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https://www.readbyqxmd.com/read/28449120/sigseeker-a-peak-calling-ensemble-approach-for-constructing-epigenetic-signatures
#1
Jens Lichtenberg, Laura Elnitski, David M Bodine
Motivation: Epigenetic data are invaluable when determining the regulatory programs governing a cell. Based on use of next-generation sequencing data for characterizing epigenetic marks and transcription factor binding, numerous peak-calling approaches have been developed to determine sites of genomic significance in these data. Such analyses can produce a large number of false positive predictions, suggesting that sites supported by multiple algorithms provide a stronger foundation for inferring and characterizing regulatory programs associated with the epigenetic data...
April 25, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28448740/sequencing-on-the-solid-5500xl-system-in-depth-characterization-of-the-gc-bias
#2
Simone Roeh, Peter Weber, Monika Rex-Haffner, Jan M Deussing, Elisabeth B Binder, Mira Jakovcevski
Different types of sequencing biases have been described and subsequently improved for a variety of sequencing systems, mostly focusing on the widely used Illumina systems. Similar studies are missing for the SOLiD 5500xl system, a sequencer which produced many data sets available to researchers today. Describing and understanding the bias is important to accurately interpret and integrate these published data in various ongoing research projects. We report a particularly strong GC bias for this sequencing system when analyzing a defined gDNA mix of five microbes with a wide range of different GC contents (20-72%) when comparing to the expected distribution and Illumina MiSeq data from the same DNA pool...
April 27, 2017: Nucleus
https://www.readbyqxmd.com/read/28442062/retinoic-acid-triggers-c-kit-gene-expression-in-spermatogonial-stem-cells-through-an-enhanceosome-constituted-between-transcription-factor-binding-sites-for-retinoic-acid-response-element-rare-spleen-focus-forming-virus-proviral-integration-oncogene-spfi1-pu
#3
Swanand Koli, Ayan Mukherjee, Kudumula Venkata Rami Reddy
Restricted availability of retinoic acid (RA) in the testicular milieu regulates transcriptional activity of c-kit (KIT, CD117), which aids in the determination of spermatogonial stem-cell differentiation. The effect of RA on c-kit has been reported previously, but its mode of genomic action remains unresolved. We studied the molecular machinery guiding RA responsiveness to the c-kit gene using spermatogonial stem-cell line C18-4 and primary spermatogonial cells. A novel retinoic acid response element (RARE) positioned at -989 nucleotides upstream of the transcription start site (TSS) was identified, providing a binding site for a dimeric RA receptor (i...
March 2017: Reproduction, Fertility, and Development
https://www.readbyqxmd.com/read/28440495/relationship-between-epigenetic-changes-in-wnt-antagonists-and-acute-leukemia
#4
Hua-Rong Zhou, Hai-Ying Fu, Dan-Sen Wu, Yuan-Yuan Zhang, Si-Han Huang, Cong-Jie Chen, Jian-Guo Yan, Jin-Long Huang, Jian-Zhen Shen
The present study was designed to investigate the relationship among epigenetic changes in Wnt antagonists, histone H4K20me1 and the expression of tumor-suppressor genes in acute leukemia (AL) to better understand the pathogenesis of leukemia. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was performed to detect messenger RNA (mRNA) expression levels of Wnt antagonists (Wnt5a, HDPR1, DKK1 and DKK3) in patients with AL and in normal controls; pyrophosphate sequencing was performed to detect the methylation status of the Wnt5a promoter; and western blotting was performed to detect the overall expression levels of Wnt5a protein and histone H4K20me1 in patients with acute myeloid leukemia (AML) and in normal controls...
May 2017: Oncology Reports
https://www.readbyqxmd.com/read/28440307/lps-independent-activation-of-the-pro-inflammatory-receptor-trem1-by-c-ebp%C3%AE%C2%B5-in-granulocytes
#5
Hyung C Suh, Touati Benoukraf, Pavithra Shyamsunder, Tong Yin, Qi Cao, Jonathan Said, Stephen Lee, Ricky Lim, Henry Yang, Jacqueline Salotti, Peter F Johnson, Vikas Madan, H Phillip Koeffler
C/EBPε is a critical transcriptional factor for granulocyte differentiation and function. Individuals with germline mutations of C/EBPε fail to develop normal granulocytes and suffer from repeated infections. In order to gain a global view of the transcriptional machinery regulated by C/EBPε, we performed whole-genome ChIP-Seq using mouse bone marrow cells. To complement the C/EBPε DNA binding analyses, RNA-Sequencing was done in parallel using sorted mature and immature granulocytes from WT and C/EBPε KO bone marrow...
