A novel workflow for the qualitative analysis of DNA methylation data

DNA methylation is an epigenetic modification that plays a pivotal role in major biological mechanisms, such as gene regulation, genomic imprinting, and genome stability. Different combinations of methylated cytosines for a given DNA locus generate different epialleles and alterations of these latter have been associated with several pathological conditions. Existing computational methods and statistical tests relevant to DNA methylation analysis are mostly based on the comparison of average CpG sites methylation levels and they often neglect non-CG methylation. Here, we present EpiStatProfiler, an R package that allows the analysis of CpG and non-CpG based epialleles starting from bisulfite sequencing data through a collection of dedicated extraction functions and statistical tests. EpiStatProfiler is provided with a set of useful auxiliary features, such as customizable genomic ranges, strand-specific epialleles analysis, locus annotation and gene set enrichment analysis. We showcase the package functionalities on two public datasets by identifying putative relevant loci in mice harboring the Huntington's disease-causing Htt gene mutation and in Ctcf +/- mice compared to their wild-type counterparts. To our knowledge, EpiStatProfiler is the first package providing functionalities dedicated to the analysis of epialleles composition derived from any kind of bisulfite sequencing experiment

MC profiling: a novel approach to analyze DNA methylation heterogeneity in genome-wide bisulfite sequencing data

: DNA methylation is an epigenetic mark implicated in crucial biological processes. Most of the knowledge about DNA methylation is based on bulk experiments, in which DNA methylation of genomic regions is reported as average methylation. However, average methylation does not inform on how methylated cytosines are distributed in each single DNA molecule. Here, we propose Methylation Class (MC) profiling as a genome-wide approach to the study of DNA methylation heterogeneity from bulk bisulfite sequencing experiments. The proposed approach is built on the concept of MCs, groups of DNA molecules sharing the same number of methylated cytosines. The relative abundances of MCs from sequencing reads incorporates the information on the average methylation, and directly informs on the methylation level of each molecule. By applying our approach to publicly available bisulfite-sequencing datasets, we individuated cell-to-cell differences as the prevalent contributor to methylation heterogeneity. Moreover, we individuated signatures of loci undergoing imprinting and X-inactivation, and highlighted differences between the two processes. When applying MC profiling to compare different conditions, we identified methylation changes occurring in regions with almost constant average methylation. Altogether, our results indicate that MC profiling can provide useful insights on the epigenetic status and its evolution at multiple genomic regions

Epigenetic remodelling of Fxyd1 promoters in developing heart and brain tissues

FXYD1 is a key protein controlling ion channel transport. FXYD1 exerts its function by regulating Na+/K+-ATPase activity, mainly in brain and cardiac tissues. Alterations of the expression level of the FXYD1 protein cause diastolic dysfunction and arrhythmias in heart and decreased neuronal dendritic tree and spine formation in brain. Moreover, FXYD1, a target of MeCP2, plays a crucial role in the pathogenesis of the Rett syndrome, a neurodevelopmental disorder. Thus, the amount of FXYD1 must be strictly controlled in a tissue specific manner and, likely, during development. Epigenetic modifications, particularly DNA methylation, represent the major candidate mechanism that may regulate Fxyd1 expression. In the present study, we performed a comprehensive DNA methylation analysis and mRNA expression level measurement of the two Fxyd1 transcripts, Fxyd1a and Fxyd1b, in brain and heart tissues during mouse development. We found that DNA methylation at Fxyd1a increased during brain development and decreased during heart development along with coherent changes in mRNA expression levels. We also applied ultra-deep methylation analysis to detect cell to cell methylation differences and to identify possible distinct methylation profile (epialleles) distribution between heart and brain and in different developmental stages. Our data indicate that the expression of Fxyd1 transcript isoforms inversely correlates with DNA methylation in developing brain and cardiac tissues suggesting the existence of a temporal-specific epigenetic program. Moreover, we identified a clear remodeling of epiallele profiles which were distinctive for single developmental stage both in brain and heart tissues

