Search results for "chromosome"

Homozygous deletions localize novel tumor suppressor genes in B-cell lymphomas

2007

AbstractIntegrative genomic and gene-expression analyses have identified amplified oncogenes in B-cell non-Hodgkin lymphoma (B-NHL), but the capability of such technologies to localize tumor suppressor genes within homozygous deletions remains unexplored. Array-based comparative genomic hybridization (CGH) and gene-expression microarray analysis of 48 cell lines derived from patients with different B-NHLs delineated 20 homozygous deletions at 7 chromosome areas, all of which contained tumor suppressor gene targets. Further investigation revealed that only a fraction of primary biopsies presented inactivation of these genes by point mutation or intragenic deletion, but instead some of them w…

The Cryptocercus punctulatus species complex (Dictyoptera: Cryptocercidae) in the eastern United States: comparison of cuticular hydrocarbons, chromo…

2008

1055-7903; The goal of the current study was to determine if cuticular hydrocarbons could be used to empirically delimit taxa within the Cryptocercus punctulatus species complex in the eastern United States. Cockroaches were collected from rotting logs in 22 locations across four states. Hydrocarbon phenotypes and two mitochondrial (16S and COII) genes and one nuclear (ITS2) gene were independently analyzed to determine their relationship with chromosome number. Five distinct hydrocarbon phenotypes were found, but these were only partly congruent with chromosome number and thus with purported species descriptions. Molecular and cuticular hydrocarbon data each indicate that Cryptocercus with…

An initial comparative map of copy number variations in the goat (Capra hircus) genome

2010

Abstract Background The goat (Capra hircus) represents one of the most important farm animal species. It is reared in all continents with an estimated world population of about 800 million of animals. Despite its importance, studies on the goat genome are still in their infancy compared to those in other farm animal species. Comparative mapping between cattle and goat showed only a few rearrangements in agreement with the similarity of chromosome banding. We carried out a cross species cattle-goat array comparative genome hybridization (aCGH) experiment in order to identify copy number variations (CNVs) in the goat genome analysing animals of different breeds (Saanen, Camosciata delle Alpi,…

Variable-order reference-free variant discovery with the Burrows-Wheeler Transform

2020

Abstract Background In [Prezza et al., AMB 2019], a new reference-free and alignment-free framework for the detection of SNPs was suggested and tested. The framework, based on the Burrows-Wheeler Transform (BWT), significantly improves sensitivity and precision of previous de Bruijn graphs based tools by overcoming several of their limitations, namely: (i) the need to establish a fixed value, usually small, for the order k, (ii) the loss of important information such as k-mer coverage and adjacency of k-mers within the same read, and (iii) bad performance in repeated regions longer than k bases. The preliminary tool, however, was able to identify only SNPs and it was too slow and memory con…

Role of THAP11 in the transcriptional regulation and chromatin structure of the human MYC locus

C-MYC è uno dei geni più frequentemente deregolati nei tumori umani. Una comprensione dettagliata della regolazione trascrizionale di questo gene è essenziale per comprendere meglio gli aspetti molecolari delle sue diverse funzioni. Usando diversi tipi di analisi (EMSA, 2D-IPG e analisi MALDI), nei nostri laboratori abbiamo caratterizzato un elemento con funzione di enhancer blocker (HB2.8) situato 32Kb valle del gene c-MYC . Saggi di trasfezione transiente e stabile hanno dimostrato che l'attività dell’elemento enhancer-blocker può essere attribuita esclusivamente ad un sub-regione di DNA di circa 400 bp chiamato AA0.4. Ulteriori test per valutare l'attività enhancer blocker di questa sequ…

CTCF and BORIS Regulate Rb2/p130 Gene Transcription: A Novel Mechanism and a New Paradigm for Understanding the Biology of Lung Cancer

2011

Abstract Although innumerable investigations regarding the biology of lung cancer have been carried out, many aspects thereof remain to be addressed, including the role played by the retinoblastoma-related protein Rb2/p130 during the evolution of this disease. Here we report novel findings on the mechanisms that control Rb2/p130 gene expression in lung fibroblasts and characterize the effects of Rb2/p130 deregulation on the proliferative features of lung cancer cells. We revealed for the first time that in lung fibroblasts the expression of Rb2/p130 gene is directly controlled by the chromatin insulator CCCTC-binding factor, CTCF, which by binding to the Rb2/p130 gene promoter induces, and/…

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…

HUMAN CHROMOSOME 4 SYNTENIC ASSOCIATIONS IN PLACENTAL MAMMALS

2009

Prospero hierae (Hyacinthaceae), a New Species from Marettimo Island (Sicily)

2009

A new species, Prospero hierae C. Brullo, S. Brullo, Giusso, Pavone & Salmeri (Hyacinthaceae), from Island of Marettimo (Egadi Archipelago, Sicily) is described and illustrated. Its chromosome number (2n = 14), leaf anatomy and ecology are examined. This small species with glaucous, adaxially flat leaves is closely related with the taxa belonging to the Prospero autumnale group and, in particular, it shows more affinities with P. corsicum, P. pulchellum and P. minimum.

RECONSTRUCTION OF GENOMIC REARRANGEMENTS IN AFRICAN DORMICE (RODENTIA-GLIRIDAE) BY CROSS-SPECIES CHROMOSOME PAINTING AND HUMAN SYNTENIC ASSOCIATION A…

2008

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