Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes

Crisp Peter A.; Marand Alexandre P.; Noshay Jaclyn M.Zhou PengLu ZefuSchmitz Robert J.Springer Nathan M.

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Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes

机译：Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes

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The genomic sequences of crops continue to be produced at a frenetic pace. It remains challenging to develop complete annotations of functional genes and regulatory elements in these genomes. Chromatin accessibility assays enable discovery of functional elements; however, to uncover the full portfolio of cis-elements would require profiling of many combinations of cell types, tissues, developmental stages, and environments. Here, we explore the potential to use DNA methylation profiles to develop more complete annotations. Using leaf tissue in maize, we define similar to 100,000 unmethylated regions (UMRs) that account for 5.8 of the genome; 33,375 UMRs are found greater than 2 kb from genes. UMRs are highly stable in multiple vegetative tissues, and they capture the vast majority of accessible chromatin regions from leaf tissue. However, many UMRs are not accessible in leaf, and these represent regions with potential to become accessible in specific cell types or developmental stages. These UMRs often occur near genes that are expressed in other tissues and are enriched for binding sites of transcription factors. The leaf-inaccessible UMRs exhibit unique chromatin modification patterns and are enriched for chromatin interactions with nearby genes. The total UMR space in four additional monocots ranges from 80 to 120 megabases, which is remarkably similar considering the range in genome size of 271 megabases to 4.8 gigabases. In summary, based on the profile from a single tissue, DNA methylation signatures provide powerful filters to distill large genomes down to the small fraction of putative functional genes and regulatory elements.

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《Proceedings of the National Academy of Sciences of the United States of America.》 |2020年第38期|23991-24000|共10页
作者
Crisp Peter A.; Marand Alexandre P.; Noshay Jaclyn M.Zhou PengLu ZefuSchmitz Robert J.Springer Nathan M.;
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作者单位

Dept Plant & Microbial Biol,Univ Minnesota;

Dept Genet,Univ Georgia;

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收录信息美国《科学引文索引》(SCI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
原文格式 PDF
正文语种英语
中图分类自然科学总论;
关键词
DNA methylation; chromatin accessibility; cis-regulatory elements; TRANSCRIPTION FACTOR; MAIZE; METHYLATION; DYNAMICS; ELEMENTS; ARABIDOPSIS; REVEALS; DEMETHYLATION; ENCYCLOPEDIA; LEAVES;

Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes

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