Biology subjects

Fair, S.

Publications and source records attributed to Fair, S..

3 recordsLinked to original sources

bioRxiv2024

The role of β-defensin 103 (DEFB103) copy number variation in bull fertility

Pregnancy rates for elite bulls used in artificial insemination (AI) can vary significantly and therefore the identification of molecular markers for fertility and targets to improve bull selection is important. {beta}-defensins are peptides which have diverse regulatory roles in sperm function across multiple species. In this study, Holstein-Friesian bulls were screened based on field fertility data to identify two groups (High and Low fertility (HF and LF, respectively)) of n=10 bulls per group which were genotyped for copy number variation (CNV) in the DEFB103 gene. Overall, low DEFB103 copy number (CN) was associated with increased sperm motility across all bulls (n=20, p<0.05). As genetic diversity of DEFB103 CN was only apparent in the LF group, three bulls per CNV class (low, intermediate and high CN) were chosen for functional analysis. Sperm from LF bulls with low CN exhibited higher binding to the oviduct epithelium in vitro, while high CN affected sperm membrane fluidity in non-capacitating conditions in vitro (p<0.05). To investigate the functional effect of DEFB103 CNV on the uterine response in vivo, 18 heifers were inseminated with sperm from bulls with low, intermediate and high CN. Transcriptomic analysis on uterine tissue harvested 12 h post-insemination showed significant differential expression of 58 genes (FDR<0.1) involved in sperm migration, immune signalling and chemotaxis. These novel results confirm an important role for DEFB103 CN in both sperm function and the uterine response to bull sperm, thereby potentially influencing pregnancy outcomes in cattle. Summary SentenceDEFB103 copy number (CN) is associated with sperm motility and binding to the oviduct epithelium and uterine gene expression, thereby potentially influencing fertility outcomes.

genomics↗

bioRxiv2024

β-defensin gene copy number variation in cattle

{beta}-defensins are peptides with antimicrobial roles, characterized by a conserved tertiary structure. Beyond antimicrobial functions, they exhibit diverse roles in both the immune response and fertility, including involvement in sperm maturation and function. Copy number variation (CNV) of {beta}-defensin genes is extensive across mammals, including cattle, with possible implications for reproductive traits and disease resistance. In this study, we comprehensively catalogue 55 {beta}-defensin genes in cattle. By constructing a phylogenetic tree to identify human orthologues and lineage-specific expansions, we identify 1:1 human orthologues for 35 bovine {beta}-defensins. We also discover extensive {beta}-defensin gene CNV across breeds, with DEFB103 in particular showing extensive multiallelic CNV. By comparing {beta}-defensin expression levels in testis from calves and adult bulls, we find that 14 {beta}-defensins, including DEFB103, increase in expression during sexual maturation. Analysis of {beta}-defensin gene expression levels in the caput of adult bull epididymis, and {beta}-defensin gene copy number, in 94 matched samples shows expression level of four {beta}-defensins are correlated with genomic copy number, including DEFB103. We therefore demonstrate extensive copy number variation in bovine {beta}-defensin genes, in particular DEFB103, with potential functional consequences for fertility.

genetics↗

bioRxiv2021

THO and TRAMP complexes prevent transcription-replication conflicts, DNA breaks, and CAG repeat contractions

Expansion of structure-forming CAG/CTG repetitive sequences is the cause of several neurodegenerative disorders and deletion of repeats is a potential therapeutic strategy. Transcription-associated mechanisms are known to cause CAG repeat instability. In this study, we discovered that Thp2, an RNA export factor and member of the THO complex, and Trf4, a key component of the TRAMP complex involved in nuclear RNA degradation, are necessary to prevent CAG fragility and repeat contractions in a S. cerevisiae model system. Depletion of both Thp2 and Trf4 proteins causes a highly synergistic increase in CAG repeat fragility, indicating a complementary role of the THO and TRAMP complexes in preventing genome instability. Loss of either Thp2 or Trf4 causes an increase in RNA polymerase stalling at the CAG repeats and genome-wide transcription-replication conflicts (TRCs), implicating impairment of transcription elongation as a cause of CAG fragility and instability in their absence. Analysis of the effect of RNase H1 overexpression on CAG fragility and TRCs suggests that co-transcriptional R-loops are the main cause of CAG fragility in the thp2{Delta} mutants. In contrast, CAG fragility and TRCs in the trf4{Delta} mutant can be compensated for by RPA overexpression, suggesting that excess unprocessed RNA in TRAMP4 mutants leads to reduced RPA availability and high levels of TRCs. Our results show the importance of RNA surveillance pathways in preventing RNAPII stalling, TRCs, and DNA breaks, and show that RNA export and RNA decay factors work collaboratively to maintain genome stability.

genetics↗