Viruses coordinatively exploit host TLE1 for replication
Description
This dataset delineates alterations in host genes transcriptionally regulated by Transducin-like enhancer of split 1 (TLE1) following influenza virus infection. TLE1, a transcriptional co-repressor encoded at chromosome 9q21.32, is clinically utilized as a diagnostic marker for synovial sarcoma. However, our analysis reveals that TLE1-regulated gene sets identified by ChIP enrichment are distinct post-infection, indicating its previously uncharacterized role in modulating transcriptional reprogramming during viral challenge. These findings provide novel insights for identifying host-directed antiviral targets and elucidate mechanisms by which influenza virus subverts host gene expression to facilitate replication and pathogenesis, thereby highlighting potential therapeutic interventions.
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Steps to reproduce
In this study, the raw ChIP-seq sequencing data were quality controlled and adapter trimmed using Trim Galore, and then high-quality sequences were mapped to the human reference genome hg19 using Bowtie2. The mapping results were converted to BAM format and sorted using Samtools, and then PCR duplicates and ENCODE blacklist regions were removed using Picard tools to ensure data quality. Peak detection was performed using MACS 1.4 at a P-value threshold of 1×10⁻⁵, with paired input samples used as controls. Peak quality was assessed by calculating the signal-to-noise ratio and FRiP values, and genomic annotation was performed using ChIPseeker. For DNA motif analysis, sequences were extracted from the peak center regions and de novo motif discovery was performed using MEME-ChIP. Differential binding analysis was performed using the DiffBind package and integrated with functional enrichment analysis and expression data to comprehensively reveal the regulatory networks and biological functions of transcription factors. All analysis steps strictly followed ENCODE standards to ensure the reliability and reproducibility of the results.
Institutions
- University of Hong Kong