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Integration of Cytological Features with Molecular and Epigenetic Properties of Rice Chromosome 4

Molecular Plant 2008年第5期1卷 816-829页

作者： Ben-Liang Yin Lan GUO Dong-Fen Zhang William Terzaghi Xiang-Feng Wang Ting-Ting Liu Hang He Zhu-Kuan Cheng Xing Wang Deng National Institute of Biological Sciences Beijing 102206 China Peking-Yale Jo-int Research Center-fo-r-Plant'Molecular-an-dAgrobiotechnology College of Life Sciences Peking University Beijing 100871 China Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 China Department of Molecular Cellular and Developmental Biology Yale University New Haven CT 06520-8104 USA Department of Biology Wilkes University Wilkes-Barre PA 18766 USA

It has been reported that rice chromosome 4 has eight major heterochromatic knobs within the heterochromatic half and that this organization correlates with chromosomal-level transcriptional activity. To better understand this chromosomal organization, we created a model based on the statistical distribution of various types of gene models to divide chromosome 4 into 17 euchromatic and heterochromatic regions that correspond with the cytological staining. Fluorescence in-situ hybridization （FISH） experiments using a set of bacterial artificial chromosome （BAC） clones from chromosome 4 placed all 18 clones in the region predicted by the model. Elevated levels of H3K4 di- and tri-methylation.detected by chromatin-immunoprecipitation （CHIP） on chip were correlated with euchromatic regions whereas lower levels of these two modifications were detected in heterochromatic regions. Small RNAs were more abundant in the heterochromatic regions. To validate these findings, H3K4 trimethylation. H3K9 acetylation, H4K12 acetylation, and H3K9 di- and tri-methylation.of 19 individual genes were measured by ChlP-PCR. Genes in heterochromatic regions had elevated H3K9 di- and tri-methylation.while genes in euchromatic regions had elevated levels of the other three modifications. We also assayed cytosine methylation.of these genes using the restriction enzymes McrBC, Hapll, and Msp I. This analysis indicated that cytosines of transposable elements and some genes located in heterochromatic regions were methylated while cytosines of the other genes were unmethylated. These results suggest that local transcriptional activity may reflect the organization of the corresponding part of the chromosome. They also indicate that epigenetic regulation plays an important role in correlating chromosomal organization with transcriptional activity.

关键词： chromosome organization FISH histone modification dna methylation.

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F-MSAP:A practical system to detect methylation.in chicken genome

引用

Science Bulletin 2005年第18期 73-78页

作者： XU Qing, SUN Dongxiao & ZHANG Yuan College of Animal Science and Technology, China Agricultural Univer-sity, Beijing 100094, China

By replacing radiation with fluorescent system in the technique of methylation.sensitive amplified polymor-phism (MSAP) and optimizing reaction conditions, a modi-fied technique to detect dna methylation.called F-MSAP (fluorescent labeled methylation.sensitive amplified poly-morphism) was developed. In the present study, cytosine methylation.patterns of genomic dna were investigated in two inbred chickens and their F1 hybrids. Three types of methylation.patterns were observed in each individual, namely fully methylated, hemi-methylated or not methylated types. The average incidence of methylation.was approxi-mately 40%. The percentage that the F1 hybrid individual inherits the methylation.for any given sites from either/both parent amounted to 95%, while the percentage of altered methylation.patterns in F1 individual was only 5%, including 14 increased and 12 decreased methylation.types, demon-strating that F-MSAP was highly efficient for large-scale detection of cytosine methylation.in chicken genome. Our technique can be further extended to other animals or plants with complex genome and rich in methylation.polymor-phism.

关键词： methylation.sensitive amplified polymorphism fluores-cent labeled chicken genome dna methylation.

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