Induced Pluripotent Stem Cells in the Era of Precise Genome Editing

Genome editing has enhanced our ability to understand the role of genetics in a number of diseases by facilitating the development of more precise cellular and animal models to study pathophysiological processes. These advances have shown extraordinary promise in a multitude of areas, from basic research to applied bioengineering and biomedical research. Induced pluripotent stem cells (iPSCs) are known for their high replicative capacity and are excellent targets for genetic manipulation as they can be clonally expanded from a single cell without compromising their pluripotency. Clustered, regularly interspaced short palindromic repeats (CRISPR) and CRISPR/Cas RNA-guided nucleases have rapidly become the method of choice for gene editing due to their high specificity, simplicity, low cost, and versatility. Coupling the cellular versatility of iPSCs differentiation with CRISPR/Cas9-mediated genome editing technology can be an effective experimental technique for providing new insights into the therapeutic use of this technology. However, before using these techniques for gene therapy, their therapeutic safety and efficacy following models need to be assessed. In this review, we cover the remarkable progress that has been made in the use of genome editing tools in iPSCs, their applications in disease research and gene therapy as well as the hurdles that remain in the actual implementation of CRISPR/Cas systems.

Optimising Electroporation Condition for CRISPR/Cas-Mediated Knockout in Zona-Intact Buffalo Zygotes

Somatic cell nuclear transfer or cytoplasm microinjection has widely been used to produce genome-edited farm animals; however, these methods have several drawbacks which reduce their efficiency. In the present study, we describe an easy adaptable approach for the introduction of mutations using CRISPR-Cas9 electroporation of zygote (CRISPR-EP) in buffalo. The goal of the study was to determine the optimal conditions for an experimental method in which the CRISPR/Cas9 system is introduced into in vitro-produced buffalo zygotes by electroporation. Electroporation was performed using different combinations of voltage, pulse and time, and we observed that the electroporation in buffalo zygote at 20 V/mm, 5 pulses, 3 msec at 10 h post insemination (hpi) resulted in increased membrane permeability and higher knockout efficiency without altering embryonic developmental potential. Using the above parameters, we targeted buffalo POU5F1 gene as a proof of concept and found no variations in embryonic developmental competence at cleavage or blastocyst formation rate between control, POU5F1-KO, and electroporated control (EC) embryos. To elucidate the effect of POU5F1-KO on other pluripotent genes, we determined the relative expression of SOX2, NANOG, and GATA2 in the control (POU5F1 intact) and POU5F1-KO-confirmed blastocyst. POU5F1-KO significantly (p ≤ 0.05) altered the expression of SOX2, NANOG, and GATA2 in blastocyst stage embryos. In conclusion, we standardized an easy and straightforward protocol CRISPR-EP method that could be served as a useful method for studying the functional genomics of buffalo embryos.

Characterization of Green Fluorescent Protein in Heart Valves of a Transgenic Swine Model for Partial Heart Transplant Research

A transgenic strain of pigs was created to express green fluorescent protein (GFP) ubiquitously using a pCAGG promoter. Here, we characterize GFP expression in the semilunar valves and great arteries of GFP-transgenic (GFP-Tg) pigs. Immunofluorescence was performed to visualize and quantify GFP expression and colocalization with nuclear staining. GFP expression was confirmed in both the semilunar valves and great arteries of GFP-Tg pigs compared to wild-type tissues (aorta, p = 0.0002; pulmonary artery, p = 0.0005; aortic valve; and pulmonic valve, p < 0.0001). The quantification of GFP expression in cardiac tissue allows this strain of GFP-Tg pigs to be used for future research in partial heart transplantation.

Limited Expansion of Human Hepatocytes in FAH/RAG2-Deficient Swine

BACKGROUND

The mammalian liver's regenerative ability has led researchers to engineer animals as incubators for expansion of human hepatocytes. The expansion properties of human hepatocytes in immunodeficient mice are well known. However, little has been reported about larger animals that are more scalable and practical for clinical purposes. Therefore, we engineered immunodeficient swine to support expansion of human hepatocytes and identify barriers to their clinical application.

METHODS

Immunodeficient swine were engineered by knockout of recombinase activating gene 2 (RAG2) and fumarylacetoacetate hydrolase (FAH). Immature human hepatocytes (ihHCs) were injected into fetal swine by intrauterine cell transplantation (IUCT) at day 40 of gestation. Human albumin was measured as a marker of engraftment. Cytotoxicity against ihHCs was measured in transplanted piglets and control swine.

