ZFIN ID: ZDB-PERS-010504-3
Peng, Jinrong
Email: pengjr@zju.edu.cn
Affiliation: Jinrong Peng Lab
Address: College of Animal Sciences, Zhejiang University, 866 Yu Hang Tang Road, Hangzhou, China 310058
Country: China
Phone: 86-571-86971513

1. Microarray and Functional Genomics:

Microarray (DNA chips) is a newly developed technology for functional genomics studies. cDNA array is one of the microarray formats, useful in profiling global gene expression patterns in different tissues or same tissue at different developmental stages or mutant vs wild type. The information obtained from the global expression pattern can be used to identify new genes prior to any knowledge of the whole genome sequence. The Functional Genomics Lab has been assigned to set up a microarray facility at IMA to facilitate the identification of genes important for agriculture and fisheries and to strengthen the research capability at IMA. My group is currently focusing on developing zebrafish microarray that will be used for the studies of zebrafish development at IMA.

In recent years, increasing evidence has demonstrated that zebrafish share with mammals not only similarities in many developmental pathways but also similar mechanisms of disease occurrence. Together with its advantage in genetic studies and genome organization, zebrafish has been chosen as a model system for the studies of vertebrate development. The interests in this lab lie mainly on the study of liver development, since liver development is one of the least studied areas in vertebrates. By using a zebrafish array, we can not only identify new genes specifically expressed in liver, but also profile gene expression patterns throughout fish development.

2. Towards Dissecting GA signalling in Arabidopsis:

Gibberellins (GA) are one class of phytohormones that have profound and diverse effects on plant growth and development. These effects include the induction of seed germination, the promotion of hypocotyl and stem elongation, the regulation of pollen development and flower initiation etc. However, the molecular mechanisms of GA actions are basically unknown. To understand GA action, factors involved in their signal perception and transduction must be isolated and characterized.

The Arabidopsis gai (for gibberellic acid insensitive) is a semi-dominant mutation, which confers a dark-green, dwarf phenotype with elevated endogenous GA levels. Dominant mutations conferring similar phenotypes are known in other plants as well, including maize (D8 mutations) and wheat (Rht mutations). The wheat Rht mutations are especially important because they are the genetic basis of the high-yielding, semi-dwarf wheat varieties of the 'green revolution'. Recently, we have cloned GAI/RGA/d8/Rht genes from Arabidopsis, maize and wheat, respectively, and found that these genes are orthologues. These genes encode proteins that resemble nuclear transcription factors and contain an SH2-like domain. We have proposed that these proteins are plant equivalents of the metazoan STATs and that a conserved phosphotyroine may participate in GA signalling. One of the main aims of this group is to identify more genes that are involved in GA signalling and to gain an understanding of the biochemical functions of their encoded products.

