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  • Chromatin and Epigenetics  (39)
  • 04. Solid Earth::04.04. Geology::04.04.09. Structural geology
  • JSTOR Archive Collection Business II
  • Oxford University Press  (44)
  • Wiley  (6)
  • 1
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    Reply to: Comment on ‘Insights from the Mw 6.3, 2009 L’Aquila earthquake (central Apennines) - Unveiling new seismogenic sources through their surface signatures: the adjacent San Pio Fault’ (2011)
    Wiley
    Details
    Publication Date: 2017-04-04
    Description: We reply to a comment by Messina et al., who strongly criticized our paper on the San Pio Fault, by showing that in areas of complex geology such as the central Apennines, where the current tectonic setting results from the superposition of different tectonic regimes, the equation: “most visible active fault = major seismogenic fault” can be misleading.
    Description: Published
    Description: 421-423
    Description: 3.2. Tettonica attiva
    Description: JCR Journal
    Description: restricted
    Keywords: Seismotectonics ; morphotectonics ; active fault ; San Pio basin ; 04. Solid Earth::04.04. Geology::04.04.01. Earthquake geology and paleoseismology ; 04. Solid Earth::04.04. Geology::04.04.03. Geomorphology ; 04. Solid Earth::04.04. Geology::04.04.09. Structural geology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 2
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    UPb and 40Ar39Ar geochronology of Palaeozoic units in the northern Apennines: determining protolith age and alpine evolution using the Calamita Schist and Ortano Porphyroid (2012)
    Wiley
    Details
    Publication Date: 2017-04-04
    Description: In the northern Apennines, the Palaeozoic basement involved in the Late Oligocene–Middle Miocene nappe stack contains metamorphic units for which hypothetical ages have been assigned on the basis of lithological correlations with the Palaeozoic formations of the Variscan chain in Sardinia. This uncertainty concerning the age poses limitations to reconstructing the Palaeozoic stratigraphy, defining the Alpine and pre-Alpine histories and correlations with other domains of the Variscan chain. We present the UPb age of detrital zircon and the 40Ar39Ar age of metamorphic muscovite for the Calamita Schist and Ortano Porphyroid, two metamorphic units of undetermined Palaeozoic age cropping out in the eastern Elba Island. The radioisotopic data allows us to: (i) define the Early Carboniferous and Middle Ordovician ages for the Calamita Schist and Ortano Porphyroid, respectively, as well as their derivation (flysch deposit and magmatic rocks); (ii) pose some constraints concerning their alpine tectonic and metamorphic histories. These new data generate a more precise reconstruction of the Palaeozoic sequence in the northern Apennines, and they document that the Palaeozoic basement involved in the alpine deformation underwent internal stacking with an inversion of the original sequence. Copyright © 2010 John Wiley & Sons, Ltd.
    Description: Published
    Description: 288-310
    Description: 3.2. Tettonica attiva
    Description: 3.3. Geodinamica e struttura dell'interno della Terra
    Description: JCR Journal
    Description: reserved
    Keywords: northern Apennines ; Palaeozoic basement ; U-Pb zircon ; 40Ar-39Ar muscovite ; 04. Solid Earth::04.04. Geology::04.04.02. Geochronology ; 04. Solid Earth::04.04. Geology::04.04.09. Structural geology ; 04. Solid Earth::04.07. Tectonophysics::04.07.07. Tectonics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 3
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    U-Pb and 40Ar-39Ar geochronology of Palaeozoic units in the northern Apennines: determining protolith age and alpine evolution using the Calamita Schist and Ortano Porphyroid (2011)
    Wiley
    Details
    Publication Date: 2017-04-04
    Description: In the northern Apennines, the Palaeozoic basement involved in the Late Oligocene–Middle Miocene nappe stack contains metamorphic units for which hypothetical ages have been assigned on the basis of lithological correlations with the Palaeozoic formations of the Variscan chain in Sardinia. This uncertainty concerning the age poses limitations to reconstructing the Palaeozoic stratigraphy, defining the Alpine and pre-Alpine histories and correlations with other domains of the Variscan chain. We present the U-Pb age of detrital zircon and the 40Ar-39Ar age of metamorphic muscovite for the Calamita Schist and Ortano Porphyroid, two metamorphic units of undetermined Palaeozoic age cropping out in the eastern Elba Island. The radioisotopic data allows us to: (i) define the Early Carboniferous and Middle Ordovician ages for the Calamita Schist and Ortano Porphyroid, respectively, as well as their derivation (flysch deposit and magmatic rocks); (ii) pose some constraints concerning their alpine tectonic and metamorphic histories. These new data generate a more precise reconstruction of the Palaeozoic sequence in the northern Apennines, and they document that the Palaeozoic basement involved in the alpine deformation underwent internal stacking with an inversion of the original sequence.
