PXD063373

PXD063373 is an original dataset announced via ProteomeXchange.

Title	Enhancer DNA pull-down of proteins extracted from PA2 tissue of mouse E11.5 embryos
Description	Enhancers, through the combinatorial action of transcription factors (TFs), dictate both the spatial specificity and the levels of gene expression, and their aberrations can result in diseases. While HMX1 downstream enhancer is associated to ear malformations, the mechanisms underlying bilateral constricted ear (BCE) remain unclear. Here, we identify a copy number variation (CNV) containing three enhancers—collectively termed the positional identity hierarchical enhancer cluster (PI-HEC)—that drives BCE by coordinately regulating HMX1 expression. Each enhancer exhibits distinct activity-location-structure features, and the dominant enhancer with high mobility group (HMG)-box and homeodomain TF motifs modulating its activity and specificity, respectively. Mouse models demonstrate that neural crest-derived fibroblasts with aberrant Hmx1 expression in the basal pinna, along with ectopic distal pinna expression, disrupt outer ear development, affecting cartilage, muscle, and epidermis. Our findings elucidate mammalian ear morphogenesis and underscore the complexity of synergistic regulation among enhancers and between enhancers and transcription factors.
HostingRepository	PRIDE
AnnounceDate	2025-04-28
AnnouncementXML	Submission_2025-04-27_20:00:03.912.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Xiaopeng Xu
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-27 19:30:19	ID requested
⏵ 1	2025-04-27 20:00:04	announced

Dataset with its publication pending

submitter keyword: DNA pull-down,Mouse E11.5 embryos

Yong-Biao Zhang
contact affiliation	School of Bioengineering Medicine, Beihang University, Beijing 100191, China
contact email	zhangyongbiao@gmail.com
lab head
Xiaopeng Xu
contact affiliation	Guangzhou Laboratory
contact email	xu_xiaopeng@gzlab.ac.cn
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD063373
     1. Label: PRIDE project
     2. Name: Enhancer DNA pull-down of proteins extracted from PA2 tissue of mouse E11.5 embryos