TY - JOUR
T1 - An integrated platform for genome-wide mapping of chromatin states using high-throughput chip-sequencing in tumor tissues
AU - Terranova, Christopher
AU - Tang, Ming
AU - Orouji, Elias
AU - Maitituoheti, Mayinuer
AU - Raman, Ayush
AU - Amin, Samirkumar
AU - Liu, Zhiyi
AU - Rai, Kunal
N1 - Funding Information:
We thank Marcus Coyle, Curtis Gumbs, SMF core at MDACC for sequencing support. The work described in this article was supported by grants from the NIH grant (CA016672) to SMF Core and NCI awards (1K99CA160578 and R00CA160578) to K. R.
Publisher Copyright:
© 2018, Journal of Visualized Experiments. All rights reserved.
PY - 2018/4/5
Y1 - 2018/4/5
N2 - Histone modifications constitute a major component of the epigenome and play important regulatory roles in determining the transcriptional status of associated loci. In addition, the presence of specific modifications has been used to determine the position and identity non-coding functional elements such as enhancers. In recent years, chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) has become a powerful tool in determining the genome-wide profiles of individual histone modifications. However, it has become increasingly clear that the combinatorial patterns of chromatin modifications, referred to as Chromatin States, determine the identity and nature of the associated genomic locus. Therefore, workflows consisting of robust high-throughput (HT) methodologies for profiling a number of histone modification marks, as well as computational analyses pipelines capable of handling myriads of ChIP-Seq profiling datasets, are needed for comprehensive determination of epigenomic states in large number of samples. The HT-ChIP-Seq workflow presented here consists of two modules: 1) an experimental protocol for profiling several histone modifications from small amounts of tumor samples and cell lines in a 96-well format; and 2) a computational data analysis pipeline that combines existing tools to compute both individual mark occupancy and combinatorial chromatin state patterns. Together, these two modules facilitate easy processing of hundreds of ChIP-Seq samples in a fast and efficient manner. The workflow presented here is used to derive chromatin state patterns from 6 histone mark profiles in melanoma tumors and cell lines. Overall, we present a comprehensive ChIP-seq workflow that can be applied to dozens of human tumor samples and cancer cell lines to determine epigenomic aberrations in various malignancies.
AB - Histone modifications constitute a major component of the epigenome and play important regulatory roles in determining the transcriptional status of associated loci. In addition, the presence of specific modifications has been used to determine the position and identity non-coding functional elements such as enhancers. In recent years, chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) has become a powerful tool in determining the genome-wide profiles of individual histone modifications. However, it has become increasingly clear that the combinatorial patterns of chromatin modifications, referred to as Chromatin States, determine the identity and nature of the associated genomic locus. Therefore, workflows consisting of robust high-throughput (HT) methodologies for profiling a number of histone modification marks, as well as computational analyses pipelines capable of handling myriads of ChIP-Seq profiling datasets, are needed for comprehensive determination of epigenomic states in large number of samples. The HT-ChIP-Seq workflow presented here consists of two modules: 1) an experimental protocol for profiling several histone modifications from small amounts of tumor samples and cell lines in a 96-well format; and 2) a computational data analysis pipeline that combines existing tools to compute both individual mark occupancy and combinatorial chromatin state patterns. Together, these two modules facilitate easy processing of hundreds of ChIP-Seq samples in a fast and efficient manner. The workflow presented here is used to derive chromatin state patterns from 6 histone mark profiles in melanoma tumors and cell lines. Overall, we present a comprehensive ChIP-seq workflow that can be applied to dozens of human tumor samples and cancer cell lines to determine epigenomic aberrations in various malignancies.
KW - Cancer research
KW - ChIP-Seq
KW - Chromatin immunoprecipitation
KW - Chromatin state profiles
KW - Histone modification
KW - Human tumor tissue
KW - Issue 134
KW - Metastatic melanoma
KW - Next-generation sequencing
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U2 - 10.3791/56972
DO - 10.3791/56972
M3 - Article
C2 - 29683440
AN - SCOPUS:85045525832
SN - 1940-087X
VL - 2018
JO - Journal of Visualized Experiments
JF - Journal of Visualized Experiments
IS - 134
M1 - e56972
ER -