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https://www.readbyqxmd.com/read/28526320/mercury-exposure-induces-cytoskeleton-disruption-and-loss-of-renal-function-through-epigenetic-modulation-of-mmp9-expression
#1
Hafizurrahman Khan, Radha Dutt Singh, Ratnakar Tiwari, Siddhartha Gangopadhyay, Somendu Kumar Roy, Dhirendra Singh, Vikas Srivastava
Mercury is one of the major heavy metal pollutants occurring in elemental, inorganic and organic forms. Due to ban on most inorganic mercury containing products, human exposure to mercury generally occurs as methylmercury (MeHg) by consumption of contaminated fish and other sea food. Animal and epidemiological studies indicate that MeHg affects neural and renal function. Our study is focused on nephrotoxic potential of MeHg. In this study, we have shown for the first time how MeHg could epigenetically modulate matrix metalloproteinase 9(MMP9) to promote nephrotoxicity using an animal model of sub chronic MeHg exposure...
May 16, 2017: Toxicology
https://www.readbyqxmd.com/read/28522256/sporadic-early-onset-diffuse-gastric-cancers-have-high-frequency-of-somatic-cdh1-alterations-but-low-frequency-of-somatic-rhoa-mutations-compared-with-late-onset-cancers
#2
Soo Young Cho, Jun Won Park, Yang Liu, Young Soo Park, Ju Hee Kim, Hanna Yang, Hyejin Um, Woo Ri Ko, Byung Il Lee, Sun Young Kwon, Seung Wan Ryu, Chae Hwa Kwon, Do Youn Park, Jae-Hyuk Lee, Sang Il Lee, Kyu Sang Song, Hoon Hur, Sang-Uk Han, Heekyung Chang, Su-Jin Kim, Byung-Sik Kim, Jeong-Hwan Yook, Moon-Won Yoo, Beom-Su Kim, In-Seob Lee, Myeong-Cherl Kook, Nina Thiessen, An He, Chip Stewart, Andrew Dunford, Jaegil Kim, Juliann Shih, Gordon Saksena, Andrew D Cherniack, Steven Schumacher, Amaro-Taylor Weiner, Mara Rosenberg, Gad Getz, Eun Gyeong Yang, Min Hee Ryu, Adam J Bass, Hark Kyun Kim
BACKGROUND & AIMS: Early-onset gastric cancer, which develops in younger patients than most gastric cancers, is usually detected at advanced stages, has diffuse histologic features, and occurs more frequently in women. We investigated somatic genomic alterations associated with the unique characteristics of sporadic diffuse gastric cancers (DGCs) from younger patients. METHODS: We conducted whole exome and RNA sequence analyses of 80 resected DGC samples from patients 45 years old or younger in Korea...
May 15, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28517952/dna-methylation-and-transcription-onset-in-the-brain
#3
Renaud Massart, Matthew Suderman, Valerie Mongrain, Moshe Szyf
AIM: The goal of this study was to test the state of methylation of transcription start positions in DNA that are actively involved in transcription. MATERIALS & METHODS: We used sequential ChIP-bisulfite-sequencing with an antibody to RNpolII-PS5 to map the state of methylation of actively transcribing transcription start sites (TSS). RESULTS: TSS that RNApolII-PS5 physically bind to, are ubiquitously unmethylated. TSS that appear to be both heavily methylated and transcriptionally active are truly a mixture of unmethylated TSS with bound RNApolII-PS5 in some nuclei and unbound methylated TSS in other nuclei...
May 18, 2017: Epigenomics
https://www.readbyqxmd.com/read/28516124/bioinformatic-analysis-for-profiling-drug-induced-chromatin-modification-landscapes-in-mouse-brain-using-chlp-seq-data
#4
Yong-Hwee Eddie Loh, Jian Feng, Eric Nestler, Li Shen
Chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) is a powerful technology to profile genome-wide chromatin modification patterns and is increasingly being used to study the molecular mechanisms of brain diseases such as drug addiction. This protocol discusses the typical procedures involved in ChIP-seq data generation, bioinformatic analysis, and interpretation of results, using a chronic cocaine treatment study as a template. We describe an experimental design that induces significant chromatin modifications in mouse brain, and the use of ChIP-seq to derive novel information about the chromatin regulatory mechanisms involved...
