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Bing-Bing Wang

Publications and source records attributed to Bing-Bing Wang.

7 recordsLinked to original sources
PubMed2006

Genomewide comparative analysis of alternative splicing in plants.

Alternative splicing (AS) has been extensively studied in mammalian systems but much less in plants. Here we report AS events deduced from EST/cDNA analysis in two model plants: Arabidopsis and rice. In Arabidopsis, 4,707 (21.8%) of the genes with EST/cDNA evidence show 8,264 AS events. Approximately 56% of these events are intron retention (IntronR), and only 8% are exon skipping. In rice, 6,568 (21.2%) of the expressed genes display 14,542 AS events, of which 53.5% are IntronR and 13.8% are exon skipping. The consistent high frequency of IntronR suggests prevalence of splice site recognition by intron definition in plants. Different AS events within a given gene occur, for the most part, independently. In total, 36-43% of the AS events produce transcripts that would be targets of the non-sense-mediated decay pathway, if that pathway were to operate in plants as in humans. Forty percent of Arabidopsis AS genes are alternatively spliced also in rice, with some examples strongly suggesting a role of the AS event as an evolutionary conserved mechanism of posttranscriptional regulation. We created a comprehensive web-interfaced database to compile and visualize the evidence for alternative splicing in plants (Alternative Splicing in Plants, available at www.plantgdb.org/ASIP).

Alternative Splicing↗
PubMed2006

Molecular characterization and phylogeny of U2AF35 homologs in plants.

U2AF (U2 small nuclear ribonucleoprotein auxiliary factor) is an essential splicing factor with critical roles in recognition of the 3'-splice site. In animals, the U2AF small subunit (U2AF35) can bind to the 3'-AG intron border and promote U2 small nuclear RNP binding to the branch-point sequences of introns through interaction with the U2AF large subunit. Two copies of U2AF35-encoding genes were identified in Arabidopsis (Arabidopsis thaliana; atU2AF35a and atU2AF35b). Both are expressed in all tissues inspected, with atU2AF35a expressed at a higher level than atU2AF35b in most tissues. Differences in the expression patterns of atU2AF35a and atU2AF35b in roots were revealed by a promoter::beta-glucuronidase assay, with atU2AF35b expressed strongly in whole young roots and root tips and atU2AF35a limited to root vascular regions. Altered expression levels of atU2AF35a or atU2AF35b cause pleiotropic phenotypes (including flowering time, leaf morphology, and flower and silique shape). Novel slicing isoforms were generated from FCA pre-mRNA by splicing of noncanonical introns in plants with altered expression levels of atU2AF35. U2AF35 homologs were also identified from maize (Zea mays) and other plants with large-scale expressed sequence tag projects. A C-terminal motif (named SERE) is highly conserved in all seed plant protein homologs, suggesting it may have an important function specific to higher plants.

Alternative Splicing↗
PubMed2005

Two novel arginine/serine (SR) proteins in maize are differentially spliced and utilize non-canonical splice sites.

The serine-arginine (SR)-rich splicing proteins are highly conserved RNA binding nuclear phosphor-proteins that play important roles in both regular and alternative splicing. Here we describe two novel putative SR genes from maize, designated zmRSp31A and zmRSp31B. Both genes contain characteristic RNA binding motifs RNP-1 and RNP-2, a serine/arginine-rich (RS) domain and share significant sequence similarity to the Arabidopsis atRSp31 family of SR proteins. Both zmRSp31A and zmRSp31B produce multiple transcripts by alternative splicing, of which majority of the alternatively spliced transcripts utilize non-canonical splice sites. zmRSp31A and zmRSp31B produce at least six and four transcripts, respectively, of which only one corresponds to the wild type proteins for each gene. All the alternatively spliced transcripts of both the genes, with one exception, are predicted to encode small truncated proteins containing only the RNP-2 domain of their first RNA recognition motif and completely lack the carboxyl terminal RS domain. We provide evidence that some of the alternatively spliced transcripts of both genes are associated with polysomes and interact with the translational machinery.

Alternative Splicing↗
PubMed2005

Comparative EST analyses in plant systems.

Expressed sequence tag (EST) data are a major contributor to the known plant sequence space. Organization of the data into non-redundant clusters representing tentative unique genes provides snapshots of the gene repertoires of a species. This chapter reviews availability of sequences and sequence analysis results and describes several resources and tools that should facilitate broad-based utilization of EST data for gene structure annotation, gene discovery, and comparative genomics.

Alternative Splicing↗
PubMed2004

The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing.

A total of 74 small nuclear RNA (snRNA) genes and 395 genes encoding splicing-related proteins were identified in the Arabidopsis genome by sequence comparison and motif searches, including the previously elusive U4atac snRNA gene. Most of the genes have not been studied experimentally. Classification of these genes and detailed information on gene structure, alternative splicing, gene duplications and phylogenetic relationships are made accessible as a comprehensive database of Arabidopsis Splicing Related Genes (ASRG) on our website.

Alternative Splicing↗
PubMed2004

Fluorescence and aggregation behavior of poly(amidoamine) dendrimers peripherally modified with aromatic chromophores: the effect of dendritic architectures.

PAMAM dendrimers of the zeroth to fifth generation (G0-5) have been peripherally modified with phenyl, naphthyl, pyrenyl, and dansyl chromophores. Their fluorescence behaviors are strongly affected by the dendritic architectures at different generations. These dendrimers modified with hydrophobic chromphores can self-organize into vesicular aggregates at the low generations G0-3 in water. The size and aggregation number of these vesicles decrease with increasing generation from G0 to G3. Critical aggregation concentration determined by fluorescence spectroscopy reveals that these aggregates can be favorably formed in the order of G3 > G2 > G1. In contrast to the vesicles made from traditional amphiphilic compounds, these dendrimer-based vesicles are very adhesive due to the H-bonding interaction and entanglement of dendritic branches located in the outer layer. A large number of multivesicle assemblies, i.e., "twins" and "quins" consisting of two and five vesicles, were clearly identifiable with transmission electron (TEM) and atomic force microscopy. For the dendrimers with peripheral pyrenyl chromophores, triangle-like vesicles were observed in water. The hydrophobic interphase thickness of the vesicular bilayer is ca. 2.0-3.2 nm determined by fluorescence resonance energy transfer methods, which agrees well with the thickness directly observed with TEM.

Journal Article↗