Xiusheng Zhu, Lei Huang, Chao Wang, Guoli Li, Biao Deng et al.
Silencers, the yin to enhancers’ yang, play a pivotal role in fine-tuning gene expression throughout the genome. However, despite their recognized importance, comprehensive identification of these regulatory elements in the genome is still in its early stages. We developed a method called Ss-STARR-seq to directly determine the activity of silencers in the whole genome. In this study, we applied Ss-STARR-seq to human cell lines K562, LNCaP, and 293 T, and identified 134,171, 137,753, and 125,307 silencers on a genome-wide scale, respectively, these silencers function in various cells in a cell-specific manner. Silencers exhibited a substantial enrichment of transcriptional-inhibitory motifs, including REST, and demonstrated overlap with the binding sites of repressor transcription factors within the endogenous environment. Interestingly, H3K27me3 did not reflect silencer activity but facilitated the silencer’s inhibitory role on gene expression. Additionally, the silencer did not have any significant histone markers at the genome-wide level. Our findings unveil that aspect-silencers not only transition into enhancers throughout diverse cell lines but also achieve functional conversion with insulators. Regarding to biological effects, knockout experiments underscored the functional redundancy and specificity of silencers in regulating gene expression and cell proliferation. In summary, this study pioneers the elucidation of the genome-wide silencer landscape in human cells, delineates their global regulatory features, and identifies specific silencers influencing cancer cell proliferation.
Xiusheng Zhu, Lei Huang, Chao Wang, Guoli Li, Biao Deng, Dashuai Kong, Xiaoxiao Wang, Rongrong Chang, Yi Gu, Qiuhan Wen, Siyuan Kong, Yuwen Liu, Yubo Zhang. Uncovering the whole genome silencers of human cells via Ss-STARR-seq. 2025-01-16. https://doi.org/10.1038/s41467-025-55852-8
Approximately 300 bp randomly sheared human genomic fragments were cloned downstream of the hPGK promoter in the GFP-containing Ss-STARR-seq episomal reporter and transfected into K562 cells. CRADLE was used to call silencer intervals from input-library DNA versus cellular reporter RNA; the table contains the deposited interval-level activity calls.
Approximately 300 bp randomly sheared human genomic fragments were cloned downstream of the hPGK promoter in the GFP-containing Ss-STARR-seq episomal reporter and transfected into LNCaP cells. CRADLE was used to call silencer intervals from input-library DNA versus cellular reporter RNA; the table contains the deposited interval-level activity calls.
Approximately 300 bp randomly sheared human genomic fragments were cloned downstream of the hPGK promoter in the GFP-containing Ss-STARR-seq episomal reporter and transfected into HEK293T (293T) cells. CRADLE was used to call silencer intervals from input-library DNA versus cellular reporter RNA; the table contains the deposited interval-level activity calls.
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.
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