April 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28439859/genome-wide-profiling-of-histone-modifications-and-histone-variants-in-arabidopsis-thaliana-and-marchantia-polymorpha
#6
Ramesh Yelagandula, Akihisa Osakabe, Elin Axelsson, Frederic Berger, Tomokazu Kawashima
Histone modifications and histone variants barcode the genome and play major roles in epigenetic regulations. Chromatin immunoprecipitation (ChIP) coupled with next-generation sequencing (NGS) is a well-established method to investigate the landscape of epigenetic marks at a genomic level. Here, we describe procedures for conducting ChIP, subsequent NGS library construction, and data analysis on histone modifications and histone variants in Arabidopsis thaliana. We also describe an optimized nuclear isolation procedure to prepare chromatin for ChIP in the liverwort, Marchantia polymorpha, which is the emerging model plant ideal for evolutionary studies...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28429804/identifying-tagging-snps-for-african-specific-genetic-variation-from-the-african-diaspora-genome
#7
Henry Richard Johnston, Yi-Juan Hu, Jingjing Gao, Timothy D O'Connor, Gonçalo R Abecasis, Genevieve L Wojcik, Christopher R Gignoux, Pierre-Antoine Gourraud, Antoine Lizee, Mark Hansen, Rob Genuario, Dave Bullis, Cindy Lawley, Eimear E Kenny, Carlos Bustamante, Terri H Beaty, Rasika A Mathias, Kathleen C Barnes, Zhaohui S Qin
A primary goal of The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to develop an 'African Diaspora Power Chip' (ADPC), a genotyping array consisting of tagging SNPs, useful in comprehensively identifying African specific genetic variation. This array is designed based on the novel variation identified in 642 CAAPA samples of African ancestry with high coverage whole genome sequence data (~30× depth). This novel variation extends the pattern of variation catalogued in the 1000 Genomes and Exome Sequencing Projects to a spectrum of populations representing the wide range of West African genomic diversity...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28429364/application-of-gene-detection-technique-in-the-antenatal-diagnosis-of-hereditary-hearing-loss
#8
Y Fang, M-S Gu, F Suo, C-X Wang, X-H Liu, F-M Liu
OBJECTIVE: Gene chip and gene sequencing techniques were used to detect the main pathogenic genes in pregnant women with hereditary hearing loss. PATIENTS AND METHODS: From May 2015 to May 2016, 1080 pregnant in Xuzhou Maternal and Child Health Hospital were enrolled in this study. Women age range was 18 to 40 years. 4 genes and 9 mutation sites, including 4 sites (35delG, 176, 235delC and 299) in GJB2 gene, 2 sites (2168A>G and IVS-7-2A>G) in SLC26A4 (PDS) gene, 2 sites (1494C>T and 1555A>G) in 12s rRNA gene and 1 site (538C>T) in GJB3 gene, were detected using the GeeDom® 9-item hereditary hearing loss gene detection kit...
April 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/28428261/ebf2-transcriptionally-regulates-brown-adipogenesis-via-the-histone-reader-dpf3-and-the-baf-chromatin-remodeling-complex
#9
Suzanne N Shapira, Hee-Woong Lim, Sona Rajakumari, Alexander P Sakers, Jeff Ishibashi, Matthew J Harms, Kyoung-Jae Won, Patrick Seale
The transcription factor early B-cell factor 2 (EBF2) is an essential mediator of brown adipocyte commitment and terminal differentiation. However, the mechanisms by which EBF2 regulates chromatin to activate brown fat-specific genes in adipocytes were unknown. ChIP-seq (chromatin immunoprecipitation [ChIP] followed by deep sequencing) analyses in brown adipose tissue showed that EBF2 binds and regulates the activity of lineage-specific enhancers. Mechanistically, EBF2 physically interacts with the chromatin remodeler BRG1 and the BAF chromatin remodeling complex in brown adipocytes...
April 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28427323/detection-of-qtl-for-traits-related-to-adaptation-to-sub-optimal-climatic-conditions-in-chickens
#10
Ching-Yi Lien, Michèle Tixier-Boichard, Shih-Wen Wu, Woei-Fuh Wang, Chen Siang Ng, Chih-Feng Chen
BACKGROUND: Growth traits can be used as indicators of adaptation to sub-optimal conditions. The current study aimed at identifying quantitative trait loci (QTL) that control performance under variable temperature conditions in chickens. METHODS: An F2 population was produced by crossing the Taiwan Country chicken L2 line (selected for body weight, comb area, and egg production) with an experimental line of Rhode Island Red layer R- (selected for low residual feed consumption)...
