A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state.
A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state.
复制标题
九头蛇基因组的染色体规模的表观遗传学图谱揭示了细胞状态的保守调节。
DOI：
10.1101/gr.277040.122
复制
发表时间：
2023-02
期刊：
影响因子：
7
通讯作者：
Juliano, Celina E.
中科院分区：
文献类型：
--
作者：
Cazet, Jack F.;Siebert, Stefan;Little, Hannah Morris;Bertemes, Philip;Primack, Abby S.;Ladurner, Peter;Achrainer, Matthias;Fredriksen, Mark T.;Moreland, R. Travis;Singh, Sumeeta;Zhang, Suiyuan;Wolfsberg, Tyra G.;Schnitzler, Christine E.;Baxevanis, Andreas D.;Simakov, Oleg;Hobmayer, Bert;Juliano, Celina E.
淡水水螅的上皮和间质干细胞是刺胞动物中最具特征的干细胞系统，为细胞类型进化和动物干细胞的起源提供了有价值的见解。然而，很少有人知道的转录调控机制，决定如何维持这些干细胞，以及它们如何产生其多样化的分化后代。为了解决这些问题，需要彻底了解水螅的转录调控。为此，我们产生了广泛的新资源来表征水螅中的转录调控，包括水螅寡聚体和水螅AEP株的新基因组组装，更新的全动物单细胞RNA-seq图谱，以及染色质相互作用的全基因组图谱，染色质可及性，序列保守性和组蛋白修饰。这些数据揭示了在水螅基因组中存在着大规模的染色质相互作用结构域，其中含有转录共调控基因。我们还发现了两种以前分子上未表征的细胞类型的转录谱：isorhiza-type nervocytes和体细胞性腺外胚层。最后，我们确定了细胞类型特异性转录的新型候选调节因子，其中一些可能至少自4亿多年前水螅和水母Clytia hemphaerica分化以来一直保守。
The epithelial and interstitial stem cells of the freshwater polyp Hydra are the best-characterized stem cell systems in any cnidarian, providing valuable insight into cell type evolution and the origin of stemness in animals. However, little is known about the transcriptional regulatory mechanisms that determine how these stem cells are maintained and how they give rise to their diverse differentiated progeny. To address such questions, a thorough understanding of transcriptional regulation in Hydra is needed. To this end, we generated extensive new resources for characterizing transcriptional regulation in Hydra, including new genome assemblies for Hydra oligactis and the AEP strain of Hydra vulgaris, an updated whole-animal single-cell RNA-seq atlas, and genome-wide maps of chromatin interactions, chromatin accessibility, sequence conservation, and histone modifications. These data revealed the existence of large kilobase-scale chromatin interaction domains in the Hydra genome that contain transcriptionally coregulated genes. We also uncovered the transcriptomic profiles of two previously molecularly uncharacterized cell types: isorhiza-type nematocytes and somatic gonad ectoderm. Finally, we identified novel candidate regulators of cell type–specific transcription, several of which have likely been conserved at least since the divergence of Hydra and the jellyfish Clytia hemisphaerica more than 400 million years ago.
登录
查看更多内容
影响因子：
64.8
作者：
Armstrong J;Hickey G;Diekhans M;Fiddes IT;Novak AM;Deran A;Fang Q;Xie D;Feng S;Stiller J;Genereux D;Johnson J;Marinescu VD;Alföldi J;Harris RS;Lindblad-Toh K;Haussler D;Karlsson E;Jarvis ED;Zhang G;Paten B
通讯作者：
Paten B
影响因子：
0.7
作者：
David, Charles N.
通讯作者：
David, Charles N.
影响因子：
4.1
作者：
Babonis LS;Martindale MQ
通讯作者：
Martindale MQ
影响因子：
4.6
作者：
Dohrmann M;Wörheide G
通讯作者：
Wörheide G
影响因子：
64.8
作者：
通讯作者：
--