RESULTS

Higher levels of human albumin were detected in cord blood of newborn FAH/RAG2-deficient (FR) pigs compared to immunocompetent controls (196.26 ng/dL vs 39.29 ng/dL, p = 0.008), indicating successful engraftment of ihHC after IUCT and adaptive immunity in the fetus. Although rare hepatocytes staining positively for human albumin were observed, levels of human albumin did not rise after birth but declined suggesting rejection of xenografted ihHCs. Cytotoxicity against ihHCs increased after birth 3.8% (95% CI: [2.1%, 5.4%], p < 0.001) and correlated inversely to declining levels of human albumin (p = 2.1 x 10-5, R2 = 0.17). Circulating numbers of T-cells and B-cells were negligible in FR pigs. However, circulating natural killer (NK) cells exerted cytotoxicity against ihHCs. NK cell activity was lower in immunodeficient piglets after IUCT than naive controls (30.4% vs 40.1% (p = 0.011, 95% CI for difference [2.7%, 16.7%]).

CONCLUSION

Immature human hepatocytes successfully engrafted in FR swine after IUCT. NK cells were a significant barrier to expansion of hepatocytes. New approaches are needed to overcome this hurdle and allow large scale expansion of human hepatocytes in immunodeficient swine.

Deciphering the functional role of EGR1 in Prostaglandin F2 alpha induced luteal regression applying CRISPR in corpus luteum of buffalo

Background

PGF2α is essential for the induction of the corpus luteum regression which in turn reduces progesterone production. Early growth response (EGR) proteins are Cys2-His2-type zinc-finger transcription factor that are strongly linked to cellular proliferation, survival and apoptosis. Rapid elevation of EGR1 was observed after luteolytic dose of PGF2α. EGR1 is involved in the transactivation of many genes, including TGFβ1, which plays an important role during luteal regression.

Methods

The current study was conducted in buffalo luteal cells with the aim to better understand the role of EGR1 in transactivation of TGFβ1 during PGF2α induced luteal regression. Luteal cells from mid stage corpus luteum of buffalo were cultured and treated with different doses of PGF2α for different time durations. Relative expression of mRNAs encoding for enzymes within the progesterone biosynthetic pathway (3βHSD, CYP11A1 and StAR); Caspase 3; AKT were analyzed to confirm the occurrence of luteolytic event. To determine if EGR1 is involved in the PGF2α induced luteal regression via induction of TGFβ1 expression, we knocked out the EGR1 gene by using CRISPR/Cas9.

Result

The present experiment determined whether EGR1 protein expression in luteal cells was responsive to PGF2α treatment. Quantification of EGR1 and TGFβ1 mRNA showed significant up regulation in luteal cells of buffalo at 12 h post PGF2α induction. In order to validate the role of PGF2α on stimulating the expression of TGFβ1 by an EGR1 dependent mechanism we knocked out EGR1. The EGR1 ablated luteal cells were stimulated with PGF2α and it was observed that EGR1 KO did not modulate the PGF2α induced expression of TGFβ1. In PGF2α treated EGR1 KO luteal cell, the mRNA expression of Caspase 3 was significantly increased compared to PGF2α treated wild type luteal cells maintained for 12 h. We also studied the influence of EGR1 on steroidogenesis. The EGR1 KO luteal cells with PGF2α treatment showed no substantial difference either in the progesterone concentration or in StAR mRNA expression with PGF2α-treated wild type luteal cells.

Conclusion

These results suggest that EGR1 signaling is not the only factor which plays a role in the regulation of PGF2α induced TGFβ1 signaling for luteolysis.