February 5, 2017: Bio-protocol
https://www.readbyqxmd.com/read/28515787/a-computational-approach-for-the-functional-classification-of-the-epigenome
#5
Francesco Gandolfi, Anna Tramontano
BACKGROUND: In the last decade, advanced functional genomics approaches and deep sequencing have allowed large-scale mapping of histone modifications and other epigenetic marks, highlighting functional relationships between chromatin organization and genome function. Here, we propose a novel approach to explore functional interactions between different epigenetic modifications and extract combinatorial profiles that can be used to annotate the chromatin in a finite number of functional classes...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28510366/hmga2-plays-an-important-role-in-cr-vi-induced-autophagy
#6
Fan Yang, Lian Zhao, Dan Mei, Liping Jiang, Chengyan Geng, Qiujuan Li, Xiaofeng Yao, Yong Liu, Ying Kong, Jun Cao
Cr (VI) is mutagenic and carcinogenic, but the mechanism is unclear. In this study, the involvement of high mobility group A2 (HMGA2) in Cr (VI)-induced autophagy was investigated. Cr (VI) treatment induced formation of autophagosomes, increased expression of LC3II, Atg12-Atg5, Atg4, Atg10, HMGA1 and HMGA2 proteins, and decreased the expression of p62 in A549 cells. Silencing of HMGA2 gene by siRNA blocked Cr (VI)-induced formation of autophagosomes, expression of LC3II, Atg12-Atg5, Atg10 and reduction of p62...
May 16, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28505182/using-nextrad-sequencing-to-infer-movement-of-herbivores-among-host-plants
#7
Zhen Fu, Brendan Epstein, Joanna L Kelley, Qi Zheng, Alan O Bergland, Carmen I Castillo Carrillo, Andrew S Jensen, Jennifer Dahan, Alexander V Karasev, William E Snyder
Herbivores often move among spatially interspersed host plants, tracking high-quality resources through space and time. This dispersal is of particular interest for vectors of plant pathogens. Existing molecular tools to track such movement have yielded important insights, but often provide insufficient genetic resolution to infer spread at finer spatiotemporal scales. Here, we explore the use of Nextera-tagmented reductively-amplified DNA (NextRAD) sequencing to infer movement of a highly-mobile winged insect, the potato psyllid (Bactericera cockerelli), among host plants...
2017: PloS One
https://www.readbyqxmd.com/read/28504937/ultrasonic-fingerprint-sensor-with-transmit-beamforming-based-on-a-pmut-array-bonded-to-cmos-circuitry
#8
Xiaoyue Jiang, Hao-Yen Tang, Yipeng Lu, Eldwin Ng, Julius Tsai, Bernhard Boser, David Horsley
In this paper, we present a single-chip 65x42 element ultrasonic pulse-echo fingerprint sensor with transmit beamforming based on piezoelectric micromachined ultrasonic transducers (PMUTs) directly bonded to a CMOS readout ASIC. The readout ASIC was realized in a standard 180 nm CMOS process with a 24V high voltage transistor option. Pulse-echo measurements are performed column-by-column in sequence using either one column or five columns to transmit the ultrasonic pulse at 20 MHz. Transmit beamforming is used to focus the ultrasonic beam at the imaging plane where the finger is located, increasing the ultrasonic pressure and narrowing the 3dB beam-width to 50 microns, a factor of 6...
May 11, 2017: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
https://www.readbyqxmd.com/read/28502869/comparative-analysis-of-osteoblast-gene-expression-profiles-and-runx2-genomic-occupancy-of-mouse-and-human-osteoblasts-in-vitro
#9
Kati Tarkkonen, Reija Hieta, Ville Kytölä, Matti Nykter, Riku Kiviranta
Fast progress of the next generation sequencing (NGS) technology has allowed global transcriptional profiling and genome-wide mapping of transcription factor binding sites in various cellular contexts. However, limited number of replicates and high amount of data processing may weaken the significance of the findings. Comparative analyses of independent data sets acquired in the different laboratories would greatly increase the validity of the data. Runx2 is the key transcription factor regulating osteoblast differentiation and bone formation...
May 11, 2017: Gene
https://www.readbyqxmd.com/read/28499349/epimetheus-a-multi-profile-normalizer-for-epigenomic-sequencing-data
#10
Mohamed-Ashick M Saleem, Marco-Antonio Mendoza-Parra, Pierre-Etienne Cholley, Matthias Blum, Hinrich Gronemeyer
BACKGROUND: Exponentially increasing numbers of NGS-based epigenomic datasets in public repositories like GEO constitute an enormous source of information that is invaluable for integrative and comparative studies of gene regulatory mechanisms. One of today's challenges for such studies is to identify functionally informative local and global patterns of chromatin states in order to describe the regulatory impact of the epigenome in normal cell physiology and in case of pathological aberrations...
