Catalogue Search | MBRL
Are you sure you want to remove the book from the shelf?
{{itemTitle}}
10,724
result(s) for
"1988"
Sort by:
Subtraction-free and bisulfite-free specific sequencing of 5-methylcytosine and its oxidized derivatives at base resolution
Although various methods have been developed for sequencing cytosine modifications, it is still challenging for specific and quantitative sequencing of individual modification at base-resolution. For example, to obtain both true 5-methylcytosine (5mC) and true 5-hydroxymethylcytosine (5hmC) information, the two major epigenetic modifications, it usually requires subtraction of two methods, which increases noise and requires high sequencing depth. Recently, we developed TET-assisted pyridine borane sequencing (TAPS) for bisulfite-free direct sequencing of 5mC and 5hmC. Here we demonstrate that two sister methods, TAPSβ and chemical-assisted pyridine borane sequencing (CAPS), can be effectively used for subtraction-free and specific whole-genome sequencing of 5mC and 5hmC, respectively. We also demonstrate pyridine borane sequencing (PS) for whole-genome profiling of 5-formylcytosine and 5-carboxylcytosine, the further oxidized derivatives of 5mC and 5hmC. This work completes the set of versatile borane reduction chemistry-based methods as a comprehensive toolkit for direct and quantitative sequencing of all four cytosine epigenetic modifications.
Specific and quantitative sequencing of cytosine modifications is challenging at base-resolution. Here the authors present TAPSβ and CAPS for subtraction-free whole genome sequencing of 5mC and 5hmC.
Journal Article
Enhancing democracy
Since the end of the Pinochet regime, Chilean public policy has sought to rebuild democratic governance in the country. This book examines the links between the state and civil society in Chile and the ways social policies have sought to ensure the inclusion of the poor in society and democracy. Although Chile has gained political stability and grown economically, the ability of social policies to expand democratic governance and participation has proved limited, and in fact such policies have become subordinate to an elitist model of democracy and resulted in a restrictive form of citizen participation.
eBook
Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm
The oil palm fruit ‘mantled’ abnormality is a somaclonal variant that markedly reduces yield; here, a genome-wide DNA methylation analysis finds that hypomethylation of a single Karma family retrotransposon embedded in a homeotic gene intron is common to all mantled clones and is associated with aberrant splicing and termination of the gene transcript, and that loss of methylation predicts a loss of oil palm yield.
How Bad Karma epiallele can ruin oil palm oil crops
A flower and fruit abnormality known as 'mantled' can develop in some agricultural oil palm cultivars derived from tissue culture and the resulting mantled palms can become unproductive. Mantling is widely regarded as an epigenetic trait, but has not been fully explained. Meilina Ong-Abdullah
et al
. have undertaken a genome-wide, unbiased, DNA methylation analysis to look for loci epigenetically associated with the mantled phenotype. They find that hypomethylation of a single
Karma
family retrotransposon embedded in the intron of a homeotic gene is common to all mantled clones and associated with aberrant splicing and termination of the gene transcript. Loss of methylation — dubbed the
Bad Karma
epiallele — predicts a loss of oil palm yield and this property should enable screening for higher-performing clones at the plantlet stage.
Somaclonal variation arises in plants and animals when differentiated somatic cells are induced into a pluripotent state, but the resulting clones differ from each other and from their parents. In agriculture, somaclonal variation has hindered the micropropagation of elite hybrids and genetically modified crops, but the mechanism responsible remains unknown
1
. The oil palm fruit ‘mantled’ abnormality is a somaclonal variant arising from tissue culture that drastically reduces yield, and has largely halted efforts to clone elite hybrids for oil production
2
,
3
,
4
. Widely regarded as an epigenetic phenomenon
5
, ‘mantling’ has defied explanation, but here we identify the
MANTLED
locus using epigenome-wide association studies of the African oil palm
Elaeis guineensis
. DNA hypomethylation of a LINE retrotransposon related to rice
Karma
, in the intron of the homeotic gene
DEFICIENS
, is common to all mantled clones and is associated with alternative splicing and premature termination. Dense methylation near the
Karma
splice site (termed the
Good Karma
epiallele) predicts normal fruit set, whereas hypomethylation (the
Bad Karma
epiallele) predicts homeotic transformation, parthenocarpy and marked loss of yield. Loss of
Karma
methylation and of small RNA in tissue culture contributes to the origin of mantled, while restoration in spontaneous revertants accounts for non-Mendelian inheritance. The ability to predict and cull mantling at the plantlet stage will facilitate the introduction of higher performing clones and optimize environmentally sensitive land resources.
Journal Article
Rihanna
In this book, readers will learn how a shy girl from a small island in the Caribbean became the colorful singer who tours the world today.
Book
DNA N6-methyladenine is dynamically regulated in the mouse brain following environmental stress
Chemical modifications on DNA molecules, such as 5-methylcytosine and 5-hydroxymethylcytosine, play important roles in the mammalian brain. A novel DNA adenine modification,
N
(6)-methyladenine (6mA), has recently been found in mammalian cells. However, the presence and function(s) of 6mA in the mammalian brain remain unclear. Here we demonstrate 6mA dynamics in the mouse brain in response to environmental stress. We find that overall 6mA levels are significantly elevated upon stress. Genome-wide 6mA and transcriptome profiling reveal an inverse association between 6mA dynamic changes and a set of upregulated neuronal genes or downregulated LINE transposon expression. Genes bearing stress-induced 6mA changes significantly overlap with loci associated with neuropsychiatric disorders. These results suggest an epigenetic role for 6mA in the mammalian brain as well as its potential involvement in neuropsychiatric disorders.
N6-methyladenine is a covalent epigenetic modification of the genome. Here, Yao and colleagues show that N6-methyladenine level in the mouse brain is dynamic following environmental stress, and the subsequent differential gene expression is correlated with LINE transposon expression.
Journal Article
Rihanna : singing sensation
This brief biography takes a look at the life and career of Barbadian pop singer Rihanna.
Book
Identification of methylated deoxyadenosines in vertebrates reveals diversity in DNA modifications
The identification of
N
6
-methyldeoxyadenosine in the DNA of
Xenopus laevis
, mice and humans extends the presence of this mark to vertebrates, thus fostering the potential importance of this mark as a carrier of epigenetic information.
Methylation of cytosine deoxynucleotides generates 5-methylcytosine (m
5
dC), a well-established epigenetic mark. However, in higher eukaryotes much less is known about modifications affecting other deoxynucleotides. Here, we report the detection of
N
6
-methyldeoxyadenosine (m
6
dA) in vertebrate DNA, specifically in
Xenopus laevis
but also in other species including mouse and human. Our methylome analysis reveals that m
6
dA is widely distributed across the eukaryotic genome and is present in different cell types but is commonly depleted from gene exons. Thus, direct DNA modifications might be more widespread than previously thought.
Journal Article