Genome-wide gene expression analyses reveal unique cellular characteristics related to the amenability of HPC/HSCs into high-quality induced pluripotent stem cells

is Table S2 presenting characteristics of the SF-iPSCs and TTF-iPSCs. (DOC 28 kb

Jump-seq: Genome-Wide Capture and Amplification of 5-Hydroxymethylcytosine Sites

5-Hydroxymethylcytosine (5hmC) arises from the oxidation of 5-methylcytosine (5mC) by Fe2+ and 2-oxoglutarate-dependent 10–11 translocation (TET) family proteins. Substantial levels of 5hmC accumulate in many mammalian tissues, especially in neurons and embryonic stem cells, suggesting a potential active role for 5hmC in epigenetic regulation beyond being simply an intermediate of active DNA demethylation. 5mC and 5hmC undergo dynamic changes during embryogenesis, neurogenesis, hematopoietic development, and oncogenesis. While methods have been developed to map 5hmC, more efficient approaches to detect 5hmC at base resolution are still highly desirable. Herein, we present a new method, Jump-seq, to capture and amplify 5hmC in genomic DNA. The principle of this method is to label 5hmC by the 6-N3-glucose moiety and connect a hairpin DNA oligonucleotide carrying an alkyne group to the azide-modified 5hmC via Huisgen cycloaddition (click) chemistry. Primer extension starts from the hairpin motif to the modified 5hmC site and then continues to “land” on genomic DNA. 5hmC sites are inferred from genomic DNA sequences immediately spanning the 5-prime junction. This technology was validated, and its utility in 5hmC identification was confirmed

Linking Incomplete Reprogramming to the Improved Pluripotency of Murine Embryonal Carcinoma Cell-Derived Pluripotent Stem Cells

Somatic cell nuclear transfer (SCNT) has been proved capable of reprogramming various differentiated somatic cells into pluripotent stem cells. Recently, induced pluripotent stem cells (iPS) have been successfully derived from mouse and human somatic cells by the over-expression of a combination of transcription factors. However, the molecular mechanisms underlying the reprogramming mediated by either the SCNT or iPS approach are poorly understood. Increasing evidence indicates that many tumor pathways play roles in the derivation of iPS cells. Embryonal carcinoma (EC) cells have the characteristics of both stem cells and cancer cells and thus they might be the better candidates for elucidating the details of the reprogramming process. Although previous studies indicate that EC cells cannot be reprogrammed into real pluripotent stem cells, the reasons for this remain unclear. Here, nuclei from mouse EC cells (P19) were transplanted into enucleated oocytes and pluripotent stem cells (P19 NTES cells) were subsequently established. Interestingly, P19 NTES cells prolonged the development of tetraploid aggregated embryos compared to EC cells alone. More importantly, we found that the expression recovery of the imprinted H19 gene was dependent on the methylation state in the differential methylation region (DMR). The induction of Nanog expression, however, was independent of the promoter region DNA methylation state in P19 NTES cells. A whole-genome transcriptome analysis further demonstrated that P19 NTES cells were indeed the intermediates between P19 cells and ES cells and many interesting genes were uncovered that may be responsible for the failed reprogramming of P19 cells. To our knowledge, for the first time, we linked incomplete reprogramming to the improved pluripotency of EC cell-derived pluripotent stem cells. The candidate genes we discovered may be useful not only for understanding the mechanisms of reprogramming, but also for deciphering the transition between tumorigenesis and pluripotency

