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| 1 | Silencing of developmental genes by H3K27me3 and DNA methylation reflects the discrepant plasticity of embryonic and extraembryonic lineages显示文摘 | Xianfa Yang Boqiang Hu Yu Hou Yunbo Qiao Ran Wang Yingying Chen Yun Qian Su Feng Jun Chen Chang Liu Guangdun Peng Fuchou Tang Naihe Jing | 2018 | Cell Research2018，28，5： | 5 |
| 2 | CRISPR-Cas9-mediated genome editing in one blastomere of two-cell embryos reveals a novel Tet3 function in regulating neocortical development显示文摘学习必要基因的早功能是在发展生物学的一个重要、挑战性的问题。这里,我们为很快在二房间的阶段胚胎的一个分裂球导致 CRISPR-Cas9-mediated 变化建立了一个方法,称为的 2 房间 embryo-CRISPR-Cas9 注射(2CC ) ,学习在里面必需品的 vivo 功能(或未知) 在创始人的基因妄想的鼠标。由注射指向兴趣的基因进的 Cre mRNA 和 CRISPR-Cas9 荧光灯记者老鼠, 2CC 方法能在不同发展阶段跟踪野类型、变异的房间,为变异的房间的 phenotypic 分析的出现内部控制。用这个方法,我们在在发展中的鼠标调整有刺激性、禁止的 synaptic 传播识别了必要基因 Tet3 的新奇函数服的外皮。由产生妄想的变异的老鼠, 2CC 方法允许在多重纸巾和房间的基因功能的快速的屏蔽录入妄想的老鼠创始人,显著地扩展基因工具的当前的一套设备。 | Wang, Lingbo Li, Min-Yin Qu, Chao Miao, Wan-Ying Yin, Qi Liao, Jiaoyang Cao, Hua-Teng Huang, Min Wang, Kai Zuo, Erwei Peng, Guangdun Zhang, Shu-Xin Chen, Guodong Li, Qing Tang, Ke Yu, Qian Li, Zhoujie Wong, Catherine C. L. Xu, Guoliang Jing, Naihe Yu, Xiang Li, Jinsong | 2017 | Cell Research2017，27，6： | 5 |
| 3 | TGF-β signaling pathway in early mouse development and embryonic stem cells显示文摘TGF- 总科发信号小径实质上包括胚胎的 patterning,房间命运决心和动态运动贡献早发展的事件的宽广光谱。在这评论,我们首先介绍了要求发信号显示出这些小径的基本重要性的 TGF- 的一些关键发展过程。然后,我们讨论他们的活动怎么被调整,并且关于的新调查结果 TGF- 总科 ligands 绑在染色质在胚胎开发期间调整抄写。 | Chang Liu Guangdun Peng Naihe Jing | 2018 | Acta Biochimica et Biophysica Sinica2018，50，1： | 4 |
| 4 | Comments on ‘Molecular architecture of lineage allocation and tissue organization in early mouse embryo’显示文摘Single-cell RNA-seq,with its capability to align cells of continuously changed status by pseudo-time reconstruction,has greatly revolutionized the understanding of cell fate transition during embryo development(Shapiroetal.,2013;Hoppeetal.,2014). | Guizhong Cui Naihe jing Guangdun Peng | 2019 | Journal of Molecular Cell Biology2019，11，11： | 4 |
| 5 | Mouse knockout models reveal largely dispensable but context-dependent functions of IncRNAs during development显示文摘 | Xue Han Sai Luo Guangdun Peng Yuyang Lu Guizhong Cui Lichao Liu Pixi Yan Yafei Yin Wei Liu Ran Wang Jiejie Zhang Shanshan Ai Zai Chang Jie Na Aibin He Naihe Jing Xiaohua Shen | 2018 | Journal of Molecular Cell Biology2018，10，2： | 3 |
| 6 | Hormones induce the formation of luminal-derived basal cells in the mammary gland显示文摘In the mammary gland, it is widely believed that the luminal cells are unipotent after birth, contributing only to the luminal compartment in normal development. Here, by lineage tracing, we uncovered an unexpected potential of luminal cells that can give rise to basal cells during pregnancy. These luminal-derived basal cells (LdBCs) persisted through mammary regression and gen erated more proge ny in successive rounds of preg nan cies. LdBCs express basal markers as well as estroge n receptor a (ERa). I n ovariectomized (OVX) mice, stimulation with estrogen and progesterone promoted the formation of LdBCs. In serial transplantation assays, LdBCs were able to rec on stitute new mammary glands in a hormone-depende nt manner. Tran scriptome an alysis and genetic experiments suggest that Wnt/p-catenin signaling is essential for the formation and maintenance of LdBCs. Our data uncover an unexpected bi-potency of luminal cells in a physiological context. The discovery of ERa+ basal cells, which can respond to hormones and are endowed with stem cell-like regenerative capacity in parous mammary gland, provides new insights into the association of hormones and breast cancer. | Wenqian Song Ran Wang Weimin Jiang Qi Yin Guangdun Peng Ruikai Yang Qing Cissy Yu Jianfeng Chen Jingsong Li Tom H. Cheung Naihe Jing Yi Arial Zeng | 2019 | Cell Research2019，29，3： | 2 |
| 7 | The genome-wide molecular regulation of mouse gastrulation embryo显示文摘The diverse morphologies among vertebrate species stems from the evolution of a basic body plan that is constituted by a spatially organized ensemble of tissue lineage progenitors. At gastrulation, this body plan is established through a coordinated morphogenetic process and the delineation of tissue lineages that are driven by the activity of the genome. To explore the molecular mechanisms, in a comprehensive context, it is imperative to glean an understanding of the region-and population-specific genetic activity underpinning this fundamental developmental process. In this review, we outline the recent progress and the future directions in studies of genome activity for the regulation of mouse embryogenesis at gastrulation. | Guangdun Peng Naihe Jing | 2017 | Science China(Life Sciences)2017，60，4： | 2 |
