Big Data Research Center, Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China.

|January 12, 2024

Summary

This summary is machine-generated.

The TSCRE database catalogs dysregulated cis-regulatory elements (CREs) and super cis-regulatory elements (SCREs) in human cancers. This resource aids in identifying novel cancer biomarkers and understanding gene regulation in tumors.

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Area of Science:

Genomics and Cancer Biology
Non-coding DNA and Gene Regulation

Background:

Cis-regulatory elements (CREs) and super cis-regulatory elements (SCREs) are crucial non-coding DNA regions controlling gene transcription and development.
Altered CRE and SCRE activity is linked to oncogene and tumor suppressor dysregulation, impacting cancer progression.
A comprehensive resource for dysregulated CREs and SCREs in human cancers is needed.

Purpose of the Study:

To establish TSCRE, an open-access database cataloging tumor-specific and cell type-specific CREs and SCREs in human cancers.
To provide a valuable platform for discovering candidate cancer biomarkers and investigating gene regulatory mechanisms.

Main Methods:

Re-analysis of publicly available histone modification profiles from 1366 human patient samples across 17 cancer types.
Identification and annotation of dysregulated CREs and SCREs using 9 histone marks.
Integration of comprehensive annotations including gene associations, expression, mutations, and clinical data.

Main Results:

TSCRE contains 1,864,941 dysregulated CREs and 68,253 dysregulated SCREs.
Over 95% of identified elements are validated in public resources.
The database offers detailed annotations and integrated pathway/transcription factor enrichment analyses.

Conclusions:

TSCRE provides a comprehensive and validated resource for exploring dysregulated CREs and SCREs in human cancers.
The platform facilitates in-depth functional investigations and the discovery of potential cancer biomarkers and therapeutic targets.