Annalisa Varriale - Academia.edu (original) (raw)

Uploads

Papers by Annalisa Varriale

pagina SOMMARIO i ABSTRACT ii 1-INTRODUZIONE 1 1.1-I pesci 7 1.2-I rettili 8 1.6-Ambiente e termo... more pagina SOMMARIO i ABSTRACT ii 1-INTRODUZIONE 1 1.1-I pesci 7 1.2-I rettili 8 1.6-Ambiente e termostabilità dell’RNA ribosomale (rRNA) 18S 9 2-MATERIALI E METODI 12 2.1 DNA e campioni di tessuto biologico 12 2.2 Estrazione del DNA genomico e analisi per ultracentrifugazione 12 2.3 Idrolisi enzimatica del DNA 12 2.4 Analisi con RP-HPLC 13 2.5 Analisi dei geni ortologhi 14 2.6 Analisi delle sequenze di RNA ribosomale 18S in vertebrati 15 3-RISULTATI 16 3.1.1 Analisi del livello di metilazione in pesci 16 3.1.2 Analisi del livello di metilazione nei rettili 22 II 3.1.3 Analisi del livello di metilazione nei mammiferi 25 3.2 Correlazione del livello di metilazione con la lunghezza del genoma 28 3.3 Livello di CpG in geni ortologhi 29 3.4 Correlazione del livello di metilazione con tassonomia e filogenia 32 3.5 Correlazione tra livello di metilazione e temperatura corporea 32 3.6 Correlazione tra livello di GC derivante dall’analisi dei nucleosidi e dalla centrifugazione in gradiente di d...

Transgenerational Epigenetics, 2019

As currently defined, epigenetics concerns metastable, potentially reversible, and heritable chan... more As currently defined, epigenetics concerns metastable, potentially reversible, and heritable changes that occur in the epigenome without genetic mutations but influence rate and mode of gene expression. The field of epigenetics has grown enormously in the past years and, in particular, the possible impact of the environment on epigenetic regulation and of the latter on ecology has attracted considerable interest. In fact, environmental stimuli can induce changes in epigenetic marks, which in turn promote mutations in DNA sequence eventually followed by modifications in gene expression. In addition, because epigenetic changes can be inherited mitotically within different cell types and also meiotically across generations (transgenerational inheritance), they have been proposed to have a role in shaping the phenotype of individuals and populations with evolutionary consequences. It is then clear how epigenetics can be considered a link between environmental stimuli and gene expression...

RNA Technologies, 2017

Cytosine DNA methylation is a key, heritable, epigenetic modification widespread among major euka... more Cytosine DNA methylation is a key, heritable, epigenetic modification widespread among major eukaryotic groups and involved in main cellular processes such as integrity of DNA structure, control of transposable elements, and regulation of gene expression. In plants, its level can be influenced and modified by a number of biotic and abiotic stresses, and its variations are prone to increase, in turn, the rate of genetic mutations in DNA regions. For this reason, these mechanisms are proposed to improve the adaptability of DNA in complex environments. DNA methylation and epigenetic marks do have a fundamental role also in fine-tuning the pattern of expressed genes, during embryogenesis and seed development, and in the heterosis process, that is, the amelioration following the crosses between individuals belonging to different variants or species.

International Journal of Evolutionary Biology, 2014

DNA methylation is a key epigenetic modification in the vertebrate genomes known to be involved i... more DNA methylation is a key epigenetic modification in the vertebrate genomes known to be involved in biological processes such as regulation of gene expression, DNA structure and control of transposable elements. Despite increasing knowledge about DNA methylation, we still lack a complete understanding of its specific functions and correlation with environment and gene expression in diverse organisms. To understand how global DNA methylation levels changed under environmental influence during vertebrate evolution, we analyzed its distribution pattern along the whole genome in mammals, reptiles and fishes showing that it is correlated with temperature, independently on phylogenetic inheritance. Other studies in mammals and plants have evidenced that environmental stimuli can promote epigenetic changes that, in turn, might generate localized changes in DNA sequence resulting in phenotypic effects. All these observations suggest that environment can affect the epigenome of vertebrates by...

