Altered non‐coding RNA profiles of seminal plasma extracellular vesicles of men with poor semen quality undergoing in vitro fertilization treatment

Abstract

Background: Currently, the precise mechanisms that underline male infertility are still unclear. Accumulating data implicate non-coding RNA cargo of seminal plasma extracellular vesicles due to their association with poor semen quality and higher expression levels relative to vesicle-free seminal plasma. Method: We assessed sperm-free seminal plasma extracellular vesicle non-coding RNA profiles from 91 semen samples collected from male participants of couples seeking infertility treatment. Men were classified into two groups (poor, n = 32; normal, n = 59) based on World Health Organization semen cutoffs. Small RNA sequencing reads were mapped to standard biotype-specific transcriptomes in the order micro RNA > transfer RNA > piwi-interacting RNA > ribosomal RNA > ribosomal RNA > circular RNA > long non-coding RNA using STAR. Differential expression of normalized non-coding RNA read counts between the two groups was conducted by EdgeR (Fold change ≥1.5 and (false discovery rate [FDR] < 0.05). Result: Small RNA sequencing identified a wide variety of seminal plasma extracellular vesicle non-coding RNA biotypes including micro RNA, ribosomal RNAs, piwi-interacting RNAs, transfer RNA, long non-coding RNAs as well as circular RNAs, and fragments associated with pseudogenes, and nonsense-mediated decay. The expression levels of 57 seminal plasma extracellular vesicle non-coding RNAs (micro

Approaches for sRNA Analysis of Human RNA-Seq Data: Comparison, Benchmarking

“…Small non-coding RNA (sRNA) of less than 200 nucleotides in length are important regulatory molecules in the control of gene expression at both the transcriptional and the post-transcriptional level [ 1 , 2 , 3 ]. Research on sRNAs has accelerated over the past two decades and sRNAs have been utilized as markers of human diseases such as neurological conditions [ 4 ], cancer [ 5 ] and infertility [ 6 , 7 , 8 ], and in the identification of molecular biomarkers associating environmental exposure with health/disease outcomes [ 9 , 10 ]. The identification of sRNA in germ cells is of particular interest as they represent an additional source of parental hereditary information beyond DNA sequences and may have a potential role in programming offspring health [ 11 , 12 ].…”

Approaches for sRNA Analysis of Human RNA-Seq Data: Comparison, Benchmarking

“…Small non-coding RNA (sRNA) less than 200 nucleotides in length are important regulatory molecules in the control of gene expression at both the transcriptional and the post-transcriptional level [1][2][3]. Research on sRNAs has accelerated over the past two decades and sRNAs have been utilized as markers of human diseases such as neurological conditions [4], cancer [5] and infertility [6][7][8], and in the identification of molecular biomarkers associating environmental exposures with health/disease outcomes [9,10]. Identification of sRNA in germ cells is of particular interest as they represent an additional source of parental hereditary information beyond DNA sequences and may have a potential role in programming offspring health [11,12].…”

Approaches for sRNA Analysis of RNA-seq Data: Comparison, Benchmarking

“…Small non-coding RNA (sRNA) less than 200 nucleotides in length are important regulatory molecules in the control of gene expression at both the transcriptional and the post-transcriptional level [1][2][3]. Research on sRNAs has accelerated over the past two decades and sRNAs have been utilized as markers of human diseases such as neurological conditions [4], cancer [5] and infertility [6][7][8], and in the identification of molecular biomarkers of associations between environmental exposures and health/disease outcomes [9,10]. Identification of sRNA in germ cells is of particular interest as they represent an additional source of parental hereditary information beyond DNA sequences and may have a potential role in programming of offspring health [11,12].…”