DNA methylation association with stage progression of head and neck squamous cell carcinoma.

Head and Neck Squamous Cell Carcinoma (HNSCC) is the sixth most common cancer worldwide, which accounts for approximately 6% of all cases and is responsible for an estimated 2% of all cancer deaths. Despite progress in the treatment of squamous cell carcinomas, survival rates remain low. It is a fact that epigenetic modifications have numerous associations with biological processes and complex diseases such as cancer. Hence, a more systematic approach is needed to provide potential screening targets and have an effective therapy method. This study developed a workflow to analyze HM450 methylation arrays with mRNA expression profiles that identified novel signatures of epigenetic regulators for tumor progression. We identified differentially expressed genes and differentially methylated regions and the correlation between associated genes to identify epigenetic modifications underlying regulation roles. We have taken the differentiation direction of expressions into account during the integration of gene expression and DNA methylation modification to detect epigenetic regulators of core genes of tumor-stage progression. Enrichment analysis of selected key genes provides better insight into their functionality. Thus, we have investigated gene copy number alteration and mutations to filter differentially expressed genes, including some members of the fibroblast growth factor family and cyclin-dependent kinase inhibitor family with other potential known regulators. Our analysis has revealed the list of 61 commercial methylation probes positively correlated with 31 differentially expressed genes, which can be associated with HNSC metastasis stages. Most of these genes have already reported potential epigenetic regulators, and their role in cancer progression was studied. We suggest these selected probes of DNA methylation as potential targets of the epigenetic regulators in revealed genes that have displayed significant genetic and epigenetic modification behavior during cancer stage progression and tumor metastasis.

CAMAMED: a pipeline for composition-aware mapping-based analysis of metagenomic data.

Metagenomics is the study of genomic DNA recovered from a microbial community. Both assembly-based and mapping-based methods have been used to analyze metagenomic data. When appropriate gene catalogs are available, mapping-based methods are preferred over assembly based approaches, especially for analyzing the data at the functional level. In this study, we introduce CAMAMED as a composition-aware mapping-based metagenomic data analysis pipeline. This pipeline can analyze metagenomic samples at both taxonomic and functional profiling levels. Using this pipeline, metagenome sequences can be mapped to non-redundant gene catalogs and the gene frequency in the samples are obtained. Due to the highly compositional nature of metagenomic data, the cumulative sum-scaling method is used at both taxa and gene levels for compositional data analysis in our pipeline. Additionally, by mapping the genes to the KEGG database, annotations related to each gene can be extracted at different functional levels such as KEGG ortholog groups, enzyme commission numbers and reactions. Furthermore, the pipeline enables the user to identify potential biomarkers in case-control metagenomic samples by investigating functional differences. The source code for this software is available from https://github.com/mhnb/camamed. Also, the ready to use Docker images are available at https://hub.docker.com.

Genes on B chromosomes: old questions revisited with new tools.

BACKGROUND: B chromosomes are supernumerary dispensable parts of the karyotype which appear in some individuals of some populations in some species. Often, they have been considered as 'junk DNA' or genomic parasites without functional genes. SCOPE OF REVIEW: Due to recent advances in sequencing technologies, it became possible to investigate their DNA composition, transcriptional activity and effects on the host transcriptome profile in detail. Here, we review the most recent findings regarding the gene content of B chromosomes and their transcriptional activities and discuss these findings in the context of comparable biological phenomena, like sex chromosomes, aneuploidy and pseudogenes. MAJOR CONCLUSIONS: Recent data suggest that B chromosomes carry transcriptionally active genic sequences which could affect the transcriptome profile of their host genome. GENERAL SIGNIFICANCE: These findings are gradually changing our view that B chromosomes are solely genetically inert selfish elements without any functional genes. This at one side could partly explain the deleterious effects which are associated with their presence. On the other hand it makes B chromosome a nice model for studying regulatory mechanisms of duplicated genes and their evolutionary consequences.

B chromosomes of rye are highly conserved and accompanied the development of early agriculture.

BACKGROUND AND AIMS: Supernumerary B chromosomes (Bs) represent a specific type of selfish genetic element. As Bs are dispensable for normal growth, it is expected to observe B polymorphisms among populations. To address whether Bs maintained in geographically distinct populations of cultivated and weedy rye are polymorphic, the distribution patterns and the transcriptional activity of different B-located repeats were analysed. METHODS: Bs of cultivated and weedy rye from seven origins were analysed by fluorescence in situ hybridization (FISH) with probes specific for the pericentromeric and interstitial regions as well as the B-specific non-disjunction control region. The DNA replication, chromatin composition and transcription behaviour of the non-disjunction regions were determined. To address whether the B-marker repeats E3900 and D1100 have diverged genotypes of different origin at the sequence level, the genomic sequences of both repeats were compared between cultivated rye and weedy rye from five different origins. KEY RESULTS: B chromosomes in cultivated and weedy rye have maintained a similar molecular structure at the level of subspecies. The high degree of conservation of the non-disjunction control region regarding its transcription activity, histone composition and replication underlines the functional importance of this chromosome region for the maintenance of Bs. The conserved chromosome structure suggests a monophyletic origin of the rye B. As Bs were found in different countries, it is likely that Bs were frequently present in the seed material used in early agriculture. CONCLUSIONS: The surprisingly conserved chromosome structure suggests that although the rye Bs experienced rapid evolution including multiple rearrangements at the early evolutionary stages, this process has slowed significantly and may have even ceased during its recent evolution.

Nondisjunction in favor of a chromosome: the mechanism of rye B chromosome drive during pollen mitosis.

B chromosomes (Bs) are supernumerary components of the genome and do not confer any advantages on the organisms that harbor them. The maintenance of Bs in natural populations is possible by their transmission at higher than Mendelian frequencies. Although drive is the key for understanding B chromosomes, the mechanism is largely unknown. We provide direct insights into the cellular mechanism of B chromosome drive in the male gametophyte of rye (Secale cereale). We found that nondisjunction of Bs is accompanied by centromere activity and is likely caused by extended cohesion of the B sister chromatids. The B centromere originated from an A centromere, which accumulated B-specific repeats and rearrangements. Because of unequal spindle formation at the first pollen mitosis, nondisjoined B chromatids preferentially become located toward the generative pole. The failure to resolve pericentromeric cohesion is under the control of the B-specific nondisjunction control region. Hence, a combination of nondisjunction and unequal spindle formation at first pollen mitosis results in the accumulation of Bs in the generative nucleus and therefore ensures their transmission at a higher than expected rate to the next generation.

Analysis of microRNA signatures using size-coded ligation-mediated PCR.

The expression pattern and regulatory functions of microRNAs (miRNAs) are intensively investigated in various tissues, cell types and disorders. Differential miRNA expression signatures have been revealed in healthy and unhealthy tissues using high-throughput profiling methods. For further analyses of miRNA signatures in biological samples, we describe here a simple and efficient method to detect multiple miRNAs simultaneously in total RNA. The size-coded ligation-mediated polymerase chain reaction (SL-PCR) method is based on size-coded DNA probe hybridization in solution, followed-by ligation, PCR amplification and gel fractionation. The new method shows quantitative and specific detection of miRNAs. We profiled miRNAs of the let-7 family in a number of organisms, tissues and cell types and the results correspond with their incidence in the genome and reported expression levels. Finally, SL-PCR detected let-7 expression changes in human embryonic stem cells as they differentiate to neuron and also in young and aged mice brain and bone marrow. We conclude that the method can efficiently reveal miRNA signatures in a range of biological samples.