Spatio-temporal analysis of coding and long noncoding transcripts during maize endosperm development

Abstract The maize endosperm consists of three major compartmentalized cell types: the starchy endosperm (SE), the basal endosperm transfer cell layer (BETL), and the aleurone cell layer (AL). Differential genetic programs are activated in each cell type to construct functionally and structurally di...

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Autores principales:	Eun-Deok Kim, Yuqing Xiong, Youngjae Pyo, Dong-Hwan Kim, Byung-Ho Kang, Sibum Sung
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/81d46b676b9849c19bb3b66d017793ea
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spelling	oai:doaj.org-article:81d46b676b9849c19bb3b66d017793ea2021-12-02T15:05:12ZSpatio-temporal analysis of coding and long noncoding transcripts during maize endosperm development10.1038/s41598-017-03878-42045-2322https://doaj.org/article/81d46b676b9849c19bb3b66d017793ea2017-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-03878-4https://doaj.org/toc/2045-2322Abstract The maize endosperm consists of three major compartmentalized cell types: the starchy endosperm (SE), the basal endosperm transfer cell layer (BETL), and the aleurone cell layer (AL). Differential genetic programs are activated in each cell type to construct functionally and structurally distinct cells. To compare gene expression patterns involved in maize endosperm cell differentiation, we isolated transcripts from cryo-dissected endosperm specimens enriched with BETL, AL, or SE at 8, 12, and 16 days after pollination (DAP). We performed transcriptome profiling of coding and long noncoding transcripts in the three cell types during differentiation and identified clusters of the transcripts exhibiting spatio-temporal specificities. Our analysis uncovered that the BETL at 12 DAP undergoes the most dynamic transcriptional regulation for both coding and long noncoding transcripts. In addition, our transcriptome analysis revealed spatio-temporal regulatory networks of transcription factors, imprinted genes, and loci marked with histone H3 trimethylated at lysine 27. Our study suggests that various regulatory mechanisms contribute to the genetic networks specific to the functions and structures of the cell types of the endosperm.Eun-Deok KimYuqing XiongYoungjae PyoDong-Hwan KimByung-Ho KangSibum SungNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-14 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Eun-Deok Kim Yuqing Xiong Youngjae Pyo Dong-Hwan Kim Byung-Ho Kang Sibum Sung Spatio-temporal analysis of coding and long noncoding transcripts during maize endosperm development
description	Abstract The maize endosperm consists of three major compartmentalized cell types: the starchy endosperm (SE), the basal endosperm transfer cell layer (BETL), and the aleurone cell layer (AL). Differential genetic programs are activated in each cell type to construct functionally and structurally distinct cells. To compare gene expression patterns involved in maize endosperm cell differentiation, we isolated transcripts from cryo-dissected endosperm specimens enriched with BETL, AL, or SE at 8, 12, and 16 days after pollination (DAP). We performed transcriptome profiling of coding and long noncoding transcripts in the three cell types during differentiation and identified clusters of the transcripts exhibiting spatio-temporal specificities. Our analysis uncovered that the BETL at 12 DAP undergoes the most dynamic transcriptional regulation for both coding and long noncoding transcripts. In addition, our transcriptome analysis revealed spatio-temporal regulatory networks of transcription factors, imprinted genes, and loci marked with histone H3 trimethylated at lysine 27. Our study suggests that various regulatory mechanisms contribute to the genetic networks specific to the functions and structures of the cell types of the endosperm.
format	article
author	Eun-Deok Kim Yuqing Xiong Youngjae Pyo Dong-Hwan Kim Byung-Ho Kang Sibum Sung
author_facet	Eun-Deok Kim Yuqing Xiong Youngjae Pyo Dong-Hwan Kim Byung-Ho Kang Sibum Sung
author_sort	Eun-Deok Kim
title	Spatio-temporal analysis of coding and long noncoding transcripts during maize endosperm development
title_short	Spatio-temporal analysis of coding and long noncoding transcripts during maize endosperm development
title_full	Spatio-temporal analysis of coding and long noncoding transcripts during maize endosperm development
title_fullStr	Spatio-temporal analysis of coding and long noncoding transcripts during maize endosperm development
title_full_unstemmed	Spatio-temporal analysis of coding and long noncoding transcripts during maize endosperm development
title_sort	spatio-temporal analysis of coding and long noncoding transcripts during maize endosperm development
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/81d46b676b9849c19bb3b66d017793ea
work_keys_str_mv	AT eundeokkim spatiotemporalanalysisofcodingandlongnoncodingtranscriptsduringmaizeendospermdevelopment AT yuqingxiong spatiotemporalanalysisofcodingandlongnoncodingtranscriptsduringmaizeendospermdevelopment AT youngjaepyo spatiotemporalanalysisofcodingandlongnoncodingtranscriptsduringmaizeendospermdevelopment AT donghwankim spatiotemporalanalysisofcodingandlongnoncodingtranscriptsduringmaizeendospermdevelopment AT byunghokang spatiotemporalanalysisofcodingandlongnoncodingtranscriptsduringmaizeendospermdevelopment AT sibumsung spatiotemporalanalysisofcodingandlongnoncodingtranscriptsduringmaizeendospermdevelopment
_version_	1718388901747359744

Spatio-temporal analysis of coding and long noncoding transcripts during maize endosperm development

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