Lin, Y., Yang, Q., Lin, X., Liu, X., Qian, Y., Xu, D., Cao, N., Han, X., Zhu, Y., Hu, W., He, X., Yu, Z., Kong, X., Zhu, L., Zhong, Z., Liu, K., Zhou, B., Wang, Y., Peng, J., Zhu, W., Wang, J. (2023) Extracellular Matrix Disorganization Caused by ADAMTS16 Deficiency Leads to Bicuspid Aortic Valve With Raphe Formation. Circulation. 149(8):605-626
Jin, Q., Hu, Y., Gao, Y., Zheng, J., Chen, J., Gao, C., Peng, J. (2023) Hhex and Prox1a synergistically dictate the hepatoblast to hepatocyte differentiation in zebrafish. Biochemical and Biophysical Research Communications. 686:149182149182
Zhang, Z., Yang, C., Wang, Z., Guo, L., Xu, Y., Gao, C., Sun, Y., Zhang, Z., Peng, J., Hu, M., Jan Lo, L., Ma, Z., Chen, J. (2023) Wdr5-mediated H3K4me3 coordinately regulates cell differentiation, proliferation termination, and survival in digestive organogenesis. Cell death discovery. 9:227227
Xie, A., Ma, Z., Wang, J., Zhang, Y., Chen, Y., Yang, C., Chen, J., Peng, J. (2023) Upf3a but not Upf1 mediates the genetic compensation response induced by leg1 deleterious mutations in an H3K4me3-independent manner. Cell discovery. 9:6363
Wei, J., Wang, S., Zhu, H., Cui, W., Gao, J., Gao, C., Yu, B., Liu, B., Chen, J., Peng, J. (2023) Hepatic depletion of nucleolar protein mDEF causes excessive mitochondrial copper accumulation associated with p53 and NRF1 activation. iScience. 26:107220107220
Jin, Q., Gao, Y., Shuai, S., Chen, Y., Wang, K., Chen, J., Peng, J., Gao, C. (2022) Cdx1b protects intestinal cell fate by repressing signaling networks for liver specification. Journal of genetics and genomics = Yi chuan xue bao. 49(12):1101-1113
Gao, Y., Jin, Q., Gao, C., Chen, Y., Sun, Z., Guo, G., Peng, J. (2022) Unraveling Differential Transcriptomes and Cell Types in Zebrafish Larvae Intestine and Liver. Cells. 11(20):
Ding, F., Huang, D., Wang, M., Peng, J. (2022) An 86 amino acids motif in CAPN3 is essential for formation of the nucleolus-localized Def-CAPN3 complex. Biochemical and Biophysical Research Communications. 623:66-73
Zhu, Y., Wang, Y., Tao, B., Han, J., Chen, H., Zhu, Q., Huang, L., He, Y., Hong, J., Li, Y., Chen, J., Huang, J., Lo, L.J., Peng, J. (2021) Nucleolar GTPase Bms1 displaces Ttf1 from RFB-sites to balance progression of rDNA transcription and replication. Journal of molecular cell biology. 13(12):902-917
Jiang, M., Xiao, Y., E, W., Ma, L., Wang, J., Chen, H., Gao, C., Liao, Y., Guo, Q., Peng, J., Han, X., Guo, G. (2021) Characterization of the Zebrafish Cell Landscape at Single-Cell Resolution. Frontiers in cell and developmental biology. 9:743421
Wang, J., Bai, Y., Xie, A., Huang, H., Hu, M., Peng, J. (2021) Difference in an intermolecular disulfide-bond between two highly homologous serum proteins Leg1a and Leg1b implicates their functional differentiation. Biochemical and Biophysical Research Communications. 579:81-88
Zhu, Q., Tao, B., Chen, H., Shi, H., Huang, L., Chen, J., Hu, M., Lo, L.J., Peng, J. (2021) Rcl1 depletion impairs 18S pre-rRNA processing at the A1-site and up-regulates a cohort of ribosome biogenesis genes in zebrafish. Nucleic acids research. 49(10):5743-5759
Zhao, T., Ye, S., Tang, Z., Guo, L., Ma, Z., Zhang, Y., Yang, C., Peng, J., Chen, J. (2021) Loss-of-function of p53 isoform Δ113p53 accelerates brain aging in zebrafish. Cell Death & Disease. 12:151
Gao, C., Peng, J. (2021) All routes lead to Rome: multifaceted origin of hepatocytes during liver regeneration. Cell regeneration (London, England). 10:2
Ye, S., Zhao, T., Zhang, W., Tang, Z., Gao, C., Ma, Z., Xiong, J.W., Peng, J., Tan, W.Q., Chen, J. (2020) p53 isoform Δ113p53 promotes zebrafish heart regeneration by maintaining redox homeostasis. Cell Death & Disease. 11:568
Tao, B., Lo, L.J., Peng, J., He, J. (2020) rDNA subtypes and their transcriptional expression in zebrafish at different developmental stages. Biochemical and Biophysical Research Communications. 529(3):819-825