Exploratory Research and Hypothesis in Medicine, 2018

Background and objectives: During sperm maturation, chromatin undergoes an extensive compaction t... more Background and objectives: During sperm maturation, chromatin undergoes an extensive compaction through
the progressive replacement of histones with basic, positively-charged proteins called protamines. Interestingly,
in human and other vertebrates, 5–15% of the paternal genome retains a somatic-like structure. It has been suggested
that preserved nucleosomes have a role in promoting transcription after fertilization, however their localization
and function is still a matter of debate. The aim of the present work was to understand if the localization of
histones in human sperm DNA is affected by genome composition, a feature linked to several biological functions.
In order to do that, we mapped histone-enriched sequences along isochores, which are large chromosomal territories
characterized by fairly homogeneous guanine and cytosine (GC) composition.
Methods: We retrieved publicly available human sequences found to be histone-enriched in sperm chromatin
and localized them along isochores by using their respective coordinates.
Results: We found that the majority of genes and sequences associated with mononucleosomes, the activating
chromatin mark H3K4me3 and the repressive mark H3K27me3 reside in the GC-poor isochores. Genes harboring
the activating mark H3K4me2, instead, are preferentially located in the GC-rich isochores.
Conclusions: For genes carrying histones with specific marks, we speculate that developmental and tissue-specific
genes (carrying the H3K27me3 mark) might take advantage by residing in GC-poor isochores because in these
regions they can be shut off immediately after the end of their transcription more easily than in GC-rich isochores.
On the contrary, housekeeping genes (marked with H3K4me2) would not need this kind of regulation and reside
in GC-rich isochores. For other genes and sequences, further analyses are required in order to clarify the role of
GC composition in histone retention in sperm chromatin. In conclusion, although the complete scenario of sperm
chromatin has not been elucidated yet, correlations seem to exist between chromatin modification patterns,
isochore structure and gene expression timing in embryo development.

Molecular Biology, 2004

Synaptonemal complex (SC) isolated from spermatocyte nuclei after their exhaustive hydrolysis by ... more Synaptonemal complex (SC) isolated from spermatocyte nuclei after their exhaustive hydrolysis by DNase II contains DNA sequences tightly associated with it (SCAR DNA). Here, the compositional properties of a cloned family of golden hamster SCAR DNA were studied. For this purpose, 27 SCAR DNA clones were hybridized with compositionally fractionated golden hamster genomic DNA. The sequences of the SCAR DNA family were mainly localized in the GC-poor isochore families L1 and L2, which accounted for 63% of hybridization signals. The remaining 37% of signals pertained to the GC-rich isochore families H1 and H2. Thus, SCAR DNA proved to be distributed throughout the genome, irrespective of differences in density and sequence type between isochore families. Moreover, the SCAR DNA sequences containing the regions of homology with LINE/SINE repeats were found in all the isochore families. The compositional localization of SCAR DNA is in agreement with the hypothesis that the SC and SCAR DNA participate in chromatin reorganization during meiosis prophase I, which should result in the attachment of chromatin loops to the lateral elements of SC throughout its length.

pagina SOMMARIO i ABSTRACT ii 1-INTRODUZIONE 1 1.1-I pesci 7 1.2-I rettili 8 1.6-Ambiente e termo... more pagina SOMMARIO i ABSTRACT ii 1-INTRODUZIONE 1 1.1-I pesci 7 1.2-I rettili 8 1.6-Ambiente e termostabilità dell’RNA ribosomale (rRNA) 18S 9 2-MATERIALI E METODI 12 2.1 DNA e campioni di tessuto biologico 12 2.2 Estrazione del DNA genomico e analisi per ultracentrifugazione 12 2.3 Idrolisi enzimatica del DNA 12 2.4 Analisi con RP-HPLC 13 2.5 Analisi dei geni ortologhi 14 2.6 Analisi delle sequenze di RNA ribosomale 18S in vertebrati 15 3-RISULTATI 16 3.1.1 Analisi del livello di metilazione in pesci 16 3.1.2 Analisi del livello di metilazione nei rettili 22 II 3.1.3 Analisi del livello di metilazione nei mammiferi 25 3.2 Correlazione del livello di metilazione con la lunghezza del genoma 28 3.3 Livello di CpG in geni ortologhi 29 3.4 Correlazione del livello di metilazione con tassonomia e filogenia 32 3.5 Correlazione tra livello di metilazione e temperatura corporea 32 3.6 Correlazione tra livello di GC derivante dall’analisi dei nucleosidi e dalla centrifugazione in gradiente di d...

Transgenerational Epigenetics, 2019

As currently defined, epigenetics concerns metastable, potentially reversible, and heritable chan... more As currently defined, epigenetics concerns metastable, potentially reversible, and heritable changes that occur in the epigenome without genetic mutations but influence rate and mode of gene expression. The field of epigenetics has grown enormously in the past years and, in particular, the possible impact of the environment on epigenetic regulation and of the latter on ecology has attracted considerable interest. In fact, environmental stimuli can induce changes in epigenetic marks, which in turn promote mutations in DNA sequence eventually followed by modifications in gene expression. In addition, because epigenetic changes can be inherited mitotically within different cell types and also meiotically across generations (transgenerational inheritance), they have been proposed to have a role in shaping the phenotype of individuals and populations with evolutionary consequences. It is then clear how epigenetics can be considered a link between environmental stimuli and gene expression...

