Yuwen Liu, Shan Yu, Vineet K Dhiman, Tonya Brunetti, Heather Eckart et al.
Background: Genome-wide quantification of enhancer activity in the human genome has proven to be a challenging problem. Recent efforts have led to the development of powerful tools for enhancer quantification. However, because of genome size and complexity, these tools have yet to be applied to the whole human genome. Results: In the current study, we use a human prostate cancer cell line, LNCaP as a model to perform whole human genome STARR-seq (WHG-STARR-seq) to reliably obtain an assessment of enhancer activity. This approach builds upon previously developed STARR-seq in the fly genome and CapSTARR-seq techniques in targeted human genomic regions. With an improved library preparation strategy, our approach greatly increases the library complexity per unit of starting material, which makes it feasible and cost-effective to explore the landscape of regulatory activity in the much larger human genome. In addition to our ability to identify active, accessible enhancers located in open chromatin regions, we can also detect sequences with the potential for enhancer activity that are located in inaccessible, closed chromatin regions. When treated with the histone deacetylase inhibitor, Trichostatin A, genes nearby this latter class of enhancers are up-regulated, demonstrating the potential for endogenous functionality of these regulatory elements. Conclusion: WHG-STARR-seq provides an improved approach to current pipelines for analysis of high complexity genomes to gain a better understanding of the intricacies of transcriptional regulation.
Yuwen Liu, Shan Yu, Vineet K Dhiman, Tonya Brunetti, Heather Eckart, Kevin P White. Functional assessment of human enhancer activities using whole-genome STARR-sequencing. 2017-11-20. https://doi.org/10.1186/s13059-017-1345-5
An episomal WHG-STARR-seq library of randomly sheared human genomic fragments was tested in the human prostate cancer cell line LNCaP using the SCP1 minimal promoter. Two biological replicates were pooled for MACS2 peak calling against the input plasmid library; the packaged table contains 94,527 unique active enhancer peaks passing the reported q-value threshold.
Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.
Download all 11 files (ZIP)13059_2017_1345_MOESM1_ESM.pdf13059_2017_1345_MOESM2_ESM.xlsx13059_2017_1345_MOESM3_ESM.xlsx13059_2017_1345_MOESM4_ESM.xlsxGSE82204_150923_TSA_edgeR_gene_table.txt.gzGSE82204_160505_TSA_diff_ATAC_Seq.txt.gzGSE82204_2015-2249-2250-2251_bff_100_fseq_35bp_map_pool.sorted.top40995.bed.gzGSE82204_2015-2252-2253-2254_bff_100_fseq_35bp_map_pool.sorted.top38813.bed.gzGSE82204_enhancer_not_overlapped_dnase.txt.gzGSE82204_enhancer_overlap_dnase.txt.gzGSE82204_family.soft.gz