    Description: In press
    Description: 3.2. Tettonica attiva
    Description: 3.3. Geodinamica e struttura dell'interno della Terra
    Description: JCR Journal
    Description: reserved
    Keywords: northern Apennines ; Palaeozoic basement ; U-Pb zircon ; 40Ar-39Ar muscovite ; 04. Solid Earth::04.04. Geology::04.04.02. Geochronology ; 04. Solid Earth::04.04. Geology::04.04.09. Structural geology ; 04. Solid Earth::04.07. Tectonophysics::04.07.02. Geodynamics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 4
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    PAtCh-Cap: input strategy for improving analysis of ChIP-exo data sets and beyond (2016)
    Oxford University Press
    Details
    Publication Date: 2016-12-04
    Description: Recently, a number of advances have been implemented into the core ChIP-seq (chromatin immunoprecipitation coupled with next-generation sequencing) methodology to streamline the process, reduce costs or improve data resolution. Several of these emerging ChIP-based methods perform additional chemical steps on bead-bound immunoprecipitated chromatin, posing a challenge for generating similarly treated input controls required for artifact removal during bioinformatics analyses. Here we present a versatile method for producing technique-specific input controls for ChIP-based methods that utilize additional bead-bound processing steps. This reported method, termed protein attached chromatin capture (PAtCh-Cap), relies on the non-specific capture of chromatin-bound proteins via their carboxylate groups, leaving the DNA accessible for subsequent chemical treatments in parallel with chromatin separately immunoprecipitated for the target protein. Application of this input strategy not only significantly enhanced artifact removal from ChIP-exo data, increasing confidence in peak identification and allowing for de novo motif searching, but also afforded discovery of a novel CTCF binding motif.
    Keywords: Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Differential peak calling of ChIP-seq signals with replicates with THOR (2016)
    Oxford University Press
    Details
    Publication Date: 2016-12-01
    Description: The study of changes in protein–DNA interactions measured by ChIP-seq on dynamic systems, such as cell differentiation, response to treatments or the comparison of healthy and diseased individuals, is still an open challenge. There are few computational methods comparing changes in ChIP-seq signals with replicates. Moreover, none of these previous approaches addresses ChIP-seq specific experimental artefacts arising from studies with biological replicates. We propose THOR, a Hidden Markov Model based approach, to detect differential peaks between pairs of biological conditions with replicates. THOR provides all pre- and post-processing steps required in ChIP-seq analyses. Moreover, we propose a novel normalization approach based on housekeeping genes to deal with cases where replicates have distinct signal-to-noise ratios. To evaluate differential peak calling methods, we delineate a methodology using both biological and simulated data. This includes an evaluation procedure that associates differential peaks with changes in gene expression as well as histone modifications close to these peaks. We evaluate THOR and seven competing methods on data sets with distinct characteristics from in vitro studies with technical replicates to clinical studies of cancer patients. Our evaluation analysis comprises of 13 comparisons between pairs of biological conditions. We show that THOR performs best in all scenarios.
    Keywords: Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    NEpiC: a network-assisted algorithm for epigenetic studies using mean and variance combined signals (2016)
    Oxford University Press
    Details
    Publication Date: 2016-09-20
    Description: DNA methylation plays an important role in many biological processes. Existing epigenome-wide association studies (EWAS) have successfully identified aberrantly methylated genes in many diseases and disorders with most studies focusing on analysing methylation sites one at a time. Incorporating prior biological information such as biological networks has been proven to be powerful in identifying disease-associated genes in both gene expression studies and genome-wide association studies (GWAS) but has been under studied in EWAS. Although recent studies have noticed that there are differences in methylation variation in different groups, only a few existing methods consider variance signals in DNA methylation studies. Here, we present a network-assisted algorithm, NEpiC, that combines both mean and variance signals in searching for differentially methylated sub-networks using the protein–protein interaction (PPI) network. In simulation studies, we demonstrate the power gain from using both the prior biological information and variance signals compared to using either of the two or neither information. Applications to several DNA methylation datasets from the Cancer Genome Atlas (TCGA) project and DNA methylation data on hepatocellular carcinoma (HCC) from the Columbia University Medical Center (CUMC) suggest that the proposed NEpiC algorithm identifies more cancer-related genes and generates better replication results.
