scholarly journals CpG Island Methylation in Human Lymphocytes Is Highly Correlated with DNA Sequence, Repeats, and Predicted DNA Structure

PLoS Genetics ◽  
2006 ◽  
Vol 2 (3) ◽  
pp. e26 ◽  
Author(s):  
Christoph Bock ◽  
Martina Paulsen ◽  
Sascha Tierling ◽  
Thomas Mikeska ◽  
Thomas Lengauer ◽  
...  
PLoS Genetics ◽  
2005 ◽  
Vol preprint (2006) ◽  
pp. e26 ◽  
Author(s):  
Christoph Bock ◽  
Martina Paulsen ◽  
Sascha Tierling ◽  
Thomas Mikeska ◽  
Thomas Lengauer ◽  
...  

2008 ◽  
Vol 69 (1) ◽  
pp. 282-291 ◽  
Author(s):  
Michael T. McCabe ◽  
Eva K. Lee ◽  
Paula M. Vertino

2021 ◽  
Vol 22 (3) ◽  
pp. 1328
Author(s):  
Rui Zhou ◽  
Yi Qin Gao

The recent development of sequencing technology and imaging methods has provided an unprecedented understanding of the inter-phase chromatin folding in mammalian nuclei. It was found that chromatin folds into topological-associated domains (TADs) of hundreds of kilo base pairs (kbps), and is further divided into spatially segregated compartments (A and B). The compartment B tends to be located near to the periphery or the nuclear center and interacts with other domains of compartments B, while compartment A tends to be located between compartment B and interacts inside the domains. These spatial domains are found to highly correlate with the mosaic CpG island (CGI) density. High CGI density corresponds to compartments A and small TADs, and vice versa. The variation of contact probability as a function of sequential distance roughly follows a power-law decay. Different chromosomes tend to segregate to occupy different chromosome territories. A model that can integrate these properties at multiple length scales and match many aspects is highly desired. Here, we report a DNA-sequence based coarse-grained block copolymer model that considers different interactions between blocks of different CGI density, interactions of TAD formation, as well as interactions between chromatin and the nuclear envelope. This model captures the various single-chromosome properties and partially reproduces the formation of chromosome territories.


2021 ◽  
Vol 19 ◽  
Author(s):  
Tingting Pi ◽  
Guangping Lang ◽  
Bo Liu ◽  
Jingshan Shi

Background: High methionine-diet (HMD) causes Alzheimer's disease (AD)-like symptoms. Previous studies have shown that Dendrobium nobile Lindle. alkaloids (DNLA) had potential benefits for AD. Object: Whether DNLA can improve AD-like symptoms induced by HMD is to be explored. Method: Mice were fed with 2% HMD diet for 11 weeks, the DNLA20 control group (20 mg/kg), DNLA10 group (10 mg/kg), and DNLA20 group (20 mg/kg) were administrated with DNLA for 3 months. Morris water maze test was used to detect learning and memory ability. Neuron damage was evaluated by HE and Nissl stainings. Levels of homocysteine (Hcy), beta-amyloid 1-42 (Aβ1-42), S-adenosine methionine (SAM), and S-adenosine homocysteine (SAH) were detected by ELISA. Immunofluorescence and western blotting (WB) were used to determine the expression of proteins. CPG island methylation. Results: Morris water maze test revealed that DNLA improved learning and memory dysfunction. HE, Nissl, and immunofluorescence stainings showed that DNLA alleviated neuron damage and reduced the 5-methylcytosine (5-mC), Aβ1-40, and Aβ1-42 levels. DNLA also decreased the levels of Hcy and Aβ1-42 in the serum, along with decreased SAM/SAH levels in the liver tissue. WB results showed that DNLA down-regulated the expression of the amyloid-precursor protein (APP), presenilin-1 (PS1), beta-secretase-1 (BACE1), DNA methyltransferase1 (DNMT1), Aβ1-40, and Aβ1-42 proteins. DNLA also up-regulated the expression of the protein of insulin-degrading enzyme (IDE), neprilysin (NEP), DNMT3a, and DNMT3b. Meanwhile, DNLA increased CPG island methylation levels of APP and BACE1 genes. Conclusions: DNLA alleviated AD-like symptoms induced by HMD via the DNA methylation pathway.


2004 ◽  
Vol 67 (1/2) ◽  
pp. 159-165 ◽  
Author(s):  
M. Eva Alonso ◽  
M. Josefa Bello ◽  
Pilar Gonzalez-Gomez ◽  
Dolores Arjona ◽  
Jose M. de Campos ◽  
...  

2014 ◽  
Vol 8 (5) ◽  
pp. 2340-2344 ◽  
Author(s):  
YU SONG ◽  
YUN ZUO

2015 ◽  
Vol 7 (1) ◽  
Author(s):  
Scott M. Langevin ◽  
Melissa Eliot ◽  
Rondi A. Butler ◽  
Agnes Cheong ◽  
Xiang Zhang ◽  
...  

2009 ◽  
Vol 10 (1) ◽  
pp. 116 ◽  
Author(s):  
Christopher Previti ◽  
Oscar Harari ◽  
Igor Zwir ◽  
Coral del Val

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