April 20, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28425186/association-studies-of-low-frequency-coding-variants-in-nonsyndromic-cleft-lip-with-or-without-cleft-palate
#11
Elizabeth J Leslie, Jenna C Carlson, John R Shaffer, Carmen J Buxó, Eduardo E Castilla, Kaare Christensen, Frederic W B Deleyiannis, Leigh L Field, Jacqueline T Hecht, Lina Moreno, Ieda M Orioli, Carmencita Padilla, Alexandre R Vieira, George L Wehby, Eleanor Feingold, Seth M Weinberg, Jeffrey C Murray, Mary L Marazita
Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a group of common human birth defects with complex etiology. Although genome-wide association studies have successfully identified a number of risk loci, these loci only account for about 20% of the heritability of orofacial clefts. The "missing" heritability may be found in rare variants, copy number variants, or interactions. In this study, we investigated the role of low-frequency variants genotyped in 1995 cases and 1626 controls on the Illumina HumanCore + Exome chip...
April 19, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28425074/lincrna-p21-function-and-mechanism-in-cancer
#12
REVIEW
Shaoyun Chen, Hairong Liang, Hui Yang, Kairu Zhou, Longmei Xu, Jiaxian Liu, Bei Lai, Li Song, Hao Luo, Jianming Peng, Zhidong Liu, Yongmei Xiao, Wen Chen, Huanwen Tang
In view of the rapid development of gene chips and high-throughput sequencing technology, noncoding RNAs (ncRNas) form a high percentage of the mammalian genome. Two major subgroups of ncRNAs that have been identified are the long ncRNAs (lncRNas) and the microRNAs. A number of studies in the past few years have showed crucial functions for lncRNas in cancer. LincRNa-p21 as a p53-dependent transcriptional target gene and a potential diagnostic marker is involved in proliferation, cell cycle, metabolism and reprogramming...
May 2017: Medical Oncology
https://www.readbyqxmd.com/read/28420760/novel-lnc-rna-regulated-by-hif-1-inhibits-apoptotic-cell-death-in-the-renal-tubular-epithelial-cells-under-hypoxia
#13
Imari Mimura, Yosuke Hirakawa, Yasuharu Kanki, Natsuki Kushida, Ryo Nakaki, Yutaka Suzuki, Tetsuhiro Tanaka, Hiroyuki Aburatani, Masaomi Nangaku
Chronic tubulointerstitial hypoxia plays an important role as the final common pathway to end-stage renal disease. HIF-1 (hypoxia-inducible factor-1) is a master transcriptional factor under hypoxia, regulating downstream target genes. Genome-wide analysis of HIF-1 binding sites using high-throughput sequencers has clarified various kinds of downstream targets and made it possible to demonstrate the novel roles of HIF-1. Our aim of this study is to identify novel HIF-1 downstream epigenetic targets which may play important roles in the kidney...
April 2017: Physiological Reports
https://www.readbyqxmd.com/read/28418438/a-scalable-self-priming-fractal-branching-microchannel-net-chip-for-digital-pcr
#14
Qiangyuan Zhu, Yanan Xu, Lin Qiu, Congcong Ma, Bingwen Yu, Qi Song, Wei Jin, Qinhan Jin, Jinyu Liu, Ying Mu
As an absolute quantification method at the single-molecule level, digital PCR has been widely used in many bioresearch fields, such as next generation sequencing, single cell analysis, gene editing detection and so on. However, existing digital PCR methods still have some disadvantages, including high cost, sample loss, and complicated operation. In this work, we develop an exquisite scalable self-priming fractal branching microchannel net digital PCR chip. This chip with a special design inspired by natural fractal-tree systems has an even distribution and 100% compartmentalization of the sample without any sample loss, which is not available in existing chip-based digital PCR methods...
April 18, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28416945/a-chip-seq-data-analysis-pipeline-based-on-bioconductor-packages
#15
Seung-Jin Park, Jong-Hwan Kim, Byung-Ha Yoon, Seon-Young Kim
Nowadays, huge volumes of chromatin immunoprecipitation-sequencing (ChIP-Seq) data are generated to increase the knowledge on DNA-protein interactions in the cell, and accordingly, many tools have been developed for ChIP-Seq analysis. Here, we provide an example of a streamlined workflow for ChIP-Seq data analysis composed of only four packages in Bioconductor: dada2, QuasR, mosaics, and ChIPseeker. 'dada2' performs trimming of the high-throughput sequencing data. 'QuasR' and 'mosaics' perform quality control and mapping of the input reads to the reference genome and peak calling, respectively...
