Journal of Genetics and Genomics

Developmental systems biology flourishing on new technologies

Jing-Dong J. Han, Yi Liu, Huiling Xue, Kai Xia, Hong Yu, Shanshan Zhu, Zhang Chen, Wei Zhang, Zheng Huang, Chunyu Jin, Bo Xian, Jing Li, Lei Hou, Yixing Han, Chaoqun Niu, Timothy C. Alcon

2008, 35(10): 577-584. doi: 10.1016/S1673-8527(08)60078-8

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Abstract:
Organism development is a systems level process. It has benefited greatly from the recent technological advances in the field of systems biology. DNA microarray, phenome, interactome and transcriptome mapping, the new generation of deep sequencing technologies, and faster and better computational and modeling approaches have opened new frontiers for both systems biologists and developmental biologists to reexamine the old developmental biology questions, such as pattern formation, and to tackle new problems, such as stem cell reprogramming. As showcased in the International Developmental Systems Biology Symposium organized by Chinese Academy of Sciences, developmental systems biology is flourishing in many perspectives, from the evolution of developmental systems, to the underlying genetic and molecular pathways and networks, to the genomic, epigenomic and noncoding levels, to the computational analysis and modeling. We believe that the field will continue to reap rewards into the future with these new approaches.

The genomic landscapes of histone H3-Lys9 modifications of gene promoter regions and expression profiles in human bone marrow mesenchymal stem cells

Jiang Tan, Hui Huang, Wei Huang, Lin Li, Jianhua Guo, Baiqu Huang, Jun Lu

2008, 35(10): 585-593. doi: 10.1016/S1673-8527(08)60079-X

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Abstract:
Mesenchymal stem cells (MSCs) of nonembryonic origins possess the proliferation and multi-lineage differentiation potentials. It has been established that epigenetic mechanisms could be critical for determining the fate of stem cells, and MSCs derived from different origins exhibited different expression profiles individually to a certain extent. In this study, ChIP-on-chip was used to generate genome-wide histone H3-Lys9 acetylation and dimethylation profiles at gene promoters in human bone marrow MSCs. We showed that modifications of histone H3-Lys9 at gene promoters correlated well with mRNA expression in human bone marrow MSCs. Functional analysis revealed that many key cellular pathways in human bone marrow MSC self-renewal, such as the canonical signaling pathways, cell cycle pathways and cytokine related pathways may be regulated by H3-Lys9 modifications. These data suggest that gene activation and silencing affected by H3-Lys9 acetylation and dimethylation, respectively, may be essential to the maintenance of human bone marrow MSC self-renewal and multi-potency.

Amelioration of β654-thalassemia in mouse model with the knockdown of aberrantly spliced β-globin mRNA

Shuyang Xie, Wei Li, Zhaorui Ren, Jingzhi Zhang, Xinbin Guo, Shu Wang, Shuzhen Huang, Fanyi Zeng, Yi-Tao Zeng

2008, 35(10): 595-601. doi: 10.1016/S1673-8527(08)60080-6

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Abstract:
Large amounts of aberrantly spliced mRNA from the β⁶⁵⁴ allele was present in erythroid cells, which might impair the erythropoiesis. A therapeutic strategy for β-thalassemia was explored by knocking down the aberrantly spliced mRNA of β-globin. Lentiviral vector with siRNA fragment targets on the specific portion of β⁶⁵⁴-globin aberrantly spliced pre-mRNA was constructed. In HeLa β⁶⁵⁴ cells, the siRNA vector could reduce approximately 60% of aberrantly spliced mRNA, which was assessed by RT-PCR and qRT-PCR. Furthermore, a disease model of β⁶⁵⁴ thalassemia mice with lentiviral-mediated siRNA was produced by subzonal injection (named Hβi-Hbb^th-4/Hbb⁺ transgenic mice). Our results showed that the hemotological parameters were improved in Hβi-Hbb^th-4/Hbb⁺ transgenic mice. This study provides a potential way for β⁶⁵⁴-thalassemia therapy by knocking down the aberrantly spliced β-globin mRNA, whilst supporting that the aberrantly spliced β-globin mRNA may aggravate the disease.

Floret-specific differences in gene expression and support for the hypothesis that tapetal degeneration of Zea mays L. occurs via programmed cell death

David S. Skibbe, Xiujuan Wang, Lisa A. Borsuk, Daniel A. Ashlock, Dan Nettleton, Patrick S. Schnable

2008, 35(10): 603-616. doi: 10.1016/S1673-8527(08)60081-8

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Abstract:
The maize (Zea mays) spikelet consists of two florets, each of which contains three developmentally synchronized anthers. Morphologically, the anthers in the upper and lower florets proceed through apparently similar developmental programs. To test for global differences in gene expression and to identify genes that are coordinately regulated during maize anther development, RNA samples isolated from upper and lower floret anthers at six developmental stages were hybridized to cDNA microarrays. Approximately 9% of the tested genes exhibited statistically significant differences in expression between anthers in the upper and lower florets. This finding indicates that several basic biological processes are differentially regulated between upper and lower floret anthers, including metabolism, protein synthesis and signal transduction. Genes that are coordinately regulated across anther development were identified via cluster analysis. Analysis of these results identified stage-specific, early in development, late in development and bi-phasic expression profiles. Quantitative RT-PCR analysis revealed that four genes whose homologs in other plant species are involved in programmed cell death are up-regulated just prior to the time the tapetum begins to visibly degenerate (i.e., the mid-microspore stage). This finding supports the hypothesis that developmentally normal tapetal degeneration occurs via programmed cell death.

