Search results for " Epigenomic"
showing 7 items of 7 documents
Variable Ranking Feature Selection for the Identification of Nucleosome Related Sequences
2018
Several recent works have shown that K-mer sequence representation of a DNA sequence can be used for classification or identification of nucleosome positioning related sequences. This representation can be computationally expensive when k grows, making the complexity in spaces of exponential dimension. This issue effects significantly the classification task computed by a general machine learning algorithm used for the purpose of sequence classification. In this paper, we investigate the advantage offered by the so-called Variable Ranking Feature Selection method to select the most informative k − mers associated to a set of DNA sequences, for the final purpose of nucleosome/linker classifi…
A motif-independent metric for DNA sequence specificity
2011
Abstract Background Genome-wide mapping of protein-DNA interactions has been widely used to investigate biological functions of the genome. An important question is to what extent such interactions are regulated at the DNA sequence level. However, current investigation is hampered by the lack of computational methods for systematic evaluating sequence specificity. Results We present a simple, unbiased quantitative measure for DNA sequence specificity called the Motif Independent Measure (MIM). By analyzing both simulated and real experimental data, we found that the MIM measure can be used to detect sequence specificity independent of presence of transcription factor (TF) binding motifs. We…
Methylation status of VTRNA2-1/nc886 is stable across populations, monozygotic twin pairs and in majority of tissues. Supplementary data
2022
Supplementary Table 1. This study used 48 DNA methylation datasets, including DILGOM, FTC, ERMA, KORA, LURIC, NELLI, SATSA and YFS as well as 39 datasets available in the Gene Expression Omnibus (GEO) [29] consisting of >30 tissues and >30,000 individuals. Supplementary Table 2. Differences in the proportion of individuals with imprinted nc886 locus between sexes or in a case–control setting. Supplementary Table 3. Of these discordant pairs, one co-twin was always intermediately methylated, whereas the other co-twin was either imprinted or nonmethylated in all cases – that is, no twin pairs were identified in which one co-twin was imprinted and the other was nonmethylated. Supplementa…
Stable Oxidative Cytosine Modifications Accumulate in Cardiac Mesenchymal Cells From Type2 Diabetes Patients
2018
Rationale: Human cardiac mesenchymal cells (CMSCs) are a therapeutically relevant primary cell population. Diabetes mellitus compromises CMSC function as consequence of metabolic alterations and incorporation of stable epigenetic changes. Objective: To investigate the role of α-ketoglutarate (αKG) in the epimetabolic control of DNA demethylation in CMSCs. Methods and Results: Quantitative global analysis, methylated and hydroxymethylated DNA sequencing, and gene-specific GC methylation detection revealed an accumulation of 5-methylcytosine, 5-hydroxymethylcytosine, and 5-formylcytosine in the genomic DNA of human CMSCs isolated from diabetic donors. Whole heart genomic DNA analysis reveale…
The role of Plant Growth Promoting (PGP) bacteria in the growth of Mediterranean diet plants producing high-value compounds
2023
Loss of fertility, together with drought and aridity, results in soil unproductivity and eventually desertification. Unsustainable agricultural practices are currently stressing the soil: an undervalued resource that, in addition to food, provides a multitude of invaluable services such as regulating the microclimate, reducing contaminants, and capturing CO2. Hence, there is an increasing need to resort to sustainable approaches toward agricultural systems. Although Sicily is one of those regions most affected by water shortages, it is at the same time a reservoir of drought-resistant Mediterranean plants with high nutritional value and a rich microbiota. This project aims to promote agricu…
The histone deacetylase Rpd3 regulates the heterochromatin structure of Drosophila telomeres
2011
Telomeres are specialized structures at the end of eukaryotic chromosomes that are required to preserve genome integrity, chromosome stability and nuclear architecture. Telomere maintenance and function are established epigenetically in several eukaryotes. However, the exact chromatin enzymatic modifications regulating telomere homeostasis are poorly understood. In Drosophila melanogaster, telomere length and stability are maintained through the retrotransposition of specialized telomeric sequences and by the specific loading of protecting capping proteins, respectively. Here, we show that the loss of the essential and evolutionarily conserved histone deacetylase Rpd3, the homolog of mammal…
Genetics of longevity. Data from the studies on Sicilian centenarians
2012
Abstract The demographic and social changes of the past decades have determined improvements in public health and longevity. So, the number of centenarians is increasing as a worldwide phenomenon. Scientists have focused their attention on centenarians as optimal model to address the biological mechanisms of "successful and unsuccessful ageing". They are equipped to reach the extreme limits of human life span and, most importantly, to show relatively good health, being able to perform their routine daily life and to escape fatal age-related diseases, such as cardiovascular diseases and cancer. Thus, particular attention has been centered on their genetic background and immune system. In thi…