RNA Technologies, 2017

Cytosine DNA methylation is a key, heritable, epigenetic modification widespread among major euka... more Cytosine DNA methylation is a key, heritable, epigenetic modification widespread among major eukaryotic groups and involved in main cellular processes such as integrity of DNA structure, control of transposable elements, and regulation of gene expression. In plants, its level can be influenced and modified by a number of biotic and abiotic stresses, and its variations are prone to increase, in turn, the rate of genetic mutations in DNA regions. For this reason, these mechanisms are proposed to improve the adaptability of DNA in complex environments. DNA methylation and epigenetic marks do have a fundamental role also in fine-tuning the pattern of expressed genes, during embryogenesis and seed development, and in the heterosis process, that is, the amelioration following the crosses between individuals belonging to different variants or species.

International Journal of Evolutionary Biology, 2014

DNA methylation is a key epigenetic modification in the vertebrate genomes known to be involved i... more DNA methylation is a key epigenetic modification in the vertebrate genomes known to be involved in biological processes such as regulation of gene expression, DNA structure and control of transposable elements. Despite increasing knowledge about DNA methylation, we still lack a complete understanding of its specific functions and correlation with environment and gene expression in diverse organisms. To understand how global DNA methylation levels changed under environmental influence during vertebrate evolution, we analyzed its distribution pattern along the whole genome in mammals, reptiles and fishes showing that it is correlated with temperature, independently on phylogenetic inheritance. Other studies in mammals and plants have evidenced that environmental stimuli can promote epigenetic changes that, in turn, might generate localized changes in DNA sequence resulting in phenotypic effects. All these observations suggest that environment can affect the epigenome of vertebrates by...

Exploratory Research and Hypothesis in Medicine, 2018

Background and objectives: During sperm maturation, chromatin undergoes an extensive compaction t... more Background and objectives: During sperm maturation, chromatin undergoes an extensive compaction through
the progressive replacement of histones with basic, positively-charged proteins called protamines. Interestingly,
in human and other vertebrates, 5–15% of the paternal genome retains a somatic-like structure. It has been suggested
that preserved nucleosomes have a role in promoting transcription after fertilization, however their localization
and function is still a matter of debate. The aim of the present work was to understand if the localization of
histones in human sperm DNA is affected by genome composition, a feature linked to several biological functions.
In order to do that, we mapped histone-enriched sequences along isochores, which are large chromosomal territories
characterized by fairly homogeneous guanine and cytosine (GC) composition.
Methods: We retrieved publicly available human sequences found to be histone-enriched in sperm chromatin
and localized them along isochores by using their respective coordinates.
Results: We found that the majority of genes and sequences associated with mononucleosomes, the activating
chromatin mark H3K4me3 and the repressive mark H3K27me3 reside in the GC-poor isochores. Genes harboring
the activating mark H3K4me2, instead, are preferentially located in the GC-rich isochores.
Conclusions: For genes carrying histones with specific marks, we speculate that developmental and tissue-specific
genes (carrying the H3K27me3 mark) might take advantage by residing in GC-poor isochores because in these
regions they can be shut off immediately after the end of their transcription more easily than in GC-rich isochores.
On the contrary, housekeeping genes (marked with H3K4me2) would not need this kind of regulation and reside
in GC-rich isochores. For other genes and sequences, further analyses are required in order to clarify the role of
GC composition in histone retention in sperm chromatin. In conclusion, although the complete scenario of sperm
chromatin has not been elucidated yet, correlations seem to exist between chromatin modification patterns,
isochore structure and gene expression timing in embryo development.

Molecular Biology, 2004

Synaptonemal complex (SC) isolated from spermatocyte nuclei after their exhaustive hydrolysis by ... more Synaptonemal complex (SC) isolated from spermatocyte nuclei after their exhaustive hydrolysis by DNase II contains DNA sequences tightly associated with it (SCAR DNA). Here, the compositional properties of a cloned family of golden hamster SCAR DNA were studied. For this purpose, 27 SCAR DNA clones were hybridized with compositionally fractionated golden hamster genomic DNA. The sequences of the SCAR DNA family were mainly localized in the GC-poor isochore families L1 and L2, which accounted for 63% of hybridization signals. The remaining 37% of signals pertained to the GC-rich isochore families H1 and H2. Thus, SCAR DNA proved to be distributed throughout the genome, irrespective of differences in density and sequence type between isochore families. Moreover, the SCAR DNA sequences containing the regions of homology with LINE/SINE repeats were found in all the isochore families. The compositional localization of SCAR DNA is in agreement with the hypothesis that the SC and SCAR DNA participate in chromatin reorganization during meiosis prophase I, which should result in the attachment of chromatin loops to the lateral elements of SC throughout its length.