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Charles J Cho, Jaeeun Jung, Lushang Jiang, Eun Ji Lee, Dae-Soo Kim, Byung Sik Kim, Hee Sung Kim, Hwoon-Yong Jung, Ho-June Song, Sung Wook Hwang, Yangsoon Park, Min Kyo Jung, Chan Gi Pack, Seung-Jae Myung, Suhwan Chang
BACKGROUND: Adenosine deaminase acting on RNA 1 (ADAR1) is known to mediate deamination of adenosine-to-inosine through binding to double-stranded RNA, the phenomenon known as RNA editing. Currently, the function of ADAR1 in gastric cancer is unclear. AIMS: This study was aimed at investigating RNA editing-dependent and editing-independent functions of ADAR1 in gastric cancer, especially focusing on its influence on editing of 3' untranslated regions (UTRs) and subsequent changes in expression of messenger RNAs (mRNAs) as well as microRNAs (miRNAs)...
April 25, 2018: Digestive Diseases and Sciences
Jun Zhang
This study aimed to further clarify the underlying pathomechanism of non-union skeletal fractures.Gene expression profile dataset GSE494 obtained from six non-union skeletal fracture and six normal samples was downloaded from the Gene Expression Omnibus database. Overlapping genes in at least two platforms were analyzed, and differentially expressed genes (DEGs) between normal and disease groups were screened. Transcriptional regulatory relationships and differentially regulated modules of various transcription factors (TFs) were determined...
March 16, 2018: Journal of Back and Musculoskeletal Rehabilitation
Xin Pan, Da Li, Jianing Huo, Fanfei Kong, Hui Yang, Xiaoxin Ma
Long noncoding RNAs (lncRNAs) have been implicated in tumorigenesis and cancer progression and are tightly associated with the phenotypes of numerous cancers. However, the functional roles underlying these effects are unknown. The expression levels of LINC01016, miR-302a-3p, miR-3130-3p, NFYA, and SATB1 were evaluated by quantitative real-time polymerase chain reaction (qRT-PCR) in 33 endometrial cancer tissues and 20 normal tissues. Bioinformatics analyses, luciferase reporter analyses, chromatin immunoprecipitation (ChIP) assays, and qRT-PCR assays were performed to verify potential binding sites...
February 21, 2018: Cell Death & Disease
Weijie Guo, Zhixiang Hu, Yichao Bao, Yuchen Li, Shengli Li, Qiupeng Zheng, Dongbin Lyu, Di Chen, Tao Yu, Yan Li, Xiaodong Zhu, Jie Ding, Yingjun Zhao, Xianghuo He, Shenglin Huang
The diversity and complexity of the cancer transcriptome may contain transcripts unique to the tumor environment. Here, we report a LIN28B variant, LIN28B-TST, which is specifically expressed in hepatocellular carcinoma (HCC) and many other cancer types. Expression of LIN28B-TST is associated with significantly poor prognosis in HCC patients. LIN28B-TST initiates from a de novo alternative transcription initiation site that harbors a strong promoter regulated by NFYA but not c-Myc. Demethylation of the LIN28B-TST promoter might be a prerequisite for its transcription and transcriptional regulation...
February 20, 2018: Cell Reports
Jingtao Guo, Edward J Grow, Chongil Yi, Hana Mlcochova, Geoffrey J Maher, Cecilia Lindskog, Patrick J Murphy, Candice L Wike, Douglas T Carrell, Anne Goriely, James M Hotaling, Bradley R Cairns
Human adult spermatogonial stem cells (hSSCs) must balance self-renewal and differentiation. To understand how this is achieved, we profiled DNA methylation and open chromatin (ATAC-seq) in SSEA4+ hSSCs, analyzed bulk and single-cell RNA transcriptomes (RNA-seq) in SSEA4+ hSSCs and differentiating c-KIT+ spermatogonia, and performed validation studies via immunofluorescence. First, DNA hypomethylation at embryonic developmental genes supports their epigenetic "poising" in hSSCs for future/embryonic expression, while core pluripotency genes (OCT4 and NANOG) were transcriptionally and epigenetically repressed...
October 5, 2017: Cell Stem Cell
Chuanwei Yang, Xuemei Zhao, Naipeng Cui, Yulong Liang
Triple-negative breast cancer (TNBC) is an aggressive type of breast cancer with poor prognosis and is enriched in cancer stem cells (CSCs). However, it is not completely understood how the CSCs were maintained in TNBC. In this study, by analyzing The Cancer Genome Atlas (TCGA) provisional datasets and several small-size breast datasets, we found that cadherins (CDHs) 2, 4, 6, and 17 were frequently amplified/overexpressed in 47% of TNBC while E-cadherin (CDH1) was downregulated/mutated at 10%. The alterations of CDH2/4/6/17 were strongly associated with the elevated levels of several stem cell-related transcription factors (SC-TFs) including FOXM1, MCM2, WWTR1, SNAI1, and SOX9...
