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https://www.readbyqxmd.com/read/29691294/reciprocal-network-between-cancer-stem-like-cells-and-macrophages-facilitates-the-progression-and-androgen-deprivation-therapy-resistance-of-prostate-cancer
#1
Hai Huang, Chao Wang, Fei Liu, Hui-Zhen Li, Guang Peng, Xu Gao, Ke-Qin Dong, Hong-Ru Wang, De-Pei Kong, Min Qu, Li-He Dai, Kai-Jian Wang, Zhe Zhou, Jun Yang, Ze-Yu Yang, Yan-Qiong Cheng, Qin-Qin Tian, Dan Liu, Chuan-Liang Xu, Dan-Feng Xu, Xin-Gang Cui, Ying-Hao Sun
PURPOSE: Cancer stem-like cells (CSCs) contribute to the progression and androgen deprivation therapy (ADT) resistance of prostate cancer. Since CSCs depend on their specific niche, including tumor-associated macrophages (TAMs), elucidating the network between CSCs and TAMs may help to effectively inhibit the progression and ADT resistance of prostate cancer. EXPERIMENTAL DESIGN: The underlying intracellular mechanism that sustains the stem-like characteristics of CSCs in prostate cancer was assessed via RNA-seq, co-IP, ChIP and other assays...
April 24, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29685157/estrogen-induced-mir-196a-elevation-promotes-tumor-growth-and-metastasis-via-targeting-spred1-in-breast-cancer
#2
Cheng-Fei Jiang, Zhu-Mei Shi, Dong-Mei Li, Ying-Chen Qian, Yi Ren, Xiao-Ming Bai, Yun-Xia Xie, Lin Wang, Xin Ge, Wei-Tao Liu, Lin-Lin Zhen, Ling-Zhi Liu, Bing-Hua Jiang
BACKGROUND: Estrogen plays a critical role in breast cancer (BC) progression through estrogen receptor (ER)-mediated gene regulation. Emerging studies suggest that the malignant progress of BC cells is influenced by the cross talk between microRNAs (miRNAs) and ER-α signaling. However, the mechanism and functional linkage between estrogen and miRNAs remain unclear. METHODS: The expression levels of miR-196a and SPRED1 in BC were tested by qRT-PCR in 46 paired BC and adjacent tissues and by the GEO datasets...
April 23, 2018: Molecular Cancer
https://www.readbyqxmd.com/read/29684346/microrna-3662-expression-correlates-with-antiviral-drug-resistance-in-adult-t-cell-leukemia-lymphoma-cells
#3
Kiyoshi Yasui, Mai Izumida, Takeya Nakagawa, Yoshinao Kubo, Hideki Hayashi, Takashi Ito, Hiroaki Ikeda, Toshifumi Matsuyama
Interferon regulatory factor (IRF) 4 and the proto-oncogene c-Rel cooperate in growth and antiviral drug resistance of adult T-cell leukemia/lymphoma (ATLL). To elucidate the target of IRF4 and c-Rel in ATLL, we determined the simultaneous binding sites of IRF4 and c-Rel using ChIP-seq technology. Nine genes were identified within 2 kb of binding sites, including MIR3662. Expression of miR-3662 was regulated by IRF4, and to a lesser extent by c-Rel. Cell proliferation was inhibited by knockdown of miR-3662 and expression of miR-3662 was correlated with antiviral drug resistance in ATLL cell lines...
April 20, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29684098/binquasi-a-peak-detection-method-for-chip-sequencing-data-with-biological-replicates
#4
Emily Goren, Peng Liu, Chao Wang, Chong Wang
Motivation: ChIP-seq experiments that are aimed at detecting DNA-protein interactions require biological replication to draw inferential conclusions, however there is no current consensus on how to analyze ChIP-seq data with biological replicates. Very few methodologies exist for the joint analysis of replicated ChIP-seq data, with approaches ranging from combining the results of analyzing replicates individually to joint modeling of all replicates. Combining the results of individual replicates analyzed separately can lead to reduced peak classification performance compared to joint modeling...
April 19, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29683440/an-integrated-platform-for-genome-wide-mapping-of-chromatin-states-using-high-throughput-chip-sequencing-in-tumor-tissues
#5
Christopher Terranova, Ming Tang, Elias Orouji, Mayinuer Maitituoheti, Ayush Raman, Samirkumar Amin, Zhiyi Liu, Kunal Rai
Histone modifications constitute a major component of the epigenome and play important regulatory roles in determining the transcriptional status of associated loci. In addition, the presence of specific modifications has been used to determine the position and identity non-coding functional elements such as enhancers. In recent years, chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) has become a powerful tool in determining the genome-wide profiles of individual histone modifications...
