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ChIP-seq OR RNA-seq

Yang Liu, Rongyao Huang, Yu Liu, Wanlu Song, Yuting Wang, Yang Yang, Shengcheng Dong, Xuerui Yang
Although the DNA methylome profiles have been available in large cancer cohorts such as The Cancer Genome Atlas (TCGA), integrative analysis of the DNA methylome architectures in a pan-cancer manner is still limited. In the present study, we aimed to systematically dissect the insightful features related to the inter-tumoral DNA methylome heterogeneity in a pan-cancer context of 21 cancers in TCGA. First, pan-cancer clustering of the DNA methylomes revealed convergence of cancers and, meanwhile, new classifications of cancer subtypes, which are often associated to prognostic differences...
August 19, 2018: International Journal of Cancer. Journal International du Cancer
Yingdi Liu, Kangsheng Peng, Ruting Xie, Jiayi Zheng, Jing Guo, Rong Wei, Huiqiong Yang, Chunmiao Cai, Qing Wei
Many clustered protocadherin genes (PCDHs) within chromosome 5q31 are frequently down-regulated in colorectal cancer (CRC) due to the hypermethylation of this region, and some of them have been identified as tumor suppressors. However, the association between the expression of the clustered PCDHs and prognosis of CRC patients is still unclear. Here, we identified multiple PCDHs that were significantly down-regulated in CRC by analyzing the RNA-seq data of the Cancer Genome Atlas (TCGA) cohort. Among them, one γ-PCDH subfamily member, PCDHGA7, was found to be associated with overall survival in the patients with wild-type KRAS...
August 16, 2018: Human Pathology
Laura Lindo, Susan P McCormick, Rosa E Cardoza, Daren W Brown, Hye-Seon Kim, Nancy J Alexander, Robert H Proctor, Santiago Gutiérrez
Trichothecenes are terpenoid toxins produced by multiple fungal species with diverse lifestyles. In these fungi, the trichothecene biosynthetic gene cluster (tri) includes a gene encoding a Cys2 His2 Zn-finger protein (TRI6). Analyses of plant pathogenic Fusarium species indicate that tri6 regulates tri gene expression. Here, we analyzed TRI6 function in the saprotrophic fungus Trichoderma arundinaceum, which produces the antimicrobial trichothecene harzianum A (HA). Deletion of the TRI6-encodinggene, tri6, blocked HA production and reduced expression of tri genes, and mevalonate biosynthetic genes required for synthesis of farnesyl diphosphate (FPP), the primary metabolite that feeds into trichothecene biosynthesis...
August 16, 2018: Fungal Genetics and Biology: FG & B
Haroon Kalam, Kartikeya Singh, Komal Chauhan, Mary F Fontana, Dhiraj Kumar
Previously, we reported that infection of human macrophages with Mycobacterium tuberculosis (Mtb) results in massive alterations in the pattern of RNA splicing in the host. The finding gained significance since alternate spliced variants of a same gene may have substantially different structure, function, stability, interaction partners, localization, and so forth, owing to inclusion or exclusion of specific exons. To establish a proof-of-concept; on how infection-induced RNA splicing could impact protein functions, here we used RNA-seq data from THP-1 macrophages that were infected with clinical isolate of Mtb...
August 18, 2018: IUBMB Life
Mark D Long, Prashant K Singh, James R Russell, Gerard Llimos, Spencer Rosario, Abbas Rizvi, Patrick R van den Berg, Jason Kirk, Lara E Sucheston-Campbell, Dominic J Smiraglia, Moray J Campbell
Expression levels of retinoic acid receptor gamma (NR1B3/RARG, encodes RARγ) are commonly reduced in prostate cancer (PCa). Therefore, we sought to establish the cellular and gene regulatory consequences of reduced RARγ expression, and determine RARγ regulatory mechanisms. RARG shRNA approaches in non-malignant (RWPE-1 and HPr1-AR) and malignant (LNCaP) prostate models revealed that reducing RARγ levels, rather than adding exogenous retinoid ligand, had the greatest impact on prostate cell viability and gene expression...
