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Identification und characterization of a new class of highly conserved non-coding sequences in plants


Kritsas, Konstantinos. Identification und characterization of a new class of highly conserved non-coding sequences in plants. 2014, University of Zurich, Faculty of Science.

Abstract

Ultraconserved elements (UCEs), DNA sequences, which are 100% identical between mammalian genomes are enigmatic features whose function is not well understood. UCEs are under strong purifying selection and a number of biological functions have been proposed to explain their robust conservation, such as gene regulation, RNA processing, and maintaining genome integrity. However, all these functions are evolutionary tolerant to DNA sequence divergence without affecting their sequence specific interactions.
Here, we report the identification and characterization of highly conserved noncoding sequences in plant genomes. We have identified them after whole genome comparison studies between Arabidopsis thaliana (mouse-ear cress) and Vitis vinifera (grapevine). Arabidopsis and Vitis have diverged from their common ancestor ~115 Mya, allowing significant changes at the DNA sequence level to occur. We found 36 elements, which are >55 bp long and share at least 85% sequence identity. Interestingly, these elements exhibit properties similar to the mammalian UCEs, such that we named them UCE-like elements (ULEs). In addition to sequence constraints our data indicate that ULEs are functional elements. Further analysis showed that ULEs are under strong purifying selection. All of them have a sharp drop of A-T content just at their borders, and they are enriched next to genes involved in development. Intriguingly, the latter show preferential expression in undifferentiated cells. By comparing the genomes of Brachypodium distachyon (purple false brome) and Oryza sativa (rice), species that diverged ~50 Mya, we identified a different set of ULEs with similar properties in monocotyledons.
Surprisingly, as their animal counterparts, ULEs are depleted from segmental duplications. This observation led to the suggestion that ULEs or the regions that contain them are dosage sensitive. Our hypothesis about the function of ULEs is that they serve as agents of chromosome copy counting. According to this hypothesis, the two homologous ULEs may compare their sequence perhaps through chromosome pairing to ensure the exact number of chromosomes. We employed a cytogenetic approach, fluorescence in situ hybridization (FISH), and found evidence that ULE regions exhibit increased pairing frequency in somatic cells relative to regions that are depleted from ULEs. We further investigated the potential dosage-sensitive nature of ULEs. Perturbation of one ULE resulted in distorted transmission efficiency of the corresponding allele in the offspring. Conversely, transmission efficiency of the same mutant was not distorted in an aneuploid context. Moreover, addition of four extra copies of ULEs did not yield any obvious phenotypes. Further investigation remains necessary to confirm a general role of ULEs in surveying genome dosage and integrity.

Abstract

Ultraconserved elements (UCEs), DNA sequences, which are 100% identical between mammalian genomes are enigmatic features whose function is not well understood. UCEs are under strong purifying selection and a number of biological functions have been proposed to explain their robust conservation, such as gene regulation, RNA processing, and maintaining genome integrity. However, all these functions are evolutionary tolerant to DNA sequence divergence without affecting their sequence specific interactions.
Here, we report the identification and characterization of highly conserved noncoding sequences in plant genomes. We have identified them after whole genome comparison studies between Arabidopsis thaliana (mouse-ear cress) and Vitis vinifera (grapevine). Arabidopsis and Vitis have diverged from their common ancestor ~115 Mya, allowing significant changes at the DNA sequence level to occur. We found 36 elements, which are >55 bp long and share at least 85% sequence identity. Interestingly, these elements exhibit properties similar to the mammalian UCEs, such that we named them UCE-like elements (ULEs). In addition to sequence constraints our data indicate that ULEs are functional elements. Further analysis showed that ULEs are under strong purifying selection. All of them have a sharp drop of A-T content just at their borders, and they are enriched next to genes involved in development. Intriguingly, the latter show preferential expression in undifferentiated cells. By comparing the genomes of Brachypodium distachyon (purple false brome) and Oryza sativa (rice), species that diverged ~50 Mya, we identified a different set of ULEs with similar properties in monocotyledons.
Surprisingly, as their animal counterparts, ULEs are depleted from segmental duplications. This observation led to the suggestion that ULEs or the regions that contain them are dosage sensitive. Our hypothesis about the function of ULEs is that they serve as agents of chromosome copy counting. According to this hypothesis, the two homologous ULEs may compare their sequence perhaps through chromosome pairing to ensure the exact number of chromosomes. We employed a cytogenetic approach, fluorescence in situ hybridization (FISH), and found evidence that ULE regions exhibit increased pairing frequency in somatic cells relative to regions that are depleted from ULEs. We further investigated the potential dosage-sensitive nature of ULEs. Perturbation of one ULE resulted in distorted transmission efficiency of the corresponding allele in the offspring. Conversely, transmission efficiency of the same mutant was not distorted in an aneuploid context. Moreover, addition of four extra copies of ULEs did not yield any obvious phenotypes. Further investigation remains necessary to confirm a general role of ULEs in surveying genome dosage and integrity.

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Item Type:Dissertation (monographical)
Referees:Grossniklaus Ueli
Communities & Collections:UZH Dissertations
Dewey Decimal Classification:Unspecified
Language:English
Place of Publication:Zürich
Date:2014
Deposited On:04 Apr 2019 06:58
Last Modified:07 Apr 2020 07:17
Number of Pages:168
OA Status:Green
Related URLs:https://www.recherche-portal.ch/primo-explore/fulldisplay?docid=ebi01_prod010407823&context=L&vid=ZAD&search_scope=default_scope&tab=default_tab&lang=de_DE (Library Catalogue)

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