April 5, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29678859/gsyellow-a-swiss-knife-tag-for-functional-protein-analysis-in-monocot-and-dicot-plants
#6
Nienke Besbrugge, Jelle Van Leene, Dominique Eeckhout, Bernard Cannoot, Shubhada R Kulkarni, Nancy De Winne, Geert Persiau, Eveline Van De Slijke, Michiel Bontinck, Stijn Aesaert, Francis Impens, Kris Gevaert, Daniel van Damme, Mieke Van Lijsebettens, Dirk Inze, Klaas Vandepoele, Hilde Nelissen, Geert De Jaeger
The ability to tag proteins has boosted the emergence of generic molecular methods for protein functional analysis. Fluorescent protein tags are used to visualize protein localization and affinity tags enable the mapping of molecular interactions by, for example, tandem affinity purification (TAP) or chromatin immunoprecipitation (ChIP). To apply these widely used molecular techniques on a single transgenic plant line, we developed a multifunctional TAP tag, named GSyellow, which combines the streptavidin-binding peptide (SBP) tag with citrine yellow fluorescent protein (cYFP)...
April 20, 2018: Plant Physiology
https://www.readbyqxmd.com/read/29674394/acetyl-coa-promotes-glioblastoma-cell-adhesion-and-migration-through-ca-2-nfat-signaling
#7
Joyce V Lee, Corbett T Berry, Karla Kim, Payel Sen, Taehyong Kim, Alessandro Carrer, Sophie Trefely, Steven Zhao, Sully Fernandez, Lauren E Barney, Alyssa D Schwartz, Shelly R Peyton, Nathaniel W Snyder, Shelley L Berger, Bruce D Freedman, Kathryn E Wellen
The metabolite acetyl-coenzyme A (acetyl-CoA) is the required acetyl donor for lysine acetylation and thereby links metabolism, signaling, and epigenetics. Nutrient availability alters acetyl-CoA levels in cancer cells, correlating with changes in global histone acetylation and gene expression. However, the specific molecular mechanisms through which acetyl-CoA production impacts gene expression and its functional roles in promoting malignant phenotypes are poorly understood. Here, using histone H3 Lys27 acetylation (H3K27ac) ChIP-seq (chromatin immunoprecipitation [ChIP] coupled with next-generation sequencing) with normalization to an exogenous reference genome (ChIP-Rx), we found that changes in acetyl-CoA abundance trigger site-specific regulation of H3K27ac, correlating with gene expression as opposed to uniformly modulating this mark at all genes...
April 19, 2018: Genes & Development
https://www.readbyqxmd.com/read/29672735/parallel-factor-chip-provides-essential-internal-control-for-quantitative-differential-chip-seq
#8
Michael J Guertin, Amy E Cullen, Florian Markowetz, Andrew N Holding
A key challenge in quantitative ChIP combined with high-throughput sequencing (ChIP-seq) is the normalization of data in the presence of genome-wide changes in occupancy. Analysis-based normalization methods were developed for transcriptomic data and these are dependent on the underlying assumption that total transcription does not change between conditions. For genome-wide changes in transcription factor (TF) binding, these assumptions do not hold true. The challenges in normalization are confounded by experimental variability during sample preparation, processing and recovery...
April 17, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29672705/annopeak-a-web-application-to-annotate-and-visualize-peaks-from-chip-seq-chip-exo-seq
#9
Xing Tang, Arunima Srivastava, Huayang Liu, Raghu Machiraju, Kun Huang, Gustavo Leone
No abstract text is available yet for this article.
April 16, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29669733/evolution-of-dnaasei-hypersensitive-sites-in-mhc-regulatory-regions-of-primates
#10
Yabin Jin, Rachel M Gittelman, Yueer Lu, Xiaohui Liu, Ming D Li, Fei Ling, Joshua M Akey
It has been challenged to determine the disease-causing variant(s) for most major histocompatibility complex (MHC) associated diseases. However, it is becoming increasingly clear that regulatory variation is pervasive and a fundamentally important mechanism governing phenotypic diversity and disease susceptibility. We leveraged DNase I data from 136 human cells to characterize the regulatory landscape of the MHC region, including 4867 DNase I hypersensitive sites (DHSs). We identified thousands of regulatory elements that have been gained or lost in the human or chimpanzee genomes since their evolutionary divergence...
