Xie, J.-J. | bioRxiv Science

bioRxiv2022

eccDB: a comprehensive repository for eccDNA-mediated chromatin contacts in multi-species

The role of extrachromosomal circular DNA (eccDNA) has been highlighted. More recently, eccDNA-chromosome interactions were identified, suggesting a potential role of eccDNA in transcriptional regulation. Several databases currently provide valuable resources for the study of eccDNAs. However, these databases are primarily focused on Human eccDNAs and do not provide analysis of eccDNA-chromosome interaction and eccDNA gene expression in different tissues. Herein, to further integrate available resources for eccDNA data across multiple species, we developed the eccDB database. The current version of eccDB has collected a total of 1,317,182 eccDNAs in 424 samples from four species (homo sapiens, mus musculus, saccharomyces cerevisiae, and arabidopsis thaliana). eccDB provides regulatory and epigenetic information on eccDNA, including typical enhancers, super-enhancers, transcription factors, DNA methylation positions, risk SNPs, expression quantitative trait locus, chromatin accessibility regions, and chromHMM states. In particular, eccDB provides eccDNAs intrachromosomal and interchromosomal interaction analysis to predict the transcriptional regulatory functions of eccDNA. Moreover, eccDB identifies eccDNAs from unknown DNA sequences and analyzes the functional and evolutionary relationships of an eccDNA among different species. Overall, eccDB offers web-based analytical tools and a comprehensive resource for biologists and clinicians to decipher the molecular regulatory mechanisms of eccDNA. eccDB is freely available at http://www.xiejjlab.bio/eccDB

bioinformatics↗

bioRxiv2019

TP63, SOX2 and KLF5 Establish Core Regulatory Circuitry and Construct Cancer Specific Epigenome in Esophageal Squamous Cell Carcinoma

Transcriptional network is controlled by master transcription factors (TFs) and cis-regulatory elements through interacting with target sequences and recruiting epigenetic regulators. By integration of enhancer profiling and chromatin accessibility, we establish super-enhancer (SE) mediated core regulatory circuitry (CRC) for esophageal squamous cell carcinoma (ESCC) and identify tumor cells-dependent CRC TFs-TP63, SOX2 and KLF5. They preferentially co-occupy SE loci and form a positive interconnected auto-regulatory loop through SEs to orchestrate chromatin and transcriptional programming. SE-associated oncogene-ALDH3A1 is identified as a novel CRC target contributing to ESCC viability. Using circular chromosome conformation capture sequencing (4C-seq) and CRISPR/Cas9 genome editing, the direct interaction between TP63 promoter and functional enhancers which is mediated by CRC TFs is identified. Deletion of each enhancer decreases expression of CRC TFs and impairs cell viability, phenocopying the knockdown of each CRC TF. Targeting epigenetic regulation by inhibition of either the BET bromodomain or HDAC disrupts the CRC program and its dependent global epigenetic modification, consequently suppressing ESCC tumor growth. Importantly, combination of both compounds result in synergistic anti-tumor effect.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=162 SRC=\"FIGDIR/small/825372v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (58K):\norg.highwire.dtl.DTLVardef@1a9f923org.highwire.dtl.DTLVardef@238c90org.highwire.dtl.DTLVardef@1e14f58org.highwire.dtl.DTLVardef@120249a_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LISuper-enhancers mediated transcriptional regulatory circuitry is established for ESCC\nC_LIO_LITP63, SOX2 and KLF5 as CRC TFs co-localize super-enhancer loci to orchestrate chromatin accessibility and transcriptional dysregulation\nC_LIO_LIComplex interaction between functional enhancers and TP63 promoter is mediated by CRC TFs\nC_LIO_LIALDH3A1 is a key downstream target of ESCC CRC and is essential for ESCC cell survival\nC_LIO_LIBET degrader-ARV-771 and HDAC inhibitor-Romidepsin synergistically inhibit ESCC tumor growth\nC_LI

cancer biology↗