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Series GSE228397 Query DataSets for GSE228397
Status Public on Sep 17, 2023
Title Unique territorial and sub-chromosomal organization revealed in the holocentric moth Bombyx mori [ChIP-seq]
Organism Bombyx mori
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Genome organization in diverse eukaryotes follows conserved principles including the formation of chromosome territories (CT), chromatin compartments, and TADs. Here, we describe the 3D architecture of holocentric chromosomes in the silkworm Bombyx mori. At the genome-wide scale, B. mori chromosomes are highly territorial lacking any visible trans contact pattern. At the chromosomal scale, B. mori chromosomes segregate into three chromatin compartments: an active A and an inactive B as described in other eukaryotes, and a third type, X, with a unique contact pattern. Compartment X is strongly enriched for short-range interactions and depleted of long-range interactions, hosts a specific combination of genetic and epigenetic features and localizes towards the periphery of CT. Biophysical simulations reveal the necessity of the combined effects of affinity-based compartmentalization and activity-based loop extrusion to lead to the unique interaction patterns observed. Our analyses contribute to our understanding how chromosomes fold highlighting the evolutionary plasticity of 3D genome organization.
 
Overall design Hi-C and ChIP-seq and RNA-seq data from Bombyx mori p50 reference strain embryos post-diapause. ChIP-seq experimments are all performed in duplicates. Hi-C have been done at several embryonic time points: 2h, 24h and 48h after dipause release and on adults heads. RNA-seq has been perfomred at 24h after diapause release
 
Contributor(s) Muller H, Drinnenberg I, Gil J Jr
Citation(s) 37745315
Submission date Mar 28, 2023
Last update date Jan 09, 2024
Contact name Héloïse Muller
E-mail(s) [email protected]
Organization name Institut Curie
Lab UMR3664
Street address 26 rue d'Ulm
City Paris
ZIP/Postal code 75005
Country France
 
Platforms (1)
GPL29210 Illumina NovaSeq 6000 (Bombyx mori)
Samples (20)
GSM7120253 D506-D492C31_ChIP_p50_D2-24h_Bmori-v4_H3K4me3_rep1_IP
GSM7120254 D506-D492C27_ChIP_p50_D2-24h_Bmori-v4_H3K4me3_rep1_H3K36me3_rep2_H3K27me3_rep2_Input
GSM7120255 D1221C18_ChIP_p50_D2-24h_Bmori-v4_H3K4me3_rep2_IP
This SubSeries is part of SuperSeries:
GSE228401 Unique territorial and sub-chromosomal organization revealed in the holocentric moth Bombyx mori
Relations
BioProject PRJNA949631

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
GSE228397_RAW.tar 1.0 Gb (http)(custom) TAR (of BIGWIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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