Tandem Repeat-Based Probes Support the Loop Model of Pericentromere Packing

Area of Science:

• Genomics
• Molecular Biology
• Cytogenetics

Background:

• Constitutive heterochromatin, rich in tandem repeats (TR), forms crucial centromeric and pericentromeric regions.
• The complex organization of TR poses challenges for genome assembly, annotation, and mapping.
• Unannotated TR arrays remain in genomic databases, highlighting knowledge gaps.

Purpose of the Study:

• To investigate the organization and structure of tandem repeats within constitutive heterochromatin.
• To explore the spatial arrangement of pericentromeric TR in spermatogenic cells of the pig and Chinese hamster.
• To provide evidence supporting or refuting existing models of centromeric region structure.

Main Methods:

• Bioinformatic identification of tandem repeat (TR) sequences in pig (Sus scrofa) and Chinese hamster (Cricetulus griseus) genomes.
• Design and application of specific TR probes for fluorescence in situ hybridization (FISH).
• Microscopic analysis of probe signals in spermatogenic cells and meiotic chromosomes.

Main Results:

• TR probes in pig spermatogenic cells, particularly primary spermatocytes, often produced ring-shaped signals in DAPI-weak regions.
• FISH analysis using a probe for chromosome 5 in Chinese hamster revealed ring-shaped signals at the pachytene stage.
• Consistent ring-like signals were observed in both species' spermatogenic cells when using pericentromeric TR probes.

Conclusions:

• The observed ring-shaped signals support a loop model for the organization of centromeric regions.
• The estimated size of these proposed loops is approximately 50 kilobases (kb).
• This study enhances understanding of heterochromatin structure and its implications for genome organization.