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Series GSE115169 Query DataSets for GSE115169
Status Public on Jun 01, 2019
Title Nodal signaling maintains H3K18ac landscape to promote mesendodermal differentiation through TRIM33
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary The epigenome of a cell is established and maintained by chromatin modifiers and remodelers, which are recruited to the chromatin by specific transcription factors. In this report, we show that nodal cross-talks with the epigenome through TRIM33-H3K18ac to mediate mesendodermal genes expression. The chromatin accessibility at mesendodermal genes depends on TRIM33. Moreover, histone acetylation is essential for TRIM33 recruitment to many nodal target genes involved in mesendodermal differentiation. The distribution pattern of the H3K18ac mark changes from foci to expanded domains at the mesendodermal genes promoter during embryonic stem cells (ESCs) differentiation to embryoid bodies (EBs). This could be the cue to facilitate TRIM33 colocalized with Smad2/3 at chromatin in EBs but not in ESCs. TRIM33 interacts with the H3K18ac “writer” p300 dependent on nodal signaling, providing a positive feedback to promote activation of mesendodermal genes and association with HDAC1 plays a negative role in activation of mesendodermal genes.
Overall design ESCs were cultured on gelatin coated plates with 15% serum ESC culture medium and d2.5 EBs were cultured on bacteria plates without gelatin with 15% serum ESC culture medium withdrawl LIF. TRIM33 WT or KO ESCs and d2.5 EBs were harvested for ATAC-seq; TRIM33 WT or KO d2.5 EBs treated with activin A (50 ng/ml, R&D Systems) for 2hs or SB431542 (10 μM, TOCRIS) for 1h were harvested for RNA-seq and TRIM33 WT ESCs were harvested for RNA-SEQ.E14 ESCs were harvested for H3K18ac ChIP-seq, E 14 d2.5 EBs treated with activin A (50 ng/ml, R&D Systems) for 2hs or SB431542 (10 μM, TOCRIS) for 1h were harvested for H3K18ac ChIP-seq and H3K27ac ChIP-seq.
Contributor(s) Liu B, Luo M, Xie W, Xi Q
Citation(s) 31564646
Submission date May 31, 2018
Last update date Oct 01, 2019
Contact name Bofeng Liu
Organization name Tsinghua University
Department School of Life Science
Lab Xie Wei Lab
Street address Haidian District
City Beijing
ZIP/Postal code 100084
Country China
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (23)
GSM3168481 ATAC-seq ES WT re1
GSM3168482 ATAC-seq ES KO re1
GSM3168483 ATAC-seq EB WT re1
BioProject PRJNA473998
SRA SRP149451

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Supplementary file Size Download File type/resource
GSE115169_RAW.tar 494.8 Mb (http)(custom) TAR (of WIG)
GSE115169_RNA-seq_FPKM_list.xlsx 3.0 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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