April 18, 2018: Genetics
https://www.readbyqxmd.com/read/29665865/integrative-analysis-reveals-functional-and-regulatory-roles-of-h3k79me2-in-mediating-alternative-splicing
#11
Tianbao Li, Qi Liu, Nick Garza, Steven Kornblau, Victor X Jin
BACKGROUND: Accumulating evidence suggests alternative splicing (AS) is a co-transcriptional splicing process not only controlled by RNA-binding splicing factors, but also mediated by epigenetic regulators, such as chromatin structure, nucleosome density, and histone modification. Aberrant AS plays an important role in regulating various diseases, including cancers. METHODS: In this study, we integrated AS events derived from RNA-seq with H3K79me2 ChIP-seq data across 34 different normal and cancer cell types and found the higher enrichment of H3K79me2 in two AS types, skipping exon (SE) and alternative 3' splice site (A3SS)...
April 17, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29659946/ethylene-responsive-factor-erf110-mediates-ethylene-regulated-transcription-of-a-sex-determination-related-orthologous-gene-in-two-cucumis-species
#12
Qianyi Tao, Huanhuan Niu, Zhongyuan Wang, Wenhui Zhang, Hu Wang, Shenhao Wang, Xian Zhang, Zheng Li
In plants, unisexual flowers derived from developmental sex determination form separate stamens and pistils that facilitate cross pollination. In cucumber and melon, ethylene plays a key role in sex determination. Six sex determination-related genes have been identified involving in ethylene biosynthesis in these Cucumis species. The interactions among these genes are thought to involve ethylene signaling; however, the detailed regulatory mechanism remains unknown. In this study, hormone treatment and qPCR assays were used to confirm expression of these sex determination-related genes in cucumber and melon is ethylene sensitive...
April 5, 2018: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29659651/stat3-is-required-for-proliferation-and-exhibits-a-cell-type-specific-binding-preference-in-mouse-female-germline-stem-cells
#13
Yunzhao Gu, Jun Wu, Wenxiao Yang, Chao Xia, Xinglong Shi, Hua Li, Jielin Sun, Zhifeng Shao, Ji Wu, Xiaodong Zhao
LIF-mediated STAT3 signaling is critically involved in stem cells and development. However, its function in mouse female germline cells (FGSCs) remains elusive. In this study, we demonstrated that LIF-induced STAT3 activation contributes to the proliferation and undifferentiation maintenance of mouse FGSCs. Characterization of the STAT3-mediated transcriptional network by intersecting ChIP-seq and RNA-seq datasets revealed 405 direct target genes of STAT3, which are primarily involved in proliferation and germline development...
April 16, 2018: Molecular omics
https://www.readbyqxmd.com/read/29659575/synergistic-co-regulation-and-competition-by-a-sox9-gli-foxa-phasic-transcriptional-network-coordinate-chondrocyte-differentiation-transitions
#14
Zhijia Tan, Ben Niu, Kwok Yeung Tsang, Ian G Melhado, Shinsuke Ohba, Xinjun He, Yongheng Huang, Cheng Wang, Andrew P McMahon, Ralf Jauch, Danny Chan, Michael Q Zhang, Kathryn S E Cheah
The growth plate mediates bone growth where SOX9 and GLI factors control chondrocyte proliferation, differentiation and entry into hypertrophy. FOXA factors regulate hypertrophic chondrocyte maturation. How these factors integrate into a Gene Regulatory Network (GRN) controlling these differentiation transitions is incompletely understood. We adopted a genome-wide whole tissue approach to establish a Growth Plate Differential Gene Expression Library (GP-DGEL) for fractionated proliferating, pre-hypertrophic, early and late hypertrophic chondrocytes, as an overarching resource for discovery of pathways and disease candidates...
April 16, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29659108/bel1-like-homeodomain-11-regulates-chloroplast-development-and-chlorophyll-synthesis-in-tomato-fruit
#15
Lanhuan Meng, Zhongqi Fan, Qiang Zhang, Cuicui Wang, Ying Gao, Yikang Deng, Benzhong Zhu, Hongliang Zhu, Chen Jianye, Wei Shan, Xunren Yin, Silin Zhong, Donald Grierson, Cai-Zhong Jiang, Yunbo Luo, Da-Qi Fu
Chloroplast development and chlorophyll(Chl)metabolism in unripe tomato contribute to the growth and quality of the fruit. However, the mechanism is poorly understood. In this work, we initially studied seven homeobox-containing transcription factors (TFs) with specific ripening-associated expression patterns by virus-induced gene silencing (VIGS) technology and found that inhibiting the expression of one of these TFs, BEL1-LIKE HOMEODOMAIN11 (SlBEL11), significantly increased Chl levels in unripe tomato fruit...
