Xwang:Accomplishment

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2008 ~ 2010 (Harvard University, Dana-Farber Cancer Institute)

Computational models for cataloging smRNAs (smRNA-Seq) and RNA-mediated Transcriptional Gene Silencing

Generally, the ncRNAs that have regulatory function can be primarily classified based on sizes: long ncRNAs (>40 nt) and small ncRNAs (20~25 nt, smRNAs). Long ncRNAs usually possess miRNA-like signatures and influence specific genes localized in antisense or nearby, while smRNAs are involved in a wide spectrum of pathways and function either in trans- or cis-mode. In plant, endogenous smRNAs refer to microRNAs (miRNAs) and short-interfering RNAs (siRNA) that are produced by distinct pathways, and the latter has multiple subclasses. Two of the subclasses named trans-acting siRNAs (ta-siRNAs) and natural-antisense-transcript derived siRNAs (nat-siRNAs), arising from respective TAS genes and convergent gene pairs, will be incorporated in RISC (RNA-induced silencing complex) to mediate translational repression or mRNA degradation, while the rest of siRNA classes mostly derived from tandem repeats or transposable elements (TEs) are found in RITS (RNA-induced initiation of transcriptional silencing, [yeast]) or RdDM (RNA-directed DNA methylation, [Arabidopsis]) complex to mediate epigenetic transformations by targeting on nascent RNAs amid transcription. However, the function and biogenesis pathways of a great number of siRNA classes are poorly characterized.

A. classification of small RNAs in plants

B. smRNA-Seq reads mapped within a genomic locus are defined as a Pri-TU (primary transcript unit)

C. miRNAs are separated from the siRNAs

D. Principal Component Analysis (PCA) were used to predict the new miRNA candidate

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2007 ~ 2008 Harvard University and Yale University

Epigenome, transcriptome and smRNAome by high-throughput Solexa seqeuncing (ChIP-Seq, RNA-Seq)

Shirley's Lab and Deng Lab collaborated the Illumia/Solexa sequencing to generate four histone modifications, H3K4/K36/K27 tri-methylation, H3K9 acetylation, plus DNA methylation, mRNA and small RNA data in maize, rice and Arabidopsis. This hugely integrated epigenomic data not only provides an opportunity for us to interpret the relation between epigenetic marks and gene transcription and small RNAs, but also gives us a chance to compare between species (Wang et al., 2009, The Plant Cell).

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2006 ~ 2007 MCDB, Yale University

Mapping of H3K4me2, H3K4me2, H3K9me2, H3K27me3 and DNA methylation in rice and Arabidopsis (ChIP-Chip)

This analysis reveals combinatorial interactions between these epigenetic modifications and chromatin structure and gene expression, and we have found several interesting rules regarding those tested epigenetic marks. 1. Cytologically densely stained heterochromatin had less H3K4me2 and H3K4me3 and more methylated DNA than the less densely stained euchromatin, whereas centromeres had a unique epigenetic composition. 2. Protein-coding genes had both methylated DNA and di- and/or trimethylated H3K4. Methylation of DNA but not H3K4 was correlated with suppressed transcription. 3. If DNA and H3K4 were comethylated, transcription was only slightly reduced. 4. Transcriptional activity was positively correlated with the ratio of H3K4me3/H3K4me2: genes with predominantly H3K4me3 were actively transcribed, whereas genes with predominantly H3K4me2 were transcribed at moderate levels. 5. More protein-coding genes contained all three modifications, and more transposons contained DNA methylation in shoots than cultured cells. Differential epigenetic modifications correlated to tissue-specific expression between shoots and cultured cells. Collectively, this study provides insights into the rice epigenomes and their effect on gene expression and plant development. (2008 Feb) The Plant Cell.; 20: 259-276