Modulation of granulosa cell function via CRISPR-Cas fuelled editing of BMPR-IB gene in goats (Capra hircus)

BMPs are multifunctional growth factors implicated in regulating the ovarian function as key intra-ovarian factors. Biological effects of BMPs are mediated through binding with membrane bound receptors like BMPR-IB and initiating downstream Smad signaling pathway. FecB mutation, regarded as a loss of function mutation in the BMPR-IB gene was identified in certain sheep breeds having high fecundity. Similar type of fecundity genes in goats have not been discovered so far. Hence, the current study was designed to investigate the effects of BMPR-IB gene modulation on granulosa cell function in goats. The BMPR-IB gene was knocked out using CRISPR-Cas technology in granulosa cells and cultured in vitro with BMP-4 stimulation for three different durations In addition, the FecB mutation was introduced in the BMPR-IB gene applying Easi-CRISPR followed by BMP-4/7 stimulation for 72 h. Steroidogenesis and cell viability were studied to explore the granulosa cell function on BMPR-IB gene modulation. BMPRs were found to be expressed stage specifically in granulosa cells of goats. Higher transcriptional abundance of R-Smads, LHR and FSHR indicating sensitisation of Smad signaling and increased gonadotropin sensitivity along with a significant reduction in the cell proliferation and viability was observed in granulosa cells upon BMPR-IB modulation. The inhibitory action of BMP-4/7 on P4 secretion was abolished in both KO and KI cells. Altogether, the study has revealed an altered Smad signaling, steroidogenesis and cell viability upon modulation of BMPR-IB gene in granulosa cells similar to that are documented in sheep breeds carrying the FecB mutation.

232 Protecting pigs from viral infectivity with gene editing

Pig models were created that were fully resistant to Porcine Reproductive and Respiratory Syndrome (PRRS) and the alphacoronaviruses, transmissible gastroenteritis virus (TGEV) by DNA editing of the cluster of differentiation (CD163) gene and aminopeptidase N (ANPEP) gene via CRISPR/Cas, respectively. Litters of pigs were bred with a gene edit in exon 7 of CD163 that resulted no CD163 protein expression (CD163-/-). The pigs were either challenged with multiple PRRSV isolates at 3 weeks of age or bred at maturity for a challenge with pregnant sows. The challenges demonstrated that the pigs were completely resistant to infectivity to both Type 1 and 2 isolates as measured by clinical signs, viremia, antibody response and lung histopathology. In a follow-up study, pregnant CD163 edited pigs were challenged with PRRSV to determine if absence of CD163 in the dam should be sufficient to protect the fetuses that have functional CD163 protein. The CD163-/- sows carrying both the CD163-/- and CD163+/- fetuses were all negative for PRRSV nucleic acid and showed no sign of fetal or placental failure clearly demonstrating that the absence of CD163 in the sow is sufficient to protect a PRRSV-susceptible CD163+/- fetus. Gene editing of CD163 in pigs, via CRISPR/Cas9, successfully blocked PRRSV infectivity in young growing pigs and pregnant sows and their fetuses. Similar methods were used to determine if TGEV infectivity could be prevented by editing the ANPEP gene. Exon 2 of ANPEP was edited and resulted an ANPEP -/- genotype. ANPEP -/- pigs and age matched wild type pigs were challenged with TGEV. The presence of virus nucleic acid was determined by PCR in fecal samples. ANPEP -/- pigs were fully resistant to TGEV infectivity. These studies clearly show that precise gene editing can be successfully used in pigs to prevent viral infectivity of both PRRSV and TGEV.

Impairment of preimplantation porcine embryo development by histone demethylase KDM5B knockdown through disturbance of bivalent H3K4me3-H3K27me3 modifications

KDM5B (JARID1B/PLU1) is a H3K4me2/3 histone demethylase that is implicated in cancer development and proliferation and is also indispensable for embryonic stem cell self-renewal, cell fate, and murine embryonic development. However, little is known about the role of KDM5B during preimplantation embryo development. Here we show that KDM5B is critical to porcine preimplantation development. KDM5B was found to be expressed in a stage-specific manner, consistent with demethylation of H3K4me3, with the highest expression being observed from the 4-cell to the blastocyst stages. Knockdown of KDM5B by morpholino antisense oligonucleotides injection impaired porcine embryo development to the blastocyst stage. The impairment of embryo development might be caused by increased expression of H3K4me3 at the 4-cell and blastocyst stages, which disturbs the balance of bivalent H3K4me3-H3K27me3 modifications at the blastocyst stage. Decreased abundance of H3K27me3 at blastocyst stage activates multiple members of homeobox genes (HOX), which need to be silenced for faithful embryo development. Additionally, the histone demethylase KDM6A was found to be upregulated by knockdown of KDM5B, which indicated it was responsible for the decreased abundance of H3K27me3 at the blastocyst stage. The transcriptional levels of Ten-Eleven Translocation gene family members (TET1, TET2, and TET3) are found to be increased by knockdown of KDM5B, which indicates cross talk between histone modifications and DNA methylation. The studies above indicate that KDM5B is required for porcine embryo development through regulating the balance of bivalent H3K4me3-H3K27me3 modifications.