April 16, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29648658/pseudomonas-aeruginosa-partitioning-protein-parb-acts-as-a-nucleoid-associated-protein-binding-to-multiple-copies-of-a-pars-related-motif
#16
Adam Kawalek, Aneta A Bartosik, Krzysztof Glabski, Grazyna Jagura-Burdzy
ParA and ParB homologs are involved in accurate chromosome segregation in bacteria. ParBs participate in the separation of ori domains by binding to parS palindromes, mainly localized close to oriC. In Pseudomonas aeruginosa neither ParB deficiency nor modification of all 10 parSs is lethal. However, such mutants show not only defects in chromosome segregation but also growth retardation and motility dysfunctions. Moreover, a lack of parB alters expression of over 1000 genes, suggesting that ParB could interact with the chromosome outside its canonical parS targets...
April 10, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29648536/silencing-of-transposable-elements-may-not-be-a-major-driver-of-regulatory-evolution-in-primate-ipscs
#17
Michelle C Ward, Siming Zhao, Kaixuan Luo, Bryan J Pavlovic, Mohammad M Karimi, Matthew Stephens, Yoav Gilad
Transposable elements (TEs) comprise almost half of primate genomes and their aberrant regulation can result in deleterious effects. In pluripotent stem cells, rapidly-evolving KRAB-ZNF genes target TEs for silencing by H3K9me3. To investigate the evolution of TE silencing, we performed H3K9me3 ChIP-seq experiments in induced pluripotent stem cells from ten human and seven chimpanzee individuals. We identified four million orthologous TEs and found the SVA and ERV families to be marked most frequently by H3K9me3...
April 12, 2018: ELife
https://www.readbyqxmd.com/read/29628310/gcn4-binding-in-coding-regions-can-activate-internal-and-canonical-5-promoters-in-yeast
#18
Yashpal Rawal, Răzvan V Chereji, Vishalini Valabhoju, Hongfang Qiu, Josefina Ocampo, David J Clark, Alan G Hinnebusch
Gcn4 is a yeast transcriptional activator induced by amino acid starvation. ChIP-seq analysis revealed 546 genomic sites occupied by Gcn4 in starved cells, representing ∼30% of Gcn4-binding motifs. Surprisingly, only ∼40% of the bound sites are in promoters, of which only ∼60% activate transcription, indicating extensive negative control over Gcn4 function. Most of the remaining ∼300 Gcn4-bound sites are within coding sequences (CDSs), with ∼75 representing the only bound sites near Gcn4-induced genes...
April 2, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29626748/pul34-binding-near-the-human-cytomegalovirus-origin-of-lytic-replication-enhances-dna-replication-and-viral-growth
#19
Mark Slayton, Tanvir Hossain, Bonita J Biegalke
The human cytomegalovirus (HCMV) UL34 gene encodes sequence-specific DNA-binding proteins (pUL34) which are required for viral replication. Interactions of pUL34 with DNA binding sites represses transcription of two viral immune evasion genes, US3 and US9. 12 additional predicted pUL34-binding sites are present in the HCMV genome (strain AD169) with three binding sites concentrated near the HCMV origin of lytic replication (oriLyt). We used ChIP-seq analysis of pUL34-DNA interactions to confirm that pUL34 binds to the oriLyt region during infection...
April 4, 2018: Virology
https://www.readbyqxmd.com/read/29618724/global-dynamics-of-stage-specific-transcription-factor-binding-during-thymocyte-development
#20
Tomonori Hosoya, Ricardo D'Oliveira Albanus, John Hensley, Greggory Myers, Yasuhiro Kyono, Jacob Kitzman, Stephen C J Parker, James Douglas Engel
In vertebrates, multiple transcription factors (TFs) bind to gene regulatory elements (promoters, enhancers, and silencers) to execute developmental expression changes. ChIP experiments are often used to identify where TFs bind to regulatory elements in the genome, but the requirement of TF-specific antibodies hampers analyses of tens of TFs at multiple loci. Here we tested whether TF binding predictions using ATAC-seq can be used to infer the identity of TFs that bind to functionally validated enhancers of the Cd4, Cd8, and Gata3 genes in thymocytes...
April 4, 2018: Scientific Reports
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