RRC ID 70249
著者 Jansen C, Paraiso KD, Zhou JJ, Blitz IL, Fish MB, Charney RM, Cho JS, Yasuoka Y, Sudou N, Bright AR, Wlizla M, Veenstra GJC, Taira M, Zorn AM, Mortazavi A, Cho KWY.
タイトル Uncovering the mesendoderm gene regulatory network through multi-omic data integration.
ジャーナル Cell Rep
Abstract Mesendodermal specification is one of the earliest events in embryogenesis, where cells first acquire distinct identities. Cell differentiation is a highly regulated process that involves the function of numerous transcription factors (TFs) and signaling molecules, which can be described with gene regulatory networks (GRNs). Cell differentiation GRNs are difficult to build because existing mechanistic methods are low throughput, and high-throughput methods tend to be non-mechanistic. Additionally, integrating highly dimensional data composed of more than two data types is challenging. Here, we use linked self-organizing maps to combine chromatin immunoprecipitation sequencing (ChIP-seq)/ATAC-seq with temporal, spatial, and perturbation RNA sequencing (RNA-seq) data from Xenopus tropicalis mesendoderm development to build a high-resolution genome scale mechanistic GRN. We recover both known and previously unsuspected TF-DNA/TF-TF interactions validated through reporter assays. Our analysis provides insights into transcriptional regulation of early cell fate decisions and provides a general approach to building GRNs using highly dimensional multi-omic datasets.
巻・号 38(7)
ページ 110364
公開日 2022-2-15
DOI 10.1016/j.celrep.2022.110364
PII S2211-1247(22)00085-7
PMID 35172134
PMC PMC8917868
MeSH Animals Chromatin / metabolism Consensus Sequence / genetics DNA / metabolism Endoderm / embryology* Gastrulation / genetics Gene Expression Regulation, Developmental Gene Regulatory Networks* Genomics* Mesoderm / embryology* Protein Binding RNA / metabolism Transcription Factors / metabolism Transcription, Genetic Xenopus / embryology* Xenopus / genetics*
IF 8.109
リソース情報
ツメガエル・イモリ Xenopus tropicalis