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Unique territorial and sub-chromosomal organization revealed in the holocentric moth Bombyx mori

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Bombyx mori

PROVIDER: GSE228401 | GEO | 2023/09/17

REPOSITORIES: GEO

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Unique territorial and sub-chromosomal organization revealed in the holocentric moth Bombyx mori [RNA-seq]

Project description: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.

2023-09-17 | GSE228398 | GEO

Unique territorial and sub-chromosomal organization revealed in the holocentric moth Bombyx mori [ChIP-seq]

2023-09-17 | GSE228397 | GEO

Unique territorial and sub-chromosomal organization revealed in the holocentric moth Bombyx mori [Hi-C head]

2023-09-17 | GSE228399 | GEO

Unique territorial and sub-chromosomal organization revealed in the holocentric moth Bombyx mori [Hi-C embryo]

2023-09-17 | GSE228400 | GEO

Unique territorial and sub-chromosomal organization revealed in the holocentric moth Bombyx mori

Project description:Unique territorial and sub-chromosomal organization revealed in the holocentric moth Bombyx mori

| PRJNA949627 | ENA

Unique territorial and sub-chromosomal organization revealed in the holocentric moth Bombyx mori [RNA-seq]

Project description:Unique territorial and sub-chromosomal organization revealed in the holocentric moth Bombyx mori [RNA-seq]

| PRJNA949630 | ENA

Unique territorial and sub-chromosomal organization revealed in the holocentric moth Bombyx mori [ChIP-seq]

Project description:Unique territorial and sub-chromosomal organization revealed in the holocentric moth Bombyx mori [ChIP-seq]

| PRJNA949631 | ENA

Unique territorial and sub-chromosomal organization revealed in the holocentric moth Bombyx mori [Hi-C embryo]

Project description:Unique territorial and sub-chromosomal organization revealed in the holocentric moth Bombyx mori [Hi-C embryo]

| PRJNA949632 | ENA

Unique territorial and sub-chromosomal organization revealed in the holocentric moth Bombyx mori [Hi-C head]

Project description:Unique territorial and sub-chromosomal organization revealed in the holocentric moth Bombyx mori [Hi-C head]

| PRJNA949633 | ENA

Fine organization of Bombyx mori fibroin heavy chain gene.

Project description:The complete sequence of the Bombyx mori fibroin gene has been determined by means of combining a shotgun sequencing strategy with physical map-based sequencing procedures. It consists of two exons (67 and 15 750 bp, respectively) and one intron (971 bp). The fibroin coding sequence presents a spectacular organization, with a highly repetitive and G-rich (approximately 45%) core flanked by non-repetitive 5' and 3' ends. This repetitive core is composed of alternate arrays of 12 repetitive and 11 amorphous domains. The sequences of the amorphous domains are evolutionarily conserved and the repetitive domains differ from each other in length by a variety of tandem repeats of subdomains of approximately 208 bp which are reminiscent of the repetitive nucleosome organization. A typical composition of a subdomain is a cluster of repetitive units, Ua, followed by a cluster of units, Ub, (with a Ua:Ub ratio of 2:1) flanked by conserved boundary elements at the 3' end. Moreover some repeats are also perfectly conserved at the peptide level indicating that the evolutionary pressure is not identical along the sequence. A tentative model for the constitution and evolution of this unusual gene is discussed.

| S-EPMC102737 | biostudies-literature

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