Dynamics of TET family expression in porcine preimplantation embryos is related to zygotic genome activation and required for the maintenance of NANOG

Dynamic changes in DNA methylation are observed during embryo development. Recent studies show that the TET family is involved in these changes by converting 5-methylcytosine (5mec) to 5-hydroxymethylcytosine (5hmec). Specifically, TET3 is responsible for the conversion in the early stages, and then TET1 is a key regulator at later stages of embryo development. From previous mouse reports and our preliminary data in porcine embryos, we hypothesized that TET1 becomes the main regulator at the time of the maternal to zygotic transition (MZT). Transcript abundance of TET3 was high only at the zygote and 2-cell stage. The abundance of TET1 mRNA was high in the blastocysts and TET1 protein was present at the 4-cell stage and the blastocysts. The dynamic was similar in porcine somatic cell nuclear transfer (SCNT) embryos however; abnormally upregulated TET3 was detected at the 4-cell stage. When transcription or translation was blocked at the 2-cell stage, TET3 mRNA remained high at the 4-cell stage suggesting that degradation of TET3 is related to the MZT. Downregulation of TET3 before fertilization resulted in the reduction of 5hmec in zygotes indicating that TET3 is a key molecule for 5hmec synthesis. This misregulation of 5hmec in zygotes also affected the level of NANOG expression in the blastocysts. We show here that the porcine TET family shows dynamic expression patterns during embryogenesis, and is responsible for the appearance of 5hmec in the zygotes by TET3. This appearance of 5hmec in zygote is important for the expression of NANOG in the blastocysts.

145 CHARACTERIZATION OF THE PROTEIN ARGININE METHYLTRANSFERASE-DIMETHYLARGININE DIMETHYLAMINOHYDROLASE-NITRIC OXIDE AXIS DURING PORCINE EMBRYO DEVELOPMENT

Transcriptional deep sequencing analysis by Bauer et al. (2010) revealed a significant increase in expression of the arginine transporter SLC7A1 in in vitro–cultured porcine blastocysts compared with those cultured in vivo and this was corrected through supplemental arginine. This indicates an important role for arginine during porcine embryo development. Arginine is the precursor for nitric oxide (NO) production and previous work in mice and cattle has shown decreased development when embryos were cultured with a nitric oxide synthase (NOS) inhibitor. The NOS activity is inhibited by monomethylarginine (MMA) and asymmetric dimethylarginine (ADMA) that are released during degradation of proteins methylated by protein arginine methyltransferases (PRMT). The enzyme dimethylarginine dimethylaminohydrolase (DDAH) is responsible for degrading MMA and ADMA in the cell. Therefore, the goal of this study was to investigate whether this PRMT-DDAH-NO axis exists in pre-implantation porcine embryos. To this end, expression of PRMT1, PRMT3, PRMT5, DDAH1 and endothelial NOS (NOS3) was analysed at different stages of embryonic development using real-time quantitative RT-PCR. In addition, the effect of supplemental arginine (1.69 mM) on the expression of the aforementioned genes was investigated. Production of NO in porcine embryos was also visualised using 4-amino-5-methylamino-2,7-difluorofluorescein diacetate (DAF-FM-DA). In vitro–fertilized porcine embryos were collected at the 4-cell and blastocyst stages. The RNA was isolated from pools of 18 to 20 embryos and cDNA, was synthesised using Superscript III (Invitrogen, Carlsbad, CA, USA). Real-time PCR analysis was performed and the mean fold change in gene expression from the reference gene YWHAG was analysed by t-test after a log transformation. Expression of PRMT3 and PRMT5 was significantly higher (P < 0.05) in blastocysts versus 4-cell embryos. Expression of PRMT1, however, was higher in 4-cell embryos (P < 0.05). The expression of DDAH1 was detected in 4-cell embryos, but DDAH1 became undetectable by the blastocyst stage. Previous microarray analysis in our laboratory by Whitworth et al. (2005 Biol. Reprod. 72(6), 1437–1451) also revealed a significant up-regulation of DDAH2 expression at the 4-cell stage versus blastocysts. Expression of NOS3 was undetectable in the 4-cell and blastocyst; however, NO was detected in 4-cell and blastocyst stage embryos by using DAF-FM-DA. This suggests that a different NOS may be acting in the porcine embryo. Addition of arginine did not have a significant effect on expression of the analysed genes. These results suggest that PRMT-DDAH regulated NO production may play a role during porcine embryo development. Understanding the PRMT-DDAH-NO axis and its regulation during embryonic development will further our ability to tailor in vitro culture so that it more appropriately mimics that of an in vivo environment. Funding was provided by NIH U42 RR18877.

