Books by Dinh Truong Nguyen
Papers by Dinh Truong Nguyen
Genomics & Informatics, 2009
Sequences from the clones of full-length enriched cDNA libraries serve as valuable resources for ... more Sequences from the clones of full-length enriched cDNA libraries serve as valuable resources for functional genomics related studies, genome annotation and SNP discovery. We analyzed 7,392 high-quality chromatograms (Phred value ≥30) obtained from sequencing the 5' ends of clones derived from full-length enriched cDNA libraries of Korean native pigs including brainstem, liver, cerebellum, neocortex and spleen libraries. In addition, 50,000 EST sequence trace files obtained from GenBank were combined with our sequences to identify cSNPs in silico. The process generated 11,324 contigs, of which 2,895 contigs contained at least one SNP and among them 610 contigs had a minimum of one sequence from Korean native pigs. Of 610 contigs, we randomly selected 262 contigs and performed in silico analysis for the identification of cSNPs. From the results, we identified 1,531 putative coding single nucleotide polymorphisms (cSNPs) and the SNP detection frequency was one SNP per 465 bp. A large-scale sequencing result of clones from full-length enriched cDNA libraries and identified cSNPs will serve as a useful resource to functional genomics related projects such as a pig HapMap project in the near future.
Nature, 2012
* Numbers refer to the annotation performed by Ensembl (release 67). Results of an independent an... more * Numbers refer to the annotation performed by Ensembl (release 67). Results of an independent annotation by the NCBI can be obtained from http://www.ncbi.nlm.nih.gov/mapview/stats/ BuildStats.cgi?taxid59823&build54&ver51. { An improved ncRNA annotation with 3,601 ncRNAs and structured elements is available as a separate track in Ensembl version 70 and for download from http://rth.dk/resources/rnannotator/susscr102. N50, 50% of the genome is in fragments of this length or longer.
DNA research : an international journal for rapid publication of reports on genes and genomes, Jan 10, 2015
DNA methylation plays a major role in the epigenetic regulation of gene expression. Although a fe... more DNA methylation plays a major role in the epigenetic regulation of gene expression. Although a few DNA methylation profiling studies of porcine genome which is one of the important biomedical models for human diseases have been reported, the available data are still limited. We tried to study methylation patterns of diverse pig tissues as a study of the International Swine Methylome Consortium to generate the swine reference methylome map to extensively evaluate the methylation profile of the pig genome at a single base resolution. We generated and analysed the DNA methylome profiles of five different tissues and a cell line originated from pig. On average, 39.85 and 62.1% of cytosine and guanine dinucleotides (CpGs) of CpG islands and 2 kb upstream of transcription start sites were covered, respectively. We detected a low rate (an average of 1.67%) of non-CpG methylation in the six samples except for the neocortex (2.3%). The observed global CpG methylation patterns of pigs indicat...
Induced pluripotent stem cells (iPSCs) have been generated by enforced expression of defined sets... more Induced pluripotent stem cells (iPSCs) have been generated by enforced expression of defined sets of transcription factors in
somatic cells. It remains controversial whether iPSCs are molecularly and functionally equivalent to blastocyst-derived
embryonic stem (ES) cells. By comparing genetically identical mouse ES cells and iPSCs, we show here that their overall
messenger RNA and microRNA expression patterns are indistinguishable with the exception of a few transcripts encoded
within the imprinted Dlk1–Dio3 gene cluster on chromosome 12qF1, which were aberrantly silenced in most of the iPSC
clones. Consistent with a developmental role of the Dlk1–Dio3 gene cluster, these iPSC clones contributed poorly to
chimaeras and failed to support the development of entirely iPSC-derived animals (‘all-iPSC mice’). In contrast, iPSC clones
with normal expression of the Dlk1–Dio3 cluster contributed to high-grade chimaeras and generated viable all-iPSC mice.
Notably, treatment of an iPSC clone that had silenced Dlk1–Dio3 with a histone deacetylase inhibitor reactivated the locus
and rescued its ability to support full-term development of all-iPSC mice. Thus, the expression state of a single imprinted
gene cluster seems to distinguish most murine iPSCs from ES cells and allows for the prospective identification of iPSC clones
that have the full development potential of ES cells.
Talks by Dinh Truong Nguyen
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Books by Dinh Truong Nguyen
Papers by Dinh Truong Nguyen
somatic cells. It remains controversial whether iPSCs are molecularly and functionally equivalent to blastocyst-derived
embryonic stem (ES) cells. By comparing genetically identical mouse ES cells and iPSCs, we show here that their overall
messenger RNA and microRNA expression patterns are indistinguishable with the exception of a few transcripts encoded
within the imprinted Dlk1–Dio3 gene cluster on chromosome 12qF1, which were aberrantly silenced in most of the iPSC
clones. Consistent with a developmental role of the Dlk1–Dio3 gene cluster, these iPSC clones contributed poorly to
chimaeras and failed to support the development of entirely iPSC-derived animals (‘all-iPSC mice’). In contrast, iPSC clones
with normal expression of the Dlk1–Dio3 cluster contributed to high-grade chimaeras and generated viable all-iPSC mice.
Notably, treatment of an iPSC clone that had silenced Dlk1–Dio3 with a histone deacetylase inhibitor reactivated the locus
and rescued its ability to support full-term development of all-iPSC mice. Thus, the expression state of a single imprinted
gene cluster seems to distinguish most murine iPSCs from ES cells and allows for the prospective identification of iPSC clones
that have the full development potential of ES cells.
Talks by Dinh Truong Nguyen
somatic cells. It remains controversial whether iPSCs are molecularly and functionally equivalent to blastocyst-derived
embryonic stem (ES) cells. By comparing genetically identical mouse ES cells and iPSCs, we show here that their overall
messenger RNA and microRNA expression patterns are indistinguishable with the exception of a few transcripts encoded
within the imprinted Dlk1–Dio3 gene cluster on chromosome 12qF1, which were aberrantly silenced in most of the iPSC
clones. Consistent with a developmental role of the Dlk1–Dio3 gene cluster, these iPSC clones contributed poorly to
chimaeras and failed to support the development of entirely iPSC-derived animals (‘all-iPSC mice’). In contrast, iPSC clones
with normal expression of the Dlk1–Dio3 cluster contributed to high-grade chimaeras and generated viable all-iPSC mice.
Notably, treatment of an iPSC clone that had silenced Dlk1–Dio3 with a histone deacetylase inhibitor reactivated the locus
and rescued its ability to support full-term development of all-iPSC mice. Thus, the expression state of a single imprinted
gene cluster seems to distinguish most murine iPSCs from ES cells and allows for the prospective identification of iPSC clones
that have the full development potential of ES cells.