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Structural and functional analysis of four non-coding Y RNAs from Chinese hamster cells: identification, molecular dynamics simulations and DNA replication initiation assays

Overview of attention for article published in BMC Molecular and Cell Biology, January 2016
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Title
Structural and functional analysis of four non-coding Y RNAs from Chinese hamster cells: identification, molecular dynamics simulations and DNA replication initiation assays
Published in
BMC Molecular and Cell Biology, January 2016
DOI 10.1186/s12867-015-0053-5
Pubmed ID
Authors

Quirino Alves de Lima Neto, Francisco Ferreira Duarte Junior, Paulo Sérgio Alves Bueno, Flavio Augusto Vicente Seixas, Madzia Pauline Kowalski, Eyemen Kheir, Torsten Krude, Maria Aparecida Fernandez

Abstract

The genes coding for Y RNAs are evolutionarily conserved in vertebrates. These non-coding RNAs are essential for the initiation of chromosomal DNA replication in vertebrate cells. However thus far, no information is available about Y RNAs in Chinese hamster cells, which have already been used to detect replication origins and alternative DNA structures around these sites. Here, we report the gene sequences and predicted structural characteristics of the Chinese hamster Y RNAs, and analyze their ability to support the initiation of chromosomal DNA replication in vitro. We identified DNA sequences in the Chinese hamster genome of four Y RNAs (chY1, chY3, chY4 and chY5) with upstream promoter sequences, which are homologous to the four main types of vertebrate Y RNAs. The chY1, chY3 and chY5 genes were highly conserved with their vertebrate counterparts, whilst the chY4 gene showed a relatively high degree of diversification from the other vertebrate Y4 genes. Molecular dynamics simulations suggest that chY4 RNA is structurally stable despite its evolutionarily divergent predicted stem structure. Of the four Y RNA genes present in the hamster genome, we found that only the chY1 and chY3 RNA were strongly expressed in the Chinese hamster GMA32 cell line, while expression of the chY4 and chY5 RNA genes was five orders of magnitude lower, suggesting that they may in fact not be expressed. We synthesized all four chY RNAs and showed that any of these four could support the initiation of DNA replication in an established human cell-free system. These data therefore establish that non-coding chY RNAs are stable structures and can substitute for human Y RNAs in a reconstituted cell-free DNA replication initiation system. The pattern of Y RNA expression and functionality is consistent with Y RNAs of other rodents, including mouse and rat.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 24 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Germany 1 4%
Ireland 1 4%
Unknown 22 92%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 4 17%
Researcher 4 17%
Student > Master 4 17%
Professor 3 13%
Student > Doctoral Student 2 8%
Other 4 17%
Unknown 3 13%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 12 50%
Agricultural and Biological Sciences 5 21%
Engineering 2 8%
Unknown 5 21%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 06 January 2016.
All research outputs
#20,656,820
of 25,374,917 outputs
Outputs from BMC Molecular and Cell Biology
#935
of 1,233 outputs
Outputs of similar age
#295,154
of 400,006 outputs
Outputs of similar age from BMC Molecular and Cell Biology
#13
of 19 outputs
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