Biochemical properties of chromatin domains define genome compartmentalization.

Chromatin three-dimensional (3D) organization inside the cell nucleus determines the separation of euchromatin and heterochromatin domains. Their segregation results in the definition of active and inactive chromatin compartments, whereby the local concentration of associated proteins, RNA and DNA results in the formation of distinct subnuclear structures. Thus, chromatin domains spatially confined in a specific 3D nuclear compartment are expected to share similar epigenetic features and biochemical properties, in terms of accessibility and solubility.

Leveraging Tissue-Specific Enhancer-Target Gene Regulatory Networks Identifies Enhancer Somatic Mutations That Functionally Impact Lung Cancer.

Unlabelled: Enhancers are noncoding regulatory DNA regions that modulate the transcription of target genes, often over large distances along with the genomic sequence. Enhancer alterations have been associated with various pathological conditions, including cancer. However, the identification and characterization of somatic mutations in noncoding regulatory regions with a functional effect on tumorigenesis and prognosis remain a major challenge.

Leveraging three-dimensional chromatin architecture for effective reconstruction of enhancer-target gene regulatory interactions.

A growing amount of evidence in literature suggests that germline sequence variants and somatic mutations in non-coding distal regulatory elements may be crucial for defining disease risk and prognostic stratification of patients, in genetic disorders as well as in cancer. Their functional interpretation is challenging because genome-wide enhancer-target gene (ETG) pairing is an open problem in genomics. The solutions proposed so far do not account for the hierarchy of structural domains which define chromatin three-dimensional (3D) architecture.

HPC-REDItools: a novel HPC-aware tool for improved large scale RNA-editing analysis.

Background: RNA editing is a widespread co-/post-transcriptional mechanism that alters primary RNA sequences through the modification of specific nucleotides and it can increase both the transcriptome and proteome diversity. The automatic detection of RNA-editing from RNA-seq data is computational intensive and limited to small data sets, thus preventing a reliable genome-wide characterisation of such process.

Results: In this work we introduce HPC-REDItools, an upgraded tool for accurate RNA-editing events discovery from large dataset repositories.

HiCBricks: building blocks for efficient handling of large Hi-C datasets.

Summary: Genome-wide chromosome conformation capture based on high-throughput sequencing (Hi-C) has been widely adopted to study chromatin architecture by generating datasets of ever-increasing complexity and size. HiCBricks offers user-friendly and efficient solutions for handling large high-resolution Hi-C datasets. The package provides an R/Bioconductor framework with the bricks to build more complex data analysis pipelines and algorithms.

PeachVar-DB: A Curated Collection of Genetic Variations for the Interactive Analysis of Peach Genome Data.

Applying next-generation sequencing (NGS) technologies to species of agricultural interest has the potential to accelerate the understanding and exploration of genetic resources. The storage, availability and maintenance of huge quantities of NGS-generated data remains a major challenge. The PeachVar-DB portal, available at http://hpc-bioinformatics.

Bacteria contribute to pesticide degradation in cryoconite holes in an Alpine glacier.

Organic contaminants deposited on glacier snow and ice are subject to partitioning and degradation processes that determine their environmental fate and, consequently, their accumulation in ice bodies. Among these processes, organic compound degradation by supraglacial bacteria has been investigated to a lesser extent than photo- and chemical degradation. We investigated biodegradation of the organophosphorus insecticide chlorpyrifos (CPF), a xenobiotic tracer that accumulates on glaciers after atmospheric medium- and long-range transport, by installing in situ microcosms on an Alpine glacier to simulate cryoconite hole systems.

Potential sources of bacteria colonizing the cryoconite of an Alpine glacier.

We investigated the potential contribution of ice-marginal environments to the microbial communities of cryoconite holes, small depressions filled with meltwater that form on the surface of Forni Glacier (Italian Alps). Cryoconite holes are considered the most biologically active environments on glaciers. Bacteria can colonize these environments by short-range transport from ice-marginal environments or by long-range transport from distant areas.

Diversity and Assembling Processes of Bacterial Communities in Cryoconite Holes of a Karakoram Glacier.

Cryoconite holes are small ponds that form on the surface of glaciers that contain a dark debris, the cryoconite, at the bottom and host active ecological communities. Differences in the structure of bacterial communities have been documented among Arctic and mountain glaciers, and among glaciers in different areas of the world. In this study, we investigated the structure of bacterial communities of cryoconite holes of Baltoro Glacier, a large (62 km in length and 524 km of surface) glacier of the Karakoram, by high-throughput sequencing of the V5-V6 hypervariable regions of the 16S rRNA gene.

Temporal variability of bacterial communities in cryoconite on an alpine glacier.

Cryoconite holes, that is, small ponds that form on glacier surface, are considered the most biologically active environments on glaciers. Bacterial communities in these environments have been extensively studied, but often through snapshot studies based on the assumption of a general stability of community structure. In this study, the temporal variation of bacterial communities in cryoconite holes on the Forni Glacier (Italian Alps) was investigated by high throughput DNA sequencing.

Diversity and hydrocarbon-degrading potential of epiphytic microbial communities on Platanus x acerifolia leaves in an urban area.

Plants and their associated bacteria have been suggested to play a role in air pollution mitigation, especially in urban areas. Particularly, epiphytic bacteria might be able to degrade atmospheric hydrocarbons. However, phyllospheric bacterial communities are highly variable depending on several factors, e.

Light-dependent microbial metabolisms drive carbon fluxes on glacier surfaces.

Biological processes on glacier surfaces affect glacier reflectance, influence surface energy budget and glacier response to climate warming, and determine glacier carbon exchange with the atmosphere. Currently, carbon balance of supraglacial environment is assessed as the balance between the activity of oxygenic phototrophs and the respiration rate of heterotrophic organisms. Here we present a metagenomic analysis of tiny wind-blown supraglacial sediment (cryoconite) from Baltoro (Pakistani Karakoram) and Forni (Italian Alps) glaciers, providing evidence for the occurrence in these environments of different and previously neglected metabolic pathways.