E06BB3E62
HepG2 random-enhancer STARR-seq
A random N170 enhancer library was assayed in HepG2 cells using an episomal STARR-seq reporter. The table contains motif-match RNA/input activity effects for the 1,121 deposited motif models.
Sequence determinants of human gene regulatory elements
Biswajyoti Sahu, Tuomo Hartonen, Päivi Pihlajamaa, Bei Wei, Kashyap Dave et al.
About this study
DNA can determine where and when genes are expressed, but the full set of sequence determinants that control gene expression is unknown. Here, we measured the transcriptional activity of DNA sequences that represent an ~100 times larger sequence space than the human genome using massively parallel reporter assays (MPRAs). Machine learning models revealed that transcription factors (TFs) generally act in an additive manner with weak grammar and that most enhancers increase expression from a promoter by a mechanism that does not appear to involve specific TF–TF interactions. The enhancers themselves can be classified into three types: classical, closed chromatin and chromatin dependent. We also show that few TFs are strongly active in a cell, with most activities being similar between cell types. Individual TFs can have multiple gene regulatory activities, including chromatin opening and enhancing, promoting and determining transcription start site (TSS) activity, consistent with the view that the TF binding motif is the key atomic unit of gene expression.
Full author list & citation
Biswajyoti Sahu, Tuomo Hartonen, Päivi Pihlajamaa, Bei Wei, Kashyap Dave, Fangjie Zhu, Eevi Kaasinen, Katja Lidschreiber, Michael Lidschreiber, Carsten O. Daub, Patrick Cramer, Teemu Kivioja, Jussi Taipale. Sequence determinants of human gene regulatory elements. 2022-02-21. https://doi.org/10.1038/s41588-021-01009-4
Experiments 13
E06EB15EF
TP53-null GP5d CpG-methylated genomic STARR-seq
Approximately 500-bp sheared human genomic fragments were CpG-methylated before assay in the TP53-null GP5d clone using an episomal STARR-seq reporter. This table contains the source MACS2 narrowPeak calls for active genomic reporter fragments.
E20B8C189
HepG2 binary STARR-seq promoter motif activity
The random N150 promoter–enhancer binary STARR-seq library was assayed in HepG2 cells. This table presents the deposited promoter-motif RNA/input activity effects for the HepG2 condition.
E2F0667AA
GP5d binary random promoter–enhancer STARR-seq motif-pair assay
Random N150 sequences were paired as promoter and enhancer elements in a binary STARR-seq library and assayed in GP5d cells in two biological replicates. The table reports all 528,529 deposited GP5d replicate-1 motif pairs joined to individual promoter and enhancer motif activity effects from both replicates.
E312D2F18
hTERT-RPE1 binary STARR-seq promoter motif activity
The random N150 promoter–enhancer binary STARR-seq library was assayed in hTERT-RPE1 cells. This table presents the deposited promoter-motif RNA/input activity effects for the RPE1 condition.
E542AE7DA
GP5d TF-motif STARR-seq with Sasaki reporter
The synthetic transcription-factor motif library was cloned into the Sasaki promoter STARR-seq reporter and assayed in GP5d cells. This table contains pattern-level RNA/input activity effects for the Sasaki reporter condition.
E6D22FC11
GP5d random-enhancer STARR-seq
A random N170 enhancer library was assayed in GP5d cells in two biological replicates using STARR-seq. The table summarizes motif-match activity effects from both replicates and the corresponding HepG2 comparison output.
E6FB637CB
GP5d wild-type nonmethylated genomic STARR-seq
Approximately 500-bp sheared human genomic fragments were assayed in wild-type GP5d cells without exogenous CpG methylation using an episomal STARR-seq reporter. This table contains the source MACS2 narrowPeak calls for active genomic reporter fragments.
E70224190
GP5d binary STARR-seq template-switch TSS motif positioning
Template-switch libraries from two GP5d binary STARR-seq RNA replicates captured 5′ transcript ends and localized transcription start sites within active random promoters. The table reports motif-match counts by position and strand relative to the TSS rather than an RNA/input activity ratio.
E80723153
TP53-null GP5d nonmethylated genomic STARR-seq
Approximately 500-bp sheared human genomic fragments were assayed without exogenous CpG methylation in the TP53-null GP5d clone using an episomal STARR-seq reporter. This table contains the source MACS2 narrowPeak calls for active genomic reporter fragments.
E8A40B7CA
HepG2 nonmethylated genomic STARR-seq
Approximately 500-bp sheared human genomic fragments were assayed without exogenous CpG methylation in HepG2 cells using an episomal STARR-seq reporter. This table combines the source MACS2 narrowPeak calls from the two HepG2 biological replicates.
E8AAC2BDC
GP5d wild-type CpG-methylated genomic STARR-seq
Approximately 500-bp sheared human genomic fragments were CpG-methylated before assay in wild-type GP5d cells using an episomal STARR-seq reporter. This table contains the source MACS2 narrowPeak calls for active genomic reporter fragments.
E9F3A5D10
GP5d TF-motif STARR-seq with CpG-free EF1α reporter
A synthetic transcription-factor motif library containing 43,251 motif patterns in two 49-bp genomic contexts was cloned into the CpG-free EF1α STARR-seq reporter and assayed in GP5d cells. This table contains pattern-level RNA/input activity effects for the E1a reporter condition.
Raw source data 21 files
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 21 files (ZIP)GSE180151_STARR-seq_motif_library_GP5d_counts.lfc.tsv.gzGSE180152_STARR-seq_gDNA_hg19_1712_GP5d_Merged_peaks.narrowPeak.gzGSE180155_STARR-seq_TSS_flank60_motif_counts.tsv.gzGSE180158_family.softGSM5454433_STARR-seq_gDNA_hg19_1712_GP5d_WT_NM_peaks.narrowPeak.gzGSM5454434_STARR-seq_gDNA_hg19_1712_GP5d_WT_M_peaks.narrowPeak.gzGSM5454435_STARR-seq_gDNA_hg19_1712_GP5d_C2_NM_peaks.narrowPeak.gzGSM5454436_STARR-seq_gDNA_hg19_1712_GP5d_C2_M_peaks.narrowPeak.gzGSM5454437_HepG2_NM1_peaks.narrowPeak.gzGSM5454438_HepG2_NM2_peaks.narrowPeak.gzGSM5454440_random-STARR-seq_enhancer_GP5d_rep1.p1e-6matches.lfc.tsv.gzGSM5454441_random-STARR-seq_enhancer_GP5d_rep2.p1e-6matches.lfc.tsv.gzGSM5454442_random-STARR-seq_enhancer_HepG2.p1e-6matches.lfc.tsv.gzGSM5454455_STARRseq_RandomPE_promoter_GP5d_rep1.p1e-6matches.lfc.tsv.gzGSM5454456_STARRseq_RandomPE_promoter_GP5d_rep2.p1e-6matches.lfc.tsv.gzGSM5454457_STARRseq_RandomPE_promoter_HepG2.p1e-6matches.lfc.tsv.gzGSM5454458_STARRseq_RandomPE_promoter_RPE.p1e-6matches.lfc.tsv.gzGSM5454459_STARRseq_RandomPE_GP5d_rep1.p5e-5.pair_counts.tsv.gzsource_provenance.txtSupplementary_Information.pdfSupplementary_Tables.xlsx