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Stallion sperm transcriptome comprises functionally coherent coding and regulatory RNAs as revealed by microarray analysis and RNA-seq.

Das PJ, McCarthy F, Vishnoi M, Paria N, Gresham C, Li G, Kachroo P, Sudderth AK, Teague S, Love CC, Varner DD, Chowdhary BP, Raudsepp T - PLoS ONE (2013)

Bottom Line: A total of 19,257 sequence tags were mapped to all horse chromosomes and the mitochondrial genome.The highest density of mapped transcripts was in gene-rich ECA11, 12 and 13, and the lowest in gene-poor ECA9 and X; 7 gene transcripts originated from ECAY.The data were aligned with selected equine gene models to identify additional exons and splice variants.

View Article: PubMed Central - PubMed

Affiliation: Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America.

ABSTRACT
Mature mammalian sperm contain a complex population of RNAs some of which might regulate spermatogenesis while others probably play a role in fertilization and early development. Due to this limited knowledge, the biological functions of sperm RNAs remain enigmatic. Here we report the first characterization of the global transcriptome of the sperm of fertile stallions. The findings improved understanding of the biological significance of sperm RNAs which in turn will allow the discovery of sperm-based biomarkers for stallion fertility. The stallion sperm transcriptome was interrogated by analyzing sperm and testes RNA on a 21,000-element equine whole-genome oligoarray and by RNA-seq. Microarray analysis revealed 6,761 transcripts in the sperm, of which 165 were sperm-enriched, and 155 were differentially expressed between the sperm and testes. Next, 70 million raw reads were generated by RNA-seq of which 50% could be aligned with the horse reference genome. A total of 19,257 sequence tags were mapped to all horse chromosomes and the mitochondrial genome. The highest density of mapped transcripts was in gene-rich ECA11, 12 and 13, and the lowest in gene-poor ECA9 and X; 7 gene transcripts originated from ECAY. Structural annotation aligned sperm transcripts with 4,504 known horse and/or human genes, rRNAs and 82 miRNAs, whereas 13,354 sequence tags remained anonymous. The data were aligned with selected equine gene models to identify additional exons and splice variants. Gene Ontology annotations showed that sperm transcripts were associated with molecular processes (chemoattractant-activated signal transduction, ion transport) and cellular components (membranes and vesicles) related to known sperm functions at fertilization, while some messenger and micro RNAs might be critical for early development. The findings suggest that the rich repertoire of coding and non-coding RNAs in stallion sperm is not a random remnant from spermatogenesis in testes but a selectively retained and functionally coherent collection of RNAs.

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Related in: MedlinePlus

Summary statistics for mapped RNA sequence tags: (a) Comparison of mapped tags (AC≥1) between the two sperm samples; (b) Proportions of tags with very high (AC≥100), high (10<AC<100), and medium (1≤AC≤10) expression.
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pone-0056535-g004: Summary statistics for mapped RNA sequence tags: (a) Comparison of mapped tags (AC≥1) between the two sperm samples; (b) Proportions of tags with very high (AC≥100), high (10<AC<100), and medium (1≤AC≤10) expression.

Mentions: Next generation sequencing (NGS) of total RNA from the sperm of two reproductively normal stallions generated about 70 million raw reads and more than 3 Gb of sequence per sample; over half of these aligned with the EcuCab2 [42] reference genome (Table 2). Average coverage (AC; normalized number of transcripts) values could be calculated for over 30 million reads that mapped to all equine chromosomes, including ChrUn and the mitochondrial genome (Table 2, Table S9), whereas 19,257 sequence tags with AC ≥1 were uniquely mapped to specific locations in the horse genome (Table 2). Of these, 14,982 map locations were shared between the two samples, while 2,188 and 2,087 were unique to sample 1 and sample 2, respectively (Fig. 4a). These differences could be due to a combination of individual and technical variations, and justified the use of two biological replicates in this study. Genomic locations of all mapped tags together with their absolute and relative AC values are presented in Table S5. The data are deposited in NCBI Gene Expression Omnibus [43], [44] and are accessible through GEO series accession number GSE38725 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38725).