August 17, 2018: Oncogene
Max Darnell, Alison O'Neil, Angelo Mao, Luo Gu, Lee L Rubin, David J Mooney
Variations in a multitude of material microenvironmental properties have been observed across tissues in vivo, and these have profound effects on cell phenotype. Phenomenological experiments have suggested that certain of these features of the physical microenvironment, such as stiffness, could sensitize cells to other features; meanwhile, mechanistic studies have detailed a number of biophysical mechanisms for this sensing. However, the broad molecular consequences of these potentially complex and nonlinear interactions bridging from biophysical sensing to phenotype have not been systematically characterized, limiting the overall understanding and rational deployment of these biophysical cues...
August 17, 2018: Proceedings of the National Academy of Sciences of the United States of America
Roger Sun, Elaine Johanna Limkin, Maria Vakalopoulou, Laurent Dercle, Stéphane Champiat, Shan Rong Han, Loïc Verlingue, David Brandao, Andrea Lancia, Samy Ammari, Antoine Hollebecque, Jean-Yves Scoazec, Aurélien Marabelle, Christophe Massard, Jean-Charles Soria, Charlotte Robert, Nikos Paragios, Eric Deutsch, Charles Ferté
BACKGROUND: Because responses of patients with cancer to immunotherapy can vary in success, innovative predictors of response to treatment are urgently needed to improve treatment outcomes. We aimed to develop and independently validate a radiomics-based biomarker of tumour-infiltrating CD8 cells in patients included in phase 1 trials of anti-programmed cell death protein (PD)-1 or anti-programmed cell death ligand 1 (PD-L1) monotherapy. We also aimed to evaluate the association between the biomarker, and tumour immune phenotype and clinical outcomes of these patients...
August 14, 2018: Lancet Oncology
Abby Spangler, Emily Y Su, April M Craft, Patrick Cahan
Directed differentiation of pluripotent stem cells provides an accessible system to model development. However, the distinct cell types that emerge, their dynamics, and their relationship to progenitors in the early embryo has been difficult to decipher because of the cellular heterogeneity inherent to differentiation. Here, we used a combination of bulk RNA-Seq, single cell RNA-Seq, and bioinformatics analyses to dissect the cell types that emerge during directed differentiation of mouse embryonic stem cells as embryoid bodies and we compared them to spatially and temporally resolved transcriptional profiles of early embryos...
July 29, 2018: Stem Cell Research
Gabriel Silva, Mozart Marins, Nadda Chaichanasak, Yongdae Yoon, Ana Lúcia Fachin, Vitor Caressato Pinhanelli, Luis Octávio Regasini, Mariana Bastos Dos Santos, Gabriela Miranda Ayusso, Beatriz de Carvalho Marques, Wells W Wu, Je-Nie Phue, Rong-Fong Shen, Seung Joon Baek
Naturally-occurring chalcones and synthetic chalcone analogues have been demonstrated to have many biological effects, including anti-inflammatory, anti-malarial, anti-fungal, and anti-oxidant/anti-cancerous activities. Compared to other chalcones, trans-chalcone exhibits superior inhibitory activity in cancer cell growth as shown via in vitro assays, and exerts anti-cancerous effects via the activation of the p53 tumor suppressor protein. Thus, characterization of the specific mechanisms, by which trans-chalcone activates p53, can aid development of new chemotherapeutic drugs that can be used individually or synergistically with other drugs...
2018: PloS One
Diego Garrido-Martín, Emilio Palumbo, Roderic Guigó, Alessandra Breschi
We present ggsashimi, a command-line tool for the visualization of splicing events across multiple samples. Given a specified genomic region, ggsashimi creates sashimi plots for individual RNA-seq experiments as well as aggregated plots for groups of experiments, a feature unique to this software. Compared to the existing versions of programs generating sashimi plots, it uses popular bioinformatics file formats, it is annotation-independent, and allows the visualization of splicing events even for large genomic regions by scaling down the genomic segments between splice sites...
