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| Status |
Public on Apr 04, 2024 |
| Title |
Stem-loop and circle-loop TADs generated by directional pairing of boundary elements have distinct physical and regulatory properties |
| Organism |
Drosophila melanogaster |
| Experiment type |
Other
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| Summary |
The chromosomes in multicellular eukaryotes are organized into a series of topologically independent loops called TADs. In flies, TADs are formed by physical interactions between neighboring boundaries. Fly boundaries exhibit distinct partner preferences, and pairing interactions between boundaries are typically orientation dependent. Pairing can be head-to-tail or head-to-head. The former generates a stem-loop TAD, while the latter gives a circle-loop TAD. The TAD that encompasses the Drosophila even skipped (eve) gene is formed by the head-to-tail pairing of the nhomie and homie boundaries. To explore the relationship between loop topology and the physical and regulatory landscape, we flanked the nhomie boundary region with two attP sites. The attP sites were then used to generate four boundary replacements: λ DNA, nhomie forward (WT orientation), nhomie reverse (opposite of WT), and homie forward (same as WT homie). The nhomie forward replacement restores the WT physical and regulatory landscape: In MicroC experiments, the eve TAD is a volcano triangle topped by a plume, and the eve gene and its regulatory elements are sequestered from interactions with neighbors. The λ DNA replacement lacks boundary function: the endpoint of the “new” eve TAD on the nhomie side is ill-defined, and eve stripe enhancers activate a nearby gene, eIF3j. While nhomie reverse and homie forward restore the eve TAD, the topology is a circle-loop, and this changes the local physical and regulatory landscape. In MicroC experiments, the eve TAD interacts with its neighbors, and the plume at the top of the eve volcano triangle is replaced by a cloud of contacts with the next-door TADs. Consistent with the loss of isolation afforded by the stem-loop topology, the eve enhancers weakly activate genes in the neighboring TADs. Conversely, eve function is partially disrupted.
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| Overall design |
microC for Drosophila st14 whole embryo samples, 2-3 independent replicates for each genotype
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| Web link |
https://doi.org/10.7554/eLife.94114
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| Contributor(s) |
Ke W, Fujioka M, Schedl P, Jaynes J |
| Citation(s) |
39110491 |
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https://doi.org/10.7554/eLife.94114
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| Submission date |
Apr 04, 2024 |
| Last update date |
Aug 09, 2024 |
| Contact name |
Wenfan Ke |
| E-mail(s) |
wk9698@princeton.edu
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| Phone |
3198553759
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| Organization name |
Princeton University
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| Department |
Department of Molecular Biology
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| Lab |
Paul Schedl lab
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| Street address |
119 Lewis Thomas Laboratory
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| City |
Princeton |
| State/province |
New Jersey |
| ZIP/Postal code |
08544 |
| Country |
USA |
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| Platforms (1) |
| GPL25244 |
Illumina NovaSeq 6000 (Drosophila melanogaster) |
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| Samples (11)
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| GSM8188919 |
lambda, st14, rep1 |
| GSM8188920 |
lambda, st14, rep2 |
| GSM8188921 |
lambda, st14, rep3 |
| GSM8188922 |
nh_forward, st14, rep1 |
| GSM8188923 |
nh_forward, st14, rep2 |
| GSM8188924 |
nh_inverted, st14, rep1 |
| GSM8188925 |
nh_inverted, st14, rep2 |
| GSM8188926 |
nh_inverted, st14, rep3 |
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| Relations |
| BioProject |
PRJNA1096375 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE263270_RAW.tar |
8.3 Gb |
(http)(custom) |
TAR (of MCOOL, TSV) |
| GSE263270_h_merged.mcool |
949.7 Mb |
(ftp)(http) |
MCOOL |
| GSE263270_lambda_merged.mcool |
1.5 Gb |
(ftp)(http) |
MCOOL |
| GSE263270_nh_forward_merged.mcool |
2.4 Gb |
(ftp)(http) |
MCOOL |
| GSE263270_nh_inverted_merged.mcool |
1.9 Gb |
(ftp)(http) |
MCOOL |
SRA Run Selector |
| Raw data are available in SRA |
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