hReg-CNCC reconstructs a regulatory network in human cranial neural crest cells and annotates variants in a developmental context

doi:10.1038/s42003-021-01970-0

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	hReg-CNCC reconstructs a regulatory network in human cranial neural crest cells and annotates variants in a developmental context
	Feng, Zhanying 1,2; Duren, Zhana 3,4; Xiong, Ziyi 5,6,7; Wang, Sijia 8,9; Liu, Fan 7,10; Wong, Wing Hung 4; Wang, Yong1,2,9,11
	2021-04-06
发表期刊	COMMUNICATIONS BIOLOGY
卷号	4 期号:1 页码:16
摘要	Cranial Neural Crest Cells (CNCC) originate at the cephalic region from forebrain, midbrain and hindbrain, migrate into the developing craniofacial region, and subsequently differentiate into multiple cell types. The entire specification, delamination, migration, and differentiation process is highly regulated and abnormalities during this craniofacial development cause birth defects. To better understand the molecular networks underlying CNCC, we integrate paired gene expression & chromatin accessibility data and reconstruct the genome-wide human Regulatory network of CNCC (hReg-CNCC). Consensus optimization predicts high-quality regulations and reveals the architecture of upstream, core, and downstream transcription factors that are associated with functions of neural plate border, specification, and migration. hReg-CNCC allows us to annotate genetic variants of human facial GWAS and disease traits with associated cis-regulatory modules, transcription factors, and target genes. For example, we reveal the distal and combinatorial regulation of multiple SNPs to core TF ALX1 and associations to facial distances and cranial rare disease. In addition, hReg-CNCC connects the DNA sequence differences in evolution, such as ultra-conserved elements and human accelerated regions, with gene expression and phenotype. hReg-CNCC provides a valuable resource to interpret genetic variants as early as gastrulation during embryonic development. The network resources are available at https://github.com/AMSSwanglab/hReg-CNCC. Zhanying Feng et al. present hReg-CNCC, a high-quality gene regulatory network for human cranial neural crest cells (CNCCs) constructed by consensus optimization modeling. It may be useful in interpreting genetic variants involved in embryonic development by linking the cis-regulatory sequences in this network with GWAS SNPs, disease risk loci, and evolutionarily-conserved regions of the genome.
DOI	10.1038/s42003-021-01970-0
收录类别	SCI
语种	英语
资助项目	Shanghai Municipal Science and Technology Major Project[2017SHZDZX01] ; CAS Light of West China Program[xbzg-zdsys-201913] ; CAS Interdisciplinary Innovation Team project, National Key R&D Program of China[2017YFC0908400] ; CAS Interdisciplinary Innovation Team project, National Key R&D Program of China[2020YFA0712402] ; National Natural Science Foundation of China (NSFC)[12025107] ; National Natural Science Foundation of China (NSFC)[11871463] ; National Natural Science Foundation of China (NSFC)[61621003] ; National Natural Science Foundation of China (NSFC)[91651507] ; Strategic Priority Research Program of Chinese Academy of Sciences[XDC01000000] ; Strategic Priority Research Program of Chinese Academy of Sciences[XDB38010400] ; China Scholarship Council PhD Fellowship ; NIH[P50-HG007735] ; NIH[R01HG010359]
WOS研究方向	Life Sciences & Biomedicine - Other Topics ; Science & Technology - Other Topics
WOS类目	Biology ; Multidisciplinary Sciences
WOS记录号	WOS:000637808400003
出版者	NATURE RESEARCH
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/58464
专题	应用数学研究所
通讯作者	Liu, Fan; Wong, Wing Hung; Wang, Yong
作者单位	1.Chinese Acad Sci, Acad Math & Syst Sci, Natl Ctr Math & Interdisciplinary Sci, CEMS,NCMIS,MDIS, Beijing, Peoples R China 2.Chinese Acad Sci, Univ Chinese Acad Sci, Sch Math, Beijing, Peoples R China 3.Clemson Univ, Dept Genet & Biochem, Ctr Human Genet, Greenwood, SC USA 4.Stanford Univ, Bio X Program, Dept Biomed Data Sci, Dept Stat, Stanford, CA 94305 USA 5.Erasmus MC Univ Med Ctr Rotterdam, Dept Genet Identificat, Rotterdam, Netherlands 6.Erasmus MC Univ Med Ctr Rotterdam, Dept Epidemiol, Rotterdam, Netherlands 7.Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genom & Precis Med, Beijing, Peoples R China 8.Chinese Acad Sci, CAS MPG Partner Inst Computat Biol, Shanghai Inst Biol Sci, Key Lab Computat Biol, Shanghai, Peoples R China 9.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming, Yunnan, Peoples R China 10.Chinese Acad Sci, China Natl Ctr Bioinformat, Beijing, Peoples R China 11.Chinese Acad Sci, Univ Chinese Acad Sci, Hangzhou Inst Adv Study, Key Lab Syst Biol, Hangzhou, Peoples R China
推荐引用方式 GB/T 7714	Feng, Zhanying,Duren, Zhana,Xiong, Ziyi,et al. hReg-CNCC reconstructs a regulatory network in human cranial neural crest cells and annotates variants in a developmental context[J]. COMMUNICATIONS BIOLOGY,2021,4(1):16.
APA	Feng, Zhanying.,Duren, Zhana.,Xiong, Ziyi.,Wang, Sijia.,Liu, Fan.,...&Wang, Yong.(2021).hReg-CNCC reconstructs a regulatory network in human cranial neural crest cells and annotates variants in a developmental context.COMMUNICATIONS BIOLOGY,4(1),16.
MLA	Feng, Zhanying,et al."hReg-CNCC reconstructs a regulatory network in human cranial neural crest cells and annotates variants in a developmental context".COMMUNICATIONS BIOLOGY 4.1(2021):16.