August 17, 2018: PLoS Computational Biology
Stéphanie Chasseigneaux, Yasmine Moraca, Véronique Cochois-Guégan, Anne-Cécile Boulay, Alice Gilbert, Stéphane Le Crom, Corinne Blugeon, Cyril Firmo, Salvatore Cisternino, Jean-Louis Laplanche, Emmanuel Curis, Xavier Declèves, Bruno Saubaméa
Brain mural cells form a heterogeneous family which significantly contributes to the maintenance of the blood-brain barrier and regulation of the cerebral blood flow. Current procedures to isolate them cannot specifically separate their distinct subtypes, in particular vascular smooth muscle cells (VSMCs) and mid-capillary pericytes (mcPCs), which differ among others by their expression of smooth muscle actin (SMA). We herein describe an innovative method allowing SMA+ VSMCs and SMA- mcPCs to be freshly isolated from the rat cerebral cortex...
August 16, 2018: Scientific Reports
Ling-Hong Miao, Yan Lin, Xin Huang, Wen-Jing Pan, Qun-Lan Zhou, Bo Liu, Ming-Chun Ren, Xian-Ping Ge, Liang-Kun Pan
The Megalobrama amblycephala ( M. amblycephala ) is one of the most important economic freshwater fish in China. The molecular mechanism under the glucose intolerance responses which affects the growth performance and feed utilization is still confused. miR-34a was reported as a key regulator in the glucose metabolism, but how did the miR-34a exert its function in the metabolism of glucose/insulin in M. amblycephala was still unclear. In this study, we intraperitoneally injected the miR-34a inhibitor (80 nmol/100 g body weight) into M...
August 16, 2018: International Journal of Molecular Sciences
Rudi Appels, Kellye Eversole, Catherine Feuillet, Beat Keller, Jane Rogers, Nils Stein, Curtis J Pozniak, Nils Stein, Frédéric Choulet, Assaf Distelfeld, Kellye Eversole, Jesse Poland, Jane Rogers, Gil Ronen, Andrew G Sharpe, Curtis Pozniak, Gil Ronen, Nils Stein, Omer Barad, Kobi Baruch, Frédéric Choulet, Gabriel Keeble-Gagnère, Martin Mascher, Andrew G Sharpe, Gil Ben-Zvi, Ambre-Aurore Josselin, Nils Stein, Martin Mascher, Axel Himmelbach, Frédéric Choulet, Gabriel Keeble-Gagnère, Martin Mascher, Jane Rogers, François Balfourier, Juan Gutierrez-Gonzalez, Matthew Hayden, Ambre-Aurore Josselin, ChuShin Koh, Gary Muehlbauer, Raj K Pasam, Etienne Paux, Curtis J Pozniak, Philippe Rigault, Andrew G Sharpe, Josquin Tibbits, Vijay Tiwari, Frédéric Choulet, Gabriel Keeble-Gagnère, Martin Mascher, Ambre-Aurore Josselin, Jane Rogers, Manuel Spannagl, Frédéric Choulet, Daniel Lang, Heidrun Gundlach, Georg Haberer, Gabriel Keeble-Gagnère, Klaus F X Mayer, Danara Ormanbekova, Etienne Paux, Verena Prade, Hana Šimková, Thomas Wicker, Frédéric Choulet, Manuel Spannagl, David Swarbreck, Hélène Rimbert, Marius Felder, Nicolas Guilhot, Heidrun Gundlach, Georg Haberer, Gemy Kaithakottil, Jens Keilwagen, Daniel Lang, Philippe Leroy, Thomas Lux, Klaus F X Mayer, Sven Twardziok, Luca Venturini, Rudi Appels, Hélène Rimbert, Frédéric Choulet, Angéla Juhász, Gabriel Keeble-Gagnère, Frédéric Choulet, Manuel Spannagl, Daniel Lang, Michael Abrouk, Georg Haberer, Gabriel Keeble-Gagnère, Klaus F X