Comprehensive Analysis of Breast Cancer Cell Lines: Genome-wide Insights from ChIP-seq Analysis
Context: Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is the central system in epigenomic exploration. Chromatin immunoprecipitation coupled with sequencing (ChIP-seq) is an important technology to identify the genome-wide location of DNA-binding proteins such as histones proteins...
Saved in:
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wolters Kluwer Medknow Publications
2024-12-01
|
| Series: | Biomedical and Biotechnology Research Journal |
| Subjects: | |
| Online Access: | https://journals.lww.com/10.4103/bbrj.bbrj_338_24 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1841554794382098432 |
|---|---|
| author | Tanishq Sahu Ruchi Yadav |
| author_facet | Tanishq Sahu Ruchi Yadav |
| author_sort | Tanishq Sahu |
| collection | DOAJ |
| description | Context:
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is the central system in epigenomic exploration. Chromatin immunoprecipitation coupled with sequencing (ChIP-seq) is an important technology to identify the genome-wide location of DNA-binding proteins such as histones proteins, transcription factors, RNA polymerase, or any protein of interest. ChIP-seq has been used to study the binding sites and efficacy of drugs in cancer cell lines etc.
Aims:
In current research, breast cancer cell line data have been used to study the effect PADI2 (peptidyl arginine deiminase) gene in the progression of breast cancer. Further, this ChIP-seq data have also been used to study the binding site of Amanitin drug in breast cancer.
Settings and Design:
Breast cancer ChIP-seq data have been retrieved from the European Nucleotide Archive database with project Id PRJNA415426 short read archive. Four samples of FASTQ files were used and analyzed for the genome-wide analysis.
Materials and Methods:
Galaxy server (https://usegalaxy.org/) was used for complete ChIP-seq data analysis; different tools such as fast-quality control (QC), multi-QC, Bowtie2, model-based analysis of ChIP-sequencing, and ChIPseeker tools were used for motif enrichment and functional analysis. Motif analysis was done through the Multiple Expectation maximizations for Motif Elicitation database (https://meme-suite.org/meme/db/motifs).
Results:
Computational investigation demonstrates the binding sequences of the T47-D breast cancer cell line as TTTTGTATTTTTAGT, and this motif occurs 2123 times in the Homo Sapiens reference genome that is hg19.
Conclusions:
This research classifies the binding site and affinity of the T47-D human breast cancer cell line. Further, wet laboratory studies are required to verify the function of the predicted motifs and their importance in drug development or research in breast cancer. |
| format | Article |
| id | doaj-art-9ad2fe48dd44402db10c31c41fc4f5d5 |
| institution | Kabale University |
| issn | 2588-9834 2588-9842 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Wolters Kluwer Medknow Publications |
| record_format | Article |
| series | Biomedical and Biotechnology Research Journal |
| spelling | doaj-art-9ad2fe48dd44402db10c31c41fc4f5d52025-01-08T09:54:52ZengWolters Kluwer Medknow PublicationsBiomedical and Biotechnology Research Journal2588-98342588-98422024-12-018452453110.4103/bbrj.bbrj_338_24Comprehensive Analysis of Breast Cancer Cell Lines: Genome-wide Insights from ChIP-seq AnalysisTanishq SahuRuchi YadavContext: Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is the central system in epigenomic exploration. Chromatin immunoprecipitation coupled with sequencing (ChIP-seq) is an important technology to identify the genome-wide location of DNA-binding proteins such as histones proteins, transcription factors, RNA polymerase, or any protein of interest. ChIP-seq has been used to study the binding sites and efficacy of drugs in cancer cell lines etc. Aims: In current research, breast cancer cell line data have been used to study the effect PADI2 (peptidyl arginine deiminase) gene in the progression of breast cancer. Further, this ChIP-seq data have also been used to study the binding site of Amanitin drug in breast cancer. Settings and Design: Breast cancer ChIP-seq data have been retrieved from the European Nucleotide Archive database with project Id PRJNA415426 short read archive. Four samples of FASTQ files were used and analyzed for the genome-wide analysis. Materials and Methods: Galaxy server (https://usegalaxy.org/) was used for complete ChIP-seq data analysis; different tools such as fast-quality control (QC), multi-QC, Bowtie2, model-based analysis of ChIP-sequencing, and ChIPseeker tools were used for motif enrichment and functional analysis. Motif analysis was done through the Multiple Expectation maximizations for Motif Elicitation database (https://meme-suite.org/meme/db/motifs). Results: Computational investigation demonstrates the binding sequences of the T47-D breast cancer cell line as TTTTGTATTTTTAGT, and this motif occurs 2123 times in the Homo Sapiens reference genome that is hg19. Conclusions: This research classifies the binding site and affinity of the T47-D human breast cancer cell line. Further, wet laboratory studies are required to verify the function of the predicted motifs and their importance in drug development or research in breast cancer.https://journals.lww.com/10.4103/bbrj.bbrj_338_24binding sitesbreast cancerchip-seqgalaxygenomicsmotif |
| spellingShingle | Tanishq Sahu Ruchi Yadav Comprehensive Analysis of Breast Cancer Cell Lines: Genome-wide Insights from ChIP-seq Analysis Biomedical and Biotechnology Research Journal binding sites breast cancer chip-seq galaxy genomics motif |
| title | Comprehensive Analysis of Breast Cancer Cell Lines: Genome-wide Insights from ChIP-seq Analysis |
| title_full | Comprehensive Analysis of Breast Cancer Cell Lines: Genome-wide Insights from ChIP-seq Analysis |
| title_fullStr | Comprehensive Analysis of Breast Cancer Cell Lines: Genome-wide Insights from ChIP-seq Analysis |
| title_full_unstemmed | Comprehensive Analysis of Breast Cancer Cell Lines: Genome-wide Insights from ChIP-seq Analysis |
| title_short | Comprehensive Analysis of Breast Cancer Cell Lines: Genome-wide Insights from ChIP-seq Analysis |
| title_sort | comprehensive analysis of breast cancer cell lines genome wide insights from chip seq analysis |
| topic | binding sites breast cancer chip-seq galaxy genomics motif |
| url | https://journals.lww.com/10.4103/bbrj.bbrj_338_24 |
| work_keys_str_mv | AT tanishqsahu comprehensiveanalysisofbreastcancercelllinesgenomewideinsightsfromchipseqanalysis AT ruchiyadav comprehensiveanalysisofbreastcancercelllinesgenomewideinsightsfromchipseqanalysis |