Beneficial Effect of Young Oocytes for Rabbit Somatic Cell Nuclear Transfer

Abstract This study was designed to examine the effect of the age of rabbit oocytes on the developmental potential of cloned embryos. The metaphase II oocytes used for nuclear transfer (NT) were collected at 10, 12, 14, and 16h post-hCG injection (hpi). The total number of oocytes collected per donor (21.4-23.7) at 12 to 16 hpi was similar, but significantly higher than that collected at 10 hpi (16.2). Additionally, a significant improvement in blastocyst development was achieved with embryos generated by electrically mediated cell fusion (56.0%), compared to those from nuclear injection (13.1 %) (Experiment 1). Markedly higher blastocyst development (45.8-54.5%) was also achieved with oocytes collected at 10-12 hpi than from those collected 14-16 hpi (8.3-14.3%) (Experiment 2). In Experiment 3, the blastocyst rates of NT embryos derived from oocytes harvested 12 hpi (39.2-42.8 %) were significantly higher than from those collected at 16 hpi (6.8-8.4 %) (p<0.05), regardless of the donor cell age. Kinase activity assays showed variable changes of activity in rabbit oocytes over the period of 10-16 hpi; however, there was no correlation with preimplantational development (blastocyst rate vs. MPF, R=0.326; blastocyst rate vs. MAPK, R=0.131). Embryo transfer of NT embryos utilizing 12 hpi oocytes resulted in one full-term but stillborn, and one live cloned rabbit; thus, an efficiency of 1.7 % (n=117) (Experiment 4). These results demonstrated that NT utilizing relatively young rabbit oocytes, harvested at 10-12h after hCG injection, was beneficial for the development of NT embryos.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/78139/1/clo.2008.0042.pd

Poly (Butylene Succinate)/Silicon Nitride Nanocomposite with Optimized Physicochemical Properties, Biocompatibility, Degradability, and Osteogenesis for Cranial Bone Repair

Congenital disease, tumors, infections, and trauma are the main reasons for cranial bone defects. Herein, poly (butylene succinate) (PB)/silicon nitride (Si3N4) nanocomposites (PSC) with Si3N4 content of 15 w% (PSC15) and 30 w% (PSC30) were fabricated for cranial bone repair. Compared with PB, the compressive strength, hydrophilicity, surface roughness, and protein absorption of nanocomposites were increased with the increase in Si3N4 content (from 15 w% to 30 w%). Furthermore, the cell adhesion, multiplication, and osteoblastic differentiation on PSC were significantly enhanced with the Si3N4 content increasing in vitro. PSC30 exhibited optimized physicochemical properties (compressive strength, surface roughness, hydrophilicity, and protein adsorption) and cytocompatibility. The m-CT and histological results displayed that the new bone formation for SPC30 obviously increased compared with PB, and PSC30 displayed proper degradability (75.3 w% at 12 weeks) and was gradually replaced by new bone tissue in vivo. The addition of Si3N4 into PB not only optimized the surface performances of PSC but also improved the degradability of PSC, which led to the release of Si ions and a weak alkaline environment that significantly promoted cell response and tissue regeneration. In short, the enhancements of cellular responses and bone regeneration of PSC30 were attributed to the synergism of the optimized surface performances and slow release of Si ion, and PSC30 were better than PB. Accordingly, PSC30, with good biocompatibility and degradability, displayed a promising and huge potential for cranial bone construction

Identification of the new gene Zrsr1 to associate with the pluripotency state in induced pluripotent stem cells (iPSCs) using high throughput sequencing technology

Finding the markers to predict the quality of induced pluripotent stem cells (iPSCs) will accelerate its practical application. The fully pluripotent iPSCs has been determined as viable all-iPSC mice can be generated through tetraploid (4N) complementation. The activation of the imprinted Dlk1-Dio3 gene cluster was reported to correlate with the pluripotency of iPSCs. However, recent studies demonstrated that the loss of imprinting at the Dlk1-Dio3 locus does not strictly correlate with the reduced pluripotency of iPSCs. In our study (ref [1]), iPSC lines with the same genetic background and proviral integration sites were established, and the pluripotency state of each iPSC line was well characterized using tetraploid (4N) complementation assay. The gene expression and global epigenetic modifications of “4N-ON” and the corresponding “4N-OFF” iPSC lines were compared through deep sequencing analysis of mRNA expression, small RNA profiling, histone modifications (H3K4me3, H3K27me3 and H3K4me2) and DNA methylation. Very few differences were detected in the iPSC lines that were investigated. However, an imprinted gene, Zrsr1 was disrupted in the “4N-OFF” iPSC lines. Here we provide more detail about the dataset and the R script with additional data for others to repeat the finding