Ensembl regulation resources Zerbino, Daniel R; Johnson, Nathan; Juetteman, Thomas ...
Database : the journal of biological databases and curation,
2016, Letnik:
2016
Journal Article
Recenzirano
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New experimental techniques in epigenomics allow researchers to assay a diversity of highly dynamic features such as histone marks, DNA modifications or chromatin structure. The study of their ...fluctuations should provide insights into gene expression regulation, cell differentiation and disease. The Ensembl project collects and maintains the Ensembl regulation data resources on epigenetic marks, transcription factor binding and DNA methylation for human and mouse, as well as microarray probe mappings and annotations for a variety of chordate genomes. From this data, we produce a functional annotation of the regulatory elements along the human and mouse genomes with plans to expand to other species as data becomes available. Starting from well-studied cell lines, we will progressively expand our library of measurements to a greater variety of samples. Ensembl's regulation resources provide a central and easy-to-query repository for reference epigenomes. As with all Ensembl data, it is freely available at http://www.ensembl.org, from the Perl and REST APIs and from the public Ensembl MySQL database server at ensembldb.ensembl.org. Database URL: http://www.ensembl.org.
A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation, ...alignment, and evolutionary constraint analyses of 23 mammalian species for all ENCODE targets. Alignments were generated using four different methods; comparisons of these methods reveal large-scale consistency but substantial differences in terms of small genomic rearrangements, sensitivity (sequence coverage), and specificity (alignment accuracy). We describe the quantitative and qualitative trade-offs concomitant with alignment method choice and the levels of technical error that need to be accounted for in applications that require multisequence alignments. Using the generated alignments, we identified constrained regions using three different methods. While the different constraint-detecting methods are in general agreement, there are important discrepancies relating to both the underlying alignments and the specific algorithms. However, by integrating the results across the alignments and constraint-detecting methods, we produced constraint annotations that were found to be robust based on multiple independent measures. Analyses of these annotations illustrate that most classes of experimentally annotated functional elements are enriched for constrained sequences; however, large portions of each class (with the exception of protein-coding sequences) do not overlap constrained regions. The latter elements might not be under primary sequence constraint, might not be constrained across all mammals, or might have expendable molecular functions. Conversely, 40% of the constrained sequences do not overlap any of the functional elements that have been experimentally identified. Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization.
Low temperature tolerance was investigated in the imbibed seed of 15 seed lots of Lactuca sativa, 6 seed lots of Lactuca virosa and 8 seed lots of Lactuca serriola. During rapid cooling (20°Ch-1) ...some seed of all seed lots survived to -16°C but none to -20°C. The majority of seed lots retained over 50% viability above -14°C and investigations with L. sativa employing differential thermal analysis indicated that this was due to isolation of the embryo from external ice by the endosperm, and subsequent embryo supercooling. Certain seed lots showed high mortality at temperatures above -10°C and correlation of mortality with the formation of extracellular ice suggested that the endosperm in these seed lots was not an effective nucleation barrier. At slower cooling rates survival to -20°C was increased due to freeze desiccation of the embryo, and variation between species and seed lots was revealed. The maximum cooling rate for 50% survival to -20°C varied from 1.5 to 3°Ch-1 (L. sativa seed lots), from 4 to 6°Ch-1 (L. virosa seed lots) and from 3 to 10°Ch-1 (L. serriola seed lots). A model to explain variation in cooling rate tolerance was developed incorporating (1) the initial equilibrium moisture content of the fully imbibed seed, (2) the rate at which freeze desiccation of the supercooled embryo took place and (3) the seed moisture content at which nucleation (at -20°C) was no longer certain. In L. sativa, variation between seed lots appeared to be governed by factor (l); low seed moisture content was closely correlated with high survival at slow cooling rates. In L. serriola, variation between the two seed lots examined appeared to be due to differences in factor (2). Organic solvent and warm water treatment of L. sativa seed suggested that saccharides rather than lipids were responsible for the barrier action of the endosperm. Attempts to store fully imbibed seed at -8+/-2°C for prolonged periods were unsuccessful. The ecological and cryobiological significance of the results was discussed.
Low temperature tolerance was investigated in the imbibed seed of 15 seed lots of Lactuca sativa, 6 seed lots of Lactuca virosa and 8 seed lots of Lactuca serriola. During rapid cooling (20°Ch-1) ...some seed of all seed lots survived to -16°C but none to -20°C. The majority of seed lots retained over 50% viability above -14°C and investigations with L. sativa employing differential thermal analysis indicated that this was due to isolation of the embryo from external ice by the endosperm, and subsequent embryo supercooling. Certain seed lots showed high mortality at temperatures above -10°C and correlation of mortality with the formation of extracellular ice suggested that the endosperm in these seed lots was not an effective nucleation barrier. At slower cooling rates survival to -20°C was increased due to freeze desiccation of the embryo, and variation between species and seed lots was revealed. The maximum cooling rate for 50% survival to -20°C varied from 1.5 to 3°Ch-1 (L. sativa seed lots), from 4 to 6°Ch-1 (L. virosa seed lots) and from 3 to 10°Ch-1 (L. serriola seed lots). A model to explain variation in cooling rate tolerance was developed incorporating (1) the initial equilibrium moisture content of the fully imbibed seed, (2) the rate at which freeze desiccation of the supercooled embryo took place and (3) the seed moisture content at which nucleation (at -20°C) was no longer certain. In L. sativa, variation between seed lots appeared to be governed by factor (l); low seed moisture content was closely correlated with high survival at slow cooling rates. In L. serriola, variation between the two seed lots examined appeared to be due to differences in factor (2). Organic solvent and warm water treatment of L. sativa seed suggested that saccharides rather than lipids were responsible for the barrier action of the endosperm. Attempts to store fully imbibed seed at -8±2°C for prolonged periods were unsuccessful. The ecological and cryobiological significance of the results was discussed.
