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Transcription and loop extrusion cooperatively shape the 3D genome of developing slime mold Dictyostelium discoideum [Hi-C]

ABSTRACT: Dictyostelium discoideum is a unicellular slime mold developing into a multicellular fruiting body upon starvation. Development is accompanied by large-scale shifts in gene expression program, but underlying rearrangements of chromatin structure remain unknown. Here, we report a unique Dictyostelium 3D genome organization represented by largely consecutive, non-hierarchical and weakly insulated loops of diverse morphology conserved at the onset of multicellular development. Loops are chromosomal neighborhoods facilitating transcription and frequently containing functionally-linked genes which coherently change expression level during development. Loop anchors are enriched with convergent gene pairs, putative enhancers and boundaries of synteny gene blocks that point at their role in genome function and evolution. Our data suggest that the loop profile arises from the interplay between transcription and cohesin-driven chromatin extrusion. In this confunction, a convergent gene pair serves as a “diode” effectively passing the extruder from upstream or downstream direction in dependence on transcription level of the paired genes.

ORGANISM(S): Dictyostelium discoideum

PROVIDER: GSE247396 | GEO | 2024/12/31

REPOSITORIES: GEO

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Transcription and loop extrusion cooperatively shape the 3D genome of developing slime mold Dictyostelium discoideum [RNA-seq]

Project description:Dictyostelium discoideum is a unicellular slime mold developing into a multicellular fruiting body upon starvation. Development is accompanied by large-scale shifts in gene expression program, but underlying rearrangements of chromatin structure remain unknown. Here, we report a unique Dictyostelium 3D genome organization represented by largely consecutive, non-hierarchical and weakly insulated loops of diverse morphology conserved at the onset of multicellular development. Loops are chromosomal neighborhoods facilitating transcription and frequently containing functionally-linked genes which coherently change expression level during development. Loop anchors are enriched with convergent gene pairs, putative enhancers and boundaries of synteny gene blocks that point at their role in genome function and evolution. Our data suggest that the loop profile arises from the interplay between transcription and cohesin-driven chromatin extrusion. In this confunction, a convergent gene pair serves as a “diode” effectively passing the extruder from upstream or downstream direction in dependence on transcription level of the paired genes.

2024-12-31 | GSE246367 | GEO

Convergent gene pairs restrict chromatin looping in Dictyostelium discoideum, acting as directional barriers for extrusion

Project description:Dictyostelium discoideum is a unicellular slime mold, developing into a multicellular fruiting body upon starvation. Development is accompanied by large-scale shifts in gene expression program, but underlying features of chromatin spatial organization remain unknown. Here, we report that the Dictyostelium 3D genome is organized into largely consecutive, non-hierarchical and weakly insulated loops positionally conserved at the onset of multicellular development. The transcription level within loops tends to be higher than in adjacent regions. Loops frequently contain functionally linked genes and genes which coherently change expression level during development. Genes at loop anchors are predominantly in the convergent orientation. Our data suggest that the loop profile may arise from the interplay between transcription and cohesin-driven chromatin extrusion. In particular, a convergent gene pair serves as a bidirectional extrusion barrier or a “diode” that controls passage of the cohesin extruder by relative transcription level of paired genes.

2024-12-31 | GSE247397 | GEO

Transcription and loop extrusion cooperatively shape the 3D genome of developing slime mold Dictyostelium discoideum [Hi-C]

Project description:Transcription and loop extrusion cooperatively shape the 3D genome of developing slime mold Dictyostelium discoideum [Hi-C]

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Transcription and loop extrusion cooperatively shape the 3D genome of developing slime mold Dictyostelium discoideum [RNA-seq]

Project description:Transcription and loop extrusion cooperatively shape the 3D genome of developing slime mold Dictyostelium discoideum [RNA-seq]

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