| 8 | Distinct enhancer signatures in the mouse gastrula delineate progressive cell fate continuum during embryo development显示文摘Primary germ layers have the potential to form all tissues in the mature organism,and their formation during gastrulation requires precise epigenetic modulation of both proximal and distal regulatory elements.Previous studies indicated that spatial and temporal patterns of gene expression in the gastrula predispose individual regions to distinct cell fates.However,the underlying epigenetic mechanisms remain largely unexplored.Here,we profile the spatiotemporal landscape of the epigenome and transcriptome of the mouse gastrula.We reveal the asynchronous dynamics of proximal chromatin states during germ layer formation as well as unique gastrula-specific epigenomic features of regulatory elements,which have strong usage turnover dynamics and clear germ layerspecific signatures.Importantly,we also find that enhancers around organogenetic genes,which are weakly expressed at the gastrulation stage,are frequently pre-marked by histone H3 lysine 27 acetylation(H3K27ac)in the gastrula.By using the transgenic mice and genome editing system,we demonstrate that a pre-marked enhancer,which is located in the intron of a brain-specific gene 25W009E07Rik,exhibits specific enhancer activity in the ectoderm and future brain tissue,and also executes important function during mouse neural differentiation.Taken together,our study provides the comprehensive epigenetic information for embryonic patterning during mouse gastrulation,demonstrates the importance of gastrula pre-marked enhancers in regulating the correct development of the mouse embryo,and thus broadens the current understanding of mammalian embryonic development and related diseases. | Xianfa Yang Boqiang Hu Jiaoyang Liao Yunbo Qiao Yingying Chen Yun Qian Su Feng Fang Yu Ji Dong Yu Hou He Xu Ran Wang Guangdun Peng Jinsong Li Fucnou Tang Naihe Jing | 2019 | Cell Research2019，29，11： | 1 |
| 9 | Author Correction:Hormones induce the formation of luminal-derived basal cells in the mammary gland显示文摘In the initial published version of this article,there was a mistake in one author name(Jingsong Li).The correct name should be“Jinsong Li”.This correction does not affect the description of the results or the conclusions of this work. | Wenqian Song Ran Wang Weimin Jiang Qi Yin Guangdun Peng Ruikai Yang Qing Cissy Yu Jianfeng Chen Jingsong Li Tom H.Cheung Naihe Jing Yi Arial Zeng | 2019 | Cell Research2019，29，4： | 1 |
| 10 | Lineage specification of early embryos and embryonic stem cells at the dawn of enabling technologies显示文摘Establishment of progenitor cell populations and lineage diversity during embryogenesis and the differentiation of pluripotent stem cells is a fascinating and intricate biological process. Conceptually, an understanding of this developmental process provides a framework to integrate stem-cell pluripotency, cell competence and differentiating potential with the activity of extrinsic and intrinsic molecular determinants.The recent advent of enabling technologies of high-resolution transcriptome analysis at the cellular,population and spatial levels proffers the capability of gaining deeper insights into the attributes of the gene regulatory network and molecular signaling in lineage specification and differentiation. In this review, we provide a snapshot of the emerging enabling genomic technologies that contribute to the study of development and stem-cell biology. | Guangdun Peng Patrick P.L.Tam Naihe Jing | 2017 | National Science Review2017，4，4： | 1 |
| 11 | Integration of Computational Analysis and Spatial Transcriptomics in Single-cell Studies显示文摘Recent advances of single-cell transcriptomics technologies and allied computational methodologies have revolutionized molecular cell biology.Meanwhile,pioneering explorations in spatial transcriptomics have opened up avenues to address fundamental biological questions in health and diseases.Here,we review the technical attributes of single-cell RNA sequencing and spatial transcriptomics,and the core concepts of computational data analysis.We further highlight the challenges in the application of data integration methodologies and the interpretation of the biological context of the findings. | Ran Wang Guangdun Peng Patrick P.L.Tam Naihe Jing | 2023 | Genomics, Proteomics & Bioinformatics2023，21，1： | 0 |