Mayer, Thomas Wicker, Frédéric Choulet, Thomas Wicker, Heidrun Gundlach, Daniel Lang, Manuel Spannagl, Daniel Lang, Manuel Spannagl, Rudi Appels, Iris Fischer, Cristobal Uauy, Philippa Borrill, Ricardo H Ramirez-Gonzalez, Rudi Appels, Dominique Arnaud, Smahane Chalabi, Boulos Chalhoub, Frédéric Choulet, Aron Cory, Raju Datla, Mark W Davey, Matthew Hayden, John Jacobs, Daniel Lang, Stephen J Robinson, Manuel Spannagl, Burkhard Steuernagel, Josquin Tibbits, Vijay Tiwari, Fred van Ex, Brande B H Wulff, Curtis J Pozniak, Stephen J Robinson, Andrew G Sharpe, Aron Cory, Moussa Benhamed, Etienne Paux, Abdelhafid Bendahmane, Lorenzo Concia, David Latrasse, Jane Rogers, John Jacobs, Michael Alaux, Rudi Appels, Jan Bartoš, Arnaud Bellec, Hélène Berges, Jaroslav Doležel, Catherine Feuillet, Zeev Frenkel, Bikram Gill, Abraham Korol, Thomas Letellier, Odd-Arne Olsen, Hana Šimková, Kuldeep Singh, Miroslav Valárik, Edwin van der Vossen, Sonia Vautrin, Song Weining, Abraham Korol, Zeev Frenkel, Tzion Fahima, Vladimir Glikson, Dina Raats, Jane Rogers, Vijay Tiwari, Bikram Gill, Etienne Paux, Jesse Poland, Jaroslav Doležel, Jarmila Číhalíková, Hana Šimková, Helena Toegelová, Jan Vrána, Pierre Sourdille, Benoit Darrier, Rudi Appels, Manuel Spannagl, Daniel Lang, Iris Fischer, Danara Ormanbekova, Verena Prade, Delfina Barabaschi, Luigi Cattivelli, Pilar Hernandez, Sergio Galvez, Hikmet Budak, Burkhard Steuernagel, Jonathan D G Jones, Kamil Witek, Brande B H Wulff, Guotai Yu, Ian Small, Joanna Melonek, Ruonan Zhou, Angéla Juhász, Tatiana Belova, Rudi Appels, Odd-Arne Olsen, Kostya Kanyuka, Robert King, Kirby Nilsen, Sean Walkowiak, Curtis J Pozniak, Richard Cuthbert, Raju Datla, Ron Knox, Krysta Wiebe, Daoquan Xiang, Antje Rohde, Timothy Golds, Jaroslav Doležel, Jana Čížková, Josquin Tibbits, Hikmet Budak, Bala Ani Akpinar, Sezgi Biyiklioglu, Gary Muehlbauer, Jesse Poland, Liangliang Gao, Juan Gutierrez-Gonzalez, Amidou N'Daiye, Jaroslav Doležel, Hana Šimková, Jarmila Číhalíková, Marie Kubaláková, Jan Šafář, Jan Vrána, Hélène Berges, Arnaud Bellec, Sonia Vautrin, Michael Alaux, Françoise Alfama, Anne-Françoise Adam-Blondon, Raphael Flores, Claire Guerche, Thomas Letellier, Mikaël Loaec, Hadi Quesneville, Curtis J Pozniak, Andrew G Sharpe, Sean Walkowiak, Hikmet Budak, Janet Condie, Jennifer Ens, ChuShin Koh, Ron Maclachlan, Yifang Tan, Thomas Wicker, Frédéric Choulet, Etienne Paux, Adriana Alberti, Jean-Marc Aury, François Balfourier, Valérie Barbe, Arnaud Couloux, Corinne Cruaud, Karine Labadie, Sophie Mangenot, Patrick Wincker, Bikram Gill, Gaganpreet Kaur, Mingcheng Luo, Sunish Sehgal, Kuldeep Singh, Parveen Chhuneja, Om Prakash Gupta, Suruchi Jindal, Parampreet Kaur, Palvi Malik, Priti Sharma, Bharat Yadav, Nagendra K Singh, JitendraP Khurana, Chanderkant Chaudhary, Paramjit Khurana, Vinod Kumar, Ajay Mahato, Saloni Mathur, Amitha Sevanthi, Naveen Sharma, Ram Sewak Tomar, Jane Rogers, John Jacobs, Michael Alaux, Arnaud Bellec, Hélène Berges, Jaroslav Doležel, Catherine Feuillet, Zeev Frenkel, Bikram Gill, Abraham Korol, Edwin van der Vossen, Sonia Vautrin, Bikram