May 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28496150/long-non-coding-rna-particle-bridges-histone-and-dna-methylation
#11
Valerie Bríd O'Leary, Sarah Hain, Doris Maugg, Jan Smida, Omid Azimzadeh, Soile Tapio, Saak Victor Ovsepian, Michael John Atkinson
PARTICLE (Gene PARTICL- 'Promoter of MAT2A-Antisense RadiaTion Induced Circulating LncRNA) expression is transiently elevated following low dose irradiation typically encountered in the workplace and from natural sources. This long non-coding RNA recruits epigenetic silencers for cis-acting repression of its neighbouring Methionine adenosyltransferase 2A gene. It now emerges that PARTICLE operates as a trans-acting mediator of DNA and histone lysine methylation. Chromatin immunoprecipitation sequencing (ChIP-seq) and immunological evidence established elevated PARTICLE expression linked to increased histone 3 lysine 27 trimethylation...
May 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28492696/complex-recombination-with-deletion-in-the-f8-and-duplication-in-the-tmlhe-mediated-by-int22h-copies-during-early-embryogenesis
#12
Changming Chen, Xiaoling Xie, Xi Wu, Yeling Lu, Xuefeng Wang, Wenman Wu, Yiqun Hu, Qiulan Ding
Haemophilia A (HA) is a common X-linked recessive bleeding disorder and almost one half of patients with severe HA are caused by intron 22 inversion (Inv22) in the F8. Inv22 is considered to be almost exclusively of meiotic origin in germ cells during spermatogenesis and only one mosaic Inv22 female carrier with the mutation possibly occurring during mitosis of the embryo has been reported so far. Previously we have identified a novel complex recombination mediated by int22h copies in a sporadic severe HA pedigree and herein we have localised the sequences flanking the breakpoint region using genome walking technique, AccuCopy technique, gene chip and real-time PCR...
May 11, 2017: Thrombosis and Haemostasis
https://www.readbyqxmd.com/read/28487543/kdm6b-modulates-mapk-pathway-mediating-multiple-myeloma-cell-growth-and-survival
#13
H Ohguchi, T Harada, M Sagawa, S Kikuchi, Y-T Tai, P G Richardson, T Hideshima, K C Anderson
Recent studies have delineated cancer type-specific roles of histone 3 lysine 27 (H3K27) demethylase KDM6B/JMJD3 depending on its H3K27 demethylase activity. Here we show that KDM6B is expressed in multiple myeloma (MM); and that shRNA-mediated knockdown and CRISPR-mediated knockout of KDM6B abrogate MM cell growth and survival. TNFα or bone marrow stromal cell culture supernatants induce KDM6B, which is blocked by IKKβ inhibitor MLN120B, suggesting KDM6B is regulated by NF-κB signaling in MM cells. RNA-sequencing and subsequent ChIP-qPCR analyses reveal that KDM6B is recruited to the loci of genes encoding components of MAPK signaling pathway including ELK1 and FOS, and upregulates these genes expression without affecting H3K27 methylation level...
May 10, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28487270/the-research-progress-of-genomic-selection-in-livestock
#14
Li Hongwei, Wang Ruijun, Wang Zhiying, Li Xuewu, Wang Zhenyu, Zhang Yanjun, Su Rui, Liu Zhihong, Li Jinquan
With the development of gene chip and breeding technology, genomic selection in plants and animals has become research hotspots in recent years. Genomic selection has been extensively applied to all kinds of economic livestock, due to its high accuracy, short generation intervals and low breeding costs. In this review, we summarize genotyping technology and the methods for genomic breeding value estimation, the latter including the least square method, RR-BLUP, GBLUP, ssGBLUP, BayesA and BayesB. We also cover basic principles of genomic selection and compare their genetic marker ranges, genomic selection accuracy and operational speed...
May 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28486493/characterization-of-joining-sites-of-a-viral-histone-h4-on-host-insect-chromosomes
#15
Sunil Kumar, Jin-Kyo Jung, Yonggyun Kim
A viral histone H4 (CpBV-H4) is encoded in a polydnavirus, Cotesia plutellae bracovirus (CpBV). It plays a crucial role in parasitism of an endoparasitoid wasp, C. plutellae, against diamondback moth, Plutella xylostella, by altering host gene expression in an epigenetic mode by its N-terminal tail after joining host nucleosomes. Comparative transcriptomic analysis between parasitized and nonparasitized P. xylostella by RNA-Seq indicated that 1,858 genes were altered at more than two folds in expression levels at late parasitic stage, including 877 up-regulated genes and 981 down-regulated genes...