Chen, F., Huang, D., Shi, H., Gao, C., Wang, Y., Peng, J. (2020) Capn3 depletion causes Chk1 and Wee1 accumulation and disrupts synchronization of cell cycle reentry during liver regeneration after partial hepatectomy. Cell regeneration (London, England). 9:8
Peng, J. (2019) Gene redundancy and gene compensation: An updated view. Journal of genetics and genomics = Yi chuan xue bao. 46(7):329-333
Ma, Z., Zhu, P., Shi, H., Guo, L., Zhang, Q., Chen, Y., Chen, S., Zhang, Z., Peng, J., Chen, J. (2019) PTC-bearing mRNA elicits a genetic compensation response via Upf3a and COMPASS components. Nature. 568(7751):259-263
Zhao, S., Chen, Y., Chen, F., Huang, D., Shi, H., Lo, L.J., Chen, J., Peng, J. (2019) Sas10 controls ribosome biogenesis by stabilizing Mpp10 and delivering the Mpp10-Imp3-Imp4 complex to nucleolus. Nucleic acids research. 47(6):2996-3012
Gao, C., Huang, W., Gao, Y., Jan Lo, L., Luo, L., Huang, H., Chen, J., Peng, J. (2018) Zebrafish hhex-null mutant develops an intrahepatic intestinal tube due to de-repression of cdx1b and pdx1. Journal of molecular cell biology. 11(6):448-462
Gao, C., Zhu, Z., Gao, Y., Lo, L.J., Chen, J., Luo, L., Peng, J. (2018) Hepatocytes in a normal adult liver are derived solely from the embryonic hepatocytes. Journal of genetics and genomics = Yi chuan xue bao. 45:173-175
Zhu, P., Ma, Z., Guo, L., Zhang, W., Zhang, Q., Zhao, T., Jiang, K., Peng, J., Chen, J. (2017) Short body length phenotype is compensated by the upregulation of nidogen family members in a deleterious nid1a mutation of zebrafish. Journal of genetics and genomics = Yi chuan xue bao. 44(11):553-556
Ma, Z., Zhu, P., Pang, M., Guo, L., Chang, N., Zheng, J., Zhu, X., Gao, C., Huang, H., Cui, Z., Xiong, J.W., Peng, J., Chen, J. (2017) A novel inducible mutagenesis screen enables to isolate and clone both embryonic and adult zebrafish mutants. Scientific Reports. 7:10381
Tao, T., Sondalle, S.B., Shi, H., Zhu, S., Perez-Atayde, A.R., Peng, J., Baserga, S.J., Look, A.T. (2017) The pre-rRNA processing factor DEF is rate limiting for the pathogenesis of MYCN-driven neuroblastoma. Oncogene. 36(27):3852-3867
Xiao, C., Gao, L., Hou, Y., Xu, C., Chang, N., Wang, F., Hu, K., He, A., Luo, Y., Wang, J., Peng, J., Tang, F., Zhu, X., Xiong, J.W. (2016) Chromatin-remodelling factor Brg1 regulates myocardial proliferation and regeneration in zebrafish. Nature communications. 7:13787
Guan, Y., Huang, D., Chen, F., Gao, C., Tao, T., Shi, H., Zhao, S., Liao, Z., Lo, L.J., Wang, Y., Chen, J., Peng, J. (2016) Phosphorylation of Def Regulates Nucleolar p53 Turnover and Cell Cycle Progression through Def Recruitment of Calpain3. PLoS Biology. 14:e1002555e1002555
Wang, Y., Zhu, Q., Huang, L., Zhu, Y., Chen, J., Peng, J., Lo, L.J. (2016) Interaction between Bms1 and Rcl1, two ribosome biogenesis factors, is evolutionally conserved in zebrafish and human. Journal of genetics and genomics = Yi chuan xue bao. 43(7):467-9
Shan, Y., Zhang, Y., Zhuo, X., Li, X., Peng, J., Fang, W. (2016) Matrix metalloproteinase-9 plays a role in protecting zebrafish from lethal infection with Listeria monocytogenes by enhacing macrophage migration. Fish & shellfish immunology. 54:179-87
Hu, M., Bai, Y., Zhang, C., Liu, F., Cui, Z., Chen, J., Peng, J. (2016) Liver-Enriched Gene 1, a Glycosylated Secretory Protein, Binds to FGFR and Mediates an Anti-stress Pathway to Protect Liver Development in Zebrafish. PLoS Genetics. 12:e1005881
Feng, G., Long, Y., Peng, J., Li, Q., Cui, Z. (2015) Transcriptomic characterization of the dorsal lobes after hepatectomy of the ventral lobe in zebrafish. BMC Genomics. 16:979
Guan, Y., Zhu, Q., Huang, D., Zhao, S., Jan Lo, L., Peng, J. (2015) An equation to estimate the difference between theoretically predicted and SDS PAGE-displayed molecular weights for an acidic peptide. Scientific Reports. 5:13370