Disruption of the CFTR gene produces a model of cystic fibrosis in newborn pigs

Almost two decades after CFTR was identified as the gene responsible for cystic fibrosis (CF), we still lack answers to many questions about the pathogenesis of the disease, and it remains incurable. Mice with a disrupted CFTR gene have greatly facilitated CF studies, but the mutant mice do not develop the characteristic manifestations of human CF, including abnormalities of the pancreas, lung, intestine, liver, and other organs. Because pigs share many anatomical and physiological features with humans, we generated pigs with a targeted disruption of both CFTR alleles. Newborn pigs lacking CFTR exhibited defective chloride transport and developed meconium ileus, exocrine pancreatic destruction, and focal biliary cirrhosis, replicating abnormalities seen in newborn humans with CF. The pig model may provide opportunities to address persistent questions about CF pathogenesis and accelerate discovery of strategies for prevention and treatment.

Production of CFTR-null and CFTR-DeltaF508 heterozygous pigs by adeno-associated virus-mediated gene targeting and somatic cell nuclear transfer

Progress toward understanding the pathogenesis of cystic fibrosis (CF) and developing effective therapies has been hampered by lack of a relevant animal model. CF mice fail to develop the lung and pancreatic disease that cause most of the morbidity and mortality in patients with CF. Pigs may be better animals than mice in which to model human genetic diseases because their anatomy, biochemistry, physiology, size, and genetics are more similar to those of humans. However, to date, gene-targeted mammalian models of human genetic disease have not been reported for any species other than mice. Here we describe the first steps toward the generation of a pig model of CF. We used recombinant adeno-associated virus (rAAV) vectors to deliver genetic constructs targeting the CF transmembrane conductance receptor (CFTR) gene to pig fetal fibroblasts. We generated cells with the CFTR gene either disrupted or containing the most common CF-associated mutation (DeltaF508). These cells were used as nuclear donors for somatic cell nuclear transfer to porcine oocytes. We thereby generated heterozygote male piglets with each mutation. These pigs should be of value in producing new models of CF. In addition, because gene-modified mice often fail to replicate human diseases, this approach could be used to generate models of other human genetic diseases in species other than mice.

Concentration and composition of free amino acids and osmolalities of porcine oviductal and uterine fluid and their effects on development of porcine IVF embryos

The concentration of free amino acids and the osmolalities in porcine oviductal (OF) and uterine fluids (UFs) on day 3 (D3) and day 5 (D5) were measured by HPLC and Vapor Pressure Osmometer, respectively. Based on these measurements we designed new media based on PZM3 by modifying the amino acid composition and osmolality. The effectiveness of the modified PZM3 on the development of porcine IVF embryos was then investigated. A total of 24 free amino acids were measured, including 20 protein and 4 nonprotein amino acids (beta-alanine, taurine, ornithine, and citrulline). There was no significant difference in the total concentration of amino acids among D3OF (13.06 +/- 3.63 mmol/L), D3UF (10.54 +/- 5.16 mmol/L), or D5UF (10.23 +/- 6.69 mmol/L). But the total concentration of amino acids in D5OF (5.89 +/- 1.47 mmol/L) was significantly lower than the three fluids above. Some individual amino acids varied significantly depending on where they were collected and from which day. The blastocyst rates of porcine IVF embryos were not improved when embryos were cultured in PZM3 with amino acids at D3OF (PZM3-D3OF, 20.3 +/- 7.9%) or D5UF (PZM3-D5UF, 14.3 +/- 10.7%) concentrations or in PZM3-D3OF for the first 48 (20.5 +/- 15.1), 72 (25.6 +/- 10.4), and 96 (18.7 +/- 10.0) hr and then transferred into PZM3-D5UF compared with PZM3 with Sigma amino acid solution (PZM3-SAA) (30.8 +/- 9.1%). However, when IVF embryos were cultured in PZM3-D5UF, the average nuclear number per blastocyst (57.6 +/- 8.3) was increased compared to PZM3-SAA (40.5 +/- 3.5). The osmolalities in D3OF, D3UF, D5OF, and D5UF were 318 +/- 8, 320 +/- 32, 321, and 293 +/- 8 mOsM, respectively. When the IVF embryos were cultured in PZM3-SAA and PZM3-D3OF at a variety of osmolalities (150-360 mOsM), higher blastocyst rates were obtained at 270-300 mOsM in the PZM3-SAA group (24.6-33.9%) and 270-290 mOsM in PZM3-D3OF group (22.4-24.2%). The blastocyst rate gradually decreased when the osmolality was increased or decreased in both groups. When the embryos were cultured in PZM3-SAA at 330 mOsM for the first 72 hr and then transferred to 250 mOsM (33.3 +/- 3.4%), the blastocyst rate was higher than original PZM3 (21.2 +/- 2.2%) (288 mOsM).

