2^nd International Conference on Transcriptomics September 12-14, 2016 Philadelphia, Pennsylvania, USA

Dajeong Lim has completed his PhD from Seoul National University. She is a Researcher in National Institute of Animal Science (NIAS), Rural Development Administration in Korea. She has published more than 30 papers in academic journals.

Some genes are expressed exclusively or differntially from one of the two parental alleles, resulting in allelic imbalance (AI) in gene expression. Genomic imprinting is a type of AI and determined allele specific expression (ASE) depending on the parent-of-origin. High-throughput transcriptome sequencing strategy can identify ASE through the use of expressed SNPs that have the capacity to detect cis-regulatory variation and imprinted genes by aligning sequence reads to individual alleles. Here, we used RNA-Seq data along with high-resolution to analyze ASE profiles and imprinted genes based on trio data. First, whole-genome resequencing data (average 10X per sample)of one family trio (sire, dam and offspring) was generated by illumina HiSeq 2500 platform. RNA-Seq data (4Gb per tissue) was also produced from twenty three tissues such as backfat, intramuscular fat. Exome SNPs of all individuals were assigned from GATK and SnpEff tools. For each heterozygous SNP, the number of maternal and paternal reads were counted. The deviation between the read numbers was analyzed with the binomial test in R software. To test inactivation of maternal or paternal SNP, we compared parental alleles and offspring’s allele between SNPs from resequencing and RNA-Seq as an additional filtering step. Then, candidate imprinted genes were checked for expression patterns in different tissues to have the tissue-specific imprinting signatures. Finally, we confirmed the expression of SNPs and tissue-specificity within imprintig gene by experimental validation.

Dawei Xu has completed his PhD in 1999 from Karolinska Institutet. He is currently working as an Associate Professor at Department of Medicine, Karolinska Institutet. He has published more than 80 papers in peer-reviewed journals.

Myeloproliferative neoplasms (MPNs) are a group of clonal neoplastic diseases originating from the myeloid lineage of the bone marrow and include essential thrombocythemia (ET), polycythemia vera (PV) and myelofibrosis (MF). A subset of patients eventually evolve into acute myeloid leukemia. A number of genetic alterations have been identified as MPN drivers, but the exact pathogenesis of MPNs remain incompletely understood. Our recent study showed a widespread dysregulation of telomere binding proteins (TBPs) or shelterins (TRF1, TRF2, TPP1, POT1, TIN2 and RAP1) in MPNs. It is well known that the aberrant expression of shelterins causes telomere dysfunction and genomic instability, however, it is unclear whether such abnormal change has other biological activities that promote the development of MPNs. In the present study, we found that the expression of TPP1, one of key TBPs, was positively correlated with expression of splicing factors SF3A1, ZRSR2 and SRSF2, while POT1 levels were negatively correlated with U2AF1 expression, in myeloid cells derived from patients with MPN. RNA sequencing results demonstrated significant alterations in RNA splicing and editing profiles in MPN patient cells compared to normal myeloid cells from healthy adults. The induction of telomere dysfunction in the MPN-derived cell line similarly leads to dramatic alterations in RNA splicing. Collectively, the dysregulated shelterin expression directly or indirectly induces significant changes in RNA splicing, thereby contributing to the MPN pathogenesis.

Han Ha Chai is a researcher at National Institute of Animal Science (NIAS), Rural Development Administration in Korea.

Variation in coloration can be determined by different types of pigments and by the structure of the integument. In particular, melanin pigments play a major role in the coloration of animals that is correlated to physiological process and disease resistance taking place not only in the integument but also inside the body. Melanin pigments could be explained with inter- and intraspecific differences in the deposition of external body surface of organisms and of internal melanin that exhibit different biophysical and chemical properties. Indeed, body coloration is related to the amount of melanin deposited in organs. In vertebrates, melanin is present in various organs and tissue such as the spleen, liver, heart, kidney, brain, eye, lung, connective tissues and muscles. Among animals, we focused on detecting differentially expressed genes (DEGs) across the RNA-seq analysis related to the internal melanin pigmentation of various parts of the body of oyge black chicken, which have darker blue feather-black fascia, jet-black eyes, a black tongue and bones from the tip of its comb to the end of its claws. Then, covariations between melanin-based coloration of integument and internal organs and tissues could be correlated with independent factors in regulatory process and biosynthetic pathways highlighting similarities and dissimilarities between the production of internal and external melanin, as well as between (the brown/black) eumelanin and (yellow/reddish-brown) pheomelanin. We approached this assuming that in some cases of protecting organism against a number of diseases and disorders, internal and external melanin pigments may have different function and the synthetic pathway may also differ on key melanogenetic genes having numerous pleiotropic effects.

