Next generation sequencing allows deeper analysis and understanding of genomes and transcriptomes including aspects to fertility
Thomas WernerGenomatix Software GmbH, Bayerstr. 85A, D-80335 München, Germany.Internal Medicine Nephrology, University of Michigan, 5520 MSRB I,1150 W Medical Center Dr, SPC 5680, Ann Arbor, MI 48109, USA.Email: werner@genomatix.de
Reproduction, Fertility and Development 23(1) 75-80 https://doi.org/10.1071/RD10247
Published: 7 December 2010
Abstract
Reproduction and fertility are controlled by specific events naturally linked to oocytes, testes and early embryonal tissues. A significant part of these events involves gene expression, especially transcriptional control and alternative transcription (alternative promoters and alternative splicing). While methods to analyse such events for carefully predetermined target genes are well established, until recently no methodology existed to extend such analyses into a genome-wide de novo discovery process. With the arrival of next generation sequencing (NGS) it becomes possible to attempt genome-wide discovery in genomic sequences as well as whole transcriptomes at a single nucleotide level. This does not only allow identification of the primary changes (e.g. alternative transcripts) but also helps to elucidate the regulatory context that leads to the induction of transcriptional changes. This review discusses the basics of the new technological and scientific concepts arising from NGS, prominent differences from microarray-based approaches and several aspects of its application to reproduction and fertility research. These concepts will then be illustrated in an application example of NGS sequencing data analysis involving postimplantation endometrium tissue from cows.
Additional keywords: alternative promoters, alternative splicing, downstream analysis, regulatory networks.
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