Of rodents and ruminants: a comparison of small noncoding RNA requirements in mouse and bovine reproduction

Paternal effects on fetal programming

Paternal programming is the concept that the environmental signals from the sire's experiences leading up to mating can alter semen and ultimately affect the phenotype of resulting offspring. Potential mechanisms carrying the paternal effects to offspring can be associated with epigenetic signatures (DNA methylation, histone modification and non-coding RNAs), oxidative stress, cytokines, and the seminal microbiome. Several opportunities exist for sperm/semen to be influenced during development; these opportunities are within the testicle, the epididymis, or accessory sex glands. Epigenetic signatures of sperm can be impacted during the pre-natal and pre-pubertal periods, during sexual maturity and with advancing sire age. Sperm are susceptible to alterations as dictated by their developmental stage at the time of the perturbation, and sperm and seminal plasma likely have both dependent and independent effects on offspring. Research using rodent models has revealed that many factors including over/under nutrition, dietary fat, protein, and ingredient composition (e.g., macro- or micronutrients), stress, exercise, and exposure to drugs, alcohol, and endocrine disruptors all elicit paternal programming responses that are evident in offspring phenotype. Research using livestock species has also revealed that sire age, fertility level, plane of nutrition, and heat stress can induce alterations in the epigenetic, oxidative stress, cytokine, and microbiome profiles of sperm and/or seminal plasma. In addition, recent findings in pigs, sheep, and cattle have indicated programming effects in blastocysts post-fertilization with some continuing into post-natal life of the offspring. Our research group is focused on understanding the effects of common management scenarios of plane of nutrition and growth rates in bulls and rams on mechanisms resulting in paternal programming and subsequent offspring outcomes. Understanding the implication of paternal programming is imperative as short-term feeding and management decisions have the potential to impact productivity and profitability of our herds for generations to come.

Analysis of C. elegans Germline Small RNA Pathways

Sequence-specific gene regulation by small RNA (sRNA) pathways is essential for the development and function of organisms in all domains of life. These regulatory complexes, containing an Argonaute protein (AGO) guided by a bound sRNA, have the potential to regulate thousands of individual target transcripts at both the co- and post-transcriptional level. Determining the repertoire of transcripts that an AGO is capable of regulating in a particular context is essential to understanding the function of these regulatory modules. Immunoprecipitation (IP) of AGOs and subsequent RNA sequencing of their bound sRNAs allows for the inference of their target transcripts by mapping the sequences of the co-precipitated sRNAs back to their complementary target transcripts. This approach can be complemented by sequencing sRNAs from ago mutants as sRNA transcripts are degraded in the absence of their AGO binding partner. Here, we describe a framework for analyzing AGO/sRNA pathways in the germline, from using CRISPR-Cas9 to tag or mutate AGOs, through protocols for the extraction, sequencing, and analysis of sRNAs from AGO IPs and ago mutants.