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SRX2576225: GSM2495559: 4C_Dup-syn_IhhTSS_rep_2; Mus musculus; OTHER
2 ILLUMINA (Illumina HiSeq 1500) runs: 5.6M spots, 1.1G bases, 471Mb downloads

Submitted by: NCBI (GEO)
Study: A multipartite enhancer ensemble coordinates pleiotropic developmental functions of Indian hedgehog
show Abstracthide Abstract
Copy number variations (CNVs) including enhancers frequently appear associated with disease, induced by pathomechanisms that are poorly understood. Here we show through transgenic reporter and genome editing studies in mice that Indian hedgehog (Ihh) is regulated by a constellation of enhancers of unusual complexity and we uncover how duplications within this enhancer architecture cause phenotypes reminiscent of those observed in human patients. At least nine enhancers with distinct combinations of activities orchestrate the expression of Ihh in the digit anlagen, growth plates, skull sutures, and digit tips. Consecutive deletions show that they function in an additive manner resulting in growth defects. Duplications, in contrast, cause not only dose-dependent upregulation of Ihh, but also misexpression, leading to phenotypes influenced by the copy number and relative positioning of individual elements. Taken together, our results uncover a complex regulatory landscape at the Ihh locus and exemplify the intricate and precise control of gene expression during morphogenetic processes. Overall design: Circular Chromosome Conformation Capture (4C-seq) at the Ihh locus in mouse forelimb tissues (digit 2-5) of mutants and WT animals at E14.5.
Sample: 4C_Dup-syn_IhhTSS_rep_2
SAMN06347085 • SRS1991472 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: Illumina HiSeq 1500
Strategy: OTHER
Source: GENOMIC
Selection: other
Layout: PAIRED
Construction protocol: 4C-seq libraries were generated from microdissected E14.5 mouse forelimb tissues (digit 2-5) as described previously (van de Werken et al., 2012). The starting material for all 4C-seq libraries was 5000000-10000000 cells. All 4C-seq experiments were carried out in heterozygous animals and were compared to wildtype. 4-bp cutters were used as primary (Csp6I) and secondary (BfaI) restriction enzymes. A total of 1 to 1.6 µg DNA was amplified by PCR (Primer sequence: Ihh_promoter_1:ACAGCTGGGGACCCTATAC; Ihh_promoter_2:CCCGTCAGGAGGACAATC). 4C-seq experiments from two different viewpoints were carried out in two biological replicates in wildtype, Dupint/+ and Dupsyn/+ mutants. All samples were sequenced with Illumina Hi-Seq technology according to standard protocols.
Experiment attributes:
GEO Accession: GSM2495559
Links:
Runs: 2 runs, 5.6M spots, 1.1G bases, 471Mb
Run# of Spots# of BasesSizePublished
SRR52721822,789,463563.5M235Mb2017-07-05
SRR52721832,773,507560.2M236Mb2017-07-05

ID:
3718617

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