DNA-methylation dependent regulation of embryo-specific 5S ribosomal DNA cluster transcription in adult tissues of sea urchin Paracentrotus lividus

Bellavia, Daniele; Dimarco, Eufrosina; Naselli, Flores; Caradonna, Fabio

doi:10.1016/j.ygeno.2013.08.001

Cited by 8 publications

(3 citation statements)

References 45 publications

(15 reference statements)

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“…This is in line with the findings in Xenopus and sea urchins, where 5S rRNA synthesis can be detected in the early blastula stage (Miller 1974). The regulation of the transcription of the 5S rRNA types in zebrafish is likely regulated epigenetically or by chromatin arrangement, as is shown for Xenopus (Bouvet et al 1994) and other organisms (Mathieu et al 2003;Douet and Tourmente 2007;Bellavia et al 2013). For instance, the long arm of chromosome 4 in zebrafish, where the maternal-type 5S rDNA clusters are located, has very few protein-coding genes and high heterochromatin content (Howe et al 2013), which could be a way to suppress the maternal-type 5S rRNA expression during embryogenesis and in adult tissues.…”

Section: Developmental-stage-specific Expression Of 5s Rrna Variantssupporting

confidence: 89%

Linking maternal and somatic 5S rRNA types with different sequence-specific non-LTR retrotransposons

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et al. 2016

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5S rRNA is a ribosomal core component, transcribed from many gene copies organized in genomic repeats. Some eukaryotic species have two 5S rRNA types defined by their predominant expression in oogenesis or adult tissue. Our next-generation sequencing study on zebrafish egg, embryo, and adult tissue identified maternal-type 5S rRNA that is exclusively accumulated during oogenesis, replaced throughout the embryogenesis by a somatic-type, and thus virtually absent in adult somatic tissue. The maternal-type 5S rDNA contains several thousands of gene copies on chromosome 4 in tandem repeats with small intergenic regions, whereas the somatic-type is present in only 12 gene copies on chromosome 18 with large intergenic regions. The nine-nucleotide variation between the two 5S rRNA types likely affects TFIII binding and riboprotein L5 binding, probably leading to storage of maternal-type rRNA. Remarkably, these sequence differences are located exactly at the sequence-specific target site for genome integration by the 5S rRNA-specific Mutsu retrotransposon family. Thus, we could define maternal-and somatic-type MutsuDr subfamilies. Furthermore, we identified four additional maternal-type and two new somatic-type MutsuDr subfamilies, each with their own target sequence. This target-site specificity, frequently intact maternal-type retrotransposon elements, plus specific presence of Mutsu retrotransposon RNA and piRNA in egg and adult tissue, suggest an involvement of retrotransposons in achieving the differential copy number of the two types of 5S rDNA loci.

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Section: Developmental-stage-specific Expression Of 5s Rrna Variantssupporting

confidence: 89%

Linking maternal and somatic 5S rRNA types with different sequence-specific non-LTR retrotransposons

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et al. 2016

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“…On the other hand, expression of the oocyte-type 5S rRNA is restricted to oogenesis and early developmental stages (Peterson et al, 1980). Expression and methylation-dependent regulation of embryonic and somatic types of 5S rRNA was also recently demonstrated in the sea urchin Paracentrotus lividus (Dimarco et al 2012;Bellavia et al 2013).…”

Section: Introductionmentioning

confidence: 95%

Assessing 5S ribosomal RNA heterogeneity in Arabidopsis thaliana using short RNA next generation sequencing data

Szymański¹,

Karłowski²

2017

Acta Biochim Pol

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In eukaryotes, ribosomal 5S rRNAs are products of multigene families organized within clusters of tandemly repeated units. Accumulation of genomic data obtained from a variety of organisms demonstrated that the potential 5S rRNA coding sequences show a large number of variants, often incompatible with folding into a correct secondary structure. Here, we present results of an analysis of a large set of short RNA sequences generated by the next generation sequencing techniques, to address the problem of heterogeneity of the 5S rRNA transcripts in Arabidopsis and identification of potentially functional rRNA-derived fragments.

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“…1) of the CYP2E1 gene. In a previous paper we made a distinction among three kinds of cytosine, each potentially methylation site: the cytosine "CpG", "CHH" or "CHG", where H are all nucleotides except G (Bellavia et al, 2013). In the region described by Hu et al (1995), containing the potential methylation sites of CYP2E1 gene not canonically attributable to CpG island, there were two CpG sites present, specifically detected by isoschizomers HpaII and MspI (Biolabs, Europe), since the other sites are CHH or CHG. We focused our investigation on these two CpG sites whose methylation could be revealed by MSRE-PCR.…”

Section: Dna Methylation Analysismentioning

confidence: 99%

Role and importance of polymorphisms with respect to DNA methylation for the expression of CYP2E1 enzyme

Naselli

Catanzaro

Bellavia

et al. 2014

Gene

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This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research and education use, including for instruction at the authors institution and sharing with colleagues.Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. Different individuals possess slightly different genetic information and show genetically-determined differences in several enzyme activities due to genetic variability. Following an integrated approach, we studied the polymorphisms and methylation of sites contained in the 5′ flanking region of the metabolizing enzyme CYP2E1 in correlation to its expression in both tumor and non-neoplastic liver cell lines, since to date little is known about the influence of these (epi)genetic elements in basal conditions and under induction by the specific inductor and a demethylating agent. In treated cells, reduced DNA methylation, assessed both at genomic and gene level, was not consistently associated with the increase of enzyme expression. Interestingly, the Rsa/Pst haplotype differentially influenced CYP2E1 enzyme expression. In addition, regarding the Variable Number of Tandem Repeats polymorphism, cells with A4/A4 genotype showed a greater expression inhibition (ranging from 20% to 30%) compared with others carrying the A2/A2 one, while those cells bringing A2/A3 genotype showed an increase of expression (of 25%, about). Finally, we demonstrated for the first time that the A2 and A3 CYP2E1 alleles play a more important role in the expression of the enzyme, compared with other (epi)genetic factors, since they are binding sites for trans-acting proteins.

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DNA-methylation dependent regulation of embryo-specific 5S ribosomal DNA cluster transcription in adult tissues of sea urchin Paracentrotus lividus

Cited by 8 publications

References 45 publications

Linking maternal and somatic 5S rRNA types with different sequence-specific non-LTR retrotransposons

Linking maternal and somatic 5S rRNA types with different sequence-specific non-LTR retrotransposons

Assessing 5S ribosomal RNA heterogeneity in Arabidopsis thaliana using short RNA next generation sequencing data

Role and importance of polymorphisms with respect to DNA methylation for the expression of CYP2E1 enzyme

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