Ruminant-specific retrotransposons shape regulatory evolution of bovine immunity

Cattle are an important livestock species, and mapping the genomic architecture of agriculturally relevant traits such as disease susceptibility is a major challenge in the bovine research community. Lineage-specific transposable elements (TEs) are increasingly recognized to contribute to gene regulatory evolution and variation, but this possibility has been largely unexplored in ruminant genomes. We conducted epigenomic profiling of the type II interferon (IFN) response in bovine cells, and found thousands of ruminant-specific TEs including MER41_BT and Bov-A2 elements predicted to act as IFN-inducible enhancer elements. CRISPR knockout experiments in bovine cells established that critical immune factors including IFNAR2 and IL2RB are transcriptionally regulated by TE-derived enhancers. Finally, population genomic analysis of 39 individuals revealed that a subset of TE-derived enhancers represent polymorphic insertion sites in modern cattle. Our study reveals that lineage-specific TEs have shaped the evolution of ruminant IFN responses, and potentially continue to contribute to immune gene regulatory differences across modern breeds and individuals. Together with previous work in human cells, our findings demonstrate that lineage-specific TEs have been independently co-opted to regulate IFN-inducible gene expression in multiple species, supporting TE co-option as a recurrent mechanism driving the evolution of IFN-inducible transcriptional networks.

A Novel Panel of 43 Insertion/Deletion Loci for Human Identifications of Forensic Degraded DNA Samples: Development and Validation

Insertion/deletion polymorphism is a promising genetic marker in the forensic genetic fields, especially in the forensic application of degraded sample at crime scene. In this research, a novel five-dye multiplex amplification panel containing 43 highly polymorphic Insertion/deletion (InDel) loci and one Amelogenin gene locus is designed and constructed in-house for the individual identification in East Asian populations. The amplicon sizes of 43 InDel loci are less than 200 bp, which help to ensure that full allele profiles can be obtained from degraded DNA sample. A series of optimizations and developmental validations including optimization of PCR conditions, detection efficiency of the degraded and casework samples, sensitivity, reproducibility, precision, tolerance for inhibitors, species specificity and DNA mixtures are performed according to the Scientific Working Group on DNA Analysis Methods (SWGDAM) guideline. The results of the internal validation demonstrated that this novel InDel panel was a reliable, sensitive and accurate system with good tolerances to different inhibitors, and performed the considerable detection efficiency for the degraded or mixed samples, which could be used in the forensic applications.

Identification of Alternative Variants and Insertion of the Novel PolymorphicAluYl17inTSEN54Gene during Primate Evolution

TSEN54encodes a subunit of the tRNA-splicing endonuclease complex, which catalyzes the identification and cleavage of introns from precursor tRNAs. Previously, we identified anAluSx-derived alternative transcript inTSEN54of cynomolgus monkey. Reverse transcription-polymerase chain reaction (RT-PCR) amplification andTSEN54sequence analysis of primate and human samples identified five novel alternative transcripts, including theAluSxexonized transcript. Additionally, we performed comparative expression analysis via RT-qPCR in various cynomolgus, rhesus monkey, and human tissues. RT-qPCR amplification revealed differential expression patterns. Furthermore, genomic PCR amplification and sequencing of primate and human DNA samples revealed thatAluSxelements were integrated in human and all of the primate samples tested. Intriguingly, in langur genomic DNA, an additionalAluYelement was inserted intoAluSxof intron eight ofTSEN54. The newAluYelement showed polymorphic insertion. Using standardized nomenclature forAlurepeats, the polymorphicAluYof the langurTSEN54was designated as being of theAluYl17subfamily. Our results suggest that integration of theAluSxelement inTSEN54contributed to diversity in transcripts and induced lineage- or species-specific evolutionary events such as alternative splicing and polymorphic insertion during primate evolution.