陳柏仰

陳柏仰
Chen, Pao-Yang
助研究員

2012 助研究員, 美國加州大學洛杉磯分校,
分子細胞及發展生物學系。

2008-2012 博士後研究, 美國加州大學洛杉磯分校,
分子細胞及發展生物學系。

2008 博士, 英國牛津大學,統計系。

TEL: 

+886-2-2787-1140 (Office)
+886-2-2787-1139 (Lab)

我們是一個結合實驗及生物資訊的實驗室,研究著力於分析基因體學 (genomic) 和表觀基因體學 (epigenomic) 的資料。我們同時發展新的實驗技術及統計分析方法,來探討基因與調控的問題,研究的對象包括真菌、植物、動物以及人類。

次時代高通量基因定序:
我們是一個結合實驗及生物資訊的實驗室,研究著力於分析基因體學 (genomic) 和表觀基因體學 (epigenomic) 的資料。我們同時發展新的實驗技術及統計分析方法,來探討基因與調控的問題,研究的對象包括真菌、植物、動物以及人類。

植物中的DNA甲基化:
DNA甲基化是表觀遺傳調控上的重要機制,通常用於穩定以及抑制基因表現。我們會以植物做為研究主軸,因為植物採樣便利,容易進行遺傳工程的操作; 此外,模式植物的註解也很清楚。 植物的表觀基因組可以幫助釐清的DNA甲基轉移酶的作用機制,以及有助於了解基因啟動子和基因序列調控的演化,探討植物如何快速適應環境則變化。

植物,動物和人類的DNA甲基化:
動物和植物的基因組DNA甲基化的遺傳標記隱藏著很重要的生物學意義。我們的實驗室與國內外多個實驗室有合作計畫,共同研究各樣植物和動物的DNA甲基化模式。例如,我們希望對基因改良的水稻基因體及表觀基因體進行詳細的研究分析。這個結果將增進水稻基因改良的品質以及轉殖的效率。還有,我們將藉由收集臍帶血和胎盤檢體,研究試管嬰兒的全基因體DNA甲基化 (methylome) 的分布,來釐清試管胚胎植入對胚胎的表關遺傳圖譜的影響力。新的定序技術讓我們可以分析全基因體的DNA甲基化模式,初步的結果令人振奮。

 

All publication list

 

Selected publication list

 

  • Fei-Man Hsu, Moloya Gohain, Pearl Chang, Jui-Hsien Lu, Pao-Yang Chen (2018) Bioinformatics of Epigenetic Data Generated from Next-Generation Sequencing Epigenetics in Human Disease, 2nd edition, Elsevier Invited chapter in production.
     
  • Jer-Young Lin, Brandon Le, Min Chen, Kelli F. Henry, Jungim Hur, Tzung-Fu Hsieh, Pao-Yang Chen, Julie M. Pelletier, Matteo Pellegrini, Robert L. Fischer, John J. Harada, Robert B. Goldberg (2017) Similarity between soybean and Arabidopsis seed methylomes and loss of non-CG methylation does not affect seed development Proceedings of the National Academy of Sciences doi: 10.1073/pnas.1716758114.
     
  • Ming-Ren Yen, Der-Fen Suen, Fei-Man Hsu, Yi-Hsiu Tsai, Hongyong Fu, Wolfgang Schmidt, and Pao-Yang Chen (2017) Deubiquitinating enzyme OTU5 contributes to DNA methylation patterns and is critical for phosphate nutrition signals Plant Physiology doi: 10.1104/pp.17.01188.
     
  • Huei-Mei Hsieh, Mei-Chu Chung, Pao-Yang Chen, Fei-Man Hsu, Wen-Wei Liao, Ai-Ning Sung, Chun-Ru Lin, Chung-Ju Wang, Yu-Hsin Kao, Mei-Jane Fang, Chi-Yung Lai, Chieh-Chen Huang, Jyh-Ching Chou, Wen-Neng Chou, Bill Chia-Han Chang and Yu-Ming Ju (2017) A termite symbiotic mushroom maximizing sexual activity at growing tips of vegetative hyphae. Botanical Studies 58:39.
     
  • Fei-Man Hsu, Pao-Yang Chen (2017) Game theory in epigenetic reprogramming: Comment on: Epigenetic game theory: How to compute the epigenetic control of maternal-to-zygotic transition by Qian Wang et al. Physics of Life Reviews 20: 143 (Invited commentary).

     
  • Wai-Shin Yong, Fei-Man Hsu, Pao-Yang Chen (2016) Profiling genome-wide DNA methylation. Epigenetics & Chromatin 9: 2
     
  • Fei-Man Hsu, Ming-Ren Yen, Chi-Ting Wang, Chien-Yu Lin, Chung-Ju Rachel Wang and Pao-Yang Chen (2017) Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize. Epigenetics & Chromatin 10 (1): 42.
     
  • Joseph Hargan-Calvopina, Sara Taylor, Helene Cook, Zhongxun Hu, Serena A. Lee, Ming-Ren Yen, Yih-Shien Chiang, Pao-Yang Chen, Amander T. Clark (2016) Stage-specific demethylation in primordial germ cells safeguards against precocious differentiation. Developmental Cell 39(1): 12. 

