Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

Integrative Genomics Viewer

Somatic cells can be reprogrammed to induced pluripotent stem cells (iPSCs) by expression of defined embryonic factors. However, little is known of the molecular mechanisms underlying the reprogramming process. Here we explore somatic cell reprogramming by exploiting a secondary mouse embryonic fibroblast model that forms iPSCs with high efficiency upon inducible expression of Oct4, Klf4, c-Myc, and Sox2. Temporal analysis of gene expression revealed that reprogramming is a multistep process that is characterized by initiation, maturation, and stabilization phases. Functional analysis by systematic RNAi screening further uncovered a key role for BMP signaling and the induction of mesenchymal-to-epithelial transition (MET) during the initiation phase. We show that this is linked to BMP-dependent induction of miR-205 and the miR-200 family of microRNAs that are key regulators of MET. These studies thus define a multistep mechanism that incorporates a BMP-miRNA-MET axis during somatic cell reprogramming. PAPERCLIP:

Functional genomics reveals a bmp driven mesenchymal-to-epithelial transition in the initiation of somatic cell reprogramming (oral presentation)

Phosphatidylinositide 3 kinases (PI3Ks) and their downstream mediators AKT and mammalian target of rapamycin (mTOR) constitute the core components of the PI3K/AKT/mTOR signalling cascade, regulating cell proliferation, survival and metabolism. Although these functions are well-defined in the context of tumorigenesis, recent studies - in particular those using pluripotent stem cells - have highlighted the importance of this pathway to development and cellular differentiation. Here, we review the recent in vitro and in vivo evidence for the role PI3K/AKT/mTOR signalling plays in the control of pluripotency and differentiation, with a particular focus on the molecular mechanisms underlying these functions.

Proliferation, survival and metabolism: the role of PI3K/AKT/mTOR signalling in pluripotency and cell fate determination.

Mitochondrial rhomboid parl regulates cytochrome c release during apoptosis via OPA1 dependent cristae remodeling

Mouse embryonic stem (ES) cells perpetuate in vitro the broad developmental potential of naive founder cells in the preimplantation embryo. ES cells self-renew relentlessly in culture but can reenter embryonic development seamlessly, differentiating on schedule to form all elements of the fetus. Here we review the properties of these remarkable cells. Arising from the stability, homogeneity, and equipotency of ES cells, we consider the concept of a pluripotent ground state. We evaluate the authenticity of ES cells in relation to cells in the embryo and examine their utility for dissecting mechanisms that confer pluripotency and that execute fate choice. We summarize current knowledge of the transcription factor circuitry that governs the ES cell state and discuss the opportunity to expose molecular logic further through iterative computational modeling and experimentation. Finally, we present a perspective on unresolved questions, including the challenge of deriving ground state pluripotent stem cells fro...

The nature of embryonic stem cells.