Stallion sperm transcriptome comprises functionally coherent coding and regulatory RNAs as revealed by microarray analysis and RNA-seq.

Das PJ, McCarthy F, Vishnoi M, Paria N, Gresham C, Li G, Kachroo P, Sudderth AK, Teague S, Love CC, Varner DD, Chowdhary BP, Raudsepp T - PLoS ONE (2013)

Summary statistics for mapped RNA sequence tags: (a) Comparison of mapped tags (AC≥1) between the two sperm samples; (b) Proportions of tags with very high (AC≥100), high (10<AC<100), and medium (1≤AC≤10) expression.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3569414&req=5

pone-0056535-g004: Summary statistics for mapped RNA sequence tags: (a) Comparison of mapped tags (AC≥1) between the two sperm samples; (b) Proportions of tags with very high (AC≥100), high (10<AC<100), and medium (1≤AC≤10) expression.
Mentions: Next generation sequencing (NGS) of total RNA from the sperm of two reproductively normal stallions generated about 70 million raw reads and more than 3 Gb of sequence per sample; over half of these aligned with the EcuCab2 [42] reference genome (Table 2). Average coverage (AC; normalized number of transcripts) values could be calculated for over 30 million reads that mapped to all equine chromosomes, including ChrUn and the mitochondrial genome (Table 2, Table S9), whereas 19,257 sequence tags with AC ≥1 were uniquely mapped to specific locations in the horse genome (Table 2). Of these, 14,982 map locations were shared between the two samples, while 2,188 and 2,087 were unique to sample 1 and sample 2, respectively (Fig. 4a). These differences could be due to a combination of individual and technical variations, and justified the use of two biological replicates in this study. Genomic locations of all mapped tags together with their absolute and relative AC values are presented in Table S5. The data are deposited in NCBI Gene Expression Omnibus [43], [44] and are accessible through GEO series accession number GSE38725 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38725).

Bottom Line: A total of 19,257 sequence tags were mapped to all horse chromosomes and the mitochondrial genome.The highest density of mapped transcripts was in gene-rich ECA11, 12 and 13, and the lowest in gene-poor ECA9 and X; 7 gene transcripts originated from ECAY.The data were aligned with selected equine gene models to identify additional exons and splice variants.

View Article: PubMed Central - PubMed

Affiliation: Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America.

ABSTRACT
Mature mammalian sperm contain a complex population of RNAs some of which might regulate spermatogenesis while others probably play a role in fertilization and early development. Due to this limited knowledge, the biological functions of sperm RNAs remain enigmatic. Here we report the first characterization of the global transcriptome of the sperm of fertile stallions. The findings improved understanding of the biological significance of sperm RNAs which in turn will allow the discovery of sperm-based biomarkers for stallion fertility. The stallion sperm transcriptome was interrogated by analyzing sperm and testes RNA on a 21,000-element equine whole-genome oligoarray and by RNA-seq. Microarray analysis revealed 6,761 transcripts in the sperm, of which 165 were sperm-enriched, and 155 were differentially expressed between the sperm and testes. Next, 70 million raw reads were generated by RNA-seq of which 50% could be aligned with the horse reference genome. A total of 19,257 sequence tags were mapped to all horse chromosomes and the mitochondrial genome. The highest density of mapped transcripts was in gene-rich ECA11, 12 and 13, and the lowest in gene-poor ECA9 and X; 7 gene transcripts originated from ECAY. Structural annotation aligned sperm transcripts with 4,504 known horse and/or human genes, rRNAs and 82 miRNAs, whereas 13,354 sequence tags remained anonymous. The data were aligned with selected equine gene models to identify additional exons and splice variants. Gene Ontology annotations showed that sperm transcripts were associated with molecular processes (chemoattractant-activated signal transduction, ion transport) and cellular components (membranes and vesicles) related to known sperm functions at fertilization, while some messenger and micro RNAs might be critical for early development. The findings suggest that the rich repertoire of coding and non-coding RNAs in stallion sperm is not a random remnant from spermatogenesis in testes but a selectively retained and functionally coherent collection of RNAs.

Show MeSH
Related in: MedlinePlus