Gill, Gaganpreet Kaur, Mingcheng Luo, Sunish Sehgal, Jan Bartoš, Kateřina Holušová, Ondřej Plíhal, Matthew D Clark, Darren Heavens, George Kettleborough, Jon Wright, Miroslav Valárik, Michael Abrouk, Barbora Balcárková, Kateřina Holušová, Yuqin Hu, Mingcheng Luo, Elena Salina, Nikolai Ravin, Konstantin Skryabin, Alexey Beletsky, Vitaly Kadnikov, Andrey Mardanov, Michail Nesterov, Andrey Rakitin, Ekaterina Sergeeva, Hirokazu Handa, Hiroyuki Kanamori, Satoshi Katagiri, Fuminori Kobayashi, Shuhei Nasuda, Tsuyoshi Tanaka, Jianzhong Wu, Rudi Appels, Matthew Hayden, Gabriel Keeble-Gagnère, Philippe Rigault, Josquin Tibbits, Odd-Arne Olsen, Tatiana Belova, Federica Cattonaro, Min Jiumeng, Karl Kugler, Klaus F X Mayer, Matthias Pfeifer, Simen Sandve, Xu Xun, Bujie Zhan, Hana Šimková, Michael Abrouk, Jacqueline Batley, Philipp E Bayer, David Edwards, Satomi Hayashi, Helena Toegelová, Zuzana Tulpová, Paul Visendi, Song Weining, Licao Cui, Xianghong Du, Kewei Feng, Xiaojun Nie, Wei Tong, Le Wang, Philippa Borrill, Heidrun Gundlach, Sergio Galvez, Gemy Kaithakottil, Daniel Lang, Thomas Lux, Martin Mascher, Danara Ormanbekova, Verena Prade, Ricardo H Ramirez-Gonzalez, Manuel Spannagl, Nils Stein, Cristobal Uauy, Luca Venturini, Nils Stein, Rudi Appels, Kellye Eversole, Jane Rogers, Philippa Borrill, Luigi Cattivelli, Frédéric Choulet, Pilar Hernandez, Kostya Kanyuka, Daniel Lang, Martin Mascher, Kirby Nilsen, Etienne Paux, Curtis J Pozniak, Ricardo H Ramirez-Gonzalez, Hana Šimková, Ian Small, Manuel Spannagl, David Swarbreck, Cristobal Uauy
An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development...
August 17, 2018: Science
Jiji T Kurup, Benjamin L Kidder
RNA has been shown to interact with various proteins to regulate chromatin dynamics and gene expression. However, it is unknown whether RNAs associate with epigenetic marks such as post-translational modifications of histones, including histone 4 lysine 20 trimethylation (H4K20me3) or trimethylated histone 3 lysine 4 (H3K4me3), to regulate chromatin and gene expression. Here, we used chromatin-associated RNA immunoprecipitation (CARIP) followed by next-generation sequencing (CARIP-Seq) to survey RNAs associated with H4K20me3 and H3K4me3-marked chromatin on a global-scale in embryonic stem (ES) cells...
August 16, 2018: Journal of Biological Chemistry
Hsien-Chao Chou, Natalia Acevedo-Luna, Julie A Kuhlman, Stephan Q Schneider
BACKGROUND: The marine polychaete annelid Platynereis dumerilii has recently emerged as a prominent organism for the study of development, evolution, stem cells, regeneration, marine ecology, chronobiology and neurobiology within metazoans. Its phylogenetic position within the spiralian/ lophotrochozoan clade, the comparatively high conservation of ancestral features in the Platynereis genome, and experimental access to any stage within its life cycle, make Platynereis an important model for elucidating the complex regulatory and functional molecular mechanisms governing early development, later organogenesis, and various features of its larval and adult life...