     
  • Wen-Wei Liao, Ming-Ren Yen, Evaline Ju, Fei-Man Hsu, Larry Lam, Pao-Yang Chen (2015) MethGO: a comprehensive tool for analyzing whole genome bisulfite sequencing data. BMC Genomics 16 (Suppl 12): S11. 

     
  • Sofia Gkountela, Kelvin Zhang, Tiasha Shafiq, Joseph Hargan-Calvopina, Pao-Yang Chen and Amander T Clark(2015) DNA demethylation dynamics in the human prenatal germline. Cell 161: 1425–1436 (co-corresponding authors).
  • Taku Sasaki, Tatsuo Kanno, Shih-Chieh Liang, Pao-Yang Chen, Wen-Wei Liao, Wen-Dar Lin, Antonius J.M. Matzke and Marjori Matzke (2015) An Rtf2 domain-containing protein influences pre-mRNA splicing and is essential for embryonic development in Arabidopsis thaliana. Genetics doi:10.1534/genetics.115.176438.
  • Barbara Montanini, Pao-Yang Chen, Marco Morselli, Artur Jaroszewicz, David Lopez, Francis Martin, Simone Ottonello and Matteo Pellegrini (2014) Non-exhaustive DNA methylation-mediated transposon silencing in the black truffle genome, a complex fungal genome with massive repeat element content. Genome Biology 15(8): 411. 

     
  • Taku Sasaki, Tzuu-fen Lee, Wen-Wei Liao, Ulf Naumann, Jo-Ling Liao, Changho Eun, Ya-Yi Huang, Jason L. Fu, Pao-Yang Chen, Blake C. Meyers, Antonius J.M. Matzke and Marjori Matzke (2014) Distinct and concurrent pathways of Pol II and Pol IV-dependent siRNA biogenesis at a repetitive trans-silencer locus in Arabidopsis thaliana. The Plant Journal doi: 10.1111/tpj.12545. 

     
  • Weilong Guo, Petko Fiziev, Weihong Yan, Shawn Cokus, Xueguang Sun, Michael Q Zhang, Pao-Yang Chen and Matteo Pellegrini (2013) BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. BMC Genomics 14 (1): 774 (co-corresponding authors). 

     
  • John J. Vincent, Yun Huang, Pao-Yang Chen, Suhua Feng, Joseph H. Calvopin, Kevin Nee, Serena A. Lee, Thuc Le, Alexander J. Yoon, Kym Faull, Guoping Fan, Anjana Rao, Steven E. Jacobsen, Matteo Pellegrini, and Amander T. Clark (2013) Stage-specific roles for Tet1 and Tet2 in DNA demethylation in primordial germ 
cells. Cell Stem Cell 12 (4): 470-8.
     
  • Pao-Yang Chen and Matteo Pellegrini (2012) Methylomes, Epigenetic Regulation and Epigenomics. Molecular Cell Biology and Molecular Medicine. UK: John Wiley & Sons, Inc. 815–837 (invited chapter).
     
  • Pao-Yang Chen, Suhua Feng, Jong Wha Joanne Joo, Steve E Jacobsen and Matteo Pellegrini (2011) A comparative analysis of DNA methylation across human embryonic stem cell lines. Genome Biology 12: R62 (highly accessed).
     
  • Shota Atsumi, Tung‐Yun Wu, Iara M P Machado, Wei‐Chih Huang, Pao‐Yang Chen, Matteo Pellegrini, James C Liao (2010) Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli. Nature-EMBO Molecular Systems Biology 6(1): 499. 

     
  • Ramakrishna K. Chodavarapu, Suhua Feng, Yana V. Bernatavichute, Pao-Yang Chen, Hume Stroud, Yanchun Yu, Jonathan A. Hetzel, Frank Kuo, Jin Kim, Shawn J. Cokus, David Casero, Maria Bernal, Peter Huijser, Amander T. Clark, Ute Krämer, Sabeeha S. Merchant, Xiaoyu Zhang, Steven E. Jacobsen and Matteo Pellegrini (2010) Relationship between nucleosome positioning and DNA methylation. Nature 466(7304): 388–392. 

     
  • Suhua Feng, Shawn J. Cokus, Xiaoyu Zhang, Pao-Yang Chen, Magnolia Bostick, Mary G. Goll, Jonathan Hetzel, Jayati Jain, Steven H. Strauss, Marnie E. Healpern, Chinweike Ukomadu, Kirsten C. Sadler, Sriharsa Pradhan, Matteo Pellegrini and Steven E. Jacobsen (2010) Conservation and divergence of plant and animal methylation patterning. PNAS, 11;107 (19): 8689–94.
     

Lab Members

博士後研究 Postdoctoral Research Associate

嚴明仁 Ming-Ren Yen

 

研究助理 Research Assistant

李怡靜 Yi-Jing Lee

陸芮嫻 Jui-Hsien Lu

謝佳蓉Chia-Jung Hsieh

 

大學生

鄧景升 Chin-Sheng Teng