Gao, L., Li, D., Ma, K., Zhang, W., Xu, T., Fu, C., Jing, C., Jia, X., Wu, S., Sun, X., Dong, M., Deng, M., Chen, Y., Zhu, W., Peng, J., Wan, F., Zhou, Y., Zon, L.I., Pan, W. (2015) TopBP1 Governs Hematopoietic Stem/Progenitor Cells Survival in Zebrafish Definitive Hematopoiesis. PLoS Genetics. 11:e1005346
Chen, J., Peng, J. (2015) Δ113p53/Δ133p53: survival and integrity. Oncotarget. 6:13850-1
Shan, Y., Fang, C., Cheng, C., Wang, Y., Peng, J., Fang, W. (2015) Immersion infection of germ-free zebrafish with Listeria monocytogenes induces transient expression of innate immune response genes. Frontiers in microbiology. 6:373
Gong, L., Gong, H., Pan, X., Chang, C., Ou, Z., Ye, S., Yin, L., Yang, L., Tao, T., Zhang, Z., Liu, C., Lane, D.P., Peng, J., Chen, J. (2015) p53 isoform Δ113p53/Δ133p53 promotes DNA double-strand break repair to protect cell from death and senescence in response to DNA damage. Cell Research. 25(3):351-69
Shi, H., Tao, T., Huang, D., Ou, Z., Chen, J., Peng, J. (2015) A naturally occurring 4-bp deletion in the intron 4 of p53 creates a spectrum of novel p53 isoforms with anti-apoptosis function. Nucleic acids research. 43(2):1035-43
Gu, Q., Yang, X., Lin, L., Li, S., Li, Q., Zhong, S., Peng, J., Cui, Z. (2014) Genetic ablation of solute carrier family 7a3a leads to hepatic steatosis in zebrafish during fasting. Hepatology (Baltimore, Md.). 60(6):1929-41
Zhu, Z., Chen, J., Xiong, J.W., Peng, J. (2014) Haploinsufficiency of Def Activates p53-Dependent TGFbeta Signalling and Causes Scar Formation after Partial Hepatectomy. PLoS One. 9:e96576
Niu, X., Hong, J., Zheng, X., Melville, D.B., Knapik, E.W., Meng, A., Peng, J. (2014) The Nuclear Pore Complex Function of Sec13 Protein Is Required for Cell Survival during Retinal Development. The Journal of biological chemistry. 289:11971-85
Ou, Z., Yin, L., Chang, C., Peng, J., Chen, J. (2014) Protein Interaction Between p53 and Δ113p53 Is Required for the Anti-Apoptotic Function of Δ113p53. Journal of genetics and genomics = Yi chuan xue bao. 41(2):53-62
Tao, T., Shi, H., Guan, Y., Huang, D., Chen, Y., Lane, D.P., Chen, J., and Peng, J. (2013) Def defines a conserved nucleolar pathway that leads p53 to proteasome-independent degradation. Cell Research. 23(5):620-634
Tao, T., Shi, H., Huang, D., and Peng, J. (2013) Def functions as a cell autonomous factor in organogenesis of digestive organs in zebrafish. PLoS One. 8(4):e58858
Liu, J., Gong, L., Chang, C., Liu, C., Peng, J., and Chen, J. (2012) Development of novel visual-plus quantitative analysis systems for studying DNA double-strand break repairs in zebrafish. Journal of genetics and genomics = Yi chuan xue bao. 39(9):489-502
Wang, Y., Luo, Y., Hong, Y., Peng, J., and Lo, L. (2012) Ribosome Biogenesis Factor Bms1-like Is Essential for Liver Development in Zebrafish. Journal of genetics and genomics = Yi chuan xue bao. 39(9):451-462
Niu, X., Gao, C., Jan Lo, L., Luo, Y., Meng, C., Hong, J., Hong, W., and Peng, J. (2012) Sec13 safeguards the integrity of the endoplasmic reticulum and organogenesis of the digestive system in zebrafish. Developmental Biology. 367(2):197-207
Yang, S.L., Aw, S.S., Chang, C., Korzh, S., Korzh, V., and Peng, J. (2011) Depletion of Bhmt Elevates sonic hedgehog Transcript Level and Increases β-Cell Number in Zebrafish. Endocrinology. 152(12):4706-17
Du, L., Xu, J., Li, X., Ma, N., Liu, Y., Peng, J., Osato, M., Zhang, W., and Wen, Z. (2011) Rumba and Haus3 are essential factors for the maintenance of hematopoietic stem/progenitor cells during zebrafish hematopoiesis. Development (Cambridge, England). 138(4):619-629
Chang, C., Hu, M., Zhu, Z., Lo, L.J., Chen, J., and Peng, J. (2011) liver-enriched gene 1a and 1b Encode Novel Secretory Proteins Essential for Normal Liver Development in Zebrafish. PLoS One. 6(8):e22910
