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Series GSE241706 Query DataSets for GSE241706
Status Public on Mar 13, 2024
Title Genomic context sensitizes regulatory elements to genetic disruption [DNA]
Organisms Mus musculus; synthetic construct
Experiment type Other
Summary Enhancer function is frequently investigated piecemeal using truncated reporter assays or single deletion analysis, thus it remains unclear to what extent their function is influenced by surrounding genomic context. Using our Big-IN technology for targeted integration of large DNAs, we analyzed the regulatory architecture of the Igf2/H19 locus, a paradigmatic model of enhancer selectivity. We assembled payloads containing a 157-kb functional Igf2/H19 locus and engineered mutations to genetically direct CTCF occupancy at the imprinting control region (ICR) that switches the target gene of the H19 enhancer cluster. Contrasting the activity of payloads delivered to the endogenous locus or to a safe harbor locus (Hprt) revealed that the functional elements comprising the Igf2/H19 locus are highly sensitive to their native context. Exchanging components of the Igf2/H19 locus with the well-studied Sox2 locus showed that the H19 enhancer cluster in particular functioned poorly out of context, and required its native surroundings to activate Sox2 expression. Conversely, the Sox2 locus control region (LCR) could activate both Igf2 and H19 outside its native context, but its activity was only partially modulated by CTCF occupancy at the ICR. Analysis of regulatory DNA actuation across different cell types revealed that, while the H19 enhancers are tightly coordinated within their native locus, the Sox2 LCR acts more independently. We show that these enhancer clusters typify broader classes of loci genome-wide. Our results show that unexpected dependencies may influence even the most studied functional elements, and our synthetic regulatory genomics approach permits large-scale manipulation of complete loci to investigate how locus architecture relates to function.
 
Overall design Sequencing and coverage data produced as part of the Big-IN genome engineering sequence verification pipeline.
(1) payload sequencing data. (2) Targeted sequencing (Capture-seq) data from mouse embryonic stem cell (mESC) lines engineered to harbor landing pads (LPs) and various payloads at Igf2/H19, Sox2, and Hprt loci
 
Contributor(s) Ordoñez R, Zhang W, Ellis G, Zhu Y, Ribeiro-dos-Santos AM, Brosh R, Huang E, Hogan MS, Boeke JD, Maurano MT
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Submission date Aug 24, 2023
Last update date Mar 14, 2024
Contact name Matthew T Maurano
Organization name NYU Grossman School of Medicine
Department Institute for Systems Genetics
Lab Maurano lab
Street address 435 East 30th Street
City New York
State/province New York
ZIP/Postal code 10016
Country USA
 
Platforms (2)
GPL21626 NextSeq 550 (Mus musculus)
GPL27609 NextSeq 550 (synthetic construct)
Samples (141)
GSM7734076 BAC-Igf2_Igf2_157kb~Igf2SV-BS08196A
GSM7734077 BAC-Igf2_Igf2_miICR~Igf2SV-BS08664A
GSM7734078 BAC-Igf2_Igf2_dEnh~miICR~Igf2SV-BS08667A
This SubSeries is part of SuperSeries:
GSE241708 Genomic context sensitizes regulatory elements to genetic disruption
Relations
BioProject PRJNA1009155

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE241706_RAW.tar 4.8 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA

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