August 16, 2018: BMC Genomics
Kuan-Fu Liao, Tsung-Lang Chiu, Sung-Ying Huang, Teng-Fu Hsieh, Shu-Fang Chang, Jhen-Wei Ruan, Shee-Ping Chen, Cheng-Yoong Pang, Sheng-Chun Chiu
BACKGROUND/AIMS: Radix Angelica Sinensis (danggui in Chinese) is widely used in traditional chinese medicine (TCM). N-butylidenephthalide (BP), a bioactive compound in danggui, is a potential antitumor agent for various cancer types. However, its clinical effect and mechanism in the treatment of gastric cancer remain undetermined. METHODS: The in vivo protective effect of danggui in patients with gastric cancer were validated using data from Taiwan's National Health Insurance Research Database (NHIRD)...
August 16, 2018: Cellular Physiology and Biochemistry
Tennille Sibbritt, Chi K Ip, Poh-Lynn Khoo, Emilie Wilkie, Vanessa Jones, Jane Q J Sun, Joanne X Shen, Guangdun Peng, Jing-Dong J Han, Naihe Jing, Pierre Osteil, Mirana Ramialison, Patrick P L Tam, Nicolas Fossat
Development of the embryonic head is driven by the activity of gene regulatory networks of transcription factors. LHX1 is a homeobox transcription factor that plays an essential role in the formation of the embryonic head. The loss of Lhx1 function results in anterior truncation of the embryo caused by the disruption of morphogenetic movement of tissue precursors and the dysregulation of WNT signaling activity. Profiling the gene expression pattern in the Lhx1 mutant embryo revealed that tissues in anterior germ layers acquire posterior tissue characteristics, suggesting Lhx1 activity is required for the allocation and patterning of head precursor tissues...
August 16, 2018: Genesis: the Journal of Genetics and Development
Yael Altuvia, Amir Bar, Niv Reiss, Ehud Karavani, Liron Argaman, Hanah Margalit
Bacterial RNase III plays important roles in the processing and degradation of RNA transcripts. A major goal is to identify the cleavage targets of this endoribonuclease at a transcriptome-wide scale and delineate its in vivo cleavage rules. Here we applied to Escherichia coli grown to either exponential or stationary phase a tailored RNA-seq-based technology, which allows transcriptome-wide mapping of RNase III cleavage sites at a nucleotide resolution. Our analysis of the large-scale in vivo cleavage data substantiated the established cleavage pattern of a double cleavage in an intra-molecular stem structure, leaving 2-nt-long 3' overhangs, and refined the base-pairing preferences in the cleavage site vicinity...
August 3, 2018: Nucleic Acids Research
L G Popova, D V Belyaev, A V Shuvalov, A A Yurchenko, D A Matalin, D E Khramov, Y V Orlova, Y V Balnokin
De novo assembled transcriptomes of the marine microalga Dunaliella tertiolecta (Chlorophyta) were analyzed. Transcriptome assemblies were performed using short-read RNA-seq data deposited in the SRA database (DNA and RNA Sequence Read Archive, NCBI). A merged transcriptome was assembled using a pooled RNA-seq data set. The goal of the study was in silico identification of nucleotide sequences encoding P-type ATPases in D. tertiolecta transcriptomes. P-type ATPases play a considerable role in the adaptation of an organism to a variable environment, and this problem is particularly significant for microalgae inhabiting an environment with an unstable ionic composition...
July 2018: Molekuliarnaia Biologiia
Victor F Oliveira, Lauro A G Moares, Ester A Mota, Liana K Jannotti-Passos, Paulo M Z Coelho, Ana C A Mattos, Flávia F B Couto, Brian E Caffrey, Annalisa Marsico, Renata Guerra-Sá
Long noncoding RNAs (lncRNAs) are transcripts generally longer than 200 nucleotides with no or poor protein coding potential, and most of their functions are also poorly characterized. Recently, an increasing number of studies have shown that lncRNAs can be involved in various critical biological processes such as organism development or cancer progression. Little, however, is known about their effects in helminths parasites, such as Schistosoma mansoni . Here, we present a computational pipeline to identify and characterize lncRNAs from RNA-seq data with high confidence from S...
2018: BioMed Research International
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