2017: PloS One
https://www.readbyqxmd.com/read/28484033/ectopic-protein-interactions-within-brd4-chromatin-complexes-drive-oncogenic-megadomain-formation-in-nut-midline-carcinoma
#16
Artyom A Alekseyenko, Erica M Walsh, Barry M Zee, Tibor Pakozdi, Peter Hsi, Madeleine E Lemieux, Paola Dal Cin, Tan A Ince, Peter V Kharchenko, Mitzi I Kuroda, Christopher A French
To investigate the mechanism that drives dramatic mistargeting of active chromatin in NUT midline carcinoma (NMC), we have identified protein interactions unique to the BRD4-NUT fusion oncoprotein compared with wild-type BRD4. Using cross-linking, affinity purification, and mass spectrometry, we identified the EP300 acetyltransferase as uniquely associated with BRD4 through the NUT fusion in both NMC and non-NMC cell types. We also discovered ZNF532 associated with BRD4-NUT in NMC patient cells but not detectable in 293T cells...
May 8, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28483659/the-long-non-coding-rna-neat1-is-an-important-mediator-of-the-therapeutic-effect-of-bexarotene-on-traumatic-brain-injury-in-mice
#17
Jianjun Zhong, Li Jiang, Zhijian Huang, Hongrong Zhang, Chongjie Cheng, Han Liu, Junchi He, Jingchuan Wu, Rami Darwazeh, Yue Wu, Xiaochuan Sun
OBJECTIVE: Bexarotene treatments exert neuroprotective effects on mice following traumatic brain injury (TBI). The present study aims to investigate the potential roles of the long noncoding RNA Neat1 in the neuroprotective effects of bexarotene. MATERIALS AND METHODS: Adult male C57BL/6J mice (n=80) and newborn mice (within 24 h after birth) (n=20) were used to generate a "controlled cortical impact" (CCI) model and harvest primary cortex neurons, respectively...
May 5, 2017: Brain, Behavior, and Immunity
https://www.readbyqxmd.com/read/28481895/succinct-workflows-for-circulating-tumor-cells-after-enrichment-from-systematic-counting-to-mutational-profiling
#18
Victor Chun-Lam Wong, Josephine Mun-Yee Ko, Chi-Tat Lam, Maria Li Lung
PURPOSE: This study aims to establish a highly adaptable workflow downstream of microfluidic enrichment for facilitating systematic CTC enumeration and genetic discovery. METHODS: To facilitate CTC enumeration, we established a CK/EPCAM-combined immunostaining strategy and an automated CTC analytical pipeline using an open-source image analyzer. By virtue of this workflow, we conducted a pilot study of 56 cancer patients and 21 healthy individuals using a high-throughput spiral microfluidic chip system...
2017: PloS One
https://www.readbyqxmd.com/read/28480959/research-on-the-epigenetic-regulation-mechanism-of-the-ptpn6-gene-in-advanced-chronic-myeloid-leukaemia
#19
Xiaokun Zhang, Lin Yang, Xiaojun Liu, Ziyuan Nie, Xingzhe Wang, Yuxia Pan, Jianmin Luo
PTPN6, a tyrosine phosphatase protein, plays a negative role in cell signal transduction and is negatively correlated with tumour formation and growth. However, epigenetic regulation mechanism of the PTPN6 gene in advanced chronic myeloid leukaemia (CML) remains unclear. This study investigated bone marrow or blood samples from 44 CML patients and 10 healthy volunteers. KCL22 and K562 cells were cultured and treated with demethylation drugs and histone deacetylase inhibitors. Real time quantitative polymerase chain reaction (qPCR), methylation-specific PCR, bisulfite sequencing PCR, Western blotting, co-immunoprecipitation and chromatin immunoprecipitation (ChIP) was performed...
May 8, 2017: British Journal of Haematology
https://www.readbyqxmd.com/read/28479135/specificity-determining-dna-triplet-code-for-positioning-of-human-preinitiation-complex
#20
Matan Goldshtein, David B Lukatsky
The notion that transcription factors bind DNA only through specific, consensus binding sites has been recently questioned. No specific consensus motif for the positioning of the human preinitiation complex (PIC) has been identified. Here, we reveal that nonconsensus, statistical, DNA triplet code provides specificity for the positioning of the human PIC. In particular, we reveal a highly nonrandom, statistical pattern of repetitive nucleotide triplets that correlates with the genomewide binding preferences of PIC measured by Chip-exo...
May 4, 2017: Biophysical Journal
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