381 PRODUCTION OF A TRANSGENIC PIGLET BY A NEW SPERM INJECTION TECHNIQUE

The technique for intracytoplasmic sperm injection (ICSI) has, until now, focused on scoring the tail of the sperm prior to catching and aspiration into the injection pipette. This is in spite of the fact that damage to the head would more closely simulate what occurs during normal fertilization. In addition, to aid in visualizing the injection process so that a reduced volume can be injected, the oocyte is generally centrifuged to clear a portion of the cytoplasm. Thus, with conventional ICSI, the sperm are immobilized with polyvinylpyrrolidone, repeatedly frozen and thawed, treated with DTT or Triton X-100, and severed between the head and tail; the oocyte is centrifuged or activated. All of the above treatments are designed to compensate for the intrinsic defects in conventional ICSI. Our objective was to use a modified ICSI procedure whereby aggressively motile sperm were captured onto the broken tip of an injection pipette and then injected into noncentrifuged oocytes. Damage to the head of the sperm occurred on the pipette or while pushed through the zona pellucida. These procedures are based on the work of Yong et al. 2003 Hum. Reprod. 18, 2390, where they achieved an improvement in development in vitro as compared to conventional methods. Ovaries were collected from prepubertal gilts, and oocytes were aspirated and matured in vitro. Sperm were collected from a transgenic boar carrying the green fluorescent protein (GFP) and frozen. After thawing, aggressively motile sperm were captured and injected through the zona pellucida and into the cytoplasm of the in vitro-matured oocytes. A total of 452 injected oocytes (43-171 oocytes per recipient) were surgically transferred into the oviduct of six surrogate gilts. Two gilts (33%) became pregnant. One gave birth to a healthy male piglet. GFP expression was observed in the nose and hooves by direct epifluorescent examination of the newborn piglet. This pattern of GFP expression is identical to that in non-ICSI-derived GFP pigs in this line. This result showed for the first time that this new sperm injection technique could be used for production of a viable transgenic piglet using in vitro-matured oocytes and frozen-thawed sperm.

254 DIFFERENTIAL TRANSCRIPTION AND CYSTOPLASMIC POLYADENYLATION ELEMENTS IN PORCINE GERMINAL VESICLE AND METAPHASE II OOCYTES

