Regulation of the three-dimensional chromatin organization by transposable elements in pig spleen

Li, Yuzhuo; Fan, Hairui; Qin, Weiyun; Wang, Yejun; Chen, Shuai; Bao, Wenbin; Sun, Ming-an

doi:10.1016/j.csbj.2023.09.029

Cited by 1 publication

(3 citation statements)

References 79 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In addition, analysis of the GATA3 and H3K27ac peaks in human TSCs revealed the significant enrichment of TEs such as MER41A/B, LTR8 and MER4B (Figure 2B , C ), matching previous studies ( 11 , 13 , 15 ). Using the CTCF peaks in pig spleen, it also successfully recovered TEs such as LTR22_SS, LTR16_SSc and LTR15_SS (Figure 2D ), as recently reported ( 27 ). Together, these data suggest that TEENA is capable to detect significantly enriched TEs with good accuracy.…”

Section: Resultssupporting

confidence: 84%

“…To further test the power of TEENA, we performed multiple case studies using public data covering different data types (TF binding sites, histone marks) and species (human, pig). Inspection of the top enriched TEs (Figure 2 , Supplementary Table S2 ) suggest that TEENA well reproduced the conclusions from previous studies ( 11 , 13 , 15 , 19 , 27 ). LTRs/ERVs such as the primate-specific MER41B were identified as top enriched in the STAT1 peaks in IFNγ-stimulated human CD14 + macrophages (Figure 2A ), which agrees well with the seminal study on regulatory evolution of innate immunity in primates ( 19 ).…”

Section: Resultssupporting

confidence: 82%

“…To evaluate the performance of TEENA, we compared it with BEDtools fisher ( 32 ) and GIGGLE ( 33 ), which has been frequently adopted for TE analysis ( 9 , 14 , 15 , 27 , 36 , 46 ). Of note, a wrapper (i.e.…”

Section: Resultsmentioning

confidence: 99%

See 2 more Smart Citations

TEENA: an integrated web server for transposable element enrichment analysis in various model and non-model organisms

Li,

Lyu,

Chen

et al. 2024

Nucleic Acids Research

Self Cite

View full text Add to dashboard Cite

Transposable elements (TEs) are abundant in the genomes of various eukaryote organisms. Increasing evidence suggests that TEs can play crucial regulatory roles—usually by creating cis-elements (e.g. enhancers and promoters) bound by distinct transcription factors (TFs). TE-derived cis-elements have gained unprecedented attentions recently, and one key step toward their understanding is to identify the enriched TEs in distinct genomic intervals (e.g. a set of enhancers or TF binding sites) as candidates for further study. Nevertheless, such analysis remains challenging for researchers unfamiliar with TEs or lack strong bioinformatic skills. Here, we present TEENA (Transposable Element ENrichment Analyzer) to streamline TE enrichment analysis in various organisms. It implements an optimized pipeline, hosts the genome/gene/TE annotations of almost one hundred species, and provides multiple parameters to enable its flexibility. Taking genomic interval data as the only user-supplied file, it can automatically retrieve the corresponding annotations and finish a routine analysis in a couple minutes. Multiple case studies demonstrate that it can produce highly reliable results matching previous knowledge. TEENA can be freely accessed at: https://sun-lab.yzu.edu.cn/TEENA. Due to its easy-to-use design, we expect it to facilitate the studies of the regulatory function of TEs in various model and non-model organisms.

show abstract