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| Status |
Public on Jan 18, 2016 |
| Title |
Dissection of transcriptional and cis-regulatory control of differentiation in human pancreatic cancer [ChIP-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
The histological grade of carcinomas describes the ability of tumor cells to organize differentiated epithelial structures and has prognostic impact. Molecular control of differentiation in normal and cancer cells relies on lineage-determining transcription factors (TFs) that activate the repertoire of cis-regulatory elements controlling cell type-specific transcriptional outputs. TF recruitment to cognate genomic DNA binding sites results in the deposition of histone marks characteristic of enhancers and other cis-regulatory elements. Here we integrated transcriptomics and genome-wide analysis of chromatin marks in human pancreatic ductal adenocarcinoma (PDAC) cells of different grade to identify first, and then experimentally validate the sequence-specific TFs controlling grade-specific gene expression. We identified a core set of TFs with a pervasive binding to the enhancer repertoire characteristic of differentiated PDACs and controlling different modules of the epithelial gene expression program. Defining the regulatory networks that control the maintenance of epithelial differentiation of PDAC cells will help determine the molecular basis of PDAC heterogeneity and progression.
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| Overall design |
Chromatin from human pancreatic ductal adenocarcinoma cell lines was immunoprecipitated with different antibodies for histone modifications and transcription factors and subjected to multiparallel sequencing. Experiments were carried out in unmodified cells and genome edited clonal CFPAC1 cells.
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| Contributor(s) |
Balestrieri C, Diaferia G, Natoli G |
| Citation(s) |
26769127 |
| |
| Submission date |
Dec 29, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Chiara Balestrieri |
| E-mail(s) |
balestrieri.c@gmail.com
|
| Organization name |
IRCCS San Raffaele Scientific Institute
|
| Department |
Center for Omics Sciences
|
| Street address |
Via Olgettina 58
|
| City |
Milan |
| ZIP/Postal code |
20132 |
| Country |
Italy |
| |
|
| Platforms (2) |
| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
|
| Samples (56)
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| This SubSeries is part of SuperSeries: |
| GSE64560 |
Dissection of transcriptional and cis-regulatory control of differentiation in human pancreatic cancer. |
|
| Relations |
| BioProject |
PRJNA271302 |
| SRA |
SRP051604 |
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