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An atlas of dynamic chromatin landscapes in mouse fetal development.

ABSTRACT: The Encyclopedia of DNA Elements (ENCODE) project has established a genomic resource for mammalian development, profiling a diverse panel of mouse tissues at 8 developmental stages from 10.5 days after conception until birth, including transcriptomes, methylomes and chromatin states. Here we systematically examined the state and accessibility of chromatin in the developing mouse fetus. In total we performed 1,128 chromatin immunoprecipitation with sequencing (ChIP-seq) assays for histone modifications and 132 assay for transposase-accessible chromatin using sequencing (ATAC-seq) assays for chromatin accessibility across 72 distinct tissue-stages. We used integrative analysis to develop a unified set of chromatin state annotations, infer the identities of dynamic enhancers and key transcriptional regulators, and characterize the relationship between chromatin state and accessibility during developmental gene regulation. We also leveraged these data to link enhancers to putative target genes and demonstrate tissue-specific enrichments of sequence variants associated with disease in humans. The mouse ENCODE data sets provide a compendium of resources for biomedical researchers and achieve, to our knowledge, the most comprehensive view of chromatin dynamics during mammalian fetal development to date.

SUBMITTER: Gorkin DU

PROVIDER: S-EPMC7398618 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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An atlas of dynamic chromatin landscapes in mouse fetal development.

Gorkin David U DU Barozzi Iros I Zhao Yuan Y Zhang Yanxiao Y Huang Hui H Lee Ah Young AY Li Bin B Chiou Joshua J Wildberg Andre A Ding Bo B Zhang Bo B Wang Mengchi M Strattan J Seth JS Davidson Jean M JM Qiu Yunjiang Y Afzal Veena V Akiyama Jennifer A JA Plajzer-Frick Ingrid I Novak Catherine S CS Kato Momoe M Garvin Tyler H TH Pham Quan T QT Harrington Anne N AN Mannion Brandon J BJ Lee Elizabeth A EA Fukuda-Yuzawa Yoko Y He Yupeng Y Preissl Sebastian S Chee Sora S Han Jee Yun JY Williams Brian A BA Trout Diane D Amrhein Henry H Yang Hongbo H Cherry J Michael JM Wang Wei W Gaulton Kyle K Ecker Joseph R JR Shen Yin Y Dickel Diane E DE Visel Axel A Pennacchio Len A LA Ren Bing B

Nature 20200729 7818

The Encyclopedia of DNA Elements (ENCODE) project has established a genomic resource for mammalian development, profiling a diverse panel of mouse tissues at 8 developmental stages from 10.5 days after conception until birth, including transcriptomes, methylomes and chromatin states. Here we systematically examined the state and accessibility of chromatin in the developing mouse fetus. In total we performed 1,128 chromatin immunoprecipitation with sequencing (ChIP-seq) assays for histone modific ...[more]

PMID: 32728240

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Project description:BackgroundThe number of patients receiving anaesthesia is increasing, but the impact of general anaesthesia on the patient's immune system remains unclear. The aim of the present study is to investigate dynamics of systemic immune cell responses to anaesthesia during perioperative period at a single-cell solution.MethodsThe peripheral blood mononuclear cells (PBMCs) and clinical phenomes were harvested and recorded 1 day before anaesthesia and operation, just after anaesthesia (0 h), and 24 and 48 h after anaesthesia. Single-cell sequencing of PBMCs was performed with 10× genomics. Subsequently, data analysis was performed with R packages: Seurat, clusterProfiler and CellPhoneDB.ResultsWe found that the cluster of CD56+ NK cells changed at 0 h and the cluster of monocytes increased at 24 and 48 h after anaesthesia. The characteristic genes of CD56+ NK cells were mainly enriched in the Jak-STAT signalling pathway and in cell adhesion molecules (24 h) and carbon metabolism (48 h). The communication between CD14+ monocytes and other cells decreased substantially 0 and 48 h after operation. The number of plasma cells enriched in protein export in men was substantially higher than that in women, although the total number in patients decreased 24 h after operation. CD14+ monocytes dominated that cell-cell communications appeared in females, while CD8+ NKT cells dominated that cell-cell communications appeared in male. The number of plasma cells increased substantially in patients with major surgical trauma, with enrichments of pentose phosphate pathway. The communications between plasma cells with other cells varied between surgical severities and anaesthetic forms. The intravenous anaesthesia caused major alterations of cell types, including CD14+ monocytes, plasmas cells and MAIT cells, as compared with inhalation anaesthesia.ConclusionWe initially reported the roles of perioperative anaesthesia/surgery in temporal phenomes of circulating immune cells at a single-cell solution. Thus, the protection against immune cell changes would benefit the recovery from anaesthesia/surgery.

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An atlas of dynamic chromatin landscapes in mouse fetal development.

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An atlas of dynamic chromatin landscapes in mouse fetal development.

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