From genes to networks: in systematic points of view

We present a report of the BIOCOMP'10 - The 2010 International Conference on Bioinformatics & Computational Biology and other related work in the area of systems biology

Plant Comparative Transcriptomics Reveals Functional Mechanisms and Gene Regulatory Networks Involved in Anther Development and Male Sterility

Gene transcription and transcriptional regulation are crucial biological processes in all cellular life. Through the next-generation sequencing (NGS) technology, transcriptome data from different tissues and developmental stages can be easily obtained, which provides us a powerful tool to reveal the transcriptional landscape of investigated tissue(s) at special developmental stage(s). Anther development is an important process not only for sexual plant reproduction but also for genic male sterility (GMS) used in agriculture production. Plant comparative transcriptomics has been widely used to uncover molecular mechanism of GMS. Here, we focused on researches of anther developmental process and plant GMS genes by using comparative transcriptomics method. In detail, the contents include the following: (1) we described the commonly used flowchart in comparative transcriptomics; (2) we summarized the comparative strategies used to analyze transcriptome data; (3) we presented a case study on a maize GMS gene, ZmMs33; (4) we described the methods and results previously reported on gene co-expression and gene regulatory networks; (5) we presented the workflow of a case study on gene regulatory network reconstruction. The further development of comparative transcriptomics will provide us more powerful theoretical and application tools to investigate molecular mechanism underlying anther development and plant male sterility

Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes

Background Low temperature leads to major crop losses every year. Although several studies have been conducted focusing on diversity of cold tolerance level in multiple phenotypically divergent Arabidopsis thaliana (A. thaliana) ecotypes, genome-scale molecular understanding is still lacking. Results In this study, we report genome-scale transcript response diversity of 10 A. thaliana ecotypes originating from different geographical locations to non-freezing cold stress (10°C). To analyze the transcriptional response diversity, we initially compared transcriptome changes in all 10 ecotypes using Arabidopsis NimbleGen ATH6 microarrays. In total 6061 transcripts were significantly cold regulated (p < 0.01) in 10 ecotypes, including 498 transcription factors and 315 transposable elements. The majority of the transcripts (75%) showed ecotype specific expression pattern. By using sequence data available from Arabidopsis thaliana 1001 genome project, we further investigated sequence polymorphisms in the core cold stress regulon genes. Significant numbers of non-synonymous amino acid changes were observed in the coding region of the CBF regulon genes. Considering the limited knowledge about regulatory interactions between transcription factors and their target genes in the model plant A. thaliana, we have adopted a powerful systems genetics approach- Network Component Analysis (NCA) to construct an in-silico transcriptional regulatory network model during response to cold stress. The resulting regulatory network contained 1,275 nodes and 7,720 connections, with 178 transcription factors and 1,331 target genes. Conclusions A. thaliana ecotypes exhibit considerable variation in transcriptome level responses to non-freezing cold stress treatment. Ecotype specific transcripts and related gene ontology (GO) categories were identified to delineate natural variation of cold stress regulated differential gene expression in the model plant A. thaliana. The predicted regulatory network model was able to identify new ecotype specific transcription factors and their regulatory interactions, which might be crucial for their local geographic adaptation to cold temperature. Additionally, since the approach presented here is general, it could be adapted to study networks regulating biological process in any biological systems

Analysis of tapetally expressed genes during Arabidopsis thaliana pollen development

The formation of viable pollen relies upon a complex interaction of genes in time and space within the anther. One of the most important maternal tissues involved in the production of functional pollen is the tapetum, which is a highly active tissue that plays a major secretory role during pollen development. This project involved the molecular analysis of genes that are expressed in the anther tapetum and are critical for functional pollen development. A number of these are thought to be regulated by, or interact with MALESTERILITY1 (MS1), a transcriptional regulator of male gametogenesis (Yang et al., 2007) or ABORTED MICROSPORE (Xu et al., 2010). Work involved analysis of an ABC transporter (At3g13220), which has been shown to be critical for viable pollen formation and confirmed as directly regulated by AMS (Xu et al., 2010). Another protein, POB2, which appears to be involved in ubiquitin-based proteolytic breakdown, is thought to interact with the MS1 protein. POB2 was identified from a previous screen of a stamen specific yeast-2-hybrid library using the MS1 protein. This interaction has been subsequently confirmed in this work by further yeast two hybrid analyses and bifunctional fluorescent complementation. Further work involved verification of this interaction in vitro and in planta by pull-downs and transient expression of proteins in E. coli and Nicotiana benthamiana respectively. Other work focused on identifying factors that regulate MS1 expression; this identified novel male sterile mutants derived from screening fast neutron mutagenised seed carrying the MS1Prom:MS1-GFP functional fusion protein. Microscopic observation of the fluorescent reporter showed changes in the stage specific expression of MS1 in some of these mutants. Backcrossing of the male sterile mutants with the parental plants (carrying the MS1Prom:MS1-GFP fusion construct) and the ms1 mutant confirmed one as a new mutant and the other three as being allelic to the ms1 mutation. Gene mapping of this mutant was subsequently conducted and suggest that it may be located on chromosome 3. These results are providing insight into the regulatory network of MS1 and AMS during anther development