Identifying novel regulators of placental development using time-series transcriptome data.
Identifying novel regulators of placental development using time-series transcriptome data.
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DOI：
10.26508/lsa.202201788
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发表时间：
2023-02
影响因子：
4.4
通讯作者：
中科院分区：
文献类型：
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作者：
对小鼠胚胎7.5、8.5和9.5天胎盘的RNA-seq数据进行网络分析，发现胎盘发育的新调控因子。胎盘在怀孕期间是母亲和胎儿之间的联系，为胎儿提供氧气、营养和生长激素。然而，胎盘早期发育的调控机制和动态基因相互作用网络尚未得到充分研究。在这里，我们从胚胎7.5、8.5和9.5天的小鼠胎儿胎盘中获得rna测序数据，以鉴定具有时间点特异性表达的基因，然后推断基因相互作用网络，以分析高度连接的网络模块。我们确定了特定时间点的基因网络模块与不同的发育过程相关，并且与特定的人类胎盘细胞群具有相似的表达谱。从每个模块中，我们确定了中心基因及其直接邻近基因，这些基因被预测为控制胎盘功能。我们证实，通过我们的分析鉴定出的四种新的候选调节因子调节HTR-8/SVneo细胞系的细胞迁移。总体而言，我们利用大量rna测序数据的网络分析预测了在特定胎盘细胞类型中表达的几种新的胎盘发育调节因子。我们的发现和分析方法将对未来研究早期发育的转录景观有价值。
Network analysis of RNA-seq data generated from mouse placenta at embryonic days 7.5, 8.5, and 9.5 identifies novel regulators of placental development. The placenta serves as a connection between the mother and the fetus during pregnancy, providing the fetus with oxygen, nutrients, and growth hormones. However, the regulatory mechanisms and dynamic gene interaction networks underlying early placental development are understudied. Here, we generated RNA-sequencing data from mouse fetal placenta at embryonic days 7.5, 8.5, and 9.5 to identify genes with timepoint-specific expression, then inferred gene interaction networks to analyze highly connected network modules. We determined that timepoint-specific gene network modules were associated with distinct developmental processes, and with similar expression profiles to specific human placental cell populations. From each module, we identified hub genes and their direct neighboring genes, which were predicted to govern placental functions. We confirmed that four novel candidate regulators identified through our analyses regulate cell migration in the HTR-8/SVneo cell line. Overall, we predicted several novel regulators of placental development expressed in specific placental cell types using network analysis of bulk RNA-sequencing data. Our findings and analysis approaches will be valuable for future studies investigating the transcriptional landscape of early development.
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DOI：
10.1042/bcj20160187
发表时间：
2016-06-01
期刊：
The Biochemical journal
影响因子：
--
作者：
Das L;Kokate SB;Rath S;Rout N;Singh SP;Crowe SE;Mukhopadhyay AK;Bhattacharyya A
通讯作者：
Bhattacharyya A
影响因子：
3.8
作者：
Cross, JC
通讯作者：
Cross, JC
影响因子：
2.8
作者：
Stirling C;Andrews S;Croft T;Vickers J;Turner P;Robinson A
通讯作者：
Robinson A
影响因子：
9.9
作者：
Cox, Brian;Kotlyar, Max;Evangelou, Andreas I.;Ignatchenko, Vladimir;Ignatchenko, Alex;Whiteley, Kathie;Jurisica, Igor;Adamson, S. Lee;Rossant, Janet;Kislinger, Thomas
通讯作者：
Kislinger, Thomas
影响因子：
64.8
作者：
Dickinson ME;Flenniken AM;Ji X;Teboul L;Wong MD;White JK;Meehan TF;Weninger WJ;Westerberg H;Adissu H;Baker CN;Bower L;Brown JM;Caddle LB;Chiani F;Clary D;Cleak J;Daly MJ;Denegre JM;Doe B;Dolan ME;Edie SM;Fuchs H;Gailus-Durner V;Galli A;Gambadoro A;Gallegos J;Guo S;Horner NR;Hsu CW;Johnson SJ;Kalaga S;Keith LC;Lanoue L;Lawson TN;Lek M;Mark M;Marschall S;Mason J;McElwee ML;Newbigging S;Nutter LM;Peterson KA;Ramirez-Solis R;Rowland DJ;Ryder E;Samocha KE;Seavitt JR;Selloum M;Szoke-Kovacs Z;Tamura M;Trainor AG;Tudose I;Wakana S;Warren J;Wendling O;West DB;Wong L;Yoshiki A;International Mouse Phenotyping Consortium;Jackson Laboratory;Infrastructure Nationale PHENOMIN, Institut Clinique de la Souris (ICS);Charles River Laboratories;MRC Harwell;Toronto Centre for Phenogenomics;Wellcome Trust Sanger Institute;RIKEN BioResource Center;MacArthur DG;Tocchini-Valentini GP;Gao X;Flicek P;Bradley A;Skarnes WC;Justice MJ;Parkinson HE;Moore M;Wells S;Braun RE;Svenson KL;de Angelis MH;Herault Y;Mohun T;Mallon AM;Henkelman RM;Brown SD;Adams DJ;Lloyd KC;McKerlie C;Beaudet AL;Bućan M;Murray SA
通讯作者：
Murray SA