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Dirk Roos, Martin de Boer
Retrotransposable elements are stretches of DNA that encode proteins with the inherent ability to insert their own RNA or another RNA by reverse transcriptase as DNA into a new genomic location. In humans, the only autonomous retrotransposable elements are members of the Long INterspersed Element-1 (LINE-1) family. LINE-1s may cause gene inactivation and human disease. We present a brief summary of the published knowledge about LINE-1s in humans and the RNAs that these elements can transpose, and we focus on the effect of LINE-1-mediated retrotransposition on human neutrophil function...
May 17, 2018: European Journal of Clinical Investigation
Ye Fu, Wubin Wang, Xuejing Li, Yanli Liu, Yingying Niu, Bin Zhang, Jisheng Nie, Baolong Pan, Ruisheng Wang, Jin Yang
Benzo [a]pyrene (BaP) have been demonstrated to induce lung cancer risk in humans and many different animal models, with aberrant gene methylation as one of the epigenetic errors; however, the molecular mechanisms remain unclear. Here, we used three types of human lung-derived cells with BaP exposure as a model and attempted to investigate the long non-coding RNA (lncRNA) H19/S-adenosylhomocysteine hydrolase (SAHH) pathway that regulates gene methylation in vitro exposure to BaP. Results showed that compared to the controls, BaP-treated cells H19 expressions were increased in a dose- and time-dependent manner, whereas SAHH protein expressions were decreased...
May 9, 2018: Chemosphere
Naoki Yamamoto, Richard Garcia, Tomohiro Suzuki, Celymar Angela Solis, Yuichi Tada, Ramaiah Venuprasad, Ajay Kohli
BACKGROUND: Increasing rice demand is one of the consequences of the steadily improving socio-economic status of the African countries. New Rice for Africa (NERICA), which are interspecific hybrids between Asian and African rice varieties, are one of successful breeding products utilizing biodiversity across the two different rice crop species. Upland NERICA varieties (NU) exhibit agronomic traits of value for the harsh eco-geography, including shorter duration, higher yield and stress tolerance, compared to local African varieties...
May 15, 2018: Rice
Shijia Zhu, John Beaulaurier, Gintaras Deikus, Tao Wu, Maya Strahl, Ziyang Hao, Guanzheng Luo, James A Gregory, Andrew Chess, Chuan He, Andrew Xiao, Robert Sebra, Eric E Schadt, Gang Fang
N6-methyladenine (m6dA) has been discovered as a novel form of DNA methylation prevalent in eukaryotes, however, methods for high resolution mapping of m6dA events are still lacking. Single-molecule real-time (SMRT) sequencing has enabled the detection of m6dA events at single-nucleotide resolution in prokaryotic genomes, but its application to detecting m6dA in eukaryotic genomes has not been rigorously examined. Herein, we identified unique characteristics of eukaryotic m6dA methylomes that fundamentally differ from those of prokaryotes...
May 15, 2018: Genome Research
Heidi Marjonen, Mia Toivonen, Laura Lahti, Nina Kaminen-Ahola
Prenatal alcohol exposure (PAE) can harm the embryonic development and cause life-long consequences in offspring's health. To clarify the molecular mechanisms of PAE we have used a mouse model of early alcohol exposure, which is based on maternal ad libitum ingestion of 10% (v/v) ethanol for the first eight days of gestation (GD 0.5-8.5). Owing to the detected postnatal growth-restricted phenotype in the offspring of this mouse model and both prenatal and postnatal growth restriction in alcohol-exposed humans, we focused on imprinted genes Insulin-like growth factor 2 (Igf2), H19, Small Nuclear Ribonucleoprotein Polypeptide N (Snrpn) and Paternally expressed gene 3 (Peg3), which all are known to be involved in embryonic and placental growth and development...
2018: PloS One
Eric S Coker, Robert Gunier, Karen Huen, Nina Holland, Brenda Eskenazi
Background: Maternal social environmental stressors during pregnancy are associated with adverse birth and child developmental outcomes, and epigenetics has been proposed as a possible mechanism for such relationships. Methods: In a Mexican-American birth cohort of 241 maternal-infant pairs, cord blood samples were measured for repeat element DNA methylation ( LINE-1 and Alu ). Linear mixed effects regression was used to model associations between indicators of the social environment (low household income and education, neighborhood-level characteristics) and repeat element methylation...