Niu, X., Shi, H., and Peng, J. (2010) The role of mesodermal signals during liver organogenesis in zebrafish. Science China. Life sciences. 53(4):455-461
Chen, J., and Peng, J. (2009) p53 Isoform Delta113p53 in Zebrafish. Zebrafish. 6(4):389-395
Tao, T., and Peng, J. (2009) Liver development in zebrafish (Danio rerio). Journal of genetics and genomics = Yi chuan xue bao. 36(6):325-334
Chen, J., Ng, S.M., Chang, C., Zhang, Z., Bourdon, J.C., Lane, D.P., and Peng, J. (2009) p53 Isoform delta113p53 is a p53 target gene that antagonizes p53 apoptotic activity via BclxL activation in zebrafish. Genes & Development. 23(3):278-290
Li, Z., Wen, C., Peng, J., Korzh, V., and Gong, Z. (2009) Generation of living color transgenic zebrafish to trace somatostatin-expressing cells and endocrine pancreas organization. Differentiation; research in biological diversity. 77(2):128-134
Huang, H., Ruan, H., Aw, M.Y., Hussain, A., Guo, L., Gao, C., Qian, F., Leung, T., Song, H., Kimelman, D., Wen, Z., and Peng, J. (2008) Mypt1-mediated spatial positioning of Bmp2-producing cells is essential for liver organogenesis. Development (Cambridge, England). 135(19):3209-3218
Liu, Y., Du, L., Osato, M., Teo, E.H., Qian, F., Jin, H., Zhen, F., Xu, J., Guo, L., Huang, H., Chen, J., Geisler, R., Jiang, Y.J., Peng, J., and Wen, Z. (2007) The zebrafish udu gene encodes a novel nuclear factor and is essential for primitive erythroid cell development. Blood. 110(1):99-106
Huang, H., Lu, F.I., Jia, S., Meng, S., Cao, Y., Wang, Y., Ma, W., Yin, K., Wen, Z., Peng, J., Thisse, C., Thisse, B., and Meng, A. (2007) Amotl2 is essential for cell movements in zebrafish embryo and regulates c-Src translocation. Development (Cambridge, England). 134(5):979-988
Cheng, W., Guo, L., Zhang, Z., Soo, H.M., Wen, C., Wu, W., and Peng, J. (2006) HNF factors form a network to regulate liver-enriched genes in zebrafish. Developmental Biology. 294(2):482-496
Jin, H., Xu, J., Qian, F., Du, L., Tan, C.Y., Lin, Z., Peng, J., and Wen, Z. (2006) The 5' zebrafish scl promoter targets transcription to the brain, spinal cord, and hematopoietic and endothelial progenitors. Developmental Dynamics : an official publication of the American Association of Anatomists. 235(1):60-67
Chen, J., Ruan, H., Ng, S.M., Gao, C., Soo, H.M., Wu, W., Zhang, Z., Wen, Z., Lane, D.P., and Peng, J. (2005) Loss of function of def selectively up-regulates {Delta}113p53 expression to arrest expansion growth of digestive organs in zebrafish. Genes & Development. 19(23):2900-2911
Qian, F., Zhen, F., Ong, C., Jin, S.W., Meng Soo, H., Stainier, D.Y., Lin, S., Peng, J., and Wen, Z. (2005) Microarray analysis of zebrafish cloche mutant using amplified cDNA and identification of potential downstream target genes. Developmental Dynamics : an official publication of the American Association of Anatomists. 233(3):1163-1172
Wu, W., Liu, X., Xu, M., Peng, J.R., and Setiono, R. (2005) A hybrid SOM-SVM approach for the zebrafish gene expression analysis. Genomics, proteomics & bioinformatics. 3(2):84-93
Wen, C., Zhang, Z., Ma, W., Xu, M., Wen, Z., and Peng, J. (2005) Genome-wide identification of female-enriched genes in zebrafish. Developmental Dynamics : an official publication of the American Association of Anatomists. 232(1):171-179
Jin, P., Tian, T., Sun, Z. H., and Meng, A. M. (2004) Generation of mutants with developmental defects in zebrafish by ENU mutagenesis. Chinese science bulletin = Kexue tongbao. 49(20):2154-2158
Lo, J., Lee, S., Xu, M., Liu, F., Ruan, H., Eun, A., He, Y., Ma, W., Wang, W., Wen, Z., and Peng, J. (2003) 15,000 unique zebrafish EST clusters and their future use in microarray for profiling gene expression patterns during embryogenesis. Genome research. 13(3):455-466