OLTRE LA CRISI DEL FUTURO: GIOVANI E VISIONI DELL’AVVENIRE

I processi di cambiamento che a partire dagli anni Ottanta hanno investito le società occidentali hanno profondamente trasformato l’idea di futuro della modernità, conducendo a quella che è stata definita la «crisi del futuro». Il rinnovato interesse per lo studio del futuro seguito a queste trasformazioni ha dato vita a numerose ricerche sul rapporto tra i giovani - che, in quanto proiettati verso la condizione adulta, devono necessariamente spostare lo sguardo più in là nel tempo – e il futuro. Queste ricerche hanno messo in luce che le modalità con cui i giovani rispondono alla crisi del futuro sono molteplici. Ciò ha reso necessario adottare strumenti di ricerca in grado di cogliere l’eterogeneità delle visioni del futuro dei giovani. Questo contributo, che rientra in questo campo di ricerca, sulla base di 11 interviste in profondità, mira a ricostruire, le diverse visioni del domani dei giovani attraverso un nuovo strumento concettuale: la costellazione di futuro

Structure of the human chromosome interaction network

New Hi-C technologies have revealed that chromosomes have a complex network of spatial contacts in the cell nucleus of higher organisms, whose organisation is only partially understood. Here, we investigate the structure of such a network in human GM12878 cells, to derive a large scale picture of nuclear architecture. We find that the intensity of intra-chromosomal interactions is power-law distributed. Inter-chromosomal interactions are two orders of magnitude weaker and exponentially distributed, yet they are not randomly arranged along the genomic sequence. Intra-chromosomal contacts broadly occur between epigenomically homologous regions, whereas inter-chromosomal contacts are especially associated with regions rich in highly expressed genes. Overall, genomic contacts in the nucleus appear to be structured as a network of networks where a set of strongly individual chromosomal units, as envisaged in the 'chromosomal territory' scenario derived from microscopy, interact with each other via on average weaker, yet far from random and functionally important interactions

The heatmap of the overall contacts between chromosome pairs.

<p>While different chromosomal pairs have different degrees of interactions, the RSS analysis points out that there are no significant isolated subgroups and the system forms a single nuclear network.</p

The distribution of intra-chromosomal interactions between contact domains (here in a <i>log</i>₁₀ − <i>log</i>₁₀ plot) decays as a power law, <i>P</i>(<i>I</i>) ≃ <i>I</i>^−<i>γ</i>, with an exponent close to <i>γ</i> ≃ 2 (dashed line), which appear to be ‘universal’ across different chromosomes.

<p>So, the structures of their contact networks exhibit similar quantitative features. <i>I</i>₀ and <i>P</i>₀ are factors to rescale on top of each other the data from different chromosomes.</p

Heatmaps representing, across the different subcompartments A1-B4, the domain average excess interactions over background within single chromosomes (<i>in-cis</i>, Panel a) and between chromosomes (<i>in-trans</i>, Panel b).

<p>Intra-chromosomal contacts (a) especially occur between homologous subcompartments (diagonal), while inter-chromosomal contacts (b) are particularly frequent with subcompartment A1, rich in highly expressed genes, hinting to a functional role.</p

Our analysis of Hi-C genomic interactions shows that the nucleus of human GM12878 cells is structured as a net of networks.

<p>Each individual chromosome form a strong intra-chromosomal network of contacts, consistent with the ‘chromosomal territories’ seen by microscopy. Yet, chromosomes intermingle via weaker, yet non-random and functionally important contacts, whereby distinct chromosomal networks form a global nuclear network. Panel a: A pictorial representation of the 3D organization of chromosomes (colored spheres) within the nucleus, as emerging from our network analysis. Panel b: A real network reconstruction (using the visualization tool described in [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0188201#pone.0188201.ref014" target="_blank">14</a>]) of chromosomal contacts of chromosomes 19 and 20. For clarity of presentation, each sphere inside a chromosome represents ∼ 1<i>Mb</i> (5 contact domains) and a high threshold is set for link visualization.</p

Heatmap of the normalized in-situ Hi-C interactions between the contact domains of chromosomes 19 and 22.

<p>Bands of regions with above background signal are visible, in contrast to the corresponding random matrix (top-right, see details in the text). The differential interaction score, <i>DR</i>, of the domains of chromosome 22 with 19 (rightmost panel) quantifies the dissimilarity with the random control and highlights the clustering of genomic locations enriched in contacts with domains on the other chromosome.</p