Search results for "Nucleosome"
showing 10 items of 97 documents
An omics perspective to the molecular mechanisms of anticancer metallo-drugs in the computational microscope era
2017
Introduction: Metallo-drugs have attracted enormous interest for cancer treatment. The achievements of this drug-type are summarized by the success story of cisplatin. That being said, there have been many drawbacks with its clinical use, which prompted decades worth of research efforts to move towards safer and more effective agents, either containing platinum or different metals. Areas covered: In this review, the authors provide an atomistic picture of the molecular mechanisms involving selected metallo-drugs from structural and molecular simulation studies. They also provide an omics perspective, pointing out many unsettled aspects of the most relevant families of metallo-drugs at an ep…
CORENup: a combination of convolutional and recurrent deep neural networks for nucleosome positioning identification
2020
Abstract Background Nucleosomes wrap the DNA into the nucleus of the Eukaryote cell and regulate its transcription phase. Several studies indicate that nucleosomes are determined by the combined effects of several factors, including DNA sequence organization. Interestingly, the identification of nucleosomes on a genomic scale has been successfully performed by computational methods using DNA sequence as input data. Results In this work, we propose CORENup, a deep learning model for nucleosome identification. CORENup processes a DNA sequence as input using one-hot representation and combines in a parallel fashion a fully convolutional neural network and a recurrent layer. These two parallel …
A one class KNN for signal identification: a biological case study
2009
The paper describes an application of a one class KNN to identify different signal patterns embedded in a noise structured background. The problem becomes harder whenever only one pattern is well-represented in the signal; in such cases, one class classifier techniques are more indicated. The classification phase is applied after a preprocessing phase based on a multi layer model (MLM) that provides preliminary signal segmentation in an interval feature space. The one class KNN has been tested on synthetic and real (Saccharomyces cerevisiae) microarray data in the specific problem of DNA nucleosome and linker regions identification. Results have shown, in both cases, a good recognition rate.
Heterochromatin Networks: Topology, Dynamics, and Function (a Working Hypothesis)
2021
Open systems can only exist by self-organization as pulsing structures exchanging matter and energy with the outer world. This review is an attempt to reveal the organizational principles of the heterochromatin supra-intra-chromosomal network in terms of nonlinear thermodynamics. The accessibility of the linear information of the genetic code is regulated by constitutive heterochromatin (CHR) creating the positional information in a system of coordinates. These features include scale-free splitting-fusing of CHR with the boundary constraints of the nucleolus and nuclear envelope. The analysis of both the literature and our own data suggests a radial-concentric network as the main structural…
Multiple roles for ISWI in transcription, chromosome organization and DNA replication.
2003
ISWI functions as the ATPase subunit of multiple chromatin-remodeling complexes. These complexes use the energy of ATP hydrolysis to slide nucleosomes and increase chromatin fluidity, thereby modulating the access of transcription factors and other regulatory proteins to DNA. Here we discuss recent progress toward understanding the biological functions of ISWI, with an emphasis on its roles in transcription, chromosome organization and DNA replication.
Sliding-end-labelling
1986
Abstract A method, termed ‘sliding-end-labelling’, has been devised to avoid a frequent artifact in nucleosome positioning by indirect end labelling, namely the appearing of DNA fragments originated by two nuclease cuts, one of them lying within the region covered by the probe. The method is applied to the nucleosome positioning in the yeast SUC2 gene for invertase.
Constitutive Promoter Occupancy by the MBF-1 Activator and Chromatin Modification of the Developmental Regulated Sea Urchin α-H2A Histone Gene
2007
The tandemly repeated sea urchin alpha-histone genes are developmentally regulated. These genes are transcribed up to the early blastula stage and permanently silenced as the embryos approach gastrulation. As previously described, expression of the alpha-H2A gene depends on the binding of the MBF-1 activator to the 5' enhancer, while down-regulation relies on the functional interaction between the 3' sns 5 insulator and the GA repeats located upstream of the enhancer. As persistent MBF-1 binding and enhancer activity are detected in gastrula embryos, we have studied the molecular mechanisms that prevent the bound MBF-1 from trans-activating the H2A promoter at this stage of development. Her…
Epigenomic k-mer dictionaries: shedding light on how sequence composition influences in vivo nucleosome positioning
2014
Abstract Motivation: Information-theoretic and compositional analysis of biological sequences, in terms of k-mer dictionaries, has a well established role in genomic and proteomic studies. Much less so in epigenomics, although the role of k-mers in chromatin organization and nucleosome positioning is particularly relevant. Fundamental questions concerning the informational content and compositional structure of nucleosome favouring and disfavoring sequences with respect to their basic building blocks still remain open. Results: We present the first analysis on the role of k-mers in the composition of nucleosome enriched and depleted genomic regions (NER and NDR for short) that is: (i) exhau…
Applications of alignment-free methods in epigenomics
2013
Epigenetic mechanisms play an important role in the regulation of cell type-specific gene activities, yet how epigenetic patterns are established and maintained remains poorly understood. Recent studies have supported a role of DNA sequences in recruitment of epigenetic regulators. Alignment-free methods have been applied to identify distinct sequence features that are associated with epigenetic patterns and to predict epigenomic profiles. Here, we review recent advances in such applications, including the methods to map DNA sequence to feature space, sequence comparison and prediction models. Computational studies using these methods have provided important insights into the epigenetic reg…
Interaction between N-terminal domain of H4 and DNA is regulated by the acetylation degree.
1998
Abstract To study whether the acetylation of one or more of the four acetylatable lysines of histone H4 affects its binding to DNA, we have designed a protection experiment with a model system consisting in phage lambda DNA as substrate, Stu I as restriction endonuclease and histone H4 with different degrees of acetylation as the protective agent. It can be deduced from the experimental data that the protection afforded by the histone is not dependent on the number of positive charges lost by acetylation. Thus, non-acetylated H4 and mono-acetylated H4 cause similar protection, while di-acetylation of the histone seems to be the crucial step in significantly weakening the interaction between…