| 12 | Profiling spatial gene activity in marmoset embryos显示文摘Spatial transcriptomics of the marmoset embryo unveils insights into the molecular landscape of post-implantation development and provides a reference dataset of cell and tissue identity and the mechanistic attributes of germ layer formation.The knowledge gains of the developmental coordinates of early gastrulation point to the utility of this non-human primate for modeling post-implantation development of human embryos.The wealth of knowledge of the developmental biology of the mouse has hallmarked the laboratory mouse as a model organism for mammalian development.Significant progress has been achieved,through the analysis of genome function in geneperturbation experimentation and the profiling of omics attributes of cell populations in developing embryos,in delineating morphogenetic mechanism,cell lineage trajectory and molecular drivers underpinning the development of preimplantation and early post-implantation mouse embryo. | Guangdun Peng Patrick P.L.Tam | 2022 | Cell Research2022，32，10： | 0 |
| 13 | 原肠运动中期细胞谱系与细胞命运的空间转录组特征显示文摘哺乳动物的早期胚胎发育,特别是着床后原肠运动过程中,多能性干细胞通过多个层次的细胞命运决定,形成了胚胎器官发生、形态建成的整个发育蓝图,是生命体最重要的分子事件之一。 | Guangdun Peng Shengbao Suo Jun Chen Weiyang Chen Chang Liu Fang Yu Ran Wang Shirui Chen Na Sun Guizhong Cui Lu Song Patrick P.L.Tam 韩敬东 景乃禾 | 2017 | 科学新闻2017，0，4： | 0 |
| 14 | Ectodermal progenitors derived from epiblast stem cells by inhibition of Nodal signaling显示文摘The ectoderm has the capability to generate epidermis and neuroectoderm and plays imperative roles during the early embryonic development.Our recent study uncovered a region with ectodermal progenitor potential in mouse embryo at embryonic day 7.0 and revealed that Nodal inhibition is essential for its formation.Here,we demonstrate that through brief inhibition of Nodal signaling in vitro,mouse embryonic stem cell(ESC)-derived epiblast stem cells(ESD-EpiSCs)could be committed to transient ectodermal progenitor populations,which possess the ability to give rise to neural or epidermal ectoderm in the absence or presence of BMP4,respectively.Mechanistic studies reveal that BMP4 recruits distinct transcriptional targets in ESD-EpiSCs and ectoderm-like cells.Furthermore,FGF–Erk signaling may also be alleviated during the generation of ectoderm-like cells.Thus,our data suggest that instructive interactions among several extracellular signals participate in the commitment of ectoderm from ESD-EpiSCs,which shed new light on the understanding of the formation of ectoderm during the gastrulation in early mouse embryo development. | Lingyu Li Lu Song Chang Liu Jun Chen Guangdun Peng Ran Wang Pingyu Liu Ke Tang Janet Rossant Naihe Jing | 2015 | Journal of Molecular Cell Biology2015，7，5： | 0 |
| 15 | Connecting past and present:single-cell lineage tracing显示文摘Central to the core principle of cell theory,depicting cells'history,state and fate is a fundamental goal in modern biology.By leveraging clonal analysis and sin-gle-cell RNA-seq technologies,single-cell lineage trac-ing provides new opportunities to interrogate both cell states and lineage histories.During the past few years,many strategies to achieve lineage tracing at single-cell resolution have been developed,and three of them(in-tegration barcodes,polylox barcodes,and CRISPR barcodes)are noteworthy as they are amenable in experimentally tractable systems.Although the above strategies have been demonstrated in animal develop-ment and stem cell research,much care and effort are still required to implement these methods.Here we review the development of single-cell lineage tracing,major characteristics of the cell barcoding strategies,applications,as well as technical considerations and limitations,providing a guide to choose or improve the single-cell barcoding lineage tracing. | Cheng Chen Yuanxin Liao Guangdun Peng | 2022 | Protein & Cell2022，13，11： | 0 |
| 16 | Single-cell technologies:From research to application显示文摘In recent years,more and more single-cell technologies have been developed.A vast amount of single-cell omics data has been generated by large projects,such as the Human Cell Atlas,the Mouse Cell Atlas,the Mouse RNA Atlas,the Mouse ATAC Atlas,and the Plant Cell Atlas.Based on these single-cell big data,thousands of bioinformatics algorithms for quality control,clustering,cell-type annotation,developmental inference,cell-cell transition,cell-cell interaction,and spatial analysis are developed.With powerful experimental single-cell technology and state-of-the-art big data analysis methods based on artificial intelligence,the molecular landscape at the single-cell level can be revealed. | Lu Wen Guoqiang Li Tao Huang Wei Geng Hao Pei Jialiang Yang Miao Zhu Pengfei Zhang Rui Hou Geng Tian Wentao Su Jian Chen Dake Zhang Pingan Zhu Wei Zhang Xiuxin Zhang Ning Zhang Yunlong Zhao Xin Cao Guangdun Peng Xianwen Ren Nan Jiang Caihuan Tian Zi-Jiang Chen | 2022 | The Innovation2022，3，6： | 0 |
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