Topologically associating domains and the evolution of three‐dimensional genome architecture in rice DOI Creative Commons
Amina Kurbidaeva, Sonal Gupta, Maricris Zaidem

и другие.

The Plant Journal, Год журнала: 2025, Номер 122(4)

Опубликована: Май 1, 2025

SUMMARY We examined the nature and evolution of three‐dimensional (3D) genome conformation, including topologically associating domains (TADs), in five genomes within genus Oryza . These included three varieties from subspecies domesticated Asian rice O. sativa as well their closely related wild relatives rufipogon meridionalis used high‐resolution chromosome conformation capture technique Micro‐C, which we modified for use rice. Our analysis TADs shows that TAD boundaries have high transcriptional activity, low methylation levels, transposable element (TE) content, increased gene density. also find a significant correlation expression levels genes TADs, suggesting they do function genomic with shared regulatory features. findings indicate animal plant may share more commonalities than were initially thought, evidenced by similar genetic epigenetic signatures associated boundaries. To examine 3D divergence, employed computer vision‐based algorithm comparison chromatin contact maps complemented this assessing evolutionary conservation individual conclude overall organization is conserved rice, structural divergence correlates distance between genomes. note are not conserved, even at short timescales.

Язык: Английский

Topologically associating domains and the evolution of three‐dimensional genome architecture in rice DOI Creative Commons
Amina Kurbidaeva, Sonal Gupta, Maricris Zaidem

и другие.

The Plant Journal, Год журнала: 2025, Номер 122(4)

Опубликована: Май 1, 2025

SUMMARY We examined the nature and evolution of three‐dimensional (3D) genome conformation, including topologically associating domains (TADs), in five genomes within genus Oryza . These included three varieties from subspecies domesticated Asian rice O. sativa as well their closely related wild relatives rufipogon meridionalis used high‐resolution chromosome conformation capture technique Micro‐C, which we modified for use rice. Our analysis TADs shows that TAD boundaries have high transcriptional activity, low methylation levels, transposable element (TE) content, increased gene density. also find a significant correlation expression levels genes TADs, suggesting they do function genomic with shared regulatory features. findings indicate animal plant may share more commonalities than were initially thought, evidenced by similar genetic epigenetic signatures associated boundaries. To examine 3D divergence, employed computer vision‐based algorithm comparison chromatin contact maps complemented this assessing evolutionary conservation individual conclude overall organization is conserved rice, structural divergence correlates distance between genomes. note are not conserved, even at short timescales.

Язык: Английский

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