Chloroplast nucleoid is organized by membrane association of transcribed genes [SOLINA]. Chloroplast nucleoid is organized by membrane association of transcribed genes [SOLINA]

Chloroplasts are organelles responsible for photosynthesis. They originated form a procaryotic ancestor in the process of endosymbiosis and contain their own genomes. The chloroplast genome is packaged into a chromatin-like structure known as the nucleoid. The internal arrangement of the nucleoid, molecular mechanisms of DNA packaging and connection of the nucleoid structure to gene expression remain poorly understood. We show that Arabidopsis thaliana chloroplast nucleoids have a unique organization driven by DNA binding to the thylakoid membranes. Membrane association of specific DNA regions is correlated with high levels of transcription, high protein occupancy and reduced DNA accessibility. Genes with low levels of transcription are further away from the membranes, have lower protein occupancy and higher DNA accessibility. Gene-specific disruption of transcription in sigma factor mutants causes a corresponding reduction in membrane association, indicating that RNA polymerase activity causes DNA tethering to the membranes. We propose that transcription organizes the chloroplast nucleoid into a transcriptionally active membrane-associated core and a less active Periphery. Overall design: The data consists of 3 replicates of SOLiNA during light and darkness in Col0 wt plants; and during illumination in the sigma factor mutants sig2 and sig6.

叶绿体是介导光合作用的细胞器。其起源于内共生过程中的原核祖先，并携带自身独立的基因组。叶绿体基因组被组装为一类染色质样结构，即类核（nucleoid）。目前，类核的内部排布模式、DNA包装的分子机制，以及类核结构与基因表达的关联通路仍未被充分阐明。本研究证实，拟南芥（Arabidopsis thaliana）的叶绿体类核具有独特的组织结构，该结构依赖于DNA与类囊体膜的结合。特定DNA区段的膜结合状态与高水平转录活性、高蛋白质占据率及降低的DNA可及性呈正相关；而转录水平较低的基因则距离类囊体膜更远，对应更低的蛋白质占据率与更高的DNA可及性。σ因子（sigma factor）突变体中基因特异性的转录缺陷会导致其膜关联程度出现相应降低，这提示RNA聚合酶（RNA polymerase）的活性可介导DNA与膜的拴定。我们据此提出，转录作用将叶绿体类核组织为两个功能区域：与膜结合的转录活跃核心区域，以及活性较弱的外围区域。总体实验设计：本数据集包含3组生物学重复，分别为哥伦比亚生态型野生型（Col0 wt）拟南芥在光照与黑暗条件下的SOLiNA数据，以及σ因子突变体sig2、sig6在光照条件下的SOLiNA数据。