Gene Ontology

Publication Title: 
Nature Neuroscience

Using the Illumina 450K array and a stringent statistical analysis with age and gender correction, we report genome-wide differences in DNA methylation between pathology-free regions derived from human multiple sclerosis-affected and control brains. Differences were subtle, but widespread and reproducible in an independent validation cohort. The transcriptional consequences of differential DNA methylation were further defined by genome-wide RNA-sequencing analysis and validated in two independent cohorts.

Author(s): 
Huynh, Jimmy L.
Garg, Paras
Thin, Tin Htwe
Yoo, Seungyeul
Dutta, Ranjan
Trapp, Bruce D.
Haroutunian, Vahram
Zhu, Jun
Donovan, Michael J.
Sharp, Andrew J.
Casaccia, Patrizia
Publication Title: 
European Journal of Medical Genetics

Schizophrenia (SCZ) is a complex mental disorder contributed by both genetic and epigenetic factors. Long noncoding RNAs (lncRNAs) was recently found playing an important regulatory role in mental disorders. However, little was known about the DNA methylation of lncRNAs, although numerous SCZ studies have been performed on genetic polymorphisms or epigenetic marks in protein coding genes. We presented a comprehensive genome wide DNA methylation study of both protein coding genes and lncRNAs in female patients with paranoid and undifferentiated SCZ.

Author(s): 
Liao, Qi
Wang, Yunliang
Cheng, Jia
Dai, Dongjun
Zhou, Xingyu
Zhang, Yuzheng
Gao, Shugui
Duan, Shiwei
Publication Title: 
PloS One

Huntington's disease (HD) is an autosomal-dominant neurodegenerative disorder resulting from expansion of CAG repeats in the Huntingtin (HTT) gene. Previous studies have shown mutant HTT can alter expression of genes associated with dysregulated epigenetic modifications. One of the most widely studied chromatin modifications is trimethylated lysine 4 of histone 3 (H3K4me3).

Author(s): 
Dong, Xianjun
Tsuji, Junko
Labadorf, Adam
Roussos, Panos
Chen, Jiang-Fan
Myers, Richard H.
Akbarian, Schahram
Weng, Zhiping
Publication Title: 
Genome Medicine

BACKGROUND: Alzheimer's disease affects ~13% of people in the United States 65 years and older, making it the most common neurodegenerative disorder. Recent work has identified roles for environmental, genetic, and epigenetic factors in Alzheimer's disease risk. METHODS: We performed a genome-wide screen of DNA methylation using the Illumina Infinium HumanMethylation450 platform on bulk tissue samples from the superior temporal gyrus of patients with Alzheimer's disease and non-demented controls.

Author(s): 
Watson, Corey T.
Roussos, Panos
Garg, Paras
Ho, Daniel J.
Azam, Nidha
Katsel, Pavel L.
Haroutunian, Vahram
Sharp, Andrew J.
Publication Title: 
PloS One

MicroRNAs (miRNAs) are endogenous small non-coding RNAs which play a critical role in gene regulation in plants. Pinelliapedatisecta is one of the most important herbs in traditional Chinese medicine, but there are no microRNAs of Pinelliapedatisecta were deposited in miRBase and the research of the related miRNA biological functions is still insufficient. To detect Pinelliapedatisecta miRNAs and discover their expression difference with Pinelliaternata, we carried out a microarray profiling.

Author(s): 
Dong, Miao
Yang, Dongfeng
Lang, Qiulei
Zhou, Wei
Xu, Shaowei
Xu, Tao
Publication Title: 
BMC genomics

BACKGROUND: Lycium chinense is well known in traditional Chinese herbal medicine for its medicinal value and composition, which have been widely studied for decades. However, further research on Lycium chinense is limited due to the lack of transcriptome and genomic information. RESULTS: The transcriptome of L. chinense was constructed by using an Illumina HiSeq 2000 sequencing platform. All 56,526 unigenes with an average length of 611 nt and an N50 equaling 848 nt were generated from 58,192,350 total raw reads after filtering and assembly.

Author(s): 
Zhao, Shicheng
Tuan, Pham Anh
Li, Xiaohua
Kim, Yeon Bok
Kim, Hyeran
Park, Chun Geon
Yang, Jingli
Li, Cheng Hao
Park, Sang Un
Publication Title: 
PloS One

Youngia japonica, a weed species distributed worldwide, has been widely used in traditional Chinese medicine. It is an ideal plant for studying the evolution of Asteraceae plants because of its short life history and abundant source. However, little is known about its evolution and genetic diversity. In this study, de novo transcriptome sequencing was conducted for the first time for the comprehensive analysis of the genetic diversity of Y. japonica. The Y. japonica transcriptome was sequenced using Illumina paired-end sequencing technology. We produced 21,847,909 high-quality reads for Y.

Author(s): 
Peng, Yulan
Gao, Xinfen
Li, Renyuan
Cao, Guoxing
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