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Sea-ATI unravels novel vocabularies of plant active cistrome.
Wen, Chenjin; Yuan, Zhen; Zhang, Xiaotian; Chen, Hao; Luo, Lin; Li, Wanying; Li, Tian; Ma, Nana; Mao, Fei; Lin, Dongmei; Lin, Zhanxi; Lin, Chentao; Xu, Tongda; Lü, Peitao; Lin, Juncheng; Zhu, Fangjie.
Afiliação
  • Wen C; College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
  • Yuan Z; College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
  • Zhang X; College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
  • Chen H; College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
  • Luo L; College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
  • Li W; College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
  • Li T; College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
  • Ma N; College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
  • Mao F; College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
  • Lin D; College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
  • Lin Z; College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
  • Lin C; College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
  • Xu T; College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
  • Lü P; College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
  • Lin J; College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
  • Zhu F; College of Life Science, Haixia Institute of Science and Technology, National Engineering Research Center of JUNCAO, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China.
Nucleic Acids Res ; 51(21): 11568-11583, 2023 Nov 27.
Article em En | MEDLINE | ID: mdl-37850650
ABSTRACT
The cistrome consists of all cis-acting regulatory elements recognized by transcription factors (TFs). However, only a portion of the cistrome is active for TF binding in a specific tissue. Resolving the active cistrome in plants remains challenging. In this study, we report the assay sequential extraction assisted-active TF identification (sea-ATI), a low-input method that profiles the DNA sequences recognized by TFs in a target tissue. We applied sea-ATI to seven plant tissues to survey their active cistrome and generated 41 motif models, including 15 new models that represent previously unidentified cis-regulatory vocabularies. ATAC-seq and RNA-seq analyses confirmed the functionality of the cis-elements from the new models, in that they are actively bound in vivo, located near the transcription start site, and influence chromatin accessibility and transcription. Furthermore, comparing dimeric WRKY CREs between sea-ATI and DAP-seq libraries revealed that thermodynamics and genetic drifts cooperatively shaped their evolution. Notably, sea-ATI can identify not only positive but also negative regulatory cis-elements, thereby providing unique insights into the functional non-coding genome of plants.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Plantas / Fatores de Transcrição / Vocabulário Idioma: En Revista: Nucleic Acids Res Ano de publicação: 2023 Tipo de documento: Article País de afiliação: China
Texto completo
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Plantas / Fatores de Transcrição / Vocabulário Idioma: En Revista: Nucleic Acids Res Ano de publicação: 2023 Tipo de documento: Article País de afiliação: China