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| Status |
Public on Aug 11, 2023 |
| Title |
Transposable elements as lineage-specific enhancers in endodermal-lineage cancers (ChIP-Seq) |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Transposable elements (TE) are repetitive genomic elements that harbor binding sites for human transcription factors (TF). A regulatory role for TEs has been suggested in embryonal development and diseases such as cancer but systematic investigation of their functions has been limited by their widespread silencing in the genome. Here, we have utilized unbiased massively parallel reporter assay data using whole human genome library to identify TEs with functional enhancer activity in two human cancer types of endodermal lineage, colorectal and liver cancers. We show that the identified TE enhancers are characterized by genomic features associated with active enhancers, such as epigenetic marks and TF binding. Importantly, we identified distinct TE subfamilies that function as tissue-specific enhancers, namely MER11- and LTR12-elements in colon and liver cancers, respectively. These elements are bound by distinct TFs in each cell type, and they have predicted associations to differentially expressed genes. In conclusion, these data demonstrate how different cancer types can utilize distinct TEs as tissue-specific enhancers.
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| Overall design |
Transcription factor binding and chromatin accessibility were determined by ChIP-seq and ATAC-seq in GP5d cells. Gene expression profiling for GP5d and primary colon epithelial cells (DMSO treated or DNMT-HDAC inhibited) was performed by RNA-seq.
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| Contributor(s) |
Karttunen K, Patel D, Xia J, Fei L, Palin K, Aaltonen L, Sahu B |
| Citation(s) |
37658059 |
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| Submission date |
Dec 15, 2022 |
| Last update date |
Sep 15, 2023 |
| Contact name |
Konsta Karttunen |
| Organization name |
University of Helsinki
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| Street address |
Haartmaninkatu 8
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| City |
Helsinki |
| ZIP/Postal code |
00290 |
| Country |
Finland |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (7)
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| This SubSeries is part of SuperSeries: |
| GSE221053 |
Transposable elements as lineage-specific enhancers in endodermal-lineage cancers |
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| Relations |
| BioProject |
PRJNA912663 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE221046_RAW.tar |
1.1 Gb |
(http)(custom) |
TAR (of BROADPEAK, BW, NARROWPEAK) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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