The maintenance of a proper gene dosage is essential in cellular networks. To resolve the dosage imbalance between eutherian females (XX) and male (XY), X chromosome inactivation (XCI) occurs in females, while X-chromosome dosage compensation up-regulates the active X to balance its expression with that of autosome pairs [Ohno’s hypothesis; Ohno 1967 Sex Chromosomes and Sex-linked Genes (Springer-Verlag), p. 99]. These phenomena have been well studied in humans and mice, despite many controversies over the existence of such up-regulation. Using RNA sequencing data, we determined X chromosome dosage compensation in the bovine by analysing the global expression profiles of germ cells, embryos, and somatic tissues. Eight bovine RNA-seq data sets were obtained in from the Gene Expression Omnibus, covering bovine immature/mature oocytes (GSE59186 and GSE52415), pre-implantation conceptuses (GSE59186, GSE52415, and GSE56513), extra-embryonic tissues (PRJNA229443), and male/female somatic tissues (GSE74076, GSE63509, PRJEB6377, and GSE65125). The RNAseq data were trimmed and non-uniquely (paralogs included) mapped to the bovine reference genome assembly UMD3.1.1 using Hisat2 (version 2.0.5) aligner. The mRNA level of each gene, estimated by transformed transcripts per kilobase million was quantified by IsoEM (version 1.1.5). These RNA-seq data sets represented 4 chromosome scenarios in cells: XXXX:AAAA (diploid immature oocyte with DNA duplication), XX:AA (haploid mature oocyte with DNA duplication), XX:AA and X:AA (gradual changed X status in bovine pre-implantation conceptuses), and X:AA (extra-embryonic tissues and somatic cells in female with one active X or XY male) were analysed for dosage compensation. A total of 959 X-linked genes and 20,316 autosome genes were used to calculate the relative X to autosomal gene (A) expression (RXE): log2 (X expression) − log2 (A expression). The following dosage determinations were made: RXE values ≥ 0: complete dosage compensation (or X: A ratio ≥ 1); RXE values < 0: in-complete dosage compensation; RXE value = −1: no dosage compensation (or X: A ratio = 0.5). Our analyses showed a decreased RXE after fertilization, from −0.33 in matured oocytes to −0.50 at the 2-cell stage, indicating that the sperm that undergo meiotic sex chromosome inactivation (MSCI) bring in inactive X chromosomes to the matured oocytes. Subsequently, the activation of the bovine embryonic genome at the 4- to 8-cell stage increased RXE from −0.54 to −0.05. This was followed by a sharp RXE decline from −0.02 at the 16-cell stage, 0.1 at the 32-cell stage to −0.29 at the compact morula stage, which is known as paternal X inactivation stage in the bovine. Finally, RXE was stabilised from blastocysts −0.19 through the Day 19 conceptuses −0.25 to somatic tissue average −0.21 with a pattern of incomplete X compensation. These findings support X expression up-regulation as proposed by Ohno. No significant RXE differences were observed between bovine female and male somatic tissues, further supporting Ohno’s hypothesis, which predicts a balance in the expression of X-linked genes to that of autosomes. This study confirms Ohno’s hypothesis of X dosage compensation in bovine germ cells, early embryos, and somatic tissues.

125 incomplete compensatory up-regulation of x-linked genes in bovine germline, early embryos, and somatic tissues

SGK1 is essential for meiotic resumption in mammalian oocytes.

The meiotic spindle is one of the most vulnerable cytoplasmic organelles when performing oocyte vitrification. It has been proposed that submitting oocytes to a post-warming incubation period in maturation medium helps in the reorganization of microtubules and chromosomes. Our previous experiments found no differences in spindle morphology after submitting vitrified oocytes to a 2-h incubation period. The aim of this experiment was to determine the effect of extended culture on the reorganization of the meiotic spindle of vitrified-warmed bovine oocytes. Oocytes were purchased from a commercial vendor (n = 86) and matured during shipment. In this experiment, three treatments were evaluated: fresh oocytes (F) (n = 30), vitrified-warmed (VW; n = 26), and extended culture (EC; n = 30). Cumulus-oocyte complexes were removed at 18 h of maturation. Fresh oocytes were denuded by vortexing in hyaluronidase (1.5 mg mL−1) and immediately fixed using 4% paraformaldehyde. Oocytes undergoing vitrification were partially denuded by pipetting in hyaluronidase (1.5 mg mL−1). The vitrification protocol consisted of incubation in equilibration solution (7.5% dimethyl sulfoxide + 7.5% ethylene glycol) for 9 min and then in vitrification solution (15% dimethyl sulfoxide + 15% ethylene glycol + 0.5 M sucrose). While in vitrification solution, oocytes were mounted onto a Cryolock and plunged into liquid nitrogen in less than 1 min. Warming was performed by placing a Cryolock into 0.5 M sucrose for 3 min and then into 0.25 M sucrose for 3 min. Finally, oocytes were washed in base medium. The base medium used for cryoprotectant and warming solutions was Dulbecco's phosphate-buffered saline supplemented with 20% fetal bovine serum. Both, vitrification and warming, were performed at 38.5°C. After warming, half of the oocytes were completely denuded and fixed and the other half underwent a 6-h incubation period in maturation medium (IVF-Bioscience). To examine microtubule distribution and chromosome arrangement, fixed oocytes were submitted to an immunostaining protocol using α tubulin antibody (1:100) and anti IgG-Alexa Fluor 488 (1:1000; Thermo Fisher Scientific) and counterstained with Hoechst. The effect of extended culture on the incidence of abnormal microtubule distribution and chromosome arrangement was analysed using logistic regression with a binomial response variable (normal/abnormal). There was no difference in maturation rates among groups (F = 73.3%, VW = 77%, EC = 86.6%; P = 0.43). For microtubule distribution, oocytes fixed immediately after warming had a higher incidence of abnormal spindles (57.7%) when compared with oocytes submitted to extended culture (26.6%; P = 0.02). The most common abnormality seen in oocytes fixed after warming was small and faintly stained spindles. Microtubule distribution in fresh oocytes did not differ from oocytes in the other groups. There were no differences in chromosome arrangement among groups (P = 0.11). Future research will focus on evaluating the benefits that this technique offers to improve development following IVF using vitrified-warmed oocytes.

