Chromatin immunoprecipitation sequencing(Ch IP-seq)and the Assay for Transposase-Accessible Chromatin with high-throughput sequencing(ATAC-seq)have become essential technologies to effectively measure protein–DNA int...Chromatin immunoprecipitation sequencing(Ch IP-seq)and the Assay for Transposase-Accessible Chromatin with high-throughput sequencing(ATAC-seq)have become essential technologies to effectively measure protein–DNA interactions and chromatin accessibility.However,there is a need for a scalable and reproducible pipeline that incorporates proper normalization between samples,correction of copy number variations,and integration of new downstream analysis tools.Here we present Containerized Bioinformatics workflow for Reproducible Ch IP/ATAC-seq Analysis(Co BRA),a modularized computational workflow which quantifies Ch IP-seq and ATAC-seq peak regions and performs unsupervised and supervised analyses.Co BRA provides a comprehensive state-of-the-art Ch IP-seq and ATAC-seq analysis pipeline that can be used by scientists with limited computational experience.This enables researchers to gain rapid insight into protein–DNA interactions and chromatin accessibility through sample clustering,differential peak calling,motif enrichment,comparison of sites to a reference database,and pathway analysis.Co BRA is publicly available online at https://bitbucket.org/cfce/cobra.展开更多
BRAF is a serine/threonine kinase that harbors activating mutations in^7%of human malignancies and^60%of melanomas.Despite initial clinical responses to BRAF inhibitors,patients frequently develop drug resistance.To i...BRAF is a serine/threonine kinase that harbors activating mutations in^7%of human malignancies and^60%of melanomas.Despite initial clinical responses to BRAF inhibitors,patients frequently develop drug resistance.To identify candidate therapeutic targets for BRAF inhibitor resistant melanoma,we conduct CRISPR screens in melanoma cells harboring an activating BRAF mutation that had also acquired resistance to BRAF inhibitors.To investigate the mechanisms and pathways enabling resistance to BRAF inhibitors in melanomas,we integrate expression,ATAC-seq,and CRISPR screen data.We identify the JUN family transcription factors and the ETS family transcription factor ETV5 as key regulators of CDK6,which together enable resistance to BRAF inhibitors in melanoma cells.Our findings reveal genes contributing to resistance to a selective BRAF inhibitor PLX4720,providing new insights into gene regulation in BRAF inhibitor resistant melanoma cells.展开更多
基金funding from the National Institutes of Health,United States(Grant Nos.2PO1CA163227 and P01CA250959)。
文摘Chromatin immunoprecipitation sequencing(Ch IP-seq)and the Assay for Transposase-Accessible Chromatin with high-throughput sequencing(ATAC-seq)have become essential technologies to effectively measure protein–DNA interactions and chromatin accessibility.However,there is a need for a scalable and reproducible pipeline that incorporates proper normalization between samples,correction of copy number variations,and integration of new downstream analysis tools.Here we present Containerized Bioinformatics workflow for Reproducible Ch IP/ATAC-seq Analysis(Co BRA),a modularized computational workflow which quantifies Ch IP-seq and ATAC-seq peak regions and performs unsupervised and supervised analyses.Co BRA provides a comprehensive state-of-the-art Ch IP-seq and ATAC-seq analysis pipeline that can be used by scientists with limited computational experience.This enables researchers to gain rapid insight into protein–DNA interactions and chromatin accessibility through sample clustering,differential peak calling,motif enrichment,comparison of sites to a reference database,and pathway analysis.Co BRA is publicly available online at https://bitbucket.org/cfce/cobra.
基金supported by grants from the National Natural Science Foundation of China(Grant No.81872290)the National Key R&D Program of China(Grant No.2017YFC0908500)
文摘BRAF is a serine/threonine kinase that harbors activating mutations in^7%of human malignancies and^60%of melanomas.Despite initial clinical responses to BRAF inhibitors,patients frequently develop drug resistance.To identify candidate therapeutic targets for BRAF inhibitor resistant melanoma,we conduct CRISPR screens in melanoma cells harboring an activating BRAF mutation that had also acquired resistance to BRAF inhibitors.To investigate the mechanisms and pathways enabling resistance to BRAF inhibitors in melanomas,we integrate expression,ATAC-seq,and CRISPR screen data.We identify the JUN family transcription factors and the ETS family transcription factor ETV5 as key regulators of CDK6,which together enable resistance to BRAF inhibitors in melanoma cells.Our findings reveal genes contributing to resistance to a selective BRAF inhibitor PLX4720,providing new insights into gene regulation in BRAF inhibitor resistant melanoma cells.