2018: Clinical Epigenetics
Tatsunori Miyata, Yo-Ichi Yamashita, Yoshifumi Baba, Kazuto Harada, Takanobu Yamao, Naoki Umezaki, Masayo Tsukamoto, Yuki Kitano, Kensuke Yamamura, Kota Arima, Shigeki Nakagawa, Hirohisa Okabe, Katsunori Imai, Daisuke Hashimoto, Akira Chikamoto, Mototsugu Shimokawa, Hideo Baba
Background: The methylation level of long interspersed nucleotide element-1 (LINE-1) is a good surrogate marker of the global DNA methylation level. The relationship between LINE-1 methylation level and prognosis in primary liver cancer (PLC) patients remains unclear. Results: LINE-1 methylation levels were significantly lower in HCC and cHCC-CC tissues, but not in ICC tissues, than those in noncancerous liver parenchyma (HCC: p < 0.0001; cHCC-CC: p < 0.001; and ICC: p = 0...
April 17, 2018: Oncotarget
Manosij Ghosh, Deniz Öner, Radu C Duca, Bram Bekaert, Jeroen A J Vanoirbeek, Lode Godderis, Peter H M Hoet
Recent studies have identified carbon nanotube (CNT)-induced epigenetic changes as one of the key players in patho-physiological response. In the present study, we investigated whether CNT exposure is associated with epigenetic changes in human bronchial epithelial cells (16 HBE), in vitro . We focused on global DNA methylation, methylation of LINE-1 elements and promoter sequence of twelve functionally important genes ( SKI, DNMT1, HDAC4 , NPAT, ATM, BCL2L11, MAP3K10, PIK3R2, MYO1C, TCF3, FGFR 1 and AGRN )...
April 17, 2018: Oncotarget
Yifan Yang, Zhu Jin, Rui Dong, Chao Zheng, Yanlei Huang, Yijie Zheng, Zhen Shen, Gong Chen, Xiaoying Luo, Shan Zheng
Biliary atresia is one of the most common liver disease in infancy. The cause and pathogenesis remain largely unknown. This study aimed to investigate the potential regulatory effect of miR-29b/142-5p on IFN-γ gene methylation. miRNAs microarray was performed on four pairs of liver and blood specimens from biliary atresia and choledochal cysts. We found the overexpression of miR-142-5p and mRNA level of DNA methyltransferase (DNMT) 1, and miR-29b and DNMT3a/DNMT3b were significantly negatively correlated in biliary atresia livers...
May 10, 2018: Cell Death & Disease
A Herrmann, S Wittmann, D Thomas, C N Shepard, B Kim, N Ferreirós, T Gramberg
[This corrects the article DOI: 10.1186/s13100-018-0116-5.].
2018: Mobile DNA
Simone Sidoli
Histones are the most abundant protein family in the cells of complex organisms such as mammals and, together with DNA, they define the backbone of chromatin. Histone PTMs are key players of chromatin biology, as they function as anchors for proteins that bind and modulate chromatin readout, including gene expression. Middle-down mass spectrometry (MS) has been optimized for about 10 years to study histone N-terminal tails, but it has been rarely applied to identify the role of co-existing histone marks in biology...
May 9, 2018: Proteomics
Neil Hunter
Oocyte quality and number are key determinants of reproductive life span and success. These variables are shaped in part by the elimination of oocytes that experience problems during the early stages of meiosis. Meiotic prophase-I marks an extended period of genome vulnerability in which epigenetic reprogramming unleashes retroelements and hundreds of DNA double-strand breaks (DSBs) are inflicted to initiate the programmed recombination required for accurate chromosome segregation at the first meiotic division...
May 9, 2018: Cold Spring Harbor Symposia on Quantitative Biology
Diego Uribe, Andres Cardona, Davide Degli Esposti, Marie-Pierre Cros, Cyrille Cuenin, Zdenko Herceg, Mauricio Camargo, Fabian M Cortés-Mancera
INTRODUCTION: Epigenetic alterations play an essential role in cancer onset and progression, thus studies of drugs targeting the epigenetic machinery are a principal concern for cancer treatment. Here, we evaluated the potential of the combination of the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine (5aza-dC) and the pan-deacetylase inhibitor Trichostatin A (TSA), at low cytotoxic concentrations, to modulate the canonical Wnt/β-catenin pathway in liver cancer cells. MATERIAL AND METHODS: Pyrosequencing was used for DNA methylation analyses of LINE-1 sequences and the Wnt/β-catenin pathway antagonist DKK3, SFRP1, WIF1 and CDH1...
April 9, 2018: Annals of Hepatology
Paolo Mita, Jef D Boeke
The LINE-1/L1 retrotransposon is a transposable element still active in the human genome. Most retrotransposons in the genome are inactive or repressed by several host mechanisms. In specific contexts, active L1 retrotransposons may evade repression and copy themselves into new genomic loci. Despite a general knowledge of the L1 life cycle, little was known about the dynamics of L1 proteins and function during the different stages of the host cell cycle. Our work highlighted a well-orchestrated localization of L1 proteins and mRNA that take advantage of mitotic nuclear membrane breakdown...