Production of aneuhaploid and euhaploid sporocytes by meiotic restitution in fertile hybrids between durum wheat Langdon chromosome substitution lines and Aegilops tauschii

Lianquan Zhang, Qijiao Chen, Zhongwei Yuan, Zhiguo Xiang, Youliang Zheng, Dengcai Liu

2008, 35(10): 617-623. doi: 10.1016/S1673-8527(08)60082-X

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Abstract:
Fertile F₁ hybrids were obtained between durum wheat (Triticum durum Desf.) Langdon (LDN) and its 10 disomic substitution (LDN DS) lines with Aegilops tauschii accession AS60 without embryo rescue. Selfed seedset rates for hybrids of LDN with AS60 were 36.87% and 49.45% in 2005 and 2006, respectively. Similar or higher selfed seedset rates were observed in the hybrids of 1D (1A), 1D (1B), 3D (3A), 4D (4B), 7D (7A), and 2D (2B) with AS60, while lower in hybrids of 3D (3B) + 3BL, 5D (5A) + 5AL, 5D (5B) + 5B and 6D (6B) + 6BS with AS60 compared with the hybrids of LDN with AS60. Observation of male gametogenesis showed that meiotic restitution, both first-division restitution (FDR) and single-division meiosis (SDM) resulted in the formation of functional unreduced gametes, which in turn produced seeds. Both euhaploid and aneuhaploid gametes were produced in F₁ hybrids. This suggested a strategy to simultaneously transfer and locate major genes from the ancestral species T. turgidum or Ae. tauschii. Moreover, there was no significant difference in the aneuhaploid rates between the F₁ hybrids of LDN and LDN DS lines with AS60, suggesting that meiotic pairing between the two D chromosomes in the hybrids of LDN DS lines with AS60 did not promote the formation of aneuhaploid gametes.

Validation of EST-derived STS markers localized on Qfhs.ndsu-3BS for Fusarium head blight resistance in wheat using a ‘Wangshuibai’ derived population

Amir Mohammad Naji, Mohammad Moghaddam, Mohammad Reza Ghaffari, Hashem Pour Irandoost, Laleh Karimi Farsad, Seyed Mostafa Pirseyedi, Seyed Abolghasem Mohammadi, Behzad Ghareyazie, Mohsen Mardi

2008, 35(10): 625-629. doi: 10.1016/S1673-8527(08)60083-1

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Abstract:
A few EST-derived STS markers localized on Qfhs.ndsu-3BS, a major QTL for resistance to Fusarium head blight (FHB) in wheat, have been previously identified in the ‘Sumai 3’/‘Stoa’ population. In this study, we used a ‘Wangshuibai’ (resistant) /‘Seri82’ (susceptible) derived population, linkage group, QTL, and quantitative gene expression analysis to assess the genetic background dependence and stability of the EST-derived STS markers for use in marker aided selection to improve FHB resistance in wheat. Based on our results, a QTL in the map interval of Xsts3B-138_1−Xgwm493 on chromosome 3BS was detected for FHB resistance, which accounted for up to 16% of the phenotypic variation. BLASTN analysis indicated that Xsts3B-138_1 sequence had significant similarity with the resistance gene analogue. Real-time quantitative PCR showed that the relative expression of Xsts3B-138_1 in ‘Wangshuibai’ at 96 h after inoculation was 2.6 times higher than ‘Seri82’. Our results underlined that EST-derived STS3B-138 markers could be predominantly used in marker aided selection to improve FHB resistance in wheat.

Isolation and characterization of two genes encoding polygalacturonase-inhibiting protein from Populus deltoides

Qiang Cheng, Youzhi Cao, Huixin Pan, Mingxiu Wang, Minren Huang

2008, 35(10): 631-638. doi: 10.1016/S1673-8527(08)60084-3

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Abstract:
Polygalacturonase-inhibiting proteins (PGIPs) are extracellular proteins that belong to the leucine-rich repeat (LRR) protein superfamily. PGIPs inhibit fungal polygalacturonases (PGs) and promote accumulation of oligogalacturonides, which activate plant defense responses. PGIPs play important roles in resistance to infection of pathogens. In this study, reverse transcriptase-polymerase chain reaction (RT-PCR) and RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE) were used to isolate the full-length PGIP cDNA from Populus deltoides (GenBank accession no. of PdPGIP2 and PdPGIP4: EF684913 and EF684912). Domain analysis revealed that the deduced amino acid sequences of PdPGIP2 and PdPGIP4 had a typical PGIP topology. Phylogenetic analysis of known PGIPs indicated that the two PdPGIPs were clustered to the defense-related PGIP clade. Using real-time RT-PCR, the expression patterns of the two PdPGIPs following treatment with a fungal pathogen and defense-related signaling molecules were studied. The expression levels ofPdPGIP2 and PdPGIP4 were both up-regulated when inoculated with the phytopathogenic fungus Marssonina brunnea. Therefore, it was proposed that the two PGIPs might be involved in the resistance to Marssonina brunnea in P. deltoides.

2008 Vol. 35, No. 10