دورية أكاديمية
أعرض في EDS

3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize.

التفاصيل البيبلوغرافية
العنوان: 3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize.
المؤلفون: Sun Y; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China., Dong L; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China., Zhang Y; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China., Lin D; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People's Republic of China., Xu W; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People's Republic of China., Ke C; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China., Han L; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China., Deng L; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, People's Republic of China., Li G; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China., Jackson D; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA., Li X; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China. xingwangli@mail.hzau.edu.cn., Yang F; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China. fyang@mail.hzau.edu.cn.
المصدر: Genome biology [Genome Biol] 2020 Jun 16; Vol. 21 (1), pp. 143. Date of Electronic Publication: 2020 Jun 16.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: BioMed Central Ltd Country of Publication: England NLM ID: 100960660 Publication Model: Electronic Cited Medium: Internet ISSN: 1474-760X (Electronic) Linking ISSN: 14747596 NLM ISO Abbreviation: Genome Biol Subsets: MEDLINE
أسماء مطبوعة: Publication: London, UK : BioMed Central Ltd
Original Publication: London : Genome Biology Ltd., c2000-
مواضيع طبية MeSH: Epigenome* , Epistasis, Genetic* , Gene Expression Regulation, Plant*, Inflorescence/*metabolism , Zea mays/*genetics, Chromatin Assembly and Disassembly ; Genome, Plant ; Phenotype ; Polymorphism, Single Nucleotide ; Zea mays/metabolism
مستخلص: Background: Maize ears and tassels are two separate types of inflorescence which are initiated by similar developmental processes but gradually develop distinct architectures. However, coordinated trans and cis regulation of differentially expressed genes determining ear and tassel architecture within the 3D genome context is largely unknown.
Results: We identify 56,055 and 52,633 open chromatin regions (OCRs) in developing maize ear and tassel primordia using ATAC-seq and characterize combinatorial epigenome features around these OCRs using ChIP-seq, Bisulfite-seq, and RNA-seq datasets. Our integrative analysis of coordinated epigenetic modification and transcription factor binding to OCRs highlights the cis and trans regulation of differentially expressed genes in ear and tassel controlling inflorescence architecture. We further systematically map chromatin interactions at high-resolution in corresponding tissues using in situ digestion-ligation-only Hi-C (DLO Hi-C). The extensive chromatin loops connecting OCRs and genes provide a 3D view on cis- and trans-regulatory modules responsible for ear- and tassel-specific gene expression. We find that intergenic SNPs tend to locate in distal OCRs, and our chromatin interaction maps provide a potential mechanism for trait-associated intergenic SNPs that may contribute to phenotypic variation by influencing target gene expression through chromatin loops.
Conclusions: Our comprehensive epigenome annotations and 3D genome maps serve as valuable resource and provide a deep understanding of the complex regulatory mechanisms of genes underlying developmental and morphological diversities between maize ear and tassel.
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فهرسة مساهمة: Keywords: 3D genome; Differential expression; Epigenetic modifications; GWAS; Maize inflorescence; Trans and cis regulation
تواريخ الأحداث: Date Created: 20200618 Date Completed: 20210706 Latest Revision: 20240329
رمز التحديث: 20240329
مُعرف محوري في PubMed: PMC7296987
DOI: 10.1186/s13059-020-02063-7
PMID: 32546248
قاعدة البيانات: MEDLINE
الوصف
تدمد:1474-760X
DOI:10.1186/s13059-020-02063-7