Search Tips

Nodal signaling maintains H3K18ac landscape to promote mesendodermal differentiation through TRIM33

UID: 10394

Author(s): Luo, Maoguo, Bai, Jianbo, Liu, Bofeng, Yan, Peiqiang, Zuo, Feifei, Sun, Hongyao, Sun, Ye, Xu, Xuanhao, Song, Zhihong, Yang, Yang, Massagué, Joan*, Lan, Xun, Lu, Zhi, Chen, Ye-Guang, Deng, Haiteng, Xie, Wei, Xi, Qiaoran * MSK affiliated

Description
ATAC-seq, RNA-seq, and ChIP-seq datasets supporting the article "H3K18ac Primes Mesendodermal Differentiation upon Nodal Signaling". From GEO authors' 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."
Subject of Study
Mus musculus
Subject(s)
Gene Expression Profiling
Transcription Factors
Access via GEO

ATAC-seq, RNA-seq, and ChIP-seq data
Accession #: GSE115169

Access via SRA

RNA and ATAC Sequence reads for 23 samples
Accession #: SRP149451

Access via BioProject

Additional information about overall initiative.
Accession #: PRJNA473998

Access Restrictions
Free to All
Access Instructions
The NCBI Gene Expression Omnibus database provides open access to these files. SRA and/or tar files can be downloaded directly from the site or viewed in the NCBI SRA Run Selector (link at bottom of page).
Associated Publications
Luo M, Bai J, Liu B, et al. H3K18ac primes mesendodermal differentiation upon nodal signaling. Stem Cell Reports. 2019; 13(4):642-656.
Data Type
Genomic
Equipment Used
Illumina HiSeq 2500

High throughput sequencing system

Illumina HiSeq X Ten

Set of 10 ultra-high-throughput sequencers

Dataset Format(s)
SRA, TAR, XLSX, WIG
Dataset Size
494.8 Mb MB (TAR of WIG), 3.0 Mb (XLSX), 91.11 Gb (SRA)
Other Resources
Nodal signaling maintains H3K18ac landscape to promote mesendodermal differentiation through TRIM33 (house mouse) BioProject

The GSE115169 accession is part of the NCBI BioProject PRJNA473998

Data Catalog Record Updated
2021-10-14