Pig H3K4me3, H3K27ac, and gene expression profiles reveal reproductive tissue-specific activity of transposable elements.

Regulatory sequences and transposable elements (TEs) account for a large proportion of the genomic sequences of species; however, their roles in gene transcription, especially tissue-specific expression, remain largely unknown. Pigs serve as an excellent animal model for studying genomic sequence biology due to the extensive diversity among their wild and domesticated populations. Here, we conducted an integrated analysis using H3K27ac ChIP-seq, H3K4me3 ChIP-seq, and RNA-seq data from 10 different tissues of seven fetuses and eight closely related adult pigs. We aimed to annotate the regulatory elements and TEs to elucidate their associations with histone modifications and mRNA expression across different tissues and developmental stages. Based on correlation analysis between mRNA expression and H3K27ac and H3K4me3 peak activity, results indicated that H3K27ac exhibited stronger associations with gene expression than H3K4me3. Furthermore, 1.45% of TEs overlapped with either the H3K27ac or H3K4me3 peaks, with the majority displaying tissue-specific activity. Notably, a TE subfamily (LTR4C_SS), containing binding motifs for SIX1 and SIX4, showed specific enrichment in the H3K27ac peaks of the adult and fetal ovaries. RNA-seq analysis also revealed widespread expression of TEs in the exons or promoters of genes, including 4 688 TE-containing transcripts with distinct development stage-specific and tissue-specific expression. Of note, 1 967 TE-containing transcripts were enriched in the testes. We identified a long terminal repeat (LTR), MLT1F1, acting as a testis-specific alternative promoter in SRPK2 (a cell cycle-related protein kinase) in our pig dataset. This element was also conserved in humans and mice, suggesting either an ancient integration of TEs in genes specifically expressed in the testes or parallel evolutionary patterns. Collectively, our findings demonstrate that TEs are deeply embedded in the genome and exhibit important tissue-specific biological functions, particularly in the reproductive organs.

Characterization of the endothiapepsin-like protein in the entomopathogenic fungus Beauveria bassiana and its virulence effect on the silkworm, Bombyx mori.

Endothiapepsin is an aspartic proteinase that was first isolated from the plant pathogenic fungus Endothia parasitica. In previous studies, we reported on three endothiapepsin-like proteins in the entomopathogenic fungus Beauveria bassiana; the genes were up-regulated in B. bassiana hyper-virulent strain GXsk1011 at early stage infection in the silkworm. However, whether these proteins play a role in pathogenicity or not remains unknown. In this study, we cloned one protein, BbepnL-1 gene (BBA-07766), that has 98% homology with B. bassiana strain Bb2860, and expressed it in the yeast Pichia pastoris to investigate its function. The endothiapepsin-like protein is a secreted proteinase of molecular weight approximately 40 kDa. It has an N-glycosylation site and a mutation in the C-terminal conserved domain- a Thr was mutated to Gly in B. bassiana GXsk1011 and is different than the endothiapepsin of Endothia parasitica. The recombinant endothiapepsin-like protein showed enzyme activity and degraded the protein components of the silkworm cuticle. To further investigate the activity of the endothiapepsin-like protein, we knocked out the gene BbepnL-1 and showed that the loss of BbepnL-1 reduced the virulence in the silkworm. These results demonstrated that the endothiapepsin-like protein of B. bassiana is a virulence factor.