March 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28414715/transcriptional-regulatory-logic-of-the-diurnal-cycle-in-the-mouse-liver
#16
Jonathan Aryeh Sobel, Irina Krier, Teemu Andersin, Sunil Raghav, Donatella Canella, Federica Gilardi, Alexandra Styliani Kalantzi, Guillaume Rey, Benjamin Weger, Frédéric Gachon, Matteo Dal Peraro, Nouria Hernandez, Ueli Schibler, Bart Deplancke, Felix Naef
Many organisms exhibit temporal rhythms in gene expression that propel diurnal cycles in physiology. In the liver of mammals, these rhythms are controlled by transcription-translation feedback loops of the core circadian clock and by feeding-fasting cycles. To better understand the regulatory interplay between the circadian clock and feeding rhythms, we mapped DNase I hypersensitive sites (DHSs) in the mouse liver during a diurnal cycle. The intensity of DNase I cleavages cycled at a substantial fraction of all DHSs, suggesting that DHSs harbor regulatory elements that control rhythmic transcription...
April 2017: PLoS Biology
https://www.readbyqxmd.com/read/28412501/regulation-of-baz1a-and-nucleosome-positioning-in-the-nucleus-accumbens-in-response-to-cocaine
#17
HaoSheng Sun, Diane M Damez-Werno, Kimberly N Scobie, Ning-Yi Shao, Caroline Dias, Jacqui Rabkin, Katherine N Wright, Ezekiell Mouzon, Mohamed Kabbaj, Rachael Neve, Gustavo Turecki, Li Shen, Eric J Nestler
Chromatin regulation, in particular1 ATP-dependent chromatin remodelers, have previously been shown to be important in the regulation of reward-related behaviors in animal models of mental illnesses. Here we demonstrate that BAZ1A, an accessory subunit of the ISWI family of chromatin remodeling complexes, is downregulated in the nucleus accumbens (NAc) of mice exposed repeatedly to cocaine and of cocaine-addicted humans. Viral-mediated overexpression of BAZ1A in mouse NAc reduces cocaine reward as assessed by conditioned place preference (CPP), but increases cocaine-induced locomotor activation...
April 12, 2017: Neuroscience
https://www.readbyqxmd.com/read/28402957/chromatin-state-dynamics-during-nk-cell-activation
#18
Yang Li, Jin Wang, Jie Yin, Xinhua Liu, Minghang Yu, Ting Li, Han Yan, Xi Wang
Studies of Natural Killer (NK) cell cytotoxicity have mainly focused on the balance of activating and inhibitory receptors, signaling transduction, calcium influx, formation of immune synapse, and cytolytic degranulation. However, little is known about the chromatin state of NK cells and the impact of its changes during target recognition. In this study, we investigate the contribution of chromatin state dynamics during NK cell activation by comprehensively analyzing a set of microarray data and two sets of Chromatin Immunoprecipitation-Sequencing (ChIP-seq) data...
March 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28402947/overexpression-of-the-transcription-factor-atf3-with-a-regulatory-molecular-signature-associates-with-the-pathogenic-development-of-colorectal-cancer
#19
Feng Yan, Le Ying, Xiaofang Li, Bin Qiao, Qiaohong Meng, Liang Yu, Xiangliang Yuan, Shu-Ting Ren, David W Chan, Liyun Shi, Peihua Ni, Xuefeng Wang, Dakang Xu, Yiqun Hu
The identification of novel biomarkers of cancer is important for improved diagnosis and prognosis. With an abundant amount of resources in the publicly available database, such as the Cancer Genome Atlas (TCGA) database, an integrative strategy is used to systematically characterize the aberrant patterns of colorectal cancer (CRC) based on RNA-Seq, chromatin immunoprecipitation sequencing (ChIP-Seq), tissue microarray (TMA), gene profiling and molecular signatures. The expression of the transcription factor ATF3 was elevated in human CRC specimens in a TMA by immunochemistry analysis compared to the adjacent normal tissues...
March 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28402545/orio-online-resource-for-integrative-omics-a-web-based-platform-for-rapid-integration-of-next-generation-sequencing-data
#20
Christopher A Lavender, Andrew J Shapiro, Adam B Burkholder, Brian D Bennett, Karen Adelman, David C Fargo
Established and emerging next generation sequencing (NGS)-based technologies allow for genome-wide interrogation of diverse biological processes. However, accessibility of NGS data remains a problem, and few user-friendly resources exist for integrative analysis of NGS data from different sources and experimental techniques. Here, we present Online Resource for Integrative Omics (ORIO; https://orio.niehs.nih.gov/), a web-based resource with an intuitive user interface for rapid analysis and integration of NGS data...
April 11, 2017: Nucleic Acids Research
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