Background
The poor prognosis and rising incidence of esophageal adenocarcinoma highlight the need for improved detection methods. The potential for circulating microRNAs (miRNAs) as biomarkers in ...other cancers has been shown, but circulating miRNAs have not been well characterized in esophageal adenocarcinoma. We investigated whether circulating exosomal miRNAs have potential to discriminate individuals with esophageal adenocarcinoma from healthy controls and non-dysplastic Barrett’s esophagus.
Methods
Seven hundred fifty-eight miRNAs were profiled in serum circulating exosomes from a cohort of 19 healthy controls, 10 individuals with Barrett’s esophagus, and 18 individuals with locally advanced esophageal adenocarcinoma. MiRNA expression was assessed using all possible permutations of miRNA ratios per individual. Four hundred eight miRNA ratios were differentially expressed in individuals with cancer compared to controls and Barrett’s esophagus (Mann-Whitney
U
test,
P
< 0.05). The 179/408 ratios discriminated esophageal adenocarcinoma from healthy controls and Barrett’s esophagus (linear regression,
P
< 0.05; area under receiver operating characteristic (ROC) > 0.7,
P
< 0.05). A multi-biomarker panel (RNU6-1/miR-16-5p, miR-25-3p/miR-320a, let-7e-5p/miR-15b-5p, miR-30a-5p/miR-324-5p, miR-17-5p/miR-194-5p) demonstrated enhanced specificity and sensitivity (area under ROC = 0.99, 95 % CI 0.96–1.0) over single miRNA ratios to distinguish esophageal adenocarcinoma from controls and Barrett’s esophagus.
Conclusions
This study highlights the potential for serum exosomal miRNAs as biomarkers for the detection of esophageal adenocarcinoma.
Circulating microRNAs (miRNAs) are potential biomarkers for many diseases. However, they can originate from non-disease specific sources, such as blood cells, and compromise the investigations for ...miRNA biomarkers. While small extracellular vesicles (sEVs) have been suggested to provide a purer source of circulating miRNAs for biomarkers discovery, the most suitable blood sample for sEV miRNA biomarker studies has not been defined.
To compare the miRNA profiles between matched serum and plasma sEV preparations to determine their suitability for biomarker studies.
Matched serum and plasma samples were obtained from 10 healthy controls and 10 patients with esophageal adenocarcinoma. sEV isolates were prepared from serum and plasma using ExoQuick
and quantified using NanoSight. RNA was extracted from sEV preparations with the miRNeasy Serum/Plasma kit and profiled using the Taqman Openarray qPCR. The overall miRNA content and the expression of specific miRNAs of reported vesicular and non-vesicular origins were compared between serum and plasma sEV preparations. The diagnostic performance of a previously identified multi-miRNA biomarker panel for esophageal adenocarcinoma was also compared.
The overall miRNA content was higher in plasma sEV preparations (480 miRNAs) and contained 97.5% of the miRNAs found in the serum sEV preparations (412 miRNAs).The expression of commonly expressed miRNAs was highly correlated (Spearman's R = 0.87,
< 0.0001) between the plasma and serum sEV preparations, but was consistently higher in the plasma sEV preparations. Specific blood-cell miRNAs (hsa-miR-223-3p, hsa-miR-451a, miR-19b-3p, hsa-miR-17-5p, hsa-miR-30b-5p, hsa-miR-106a-5p, hsa-miR-150-5p and hsa-miR-92a-3p) were expressed at 2.7 to 9.6 fold higher levels in the plasma sEV preparations compared to serum sEV preparations (
< 0.05). In plasma sEV preparations, the percentage of protein-associated miRNAs expressed at relatively higher levels (Ct 20-25) was greater than serum sEV preparations (50%
31%). While the percentage of vesicle-associated miRNAs expressed at relatively higher levels was greater in the serum sEV preparations than plasma sEV preparations (70%
44%). A 5-miRNA biomarker panel produced a higher cross validated accuracy for discriminating patients with esophageal adenocarcinoma from healthy controls using serum sEV preparations compared with plasma sEV preparations (AUROC 0.80
0.54,
< 0.05).
Although plasma sEV preparations contained more miRNAs than serum sEV preparations, they also contained more miRNAs from non-vesicle origins. Serum appears to be more suitable than plasma for sEV miRNAs biomarkers studies.
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