Supplementary Legends from Positive selection of the TRIM family regulatory region in primate genomes

Viral selection pressure has acted on restriction factors that play an important role in innate immune system by inhibiting the replication of viruses during primate evolution. Tripartite motif-containing (TRIM) family members are some of these restriction factors. It is becoming increasingly clear that gene expression differences, rather than protein-coding regions changes, could play a vital role in the anti-retroviral immune mechanism. Increasingly, recent studies have created genome-scale catalogues of DNase I hypersensitive sites (DHSs), which demark potentially functional regulatory DNA. To improve our understanding of the molecular evolution mechanism of antiviral differences between species, we leveraged 14 130 DHSs derived from 145 cell types to characterize the regulatory landscape of the TRIM region. Subsequently, we compared the alignments of the DHSs across six primates and found 375 DHSs that are conserved in non-human primates but exhibit significantly accelerated rates of evolution in the human lineage (haDHSs). Furthermore, we discovered 31 human-specific potential transcription factor motifs within haDHSs, including the <i>KROX</i> and <i>SP1</i>, that both interact with <i>HIV-1</i>. Importantly, the corresponding haDHS was correlated with antiviral factor <i>TRIM23</i>. Thus, our results suggested that some viruses may contribute, through regulatory DNA differences, to organismal evolution by mediating TRIM gene expression to escape immune surveillance

Transposable elements within TRIM DHS

This files showed the transposable elements that overlapped with TRIM haDHSs and conversed DHSs and their detailed information. The first three columns represented the position of DHS, the fourth to sixth columns represented the position of transposable elements. The annotation file of transposable elements came from ReapeatsMasker output file in UCSC

Selection analysis of TRIM DHS

The TRIM DHS data was generated from 145 cell types DHS data in ENCODE. And the methodology of DHS selection analysis was based on our previous DHS research(Comprehensive identification and analysis of human accelerated regulatory DNA, Rachel et al.Genome Research)

The motifs identified in TRIM haDHSs

Using the FIMO software to identified the putative transcription binding site motifs in TRIM haDHSs. And the corresponding six-primates sequences of these motifs were downloaed from Ensembl

Supplemental Material for Jin et al., 2018

Genetics/2018/30102

Supplemental Material for Jin et al., 2018

Genetics/2018/30102