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      Contributions of RNA-seq to improve in vitro embryo production (IVP)

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          Abstract

          Abstract In Vitro Embryo Production (IVP) is widely used to improve the reproductive efficiency of livestock animals, however increasing the embryo development rates and pregnancy outcomes is still a challenge for some species. Thus, the lack of biological knowledge hinders developing specie-specific IVP protocols. Therefore, the contributions of RNA-seq to generate relevant biological knowledge and improve the efficiency of IVP in livestock animals are reviewed herein.

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          Understanding the Warburg effect: the metabolic requirements of cell proliferation.

          Craig B Thompson, Matthew Vander Heiden, Lewis Cantley (2009)
          In contrast to normal differentiated cells, which rely primarily on mitochondrial oxidative phosphorylation to generate the energy needed for cellular processes, most cancer cells instead rely on aerobic glycolysis, a phenomenon termed "the Warburg effect." Aerobic glycolysis is an inefficient way to generate adenosine 5'-triphosphate (ATP), however, and the advantage it confers to cancer cells has been unclear. Here we propose that the metabolism of cancer cells, and indeed all proliferating cells, is adapted to facilitate the uptake and incorporation of nutrients into the biomass (e.g., nucleotides, amino acids, and lipids) needed to produce a new cell. Supporting this idea are recent studies showing that (i) several signaling pathways implicated in cell proliferation also regulate metabolic pathways that incorporate nutrients into biomass; and that (ii) certain cancer-associated mutations enable cancer cells to acquire and metabolize nutrients in a manner conducive to proliferation rather than efficient ATP production. A better understanding of the mechanistic links between cellular metabolism and growth control may ultimately lead to better treatments for human cancer.
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            RNA-Seq: a revolutionary tool for transcriptomics.

            Zhong Wang, Mark Gerstein, Michael Snyder (2009)
            RNA-Seq is a recently developed approach to transcriptome profiling that uses deep-sequencing technologies. Studies using this method have already altered our view of the extent and complexity of eukaryotic transcriptomes. RNA-Seq also provides a far more precise measurement of levels of transcripts and their isoforms than other methods. This article describes the RNA-Seq approach, the challenges associated with its application, and the advances made so far in characterizing several eukaryote transcriptomes.
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              Next-generation transcriptome assembly.

              Jeffrey A Martin, Zhong Wang (2011)
              Transcriptomics studies often rely on partial reference transcriptomes that fail to capture the full catalogue of transcripts and their variations. Recent advances in sequencing technologies and assembly algorithms have facilitated the reconstruction of the entire transcriptome by deep RNA sequencing (RNA-seq), even without a reference genome. However, transcriptome assembly from billions of RNA-seq reads, which are often very short, poses a significant informatics challenge. This Review summarizes the recent developments in transcriptome assembly approaches - reference-based, de novo and combined strategies - along with some perspectives on transcriptome assembly in the near future.
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                Author and article information

                Contributors
                Priscila Di Paula Bessa Santana: Role: ND
                Artur Luis da Costa da Silva: Role: ND
                Rommel Thiago Jucá Ramos: Role: ND
                Arnaldo Algaranhar Gonçalves: Role: ND
                Nathalia Nogueira da Costa: Role: ND
                Priscilla do Carmo Azevedo Ramos: Role: ND
                Thiago Velasco Guimarães Silva: Role: ND
                Marcela da Silva Cordeiro: Role: ND
                Simone do Socorro Damasceno Santos: Role: ND
                Otávio Mitio Ohashi: Role: ND
                Moysés dos Santos Miranda: Role: ND
                Journal
                Journal ID (publisher-id): ar
                Title: Animal Reproduction
                Abbreviated Title: Anim. Reprod.
                Publisher: Colégio Brasileiro de Reprodução Animal (Belo Horizonte, MG, Brazil )
                ISSN (Print): 1806-9614
                ISSN (Electronic): 1984-3143
                Publication date (Print and electronic): June 2019
                Volume: 16
                Issue: 2
                Pages: 249-259
                Affiliations
                [02] Belém PA orgnameFederal University of Pará orgdiv1Laboratory of Genomics and Bioinformatics Brazil
                [03] Belém PA orgnameFederal University of Pará orgdiv1Institute of Biological Science orgdiv2Laboratory of In Vitro Fertilization Brazil
                [01] Capitão-Poço Pará orgnameFederal Rural University of Amazon Brazil
                Article
                Publisher ID: S1984-31432019000200249
                DOI: 10.21451/1984-3143-ar2017-0043
                SO-VID: 4a1ca1ab-e2ef-41a3-a2a1-c9048dc7ef9c
                License:

                This work is licensed under a Creative Commons Attribution 4.0 International License.

                History
                Date received : 02 November 2017
                Date accepted : 20 December 2018
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 92, Pages: 11
                Product

                SciELO Brazil

                Categories
                Subject: Reviews

                Keywords: RNA-seq,biomarker genes,in vitro embryo production,livestock animals
                Data availability:
                Keywords: RNA-seq, biomarker genes, in vitro embryo production, livestock animals

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