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Extrinsically derived TNF is primarily responsible for limiting antiviral CD8+ T cell response magnitude.
Kylie M Quinn, Wan-Ting Kan, Katherine A Watson, Brian J Liddicoat, Natasha G Swan, Hayley McQuilten, Alice E Denton, Jasmine Li, Weisan Chen, Lorena E Brown, David C Jackson, Patrick C Reading, Peter C Doherty, Katherine Kedzierska, Lukasz Kedzierski, Stephen J Turner, Nicole L La Gruta
Jun 24, 2019
TNF is a pro-inflammatory cytokine produced by both lymphoid and non-lymphoid cells. As a consequence of the widespread expression of its receptors (TNFR1 and 2), TNF plays a role in many important biological processes. In the...
A ChIP-chip approach reveals a novel role for transcription factor IRF1 in the DNA damage response.
IRF1 is a transcription factor that regulates key processes in the immune system and in tumour suppression. To gain further insight into IRF1's role in these processes, we searched for new target genes by performing chromatin...
Binding Sites Cell Line Tumor Cells Cultured Chromatin Immunoprecipitation Cross-Linking Reagents DNA Damage DNA Repair DNA-Binding Proteins Fanconi Anemia Complementation Group Proteins FIBROBLASTS Gene Expression Regulation Humans Interferon Regulatory Factor-1 Interferon-gamma Melphalan Oligonucleotide Array Sequence Analysis RNA Helicases RNA Interference Regulatory Elements Transcriptional Reproducibility of Results
In vivo, genome-wide profiling of endogenously tagged chromatin-binding proteins with spatial and temporal resolution using NanoDam in Drosophila.
Jocelyn LY Tang, Robert Krautz, Oriol Llorà-Batlle, Anna E Hakes, Paul M Fox, Andrea H Brand
Dec 09, 2022
NanoDam is a technique for genome-wide profiling of the binding targets of any endogenously tagged chromatin-binding protein in vivo, without the need for antibodies, crosslinking, or immunoprecipitation. Here, we explain the...
Global and stage specific patterns of Krüppel-associated-box zinc finger protein gene expression in murine early embryonic cells.
Andrea Corsinotti, Adamandia Kapopoulou, Carine Gubelmann, Michael Imbeault, Francesca R Santoni de Sio, Helen M Rowe, Yoann Mouscaz, Bart Deplancke, Didier Trono
Dec 12, 2019
Highly coordinated transcription networks orchestrate the self-renewal of pluripotent stem cell and the earliest steps of mammalian development. KRAB-containing zinc finger proteins represent the largest group of transcription...
Parallel factor ChIP provides essential internal control for quantitative differential ChIP-seq.
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...
CODEX
Manuel Sánchez-Castillo, David Ruau, Adam C Wilkinson, Felicia SL Ng, Rebecca Hannah, Evangelia Diamanti, Patrick Lombard, Nicola K Wilson, Berthold Gottgens
Sep 29, 2014
Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties.
ChIP-exonuclease (ChIP-exo) is a modified ChIP-seq approach for high resolution mapping of transcription factor DNA sites. We describe an Illumina-based ChIP-exo method which provides a global improvement of the data quality of...
GPAT
BACKGROUND: Recent genome wide transcription factor binding site or chromatin modification mapping analysis techniques, such as chromatin immunoprecipitation (ChIP) linked to DNA microarray analysis (ChIP on chip) or ChIP...
Transcription factor co-localization patterns affect human cell type-specific gene expression.
Regulators of genetic risk of breast cancer identified by integrative network analysis.
Mauro AA Castro, Ines de Santiago, Thomas M Campbell, Courtney Vaughn, Theresa E Hickey, Edith Ross, Wayne D Tilley, Florian Markowetz, Bruce AJ Ponder, Kerstin B Meyer
Nov 11, 2015
Breast Neoplasms Cell Line Tumor Chromatin Immunoprecipitation Cluster Analysis Estrogen Receptor alpha Female Fibroblast Growth Factor 10 Gene Expression Profiling Gene Regulatory Networks Genetic Predisposition to Disease Genome-Wide Association Study Humans Mutation Quantitative Trait Loci Reproducibility of Results Transcription Factors
BET protein inhibition shows efficacy against JAK2V617F-driven neoplasms.
BS Wyspiańska, AJ Bannister, I Barbieri, J Nangalia, A Godfrey, FJ Calero-Nieto, S Robson, I Rioja, J Li, M Wiese, E Cannizzaro, MA Dawson, B Huntly, RK Prinjha, AR Green, B Gottgens, T Kouzarides
Jun 13, 2014
Nuclear RNA sequencing of the mouse erythroid cell transcriptome.