    Keywords: Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Establishment of a promoter-based chromatin architecture on recently replicated DNA can accommodate variable inter-nucleosome spacing (2016)
    Oxford University Press
    Details
    Publication Date: 2016-09-03
    Description: Nucleosomes, the fundamental subunits of eukaryotic chromatin, are organized with respect to transcriptional start sites. A major challenge to the persistence of this organization is the disassembly of nucleosomes during DNA replication. Here, we use complimentary approaches to map the locations of nucleosomes on recently replicated DNA. We find that nucleosomes are substantially realigned with promoters during the minutes following DNA replication. As a result, the nucleosomal landscape is largely re-established before newly replicated chromosomes are partitioned into daughter cells and can serve as a platform for the re-establishment of gene expression programmes. When the supply of histones is disrupted through mutation of the chaperone Caf1, a promoter-based architecture is generated, but with increased inter-nucleosomal spacing. This indicates that the chromatin remodelling enzymes responsible for spacing nucleosomes are capable of organizing nucleosomes with a range of different linker DNA lengths.
    Keywords: Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes: implications for hepatic gene expression (2016)
    Oxford University Press
    Details
    Publication Date: 2016-08-20
    Description: To improve the epigenomic analysis of tissues rich in 5-hydroxymethylcytosine (hmC), we developed a novel protocol called TAB-Methyl-SEQ, which allows for single base resolution profiling of both hmC and 5-methylcytosine by targeted next-generation sequencing. TAB-Methyl-SEQ data were extensively validated by a set of five methodologically different protocols. Importantly, these extensive cross-comparisons revealed that protocols based on Tet1-assisted bisulfite conversion provided more precise hmC values than TrueMethyl-based methods. A total of 109 454 CpG sites were analyzed by TAB-Methyl-SEQ for mC and hmC in 188 genes from 20 different adult human livers. We describe three types of variability of hepatic hmC profiles: (i) sample-specific variability at 40.8% of CpG sites analyzed, where the local hmC values correlate to the global hmC content of livers (measured by LC-MS), (ii) gene-specific variability, where hmC levels in the coding regions positively correlate to expression of the respective gene and (iii) site-specific variability, where prominent hmC peaks span only 1 to 3 neighboring CpG sites. Our data suggest that both the gene- and site-specific components of hmC variability might contribute to the epigenetic control of hepatic genes. The protocol described here should be useful for targeted DNA analysis in a variety of applications.
    Keywords: Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Inducible DamID systems for genomic mapping of chromatin proteins in Drosophila (2016)
    Oxford University Press
    Details
    Publication Date: 2016-07-09
    Description: Dam identification (DamID) is a powerful technique to generate genome-wide maps of chromatin protein binding. Due to its high sensitivity, it is particularly suited to study the genome interactions of chromatin proteins in small tissue samples in model organisms such as Drosophila . Here, we report an intein-based approach to tune the expression level of Dam and Dam-fusion proteins in Drosophila by addition of a ligand to fly food. This helps to suppress possible toxic effects of Dam. In addition, we describe a strategy for genetically controlled expression of Dam in a specific cell type in complex tissues. We demonstrate the utility of the latter by generating a glia-specific map of Polycomb in small samples of brain tissue. These new DamID tools will be valuable for the mapping of binding patterns of chromatin proteins in Drosophila tissues and especially in cell lineages.
    Keywords: Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    De novo deciphering three-dimensional chromatin interaction and topological domains by wavelet transformation of epigenetic profiles (2016)
    Oxford University Press
    Details
    Publication Date: 2016-06-21
    Description: Defining chromatin interaction frequencies and topological domains is a great challenge for the annotations of genome structures. Although the chromosome conformation capture (3C) and its derivative methods have been developed for exploring the global interactome, they are limited by high experimental complexity and costs. Here we describe a novel computational method, called CITD, for de novo prediction of the chromatin interaction map by integrating histone modification data. We used the public epigenomic data from human fibroblast IMR90 cell and embryonic stem cell (H1) to develop and test CITD, which can not only successfully reconstruct the chromatin interaction frequencies discovered by the Hi-C technology, but also provide additional novel details of chromosomal organizations. We predicted the chromatin interaction frequencies, topological domains and their states (e.g. active or repressive) for 98 additional cell types from Roadmap Epigenomics and ENCODE projects. A total of 131 protein-coding genes located near 78 preserved boundaries among 100 cell types are found to be significantly enriched in functional categories of the nucleosome organization and chromatin assembly. CITD and its predicted results can be used for complementing the topological domains derived from limited Hi-C data and facilitating the understanding of spatial principles underlying the chromosomal organization.
    Keywords: Chromatin and Epigenetics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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