Telomeric and Sub-Telomeric Structure and Implications in Fungal Opportunistic Pathogens

Diotti, Raffaella; Esposito, Michelle; Shen, Chengchao

doi:10.3390/microorganisms9071405

Cited by 9 publications

(8 citation statements)

References 98 publications

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“…In addition, the heterochromatin that forms the ST is characterized by low nucleosome occupancy and the presence of repressive histone marks such as H4K20me3, H3K9me2/3, and H3K27me3. Those marks, in turn, recruit heterochromatin factors such as HP1 and deacetylases such as Sir2, which target H3 and H4 [ 6 , 7 , 8 , 9 ].…”

Section: Introductionmentioning

confidence: 99%

Architecture, Chromatin and Gene Organization of Toxoplasma gondii Subtelomeres

et al. 2022

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Subtelomeres (ST) are chromosome regions that separate telomeres from euchromatin and play relevant roles in various biological processes of the cell. While their functions are conserved, ST structure and genetic compositions are unique to each species. This study aims to identify and characterize the subtelomeric regions of the 13 Toxoplasma gondii chromosomes of the Me49 strain. Here, STs were defined at chromosome ends based on poor gene density. The length of STs ranges from 8.1 to 232.4 kbp, with a gene density of 0.049 genes/kbp, lower than the Me49 genome (0.15 kbp). Chromatin organization showed that H3K9me3, H2A.X, and H3.3 are highly enriched near telomeres and the 5′ end of silenced genes, decaying in intensity towards euchromatin. H3K4me3 and H2A.Z/H2B.Z are shown to be enriched in the 5′ end of the ST genes. Satellite DNA was detected in almost all STs, mainly the sat350 family and a novel satellite named sat240. Beyond the STs, only short dispersed fragments of sat240 and sat350 were found. Within STs, there were 12 functional annotated genes, 59 with unknown functions (Hypothetical proteins), 15 from multigene FamB, and 13 from multigene family FamC. Some genes presented low interstrain synteny associated with the presence of satellite DNA. Orthologues of FamB and FamC were also detected in Neospora caninum and Hammondia hammondi. A re-analysis of previous transcriptomic data indicated that ST gene expression is strongly linked to the adaptation to different situations such as extracellular passage (evolve and resequencing study) and changes in metabolism (lack of acetyl-CoA cofactor). In conclusion, the ST region of the T. gondii chromosomes was defined, the STs genes were determined, and it was possible to associate them with high interstrain plasticity and a role in the adaptability of T. gondii to environmental changes.

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Section: Introductionmentioning

confidence: 99%

Architecture, Chromatin and Gene Organization of Toxoplasma gondii Subtelomeres

et al. 2022

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“…The repeated elements within eukaryotes reflect the activities of both recombination and transposition. In A. flavus , there is evidence for recombination and genome rearrangement within subtelomeric regions close to the 120 bp of TTAGGGTCAACA telomere repeats [49, 50]. However, little is known about the dispersion of transposable and other repeated elements that contribute to genomic stability through the evolution and divergence of this species.…”

Section: Resultsmentioning

confidence: 99%

Investigating the origin of subtelomeric and centromeric AT-rich elements inAspergillus flavus

Lustig

2022

Preprint

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An in silico study of Aspergillus flavus genome stability uncovered significant variations in both coding and non-coding regions. The non-coding insertions uniformly consisted of AT-rich sequences that are evolutionarily maintained, albeit distributed at widely different sites in an array of A. flavus strains. A survey of ≥ 2kb AT-rich elements (AT ≥ 70%; ATEs) uncovered three classes. The first class is composed of homologous insertions at ectopic, non-allelic sites that contain homology to transposable elements (TEs). Strains differed significantly in frequency, position, and TE type, but displayed a common enrichment in subtelomeric regions. The TEs were heavily mutated, with patterns consistent with the ancestral activity of repeat-induced point mutations (RIP). The second class consists of ~100 kb regions at each centromere. Centromeric ATEs and TE clusters within these centromeres display a high level of sequence identity between strains. The third class consists of a conserved set of novel subtelomeric ATE repeats which lack discernible TEs and, unlike TEs, display a constant polarity relative to the telomere. Members of one of these classes are derivatives of a progenitor ATE that is predicted to have undergone extensive homologous recombination during evolution. These studies suggest that transposition and RIP are forces in the evolution of subtelomeric and centromeric structure and function.

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“…This allows faster and better adaptive responses to the changing environment. Additionally, it contributes to antigenic variation and virulence in some pathogenic yeasts and parasites [ 28 , 87–89 ]. Therefore, understanding regulation of telomeric and sub-telomeric transcription has implications beyond yeast.…”

Section: Discussionmentioning

confidence: 99%

Transcription termination complex, Rtt103-Rai1-Rat1, regulates sub-telomeric transcripts in Saccharomyces cerevisiae

Ramalingam

Mishra

2023

RNA Biology

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Telomeres are terminal structures that define the ends of linear chromosomes. They harbour specialized ribonucleoprotein complexes which play a major role in genome integrity by preventing unscheduled DNA damage repair events. Genes located adjacent to telomere repeat sequences are repressed by a phenomenon called telomere position effect (TPE) via epigenetic silencing. RNA surveillance pathways post-transcriptionally regulate any leaky transcripts arising from the telomeres. Recently, multiple non-coding RNA species originate from telomere ends, namely, TERRA (telomeric repeat‐containing RNA), ARRET, sub-telomeric XUTs and sub-telomeric CUTs have been identified. In this study, we report a role for the transcription termination complex (Rtt103-Rai1-Rat1) in regulating the abundance of the sub-telomeric transcripts in a transcription-dependent manner. We show that the Rtt103 mutants have elevated levels of TERRA and other sub-telomeric transcripts that are usually silenced. Our study suggests that Rtt103 potentially recruits the exonuclease, Rat1 in a RNA polymerase II dependent manner to degrade these transcripts and regulate their levels in the cell.

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Telomeric and Sub-Telomeric Structure and Implications in Fungal Opportunistic Pathogens

Cited by 9 publications

References 98 publications

Architecture, Chromatin and Gene Organization of Toxoplasma gondii Subtelomeres

Architecture, Chromatin and Gene Organization of Toxoplasma gondii Subtelomeres

Investigating the origin of subtelomeric and centromeric AT-rich elements inAspergillus flavus

Transcription termination complex, Rtt103-Rai1-Rat1, regulates sub-telomeric transcripts in Saccharomyces cerevisiae

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