著名華人科學(xué)家鄧興旺教授在2006年1月15日Nature Gentics上發(fā)表最新研究成果,，采用tiling微陣列（芯片）技術(shù)研究了水稻轉(zhuǎn)錄組,。

   這篇重要研究成果是其領(lǐng)導(dǎo)的位于北京的中國國家生命科學(xué)研究所工作人員作出的重要一項成果。研究了水稻的35970個功能基因（占水稻的基因的81.9%)和5464個單一的基因內(nèi)區(qū)域的表達(dá)譜的變化,。這一研究成果為深入闡述水稻的轉(zhuǎn)錄譜變化具有重要意義,。

(a) Representative gene models from chromosome 1 are aligned to the chromosomal coordinates. Arrow points indicate direction of transcription. The interrogating probes are also aligned to the chromosomal coordinates, with the fluorescence intensity value depicted as a vertical bar. The red blocks at the bottom indicate the presence of an interrogating probe in the microarray at the specific genomic location. (b) Classification of rice gene models based on array detection. (c) A sample region of chromosome 1 illustrating transcription in the intergenic regions. TARs represented by at least four consecutive signal probes were identified (green bars). The cutoff for signal probe is depicted as a dashed line corresponding to a fluorescence intensity of 250. SSRs are indicated as black bars and are aligned to the chromosomal coordinates.

Tiling array detection of annotated indica gene models.

(a) The gene models are categorized on the basis of previous expression support (CG, EG and UG) and protein homology to A. thaliana genes (HH and LH) using E  10-7. Array detection rate for gene models in each category is shown. (b) The gene models are categorized on the basis of previous expression support and alignment against japonica gene models (common and unique). Array detection rate for gene models in each group is shown. (c) Comparison of tiling array detection of rice and Arabidopsis gene models. Rice and A. thaliana gene models are categorized on the basis of protein homology in the reciprocal genomes. Expression data on the A. thaliana gene models was obtained from a previous whole-genome tiling array study
 

Identification and characterization of TARs.

(a) Distribution of signal probes in the annotated exons, introns and intergenic regions (far left). The 5,464 identified TARs were compared against the japonica sequences at the corresponding genomic positions (second from left), the rice EST collections using E  10-20 (second from right) and all major plant TCs at the protein level using E  10-10 (far right). (b) RT-PCR analysis of selected TARs. PCR targeting each TAR was carried out on reverse transcribed cDNA (RT+) and mRNA (RT-) and resolved on gel side by side. (c) Average distance (in kb) between two neighboring simple sequence repeats associated with different indica genome components as indicated. (d) Relative frequency of simple sequence repeat motifs in the four indica genome components as indicated. TEs, transposable elements; TNRs, trinucleotide repeats.

Tiling microarray analysis of chromosome-wide transcriptional activities.

(a) Number of signal probes was calculated in 100-kb windows along both strands of chromosome 1 and depicted as color-coded vertical bars. Cumulative length of interrogating and masked probes in the same 100-kb windows along the length of the chromosome is shown below. Black triangle marks the starting position of the annotated centromere3. (b) Number of signal probes and accumulative length of interrogating and masked probes in 100-kb windows along the length of chromosome 4. Results for the other 10 rice chromosomes are shown in Supplementary Figure 5. (c) Euchromatin and heterochromatin of indica rice chromosome 4 were mapped by DAPI staining (red). Supplementary Figure 6 shows the results for the other 11 chromosomes. Two selected probes P1 and P2, located at 15.3 Mb and 16.2 Mb, respectively (marked by arrows in b), were used for FISH (yellow signal). At right, the stained images converted to black and white to enhance visualization of the euchromatin and heterochromatin domains.

Transcription analysis of duplicated segments in the indica genome.

Depicted here are the duplicated segments located in chromosome 1 and 5, which are 6.5 and 8.4 Mb in size, respectively. Average probe fluorescence intensity and number of gene models are calculated in 20-kb windows along the length of each segment and represented by the color-coded bars and the red wavy line, respectively. Positions of the markers used to define the segmental duplication are indicated. The original cDNAs are represented by green lines and their homologous counterparts by blue lines. The calculated log2 ratio of average probe intensity in the genomic regions containing the cDNAs and their counterparts is shown in the center.

原始出處：

Lei Li, Xiangfeng Wang, Viktor Stolc, Xueyong Li, Dongfen Zhang, Ning Su, Waraporn Tongprasit, Songgang Li, Zhukuan Cheng, Jun Wang & Xing Wang Deng. Genome-wide transcription analyses in rice using tiling microarrays
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補充資料：

鄧興旺博士簡介

有關(guān)水稻基因組研究以及Tiling微陣列技術(shù)相關(guān)文獻(xiàn)資料

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