1. RNA element discovery from germ cell to blastocyst.
- Author
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Estill MS, Hauser R, and Krawetz SA
- Subjects
- Blastocyst cytology, Cell Differentiation, Cell Line, Chromatin genetics, Chromatin metabolism, Chromosomes, Human, X genetics, Embryonic Development genetics, Exons genetics, Female, Fertilization, Gene Expression Regulation, Developmental, Genomics, Humans, Liver cytology, Liver metabolism, Male, Meiosis genetics, Oocytes cytology, Poly A analysis, Poly A genetics, Poly A isolation & purification, RNA, Messenger isolation & purification, Repetitive Sequences, Nucleic Acid, Spermatogenesis genetics, Spermatozoa cytology, Transcription, Genetic, X Chromosome Inactivation, Algorithms, Blastocyst metabolism, Oocytes metabolism, RNA, Messenger analysis, RNA, Messenger genetics, Regulatory Sequences, Ribonucleic Acid genetics, Sequence Analysis, RNA, Spermatozoa metabolism
- Abstract
Recent studies have shown that tissue-specific transcriptomes contain multiple types of RNAs that are transcribed from intronic and intergenic sequences. The current study presents a tool for the discovery of transcribed, unannotated sequence elements from RNA-seq libraries. This RNA Element (RE) discovery algorithm (REDa) was applied to a spectrum of tissues and cells representing germline, embryonic, and somatic tissues and examined as a function of differentiation through the first set of cell divisions of human development. This highlighted extensive transcription throughout the genome, yielding previously unidentified human spermatogenic RNAs. Both exonic and novel X-chromosome REs were subject to robust meiotic sex chromosome inactivation, although an extensive de-repression occurred in the post-meiotic stages of spermatogenesis. Surprisingly, 2.4% of the 10,395 X chromosome exonic REs were present in mature sperm. Transcribed genomic repetitive sequences, including simple centromeric repeats, HERVE and HSAT1, were also shown to be associated with RE expression during spermatogenesis. These results suggest that pervasive intergenic repetitive sequence expression during human spermatogenesis may play a role in regulating chromatin dynamics. Repetitive REs switching repeat classes during differentiation upon fertilization and embryonic genome activation was evident., (© The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.)
- Published
- 2019
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