2017: Stem Cells International
Falong Lu, Yuting Liu, Azusa Inoue, Tsukasa Suzuki, Keji Zhao, Yi Zhang
How the chromatin regulatory landscape in the inner cell mass cells is established from differentially packaged sperm and egg genomes during preimplantation development is unknown. Here, we develop a low-input DNase I sequencing (liDNase-seq) method that allows us to generate maps of DNase I-hypersensitive site (DHS) of mouse preimplantation embryos from 1-cell to morula stage. The DHS landscape is progressively established with a drastic increase at the 8-cell stage. Paternal chromatin accessibility is quickly reprogrammed after fertilization to the level similar to maternal chromatin, while imprinted genes exhibit allelic accessibility bias...
June 2, 2016: Cell
Feng Bing, Yu Zhao
OBJECTIVE: To screen the biomarkers having the ability to predict prognosis after chemotherapy for breast cancers. METHODS: Three microarray data of breast cancer patients undergoing chemotherapy were collected from Gene Expression Omnibus database. After preprocessing, data in GSE41112 were analyzed using significance analysis of microarrays to screen the differentially expressed genes (DEGs). The DEGs were further analyzed by Differentially Coexpressed Genes and Links to construct a function module, the prognosis efficacy of which was verified by the other two datasets (GSE22226 and GSE58644) using Kaplan-Meier plots...
2016: OncoTargets and Therapy
Junqin Chen, Martin E Young, John C Chatham, David K Crossman, Louis J Dell'Italia, Anath Shalev
Myocardial fatty acid β-oxidation is critical for the maintenance of energy homeostasis and contractile function in the heart, but its regulation is still not fully understood. While thioredoxin-interacting protein (TXNIP) has recently been implicated in cardiac metabolism and mitochondrial function, its effects on β-oxidation have remained unexplored. Using a new cardiomyocyte-specific TXNIP knockout mouse and working heart perfusion studies, as well as loss- and gain-of-function experiments in rat H9C2 and human AC16 cardiomyocytes, we discovered that TXNIP deficiency promotes myocardial β-oxidation via signaling through a specific microRNA, miR-33a...
July 1, 2016: American Journal of Physiology. Heart and Circulatory Physiology
Xiang Lu, Qing-Tian Li, Qing Xiong, Wei Li, Ying-Dong Bi, Yong-Cai Lai, Xin-Lei Liu, Wei-Qun Man, Wan-Ke Zhang, Biao Ma, Shou-Yi Chen, Jin-Song Zhang
Cultivated soybean has undergone many transformations during domestication. In this paper we report a comprehensive assessment of the evolution of gene co-expression networks based on the analysis of 40 transcriptomes from developing soybean seeds in cultivated and wild soybean accessions. We identified 2680 genes that are differentially expressed during seed maturation and established two cultivar-specific gene co-expression networks. Through analysis of the two networks and integration with quantitative trait locus data we identified two potential key drivers for seed trait formation, GA20OX and NFYA...
June 2016: Plant Journal: for Cell and Molecular Biology
Jun Ma, Ping Wang, Yilong Yao, Yunhui Liu, Zhen Li, Xiaobai Liu, Zhiqing Li, Xihe Zhao, Zhuo Xi, Hao Teng, Jing Liu, Yixue Xue
The blood-tumor barrier (BTB) forms a major obstacle in brain tumor therapy by preventing the delivery of sufficient quantities of therapeutic drugs. Long non-coding RNAs (lncRNAs) play important roles in both normal development and diseases including cancer. Here, we elucidated the expression of lncRNA metastasis associated lung adenocarcinoma transcript 1 (MALAT1) and defined its functional role in the regulation of BTB function as well as its possible molecular mechanisms. Our results proved that MALAT1 expression was up-regulated in brain microvessels of human glioma and glioma endothelial cells (GECs) which were obtained by co-culturing endothelial cells with glioma cells...
February 2016: Biochimica et Biophysica Acta
Tao Peng, Yongjiang Yang, Yifeng Zhao, Jianchao Gao, Muhammad Abbas, Guoqiang Wang, Hong Sun, Shuguang Li
OBJECTIVE: To detect the methylation status of gastric cancer tissue genome by DNA methylation chip. METHODS: Methylation status of 6 samples of gastric cancer tissues and their matched adjacent tissues was analyzed using methylated DNA immunoprecipitation(MeDIP) combined with NibleGen chip. Significantly different methylated genes in promoter region and CpG island between two tissues were searched. Functions of these significantly different methylated genes were analyzed by Gene Ontology and Pathway assays...
October 2015: Zhonghua Wei Chang Wai Ke za Zhi, Chinese Journal of Gastrointestinal Surgery
Yijie Han, Guantao Zheng, Tianxiao Yang, Shuyi Zhang, Dong Dong, Yi-Hsuan Pan
BACKGROUND: Hibernation is a survival mechanism in the winter for some animals. Fat preserved instead of glucose produced is the primary fuel during winter hibernation of mammals. Many genes involved in lipid metabolism are regulated by the peroxisome proliferator-activated receptor alpha (PPARα). The role of PPARα in hibernation of mammals remains largely unknown. Using a multidisciplinary approach, we investigated whether PPARα is adapted to hibernation in bats. RESULTS: Evolutionary analyses revealed that the ω value of Pparα of the ancestral lineage of hibernating bats in both Yinpterochiroptera and Yangochiroptera was lower than that of non-hibernating bats in Yinpterochiroptera, suggesting that a higher selective pressure acts on Pparα in hibernating bats...