Identification of transcripts produced during porcine oocyte maturation is one of the first steps in defining pathways important to development. Practically, this information will aid in the refinement of in vitro culture processes, allowing for more efficient in vitro embryo production. To this end, mRNA was isolated from 50 in vitro-matured sow metaphase II stage oocytes (Bomed, Inc., Madison, WI, USA) (MIIs), 50 in vitro-matured gilt metaphase II-stage oocytes (MIIg), and 50 gilt germinal vesicle stage oocytes (GVO) by using the Dynabead® system (Dynal, Inc., Lake Success, NY, USA) and amplified by using the SMART system (Clontech, Palo Alto, CA, USA). The PCR products were ligated into a pSport vector and transformed into electro-competent E. coli. Colonies were randomly picked and sequenced at the University of Missouri DNA Core. Sequences were clustered with similar sequences derived from a larger expressed sequence tag (EST) project (http://genome.rnet.missouri.edu/Swine/) by using the tlcluster program developed at the University of Iowa. Following clustering, individual clusters in the cDNA libraries were compared by using Fisher's exact test (P < 0.01) to determine if they were differentially represented. Two sets of comparisons were performed, one between the MIIs and MIIg libraries, and another between the GVO library and the combination of both metaphase II libraries (MII). The number of clusters per number of clones in the library was 966/1668 (GVO), 458/820 (MIIg), and 158/819 (MIIs). There were 15/419 clusters that were different between the MIIs and MIIg libraries, and 26/1269 that were different between the MII and GVO libraries. Potential cytoplasmic polyadenylation elements (CPEs) identified from the literature were found in the GVO and MII libraries by using a custom pattern-matching program. Of the clusters with differential expression, 4/15 (MIIs vs. MIIg) and 7/26 (MII vs. GVO) contained CPEs. Table 1 contains a partial list of differentially expressed genes and the sequence of their cytoplasmic polyadenylation elements. Many genes were found to be differentially expressed in both (MII vs. GVO and MIIs vs. MIIg) comparisons. Collectively, these findings will facilitate the elucidation of important developmental pathways in swine and other animals. Table 1. Comparison of mRNA expression and cytoplasmic polyadenylation elements This work was partially funded by a University of Missouri Life Sciences Mission Enhancement grant and Food for the 21st Century.

Developmental expression of 2489 gene clusters during pig embryogenesis: an expressed sequence tag project

Identification of mRNAs that are present at early stages of embryogenesis is critical for a better understanding of development. To this end, cDNA libraries were constructed from germinal vesicle-stage oocytes, in vivo-produced four-cell- and blastocyst-stage embryos, and from in vitro-produced four-cell- and blastocyst-stage embryos. Randomly picked clones (10 848) were sequenced from the 3' end and those of sufficient quality (8066, 74%) were clustered into groups of sequence similarity (>95% identity), resulting in 2489 clusters. The sequence of the longest representative expressed sequence tag (EST) of each cluster was compared with GenBank and TIGR. Scores below 200 were considered unique, and 1114 (44.8%) did not have a match in either database. Sequencing from the 5' end yielded 12 of 37 useful annotations, suggesting that one third of the 1114 might be identifiable, still leaving over 700 unique ESTs. Virtual Northerns compared between the stages identified numerous genes where expression appears to change from the germinal vesicle oocyte to the four-cell stage, from the four-cell to blastocyst stage, and between in vitro- and in vivo-derived four-cell- and blastocyst-stage embryos. This is the first large-scale sequencing project on early pig embryogenesis and has resulted in the discovery of a large number of genes as well as possible stage-specific expression. Because many of these ESTs appear to not be in the public databases, their addition will be useful for transcriptional profiling experiments conducted on early pig embryos.

Radiation hybrid comparative mapping between human chromosome 17 and porcine chromosome 12 demonstrates conservation of gene order

A comparative study of human chromosome 17 (HSA17) and pig chromosome 12 (SSC12) was conducted using both somatic cell hybrid panel (SCHP) and radiation hybrid (RH) panel analysis. Sequences from an expressed sequence tag (EST) project in pig reproduction were examined and six genes and ESTs originally believed to map to HSA17 were selected for this study. The genes/ESTs were TATA box binding protein-associated factor (TAF2N/RBP56), alpha-2-plasmin inhibitor (SERPINF2/PLI), H3 histone family 3B (H3F3B), aminopeptidase puromycin sensitive (NPEPPS), an expressed sequence tag (ESTMI015) and P311 protein (P311). The SCHP analysis mapped five genes/ESTs (TAF2N, H3F3B, SERPINF2, NPEPPS and ESTMI015) to SSC12q11-q15 and SSC12p11-p15 with 100% concordance, and assigned P311 to SSC2 (1/2q24)-q29 with 100% concordance. Radiation hybrid analysis of all six genes confirmed the SCHP mapping results, with average retention frequency of 25%. Recent human sequence data demonstrated that P311 is actually located on HSA5q. As HSA5q and SSC2q show conserved syntenic regions predicted from bi-directional painting, our P311 mapping data is consistent with these results. An expanded comparative SSC12 RH map integrating the five new type I markers and 23 previously mapped loci was established using a LOD score threshold of 4.8. The gene order of the five genes/ESTs on the SSC12 framework RH map (H3F3B-ESTMI015-NPEPPS-TAF2N-SERPINF2) is identical to the HSA17 GB4 map but with inversion of the map as conventionally drawn.