Molecular Human Reproduction · 2014 · 81 citations · 81 references
Life SciencesCell BiologyGynecologyEmbryologyGene ExpressionTranscriptomicsOocyte MaturationOogenesisCumulus ExpansionGerminal Vesicle Stage OocytesGranulosa Cell SignalingGranulosa Cell SteroidogenesisIn Vitro MaturationOocyte DevelopmentOocyte Maturation StageTranscriptome Sequencing
Cumulus expansion and oocyte maturation are central processes in ovulation. Knowledge gained from rodent and other mammalian models has revealed some of the molecular pathways associated with these processes. However, the equivalent pathways in humans have not been thoroughly studied and remain unidentified. Compact cumulus cells (CCs) from germinal vesicle cumulus oocyte complexes (COCs) were obtained from patients undergoing in vitro maturation (IVM) procedures. Expanded CCs from metaphase 2 COC were obtained from patients undergoing IVF/ICSI. Global transcriptome profiles of the samples were obtained using state-of-the-art RNA sequencing techniques. We identified 1746 differentially expressed (DE) genes between compact and expanded CCs. Most of these genes were involved in cellular growth and proliferation, cellular movement, cell cycle, cell-to-cell signaling and interaction, extracellular matrix and steroidogenesis. Out of the DE genes, we found 89 long noncoding RNAs, of which 12 are encoded within introns of genes known to be involved in granulosa cell processes. This suggests that unique noncoding RNA transcripts may contribute to the regulation of cumulus expansion and oocyte maturation. Using global transcriptome sequencing, we were able to generate a library of genes regulated during cumulus expansion and oocyte maturation processes. Analysis of these genes allowed us to identify important new genes and noncoding RNAs potentially involved in COC maturation and cumulus expansion. These results may increase our understanding of the process of oocyte maturation and could ultimately improve the efficacy of IVM treatment.
81
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan, Ira M. Hall · Bioinformatics · 2010 · 30.4K citations · Full text
Differential expression analysis for sequence count data
Simon Anders, Wolfgang Huber · Genome biology · 2010 · 16.4K citations · Full text
TopHat: discovering splice junctions with RNA-Seq
Cole Trapnell, Lior Pachter, Steven L. Salzberg · Bioinformatics · 2009 · 12.1K citations · Full text
Landscape of transcription in human cells
Sarah Djebali, Carrie Davis, Angelika Merkel et al. · Nature · 2012 · 5.4K citations · Full text
The Gene Ontology (GO) database and informatics resource
Nucleic Acids Research · 2003 · 4.7K citations · Full text