Jennifer A Mitchell, Ieuan Clay, David Umlauf, Chih-Yu Chen, Catherine A Moir, Christopher H Eskiw, Stefan Schoenfelder, Lyubomira Chakalova, Takashi Nagano, Peter Fraser
Jul 15, 2019
In addition to protein coding genes a substantial proportion of mammalian genomes are transcribed. However, most transcriptome studies investigate steady-state mRNA levels, ignoring a considerable fraction of the transcribed...
Animals Chromatin Immunoprecipitation Erythroid Cells Gene Expression Regulation Gene Library High-Throughput Nucleotide Sequencing Mice Protein Binding RNA Polymerase II RNA Long Noncoding RNA Nuclear Regulatory Sequences Nucleic Acid Reproducibility of Results Sequence Analysis RNA Transcription Genetic Transcriptome
Stat3 promotes mitochondrial transcription and oxidative respiration during maintenance and induction of naive pluripotency.
LIF STAT3 metabolism mitochondrial respiration Pluripotency Animals Cell Differentiation Cell Proliferation Cell Respiration Chromatin Immunoprecipitation Embryonic Stem Cells Gene Expression Regulation Leukemia Inhibitory Factor Mice Mitochondria Pluripotent Stem Cells STAT3 Transcription Factor Transcription Genetic
Transcriptional networks controlling the cell cycle.
Martin Bonke, Mikko Turunen, Maria Sokolova, Anna Vähärautio, Teemu Kivioja, Minna Taipale, Mikael Björklund, Jussi Taipale
Nov 04, 2020
In this work, we map the transcriptional targets of 107 previously identified Drosophila genes whose loss caused the strongest cell-cycle phenotypes in a genome-wide RNA interference screen and mine the resulting data...
Animals CDC2 Protein Kinase Cell Cycle Cell Line Cell Size Chromatin Immunoprecipitation Cluster Analysis Drosophila Feedback Physiological Flow Cytometry Gene Expression Profiling Gene Regulatory Networks Microarray Analysis Mitosis Oligonucleotides Phosphorylation RNA Interference Sequence Analysis RNA
Endogenous purification reveals GREB1 as a key estrogen receptor regulatory factor.
Hisham Mohammed, Clive D'Santos, Aurelien A Serandour, H Raza Ali, Gordon D Brown, Alan Atkins, Oscar M Rueda, Kelly A Holmes, Vasiliki Theodorou, Jessica LL Robinson, Wilbert Zwart, Amel Saadi, Caryn S Ross-Innes, Suet-Feung Chin, Suraj Menon, John Stingl, Carlo Palmieri, Carlos Caldas, Jason S Carroll
Jan 18, 2021
Estrogen receptor-α (ER) is the driving transcription factor in most breast cancers, and its associated proteins can influence drug response, but direct methods for identifying interacting proteins have been limited. We purified...
Animals Breast Neoplasms Cell Line Tumor Chromatin Chromatin Immunoprecipitation Estrogen Receptor alpha Female Gene Expression Regulation Neoplastic Humans MCF-7 Cells Mice Mice SCID Neoplasm Proteins Protein Interaction Maps RNA Interference RNA Small Interfering Transcription Genetic Transplantation Heterologous
Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.
Ciira wa Maina, Antti Honkela, Filomena Matarese, Korbinian Grote, Hendrik G Stunnenberg, George Reid, Neil D Lawrence, Magnus Rattray
Jan 14, 2020
Gene transcription mediated by RNA polymerase II (pol-II) is a key step in gene expression. The dynamics of pol-II moving along the transcribed region influence the rate and timing of gene expression. In this work, we present a...
Combinatorial activities of SHORT VEGETATIVE PHASE and FLOWERING LOCUS C define distinct modes of flowering regulation in Arabidopsis.
Julieta L Mateos, Pedro Madrigal, Kenichi Tsuda, Vimal Rawat, René Richter, Maida Romera-Branchat, Fabio Fornara, Korbinian Schneeberger, Paweł Krajewski, George Coupland
Jun 19, 2020
BACKGROUND: The initiation of flowering is an important developmental transition as it marks the beginning of the reproductive phase in plants. The MADS-box transcription factors (TFs) FLOWERING LOCUS C (FLC) and SHORT...
Arabidopsis Arabidopsis Proteins Base Sequence Binding Sites Biological Evolution Chromatin Immunoprecipitation Flowers Gene Expression Profiling Gene Expression Regulation Plant Gene Regulatory Networks Genes Plant Genotype Gibberellins MADS Domain Proteins Meristem Molecular Sequence Data Plant Leaves principal component analysis Protein Binding Regulatory Sequences Nucleic Acid Transcription Factors Transcription Genetic
Intra- and inter-chromosomal interactions correlate with CTCF binding genome wide.
