Transcriptome and DNA methylome analyses provide insight into the heterosis in flag leaf of inter-subspecific hybrid rice

Plant Molecular Biology - Flag leaf heterosis of inter-subspecific hybrid rice is suggested to be related to leaf area, gene expression pattern and allele-specific expression, putatively related to...     

Epigenetic silencing of genomic structural variations

A great amount of copy number variations (CNVs) are identified in the human genome. Most of them are neutral; nevertheless, the role of CNVs in the pathogenesis of hereditary diseases is still significant. Especially, this is important for neuropsychiatric disorders, such as intellectual disability and autism. When analyzing the CNV-associated diseases, the controversial question is to distinguish the pathogenic CNVs among common polymorphic variants and to predict the disease risk in other children of the family. Unfortunately, the mechanisms of phenotypic expression and incomplete penetrance of CNVs remain largely unknown. Currently, incomplete penetrance and variable expressivity of CNVs are attributed mainly to allelic interaction of different genetic variations. However, epigenetic mechanisms of gene expression regulation in the context of structural variation of the genome are poorly explored. It is possible that epigenetic modifications of the genome regions with CNVs may underlie the understanding of ways of phenotypic manifestations of structural variations in the human genome.     

Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations

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Immunohistochemical demonstration of keratins in the cysts of thyroid glands, parathyroid glands, and C-cell complexes of the dog

Cyst structures were often detected in and around thyroid glands of the dog. The present study revealed the frequency of occurrence, the light microscopic features, and the immunoperoxidase reactions to anti-keratin and anti-19S-thyroglobulin antisera of each cyst located in parathyroid III, parathyroid IV, thymus IV, C-cell complexes, and thyroid parenchyma from 112 dogs. In each location, cysts showed characteristic features. In parathyroid III, the cysts were covered with single or pseudostratified epithelium composed of ciliated cells; whereas in parathyroid IV they were covered with keratinizing stratified squamous epithelium. In C-cell complexes, small cysts lined with small packed cells were predominant, and large cysts lined with single cuboidal cells or stratified squamous cells were also present. In thymus IV located in the close vicinity of parathyroid IV, cyst epithelium consisted of several types of cells showing variable features. In thyroid parenchyma, there were several types of cysts: some were covered with ciliated columnar cells, and others were covered with two or multilayers of small packed cells or cuboidal cells. In spite of these differences in appearance of the cysts located in different tissues, all their epithelia were immunoreactive to the keratin antisera, except for small cysts in C-cell complexes, which were regarded as immature structures. Thus, the presence of keratin filaments in epithelial cells seems to be a characteristic feature of all cysts. The lumens of each cyst contained variable amounts of amorphous materials, which showed colloid-like, flocculent, foamy, and granular features and were periodic acid-Schiff-positive in variable degrees, from weak to intense. Although the lumenal contents of the cysts in parathyroid III revealed no immunoreactivity for 19S-thyroglobulin, those in thyroid parenchyma, C-cell complexes, parathyroid IV, and thymus IV reacted strongly with the 19S-thyroglobulin antiserum.     

Whole genome sequencing and methylome analysis of the wild guinea pig

Background

DNA methylation is a heritable mechanism that acts in response to environmental changes, lifestyle and diseases by influencing gene expression in eukaryotes. Epigenetic studies of wild organisms are mandatory to understand their role in e.g. adaptational processes in the great variety of ecological niches. However, strategies to address those questions on a methylome scale are widely missing. In this study we present such a strategy and describe a whole genome sequence and methylome analysis of the wild guinea pig.

Results

We generated a full Wild guinea pig (Cavia aperea) genome sequence with enhanced coverage of methylated regions, benefiting from the available sequence of the domesticated relative Cavia porcellus. This new genome sequence was then used as reference to map the sequence reads of bisulfite treated Wild guinea pig sequencing libraries to investigate DNA-methylation patterns at nucleotide-specific level, by using our here described method, named ‘DNA-enrichment-bisulfite-sequencing’ (MEBS). The results achieved using MEBS matched those of standard methods in other mammalian model species. The technique is cost efficient, and incorporates both methylation enrichment results and a nucleotide-specific resolution even without a whole genome sequence available. Thus MEBS can be easily applied to extend methylation enrichment studies to a nucleotide-specific level.

Conclusions

The approach is suited to study methylomes of not yet sequenced mammals at single nucleotide resolution. The strategy is transferable to other mammalian species by applying the nuclear genome sequence of a close relative. It is therefore of interest for studies on a variety of wild species trying to answer evolutionary, adaptational, ecological or medical questions by epigenetic mechanisms.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1036) contains supplementary material, which is available to authorized users.     

An immunochemical method for detection and analysis of changes in methylome

DNA methylation is an important epigenetic modification involved in the ability of an organism to respond to stress and adaptation. It has been implicated in development, differentiation, oncogenesis, chromatin remodelling, nutrigenomics, and appears to play a pivotal role in many regulatory and adaptive functions. It is therefore important to analyze the status of DNA methylation and its changes under various developmental, carcinogenic, pharmacological, and environmental conditions. In this report we describe an immunochemical method for the detection of genome wide DNA methylation and its alterations under various conditions along with the analysis of DNA methyltransferase activity. The ability of this approach to detect and provide a map of methylomic changes in a genome facilitates assessment of various agents and conditions which can alter this important epigenetic signal. This experimental system permits rapid evaluation of potential target genes which would be modulated by DNA methylation changes and thus the gene networks that govern the processes.     

The thyroid and parathyroid glands in the Giant panda, Ailuropoda melanoleuca

Observations are submitted upon the anatomy of the thyroid and parathyroid glands of Ailuropoda melanoleuca following gland investigation in three specimens. Variations of thyroid configuration and of parathyroid topography are noted, the thyroid vasculature is described in detail and an initial contribution is made to thyroid and parathyroid histology in this genus.