Chromatin Accessibility and Transcriptional Differences in Human Stem Cell-Derived Early-Stage Retinal Organoids.
Chromatin Accessibility and Transcriptional Differences in Human Stem Cell-Derived Early-Stage Retinal Organoids.
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作者：
视网膜发生涉及早期脊椎动物发育过程中视网膜细胞类型的规范。虽然模式生物对于确定动态染色质和细胞类型特异性转录网络在这一过程中的作用至关重要，但由于对人类胎儿组织的需求，对发育中的人类视网膜的理解更加难以捉摸。多能干细胞（PSC）衍生的视网膜类器官为研究发育中的人类视网膜提供了一种实验可行的解决方案。为了研究发育早期视网膜类器官的细胞和分子变化，我们开发了SIX6-GFP和VSX2-tdTomato（或VSX2-h2b-mRuby3）双荧光报告基因。当分化为3D类器官时，它们分别在第15天表达GFP，在第25天表达tdTomato（或mRuby3）。这使我们能够利用RNA-seq和ATAC-seq从早期视网膜的多能性中探索转录和染色质相关的变化。发育中的类器官的通路分析显示多能性逐渐丧失，而视神经泡和视网膜通路逐渐变得更加普遍。将基因转录与早期视野发育中染色质可及性相关联表明，视网膜细胞染色质景观和基因表达谱发生了明显变化。虽然每个数据集单独提供了有价值的信息，但并行考虑两者提供了对分子性质眼睛发展的信息一瞥。
Retinogenesis involves the specification of retinal cell types during early vertebrate development. While model organisms have been critical for determining the role of dynamic chromatin and cell-type specific transcriptional networks during this process, an enhanced understanding of the developing human retina has been more elusive due to the requirement for human fetal tissue. Pluripotent stem cell (PSC) derived retinal organoids offer an experimentally accessible solution for investigating the developing human retina. To investigate cellular and molecular changes in developing early retinal organoids, we developed SIX6-GFP and VSX2-tdTomato (or VSX2-h2b-mRuby3) dual fluorescent reporters. When differentiated as 3D organoids these expressed GFP at day 15 and tdTomato (or mRuby3) at day 25, respectively. This enabled us to explore transcriptional and chromatin related changes using RNA-seq and ATAC-seq from pluripotency through early retina specification. Pathway analysis of developing organoids revealed a stepwise loss of pluripotency, while optic vesicle and retina pathways became progressively more prevalent. Correlating gene transcription with chromatin accessibility in early eye field development showed that retinal cells underwent a clear change in chromatin landscape, as well as gene expression profiles. While each dataset alone provided valuable information, considering both in parallel provided an informative glimpse into the molecular nature eye development.
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影响因子：
7
作者：
Duttke, Sascha H.;Chang, Max W.;Benner, Christopher
通讯作者：
Benner, Christopher
影响因子：
5.2
作者：
Capowski, Elizabeth E.;Wright, Lynda S.;Liang, Kun;Phillips, M. Joseph;Wallace, Kyle;Petelinsek, Anna;Hagstrom, Anna;Pinilla, Isabel;Borys, Katarzyna;Lien, Jessica;Min, Jee Hong;Keles, Sunduz;Thomson, James A.;Gamm, David M.
通讯作者：
Gamm, David M.
人类诱导的多能干细胞产生具有可变和养分依赖性效率的光响应性视网膜器官。
DOI：
10.1002/stem.2883
发表时间：
2018-10
期刊：
Stem cells (Dayton, Ohio)
影响因子：
--
作者：
Hallam D;Hilgen G;Dorgau B;Zhu L;Yu M;Bojic S;Hewitt P;Schmitt M;Uteng M;Kustermann S;Steel D;Nicholds M;Thomas R;Treumann A;Porter A;Sernagor E;Armstrong L;Lako M
通讯作者：
Lako M
影响因子：
14.9
作者：
Frankish A;Diekhans M;Ferreira AM;Johnson R;Jungreis I;Loveland J;Mudge JM;Sisu C;Wright J;Armstrong J;Barnes I;Berry A;Bignell A;Carbonell Sala S;Chrast J;Cunningham F;Di Domenico T;Donaldson S;Fiddes IT;García Girón C;Gonzalez JM;Grego T;Hardy M;Hourlier T;Hunt T;Izuogu OG;Lagarde J;Martin FJ;Martínez L;Mohanan S;Muir P;Navarro FCP;Parker A;Pei B;Pozo F;Ruffier M;Schmitt BM;Stapleton E;Suner MM;Sycheva I;Uszczynska-Ratajczak B;Xu J;Yates A;Zerbino D;Zhang Y;Aken B;Choudhary JS;Gerstein M;Guigó R;Hubbard TJP;Kellis M;Paten B;Reymond A;Tress ML;Flicek P
通讯作者：
Flicek P
影响因子：
48
作者：
Gibson, Daniel G.;Young, Lei;Smith, Hamilton O.
通讯作者：
Smith, Hamilton O.