Search results for "Hi-C"
showing 5 items of 5 documents
Evolutionary stability of topologically associating domains is associated with conserved gene regulation
2018
AbstractBackgroundThe human genome is highly organized in the three-dimensional nucleus. Chromosomes fold locally into topologically associating domains (TADs) defined by increased intra-domain chromatin contacts. TADs contribute to gene regulation by restricting chromatin interactions of regulatory sequences, such as enhancers, with their target genes. Disruption of TADs can result in altered gene expression and is associated to genetic diseases and cancers. However, it is not clear to which extent TAD regions are conserved in evolution and whether disruption of TADs by evolutionary rearrangements can alter gene expression.ResultsHere, we hypothesize that TADs represent essential functiona…
La Muestra Continua de Vidas Laborales (MCVL) como fuente generadora de datos para el estudio del sistema de pensiones
2015
Esta tesis tiene como elemento fundamental de análisis la denominada Muestra Continua de Vidas Laborales (MCVL), como fuente generadora de datos para el estudio del sistema de público de pensiones de España. La MCVL es un conjunto de microdatos individuales anonimizados extraídos de los registros de la Seguridad Social de España. La MCVL se obtiene a partir de un Muestreo Aleatorio Simple (MAS) sobre la población de referencia (conjunto de personas relacionadas durante todo el año con la Seguridad Social, bien como afiliadas o bien como perceptoras de prestaciones, pero con ciertos matices en dicha relación). Los objetivos principales de esta tesis son: - Contribuir a aumentar el conocimien…
7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs.
2019
Abstract Background Knowledge of the three-dimensional structure of the genome is necessary to understand how gene expression is regulated. Recent experimental techniques such as Hi-C or ChIA-PET measure long-range chromatin interactions genome-wide but are experimentally elaborate, have limited resolution and such data is only available for a limited number of cell types and tissues. Results While ChIP-seq was not designed to detect chromatin interactions, the formaldehyde treatment in the ChIP-seq protocol cross-links proteins with each other and with DNA. Consequently, also regions that are not directly bound by the targeted TF but interact with the binding site via chromatin looping are…
Best proximity points: Convergence and existence theorems for p-cyclic mappings
2010
Abstract We introduce a new class of mappings, called p -cyclic φ -contractions, which contains the p -cyclic contraction mappings as a subclass. Then, convergence and existence results of best proximity points for p -cyclic φ -contraction mappings are obtained. Moreover, we prove results of the existence of best proximity points in a reflexive Banach space. These results are generalizations of the results of Al-Thagafi and Shahzad (2009) [8] .
Computational processing and quality control of Hi-C, capture Hi-C and capture-C data
2019
Hi-C, capture Hi-C (CHC) and Capture-C have contributed greatly to our present understanding of the three-dimensional organization of genomes in the context of transcriptional regulation by characterizing the roles of topological associated domains, enhancer promoter loops and other three-dimensional genomic interactions. The analysis is based on counts of chimeric read pairs that map to interacting regions of the genome. However, the processing and quality control presents a number of unique challenges. We review here the experimental and computational foundations and explain how the characteristics of restriction digests, sonication fragments and read pairs can be exploited to distinguish…