1. Richards, D. E., Peng, J.R., and Harberd, N.P (2000) Plant GRAS and metazoan STATs: one family? Bioassay 22:573-577.

2. Peng, J.R., Richards, D. E., Hartley, N. M., Murphy, G. P., Devos, K. M., Flintham, J. E., Beales, J., Fish, L. J., Worland, A. J., Pelica, F., Sudhakar, D., Christou, P., Snape, J. W., Gale, M. D., and Harberd, N. P. (1999) �Green revolution� genes encode mutant gibberellin response modulators. Nature 400:256-261.

3. Peng, J.R., Richards, D. E., Moritz, T., Cano, A., and Harberd, N.P. (1999) Extragenic suppressors of the Arabidopsis gai mutation alter the dose-response relationship of diverse gibberellin responses. Plant Physiology 119:1199-1208.

4. Harberd, N.P., King, K.E., Carol, P., Cowling R.J., Peng, J.R., and Richards, D.E (1998) Gibberellin: inhibitor of an inhibitor of ---? BioEssays 20:1001-1008.

5. Peng, J.R., Carol, P., Richards, D.E., King, K.E., Cowling, R., Murphy, G.P., and Harberd, N.P. (1997) The Arabidopsis GAI gene defines a signalling pathway that negatively regulates gibberellin responses. Genes & Development 11:3194-3205.

6. Peng, J.R. and Harberd, N.P. (1997) Gibberellin deficiency and response mutations suppress the stem elongation phenotype of phytochrome-deficient mutants of Arabidopsis. Plant Physiology 113:1051-1058.

7. Peng, J.R, and Harberd, N.P. (1993). Derivative alleles of the Arabidopsis gibberellin-insensitive (gai) mutation confer a wild-type phenotype. Plant Cell 5:351-360.

8. Whitelam, G.C., Jonson, E., Peng, J.R., Carol, P., Anderson, M., Cowl, J., and Harberd, N.P. (1993). Phytochrome A null mutants of Arabidopsis display a wild-type phenotype in white-light. Plant Cell 5:757-768.