36 Extended culture after vitrification-warming helps in spindle recovery of bovine oocytes

High resolution ribosome fractionation and low-input ribosome profiling of bovine oocytes and preimplantation embryos has enabled us to define the translational landscapes of early embryo development at an unprecedented level. We analyzed the transcriptome, polysome- and non-polysome-bound RNA profiles of bovine oocytes (GV and MII stage) and early embryos at 2-, 8-cell, morula, and blastocyst stage, and revealed four modes of translational selectivity: i. selective translation of non-abundant mRNAs, ii. active, but modest translation of a selection of highly expressed mRNAs, iii. translationally suppressed abundant to moderately abundant mRNAs, and iv. mRNAs associated specifically with monosomes. A strong translational selection of low abundance mRNAs encoding protein components involved in metabolic pathways and lysosome was found throughout bovine oocyte and preimplantation development. In particular, genes encoding components involved in mitochondrial function were prioritized for translation. Notably, transcripts encoding proteins regulating chromatin modifications selectively translated in oocytes. We found that the translational dynamics largely reflects transcriptional profiles in oocytes and 2-cell embryos, but observed marked shift in translational control in 8-cell embryos associated with the main phase of embryonic genome activation. Subsequently, transcription and translation become better synchronized in morulae and blastocysts. Together, these data reveal a unique spatiotemporal translational regulation that accompanies bovine preimplantation development. Significance Statement Translational control during preimplantation embryo development is poorly understood, mostly due to the scarcity of samples and the corresponding inability to analyze low quantities of these materials. By developing a low-input method, we have been able to explore the transcriptome, polysome- and non-polysome-bound RNA profiles of bovine oocytes (GV and MII stage) and preimplantation embryos at 2-, 8-cell, morula, and blastocyst stages. We reveal four different modes of translational selectivity, plus novel temporal regulatory mechanisms during early embryo development. The spatiotemporal translation dynamics of bovine oocytes and preimplantation embryos offer an entirely new insight into mammalian embryo development research and new possibilities for improving efficiency of assisted reproduction technologies (ARTs).

Zongliang Jiang

Papers

125 incomplete compensatory up-regulation of x-linked genes in bovine germline, early embryos, and somatic tissues

SGK1 is essential for meiotic resumption in mammalian oocytes.

36 Extended culture after vitrification-warming helps in spindle recovery of bovine oocytes

High-resolution ribosome profiling reveals translational selectivity for transcripts in bovine preimplantation embryo development

MFN1 is required for follicle development, oocyte maturation, and female fertility