Setting boundaries for genome-wide heterochromatic DNA deletions through flanking inverted repeats in Tetrahymena thermophile
Autor: | Huai-Kuang Tsai, Meng-Chao Yao, Ju-Lan Chao, Chih-Yi Gabriela Lin, Douglas L. Chalker |
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Rok vydání: | 2019 |
Předmět: |
Euchromatin
Heterochromatin Inverted repeat Amino Acid Motifs Protozoan Proteins Biology Genome Tetrahymena thermophila 03 medical and health sciences chemistry.chemical_compound 0302 clinical medicine Protein Domains Genetics 030304 developmental biology Cell Nucleus Gene Rearrangement 0303 health sciences Tetrahymena Genomics Gene rearrangement DNA Protozoan biology.organism_classification genomic DNA Gene Expression Regulation chemistry Corrigendum Genome Protozoan Gene Deletion 030217 neurology & neurosurgery DNA |
Zdroj: | Nucleic Acids Research |
ISSN: | 1362-4962 0305-1048 |
Popis: | Eukaryotic cells pack their genomic DNA into euchromatin and heterochromatin. Boundaries between these domains have been shown to be set by boundary elements. In Tetrahymena, heterochromatin domains are targeted for deletion from the somatic nuclei through a sophisticated programmed DNA rearrangement mechanism, resulting in the elimination of 34% of the germline genome in ∼10,000 dispersed segments. Here we showed that most of these deletions occur consistently with very limited variations in their boundaries among inbred lines. We identified several potential flanking regulatory sequences, each associated with a subset of deletions, using a genome-wide motif finding approach. These flanking sequences are inverted repeats with the copies located at nearly identical distances from the opposite ends of the deleted regions, suggesting potential roles in boundary determination. By removing and testing two such inverted repeats in vivo, we found that the ability for boundary maintenance of the associated deletion were lost. Furthermore, we analyzed the deletion boundaries in mutants of a known boundary-determining protein, Lia3p and found that the subset of deletions that are affected by LIA3 knockout contained common features of flanking regulatory sequences. This study suggests a common mechanism for setting deletion boundaries by flanking inverted repeats in Tetrahymena thermophila. |
Databáze: | OpenAIRE |
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