April 1, 2018: SLAS Discovery
Xu De Wang, Guang Yue Su, Chen Zhao, Fan Zhi Qu, Peng Wang, Yu Qing Zhao
Background: AD-2 (20( R )-dammarane-3b, 12b, 20, 25-tetrol; 25-OH-PPD) is a ginsenoside and isolated from Panax ginseng , showing anticancer activity against extensive human cancer cell lines. In this study, effects and mechanisms of 1C ((20 R )-3b- O -(L-alanyl)-dammarane-12b, 20, 25-triol), a modified version of AD-2, were evaluated for its development as a novel anticancer drug. Methods: MTT assay was performed to evaluate cell cytotoxic activity. Cell cycle and levels of reactive oxygen species (ROS) were determined using flow cytometry analysis...
April 2018: Journal of Ginseng Research
Seon Ok, Sa-Rang Oh, Tae-Sung Jung, Sang-Ok Jeon, Ji-Wook Jung, Deok-Seon Ryu
We investigated the cellular and molecular mechanisms mediating the effects of Angelica gigas Nakai extract (AGNE) through the mitogen-activated protein kinases (MAPKs)/NF- κ B pathway using in vitro and in vivo atopic dermatitis (AD) models. We examined the effects of AGNE on the expression of proinflammatory cytokines and chemokines in human mast cell line-1 (HMC-1) cells. Compound 48/80-induced pruritus and 2,4-dinitrochlorobenzene- (DNCB-) induced AD-like skin lesion mouse models were also used to investigate the antiallergic effects of AGNE...
2018: Evidence-based Complementary and Alternative Medicine: ECAM
Sandra R Richardson, Geoffrey J Faulkner
The retrotransposon Long Interspersed Element 1 (LINE-1 or L1) has played a major role in shaping the sequence composition of the mammalian genome. In our recent publication, "Heritable L1 retrotransposition in the mouse primordial germline and early embryo," we systematically assessed the rate and developmental timing of de novo, heritable endogenous L1 insertions in mice. Such heritable retrotransposition events allow L1 to exert an ongoing influence upon genome evolution. Here, we place our findings in the context of earlier studies, and highlight how our results corroborate, and depart from, previous research based on human patient samples and transgenic mouse models harboring engineered L1 reporter genes...
April 30, 2018: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
Rebecka Lundgren, Susannah Gibbs, Brad Kerner
Background Gender inequity contributes to a range of poor health outcomes. Early adolescence presents a window of opportunity for gender transformative interventions to shift inequitable gender norms, attitudes and behaviors. Objective The objective of this study is to evaluate a set of individual, family and community interventions to increase gender equity among very young adolescents (VYAs) in rural Nepal. Methods Two communities received the individual-level Choices intervention as well the family and community Voices and Promises interventions (CVP)...
April 30, 2018: International Journal of Adolescent Medicine and Health
Chaonan Wei, Dongguang Guo, Ying Li, Kaizhao Zhang, Guan Liang, Ying Li, Yongjiang Ma, Jilong Liu, Yugu Li
Thymus is the primary organ for T-cell differentiation and maturation. Many studies have demonstrated that estrogen plays a crucial role in thymic epithelial cell (TEC) proliferation during thymic involution. LncRNAs are involved in various biological processes; however, estrogen mediated lncRNA expression in TECs has not been yet reported. To address this question, the mouse medullary thymic epithelial cell line 1 (MTEC1) was treated with 17β-Estradiol (E2). By using CCK8 assay and flow cytometry, we found that E2 was able to inhibit viability and proliferation of MTEC1 cells...
April 27, 2018: Physiological Genomics
Ajay Ashok, Neena Singh
The prion protein (PrPC ), a mainly neuronal protein, is known to modulate glucose homeostasis in mouse models. We explored the underlying mechanism in mouse models and the human pancreatic β-cell line 1.1B4. We report expression of PrPC on mouse pancreatic β-cells, where it promoted uptake of iron through divalent-metal-transporters. Accordingly, pancreatic iron stores in PrP knockout mice (PrP-/- ) were significantly lower than wild type (PrP+/+ ) controls. Silencing of PrPC in 1.1B4 cells resulted in significant depletion of intracellular (IC) iron, and remarkably, upregulation of glucose transporter GLUT2 and insulin...
April 26, 2018: Scientific Reports
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