2015: BMC Evolutionary Biology
Lisha P Luke, M B Mohamed Sathik, Molly Thomas, Linu Kuruvilla, K V Sumesh, K Annamalainathan
In order to meet the ever rising global demand for natural rubber, cultivation of Hevea is being extended to non-traditional regions of India where extreme climatic conditions like drought and low temperature negatively influence the crop performance. In order to ensure maximum productivity, identification of drought tolerant clones of Hevea which can cope up with stress and give better crop yield is essential. Several attempts have been made previously to identify genes that are associated with drought tolerance in Hevea...
April 2015: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
Jian Li, Yinyin Cao, Yao Wu, Weicheng Chen, Yuan Yuan, Xiaojing Ma, Guoying Huang
BACKGROUND: Mutation of NKX2-5 could lead to the development of congenital heart disease (CHD) which is a common inherited disease. This study aimed to investigate the pathogenesis of CHD in NKX2-5 knock-out embryonic mice. METHODS: The expression profile in the NKX2-5 knock-out embryonic mice (GSE528) was downloaded from Gene Expression Omnibus. The heart tissues from the null/heterozygous embryonic day 12.5 mice were compared with wild-type mice to identify differentially expressed genes (DEGs), and then DEGs corresponding to the transcriptional factors were filtered out based on the information in the TRANSFAC database...
December 2015: Journal of Cardiology
Baoyuan Qu, Xue He, Jing Wang, Yanyan Zhao, Wan Teng, An Shao, Xueqiang Zhao, Wenying Ma, Junyi Wang, Bin Li, Zhensheng Li, Yiping Tong
Increasing fertilizer consumption has led to low fertilizer use efficiency and environmental problems. Identifying nutrient-efficient genes will facilitate the breeding of crops with improved fertilizer use efficiency. This research performed a genome-wide sequence analysis of the A (NFYA), B (NFYB), and C (NFYC) subunits of Nuclear Factor Y (NF-Y) in wheat (Triticum aestivum) and further investigated their responses to nitrogen and phosphorus availability in wheat seedlings. Sequence mining together with gene cloning identified 18 NFYAs, 34 NFYBs, and 28 NFYCs...
February 2015: Plant Physiology
Young-Wook Kim, Hee-Jeong Jung, Jong-In Park, Yoonkang Hur, Ill-Sup Nou
Environmental stresses, including both abiotic and biotic stresses, cause considerable yield loss in crops and can significantly affect their development. Under field conditions, crops are exposed to a variety of concurrent stresses. Among abiotic and biotic stresses, heat and Fusarium oxysporum, are the most important factors affecting development and yield productivity of Brassica oleracea. Genes encoding the nucleotide-binding site (NBS) motif are known to be related to responses to abiotic and biotic stresses in many plants...
January 2015: Plant Physiology and Biochemistry: PPB
Muhammad Faisal, Durdana Waseem, Humaira Ismatullah, Malik Mumtaz Taqi
Single nucleotide polymorphisms (SNPs) both in coding and non-coding regions govern gene functions prompting differential vulnerability to diseases, heterogeneous response to pharmaceutical regimes and environmental anomalies. These genetic variations, SNPs, may alter an individual׳s susceptibility for alcohol dependence by remodeling DNA-protein interaction patterns in prodynorphin (PDYN) and the κ-opioid receptor (OPRK1) genes. In order to elaborate the underlying molecular mechanism behind these susceptibility differences we used bioinformatics tools to retrieve differential DNA-protein interactions at PDYN and OPRK1 SNPs significantly associated with alcohol dependence...
October 2014: Computers in Biology and Medicine
Imen Samet, Junkyu Han, Lobna Jlaiel, Sami Sayadi, Hiroko Isoda
Differentiation therapy is an attractive approach aiming at reversing malignancy and reactivating endogenous differentiation programs in cancer cells. Olive leaf extract, known for its antioxidant activity, has been demonstrated to induce apoptosis in several cancer cells. However, its differentiation inducing properties and the mechanisms involved are still poorly understood. In this study, we investigated the effect of Chemlali Olive Leaf Extract (COLE) for its potential differentiation inducing effect on multipotent leukemia K562 cells...
2014: Oxidative Medicine and Cellular Longevity
Y Gong, Y Cao, L Song, J Zhou, C Wang, B Wu
Gastric cancer is a major health problem worldwide; it is the second most common cause of cancer death in the world. Recent studies indicate that the high-mobility group (HMG) of chromosomal proteins is associated with cancer progression. However, HMGB3 has been little studied. We analyzed the co-expression network between HMGB3 and differentially-expressed genes in the GSE17187 database, identifying the relevant transcription factors, and the conserved domain of HMGB3 to understand the underlying regulation mechanisms involved in gastric cancer...
2013: Genetics and Molecular Research: GMR
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