The SEQC2 epigenomics quality control (EpiQC) study

BACKGROUND

Cytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify types of cancer and other diseases. However, the wide variety of approaches available to interrogate these modifications has created a need for harmonized materials, methods, and rigorous benchmarking to improve genome-wide methylome sequencing applications in clinical and basic research. Here, we present a multi-platform assessment and cross-validated resource for epigenetics research from the FDA's Epigenomics Quality Control Group.

RESULTS

Each sample is processed in multiple replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS MethylSeq, and SPLAT), oxidative bisulfite sequencing (TrueMethyl), enzymatic deamination method (EMSeq), targeted methylation sequencing (Illumina Methyl Capture EPIC), single-molecule long-read nanopore sequencing from Oxford Nanopore Technologies, and 850k Illumina methylation arrays. After rigorous quality assessment and comparison to Illumina EPIC methylation microarrays and testing on a range of algorithms (Bismark, BitmapperBS, bwa-meth, and BitMapperBS), we find overall high concordance between assays, but also differences in efficiency of read mapping, CpG capture, coverage, and platform performance, and variable performance across 26 microarray normalization algorithms.

CONCLUSIONS

The data provided herein can guide the use of these DNA reference materials in epigenomics research, as well as provide best practices for experimental design in future studies. By leveraging seven human cell lines that are designated as publicly available reference materials, these data can be used as a baseline to advance epigenomics research.

Increased symplasmic permeability in barley root epidermal cells correlates with defects in root hair development

It is well known that the process of plant cell differentiation depends on the symplasmic isolation of cells. Before starting the differentiation programme, the individual cell or group of cells should restrict symplasmic communication with neighbouring cells. We tested the symplasmic communication between epidermal cells in the different root zones of parental barley plants Hordeum vulgare L., cv. 'Karat' with normal root hair development, and two root hairless mutants (rhl1.a and rhl1.b). The results clearly show that symplasmic communication was limited during root hair differentiation in the parental variety, whereas in both root hairless mutants epidermal cells were still symplasmically connected in the corresponding root zone. This paper is the first report on the role of symplasmic isolation in barley root cell differentiation, and additionally shows that a disturbance in the restriction of symplasmic communication is present in root hairless mutants.

MPTP-induced central dopamine depletion exacerbates experimental autoimmune encephalomyelitis (EAE) in C57BL mice

It is obvious that the central nervous system plays a role in the regulation of an immune response. However, the mechanisms of this regulation are poorly understood. The goal of the present study was to examine the role of one of the neurotransmitters - dopamine, in this process. We used experimental autoimmune encephalomyelitis (EAE), an autoimmune disease with its effector phase in the CNS, as a model to study the effect of central dopamine depletion on the development of an immune response. Dopamine depletion was achieved by treatment with 1-methyl-4-phenyl-1, 2, 3, 6-tetrahydropiridine (MPTP; 40 mg/kg), whereas EAE was elicited by immunization with MOG 35-55 (150 microg) in complete Freund's adjuvant (CFA), supplemented with Mycobacterium tuberculosis. As determined by HPLC, striatal dopamine contents in mice treated with MPTP were significantly lower compared to vehicle-treated controls. Remarkably, striatal depletion of dopamine prior to EAE induction resulted in an earlier onset of the disease and an augmentation of its clinical signs. Moreover, the striatal dopamine-depleted mice demonstrated an increased concentration of IL-1beta and decreased concentration of TGFbeta in the spinal cord, compared to EAE mice. Since MPTP itself does not have any direct effect on immune cells, it strongly suggests that the observed changes in EAE induction and progression after MPTP administration depended on lower dopamine level. Further studies are required to find out the cellular mechanism of the dopamine action.

Beta-adrenergic receptors in corpora lutea from different stages of the estrous cycle in conscious and slaughtered cattle

The overall objective of this study was to determine the pattern of beta-adrenergic receptors in bovine luteal membranes obtained from slaughtered and from conscious cattle on different days of the estrous cycle. Two approaches were used with respect to the CL collection. In the first approach, CL (n = 20) were obtained from animals slaughtered in a local abattoir. The day of the estrous cycle was estimated based on the morphology of luteal tissue and follicles present. Using 3H-dihydroalprenolol (3H-DHA) as a ligand, we were unable to find specific binding in any of the tissues examined. Therefore, for the second approach we decided to collect CL from mature heifers or cows under local anesthesia on Days 4 (n = 15), 8 (n = 7), 12 (n = 6), and 16 (n = 3) of the estrous cycle by means of colpotomy or by lumbar incision. This procedure was chosen to reduce the influence of stress factors before CL collection. In these samples, specific beta-adrenergic binding sites were found and they varied during the estrous cycle. Maximal binding (Bmax; fmol/mg of protein) was highest on Day 4 (178.3 +/- 15.2); it then decreased significantly (73.2 +/- 14.7, 40.1 +/- 5.5, 10.8 +/- 0.8) on Days 8, 12, and 16, respectively. The dissociation constant (Kd; nM), which followed the same pattern, was 52.0 +/- 14.4, 16.3 +/- 3.9, 14.9 +/- 3.2, and 7.6 +/- 4.0) on the same days, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)

Effect of catecholamines and FSH on progesterone secretion by pig granulosa cells

Granulosa cells were recovered from small (1-3 mm in diameter) and large (greater than 6 mm in diameter) preovulatory follicles or from follicles of early pregnant pigs (3-5 mm, Day 18). Incubation of these cells (5 x 10(5)) was carried out in a shaking water bath (40 degrees C) for 2 h with or without salbutamol (10(-5) M), isoprenaline (10(-5) M), propranolol (10(-5) M) and FSH (100 ng/ml). Isoprenaline significantly increased progesterone production (P less than 0.05) by granulosa cells of small follicles and large preovulatory follicles but not by granulosa cells of follicles from early pregnant pigs. After blocking the beta-adrenoceptor with propranolol the stimulatory effect of catecholamines was not observed. FSH alone stimulated progesterone production, particularly in granulosa cells of early pregnant pigs (P less than 0.05) but FSH plus catecholamine treatment did not have any effect on progesterone release. These results suggest that catecholamines may play a regulatory role in follicle maturation and this may differ between naturally cyclic and early pregnant animals.