Ick Hyun Jo has completed his PhD from Chungbuk National University and Post-doctoral studies from National Institute of Horticultural and Herbal Science (NIHHS) in South Korea. He is the Public Agricultural Research Worker at Rural Development Administration (RDA). He has published more than 32 papers in reputed journals and serving as an Editorial Board Member for Medical Crop Science Journal.

We performed de novo transcriptome sequencing for Panax ginseng and Panax quinquefolius accessions using the 454 GS FLX Titanium System and discovered annotation-based genome-wide single-nucleotide polymorphism (SNPs) using next-generation ginseng transcriptome data without reference genome sequence. The comprehensive transcriptome characterization with the mature roots of four ginseng accessions generated 297,170 reads for ‘Cheonryang’ cultivar, 305,673 reads for ‘Yunpoong’ cultivar, 311,861 reads for the G03080 breeding line, and 308,313 reads for P. quinquefolius. In transcriptome assembly, the lengths of the sample read were 156.42 Mb for ‘Cheonryang’, 161.95 Mb for ‘Yunpoong’, 165.07 Mb for G03080 breeding line, and 166.48 Mb for P. quinquefolius. A total of 97 primer pairs were designed with the homozygous SNP presented in all four accessions. SNP genotyping using high-resolution melting (HRM) analysis was performed to validate the putative SNP markers of 97 primer pairs. Out of the 73 primer pairs, 73 primer pairs amplified the target sequence and 34 primer pairs showed polymorphic melting curves in samples from 11 P. ginseng cultivars and one P. quinquefolius accession. Among the 34 polymorphic HRM-SNP primers, four primers were useful to distinguish ginseng cultivars. In the present study, we demonstrated that de novo transcriptome assembly and mapping analyses are useful in providing four HRM-SNP primer pairs that reliably show a high degree of polymorphism among ginseng cultivars.

Jong Eun Park has completed his PhD from Seoul National University. He is a Researcher at National Institute of Animal Science (NIAS), Rural Development Administration in Korea.

High temperature is prior factor in climate change following global warming. This envionmental factor decreases the growth and productivity in livestock. The Pekin duck, Anas platyrhynchos, is one of the most famous meat duck species worldwide. Thus, transcriptome and expression profiling data for pekin duck under heat stress are important resource for identifying genes and developing molecular markers. In this study, we compared transcriptome and expression profiles of 30 samples for different heating time (35℃, 3 and 6 hours) and moisture (60% and 90%) with control. After trimming of reads, more than 30 milion reads and 96% of Q20 (per sample) were generated. From 17,160 transcripts (over 66% per sample), 3,576 transcripts with zero FPKMs (Fragments Per Kilobase Million) across more than 50% of all samples were excluded leaving 13,584 transcripts to be analyzed. After quantile normalization for remained transcripts, we identifed total 669 differentially expressed transcripts from 6 combinations of treatment (including control). The selection criterions were both absolute value of 2 fold change and significance of independent t-test (raw p-value<0.05). In further study, we will perform functional annotation, network analysis and experimetal validation to select candidate genes related with heat stress. This study will provide informative genes or markers that can be used to develope heat-tolerant duck strains.

Yongyan Sun is now a PhD candidate in Institute of Urban Environment, Chinese Academy of Sciences. She mainly focus on researches of the bioeffects of electromagnetic environment exposure on model organisms. Her supervisor Professor Peng Cai, obtained his PhD degree from Shanghai Institute of Biochemistry, Chinese Academy of Sciences and postdoctoral studies from NIDDK, NIH and Uniformed Services University of the Health Sciences, DOD of USA. He is the Chief of Physical Environment Laboratory and Deputy Director-General of IUE, Chinese Academy of Sciences.

Transcriptomics is one of functional genomic approaches widely applied in life science research in recent years. Based on the background of crosses and integration between environmental science and life science subjects, growing cutting-edged molecular technologies such as proteomics, metabolomics and etc., are applied in studying environmental problems, especially exploring biological relationships between human living environments and health. Electromagnetic environment is one of extensively existed urban environmental factors in modern life during the development of urbanization and modernization. Thus, it is indispensable and inevitable to investigate the biological effects of electromagnetic field (EMF) on human health and disease. Transcriptomic analysis, which could to some extent reflect the gene expression alteration under EMF exposure, is rewarding to much deeper understanding on molecular mechanism of living organism sensing and responsing to EMF exposure. In our study, we have explored the bio-effects of extremely low-frequency electromagnetic field (ELF-EMF) and radio frequency electromagnetic field (RF-EMF) via transcriptomic analysis on model organism, such as Saccharomyces cerevisiae, Drosophila melanogaster and Caenorhabditis elegans. Several results indicate that the living organism indeed response to EMF exposure and different model organism showed changes in various ways. Therefore, the utilization of trancriptomic approach on studying the health effect of EMF exposure lays the molecular basis for further research on mechanism of electromagnetic field sensing and responsing.