A prime goal in systems biology is the comprehensive use of existing high-throughput genomic datasets to gain a better understanding of chromatin organization and genome function. In this report, we use chromatin...
MacroH2A1 isoforms are associated with epigenetic markers for activation of lipogenic genes in fat-induced steatosis.
Christine Podrini, Apostolos Koffas, Shilpa Chokshi, Manlio Vinciguerra, Christopher J Lelliott, Jacqueline K White, Hibret A Adissu, Roger Williams, Azzura Greco
Apr 07, 2021
The importance of epigenetic changes in the development of hepatic steatosis is largely unknown. The histone variant macroH2A1 under alternative splicing gives rise to macroH2A1.1 and macroH2A1.2. In this study, we show that the...
bivalent promoter histone methylation histone variants Lipid uptake Animals Biomarkers Blotting Western Carcinoma Hepatocellular Cells Cultured Chromatin Immunoprecipitation Diet High-Fat Epigenomics Fatty Liver Female Fluorescent Antibody Technique Gene Expression Profiling Hepatocytes Histones Humans Immunoenzyme Techniques Lipid Peroxidation Liver Liver Neoplasms Male Mice Mice Inbred C57BL Mice Knockout Mitochondrial Proton-Translocating ATPases Oligonucleotide Array Sequence Analysis Promoter Regions Genetic Protein Isoforms RNA Messenger Real-Time Polymerase Chain Reaction Reverse Transcriptase Polymerase Chain Reaction
Practical guidelines for the comprehensive analysis of ChIP-seq data.
Timothy Bailey, Pawel Krajewski, Istvan Ladunga, Celine Lefebvre, Qunhua Li, Tao Liu, Pedro Madrigal, Cenny Taslim, Jie Zhang
Jun 19, 2020
Mapping the chromosomal locations of transcription factors, nucleosomes, histone modifications, chromatin remodeling enzymes, chaperones, and polymerases is one of the key tasks of modern biology, as evidenced by the...
Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci.
Kyle J Gaulton, Teresa Ferreira, Yeji Lee, Anne Raimondo, Reedik Mägi, Michael E Reschen, Anubha Mahajan, Adam Locke, N William Rayner, Neil Robertson, Robert A Scott, Inga Prokopenko, Laura J Scott, Todd Green, Thomas Sparso, Dorothee Thuillier, Loic Yengo, Harald Grallert, Simone Wahl, Mattias Frånberg, Rona J Strawbridge, Hans Kestler, Himanshu Chheda, Lewin Eisele, Stefan Gustafsson, Valgerdur Steinthorsdottir, Gudmar Thorleifsson, Lu Qi, Lennart C Karssen, Elisabeth M van Leeuwen, Sara M Willems, Man Li, Han Chen, Christian Fuchsberger, Phoenix Kwan, Clement Ma, Michael Linderman, Yingchang Lu, Soren K Thomsen, Jana K Rundle, Nicola L Beer, Martijn van de Bunt, Anil Chalisey, Hyun Min Kang, Benjamin F Voight, Gonçalo R Abecasis, Peter Almgren, Damiano Baldassarre, Beverley Balkau, Rafn Benediktsson, Matthias Blüher, Heiner Boeing, Lori L Bonnycastle, Erwin P Bottinger, Noël P Burtt, Jason Carey, Guillaume Charpentier, Peter S Chines, Marilyn C Cornelis, David J Couper, Andrew T Crenshaw, Rob M van Dam, Alex SF Doney, Mozhgan Dorkhan, Sarah Edkins, Johan G Eriksson, Tonu Esko, Elodie Eury, João Fadista, Jason Flannick, Pierre Fontanillas, Caroline Fox, Paul W Franks, Karl Gertow, Christian Gieger, Bruna Gigante, Omri Gottesman, George B Grant, Niels Grarup, Christopher J Groves, Maija Hassinen, Christian T Have, Christian Herder, Oddgeir L Holmen, Astradur B Hreidarsson, Steve E Humphries, David J Hunter, Anne U Jackson, Anna Jonsson, Marit E Jørgensen, Torben Jørgensen, Wen-Hong L Kao, Nicola D Kerrison, Leena Kinnunen, Norman Klopp, Augustine Kong, Peter Kovacs, Peter Kraft, Jasmina Kravic, Cordelia Langford, Karin Leander, Liming Liang, Peter Lichtner, Cecilia M Lindgren, Eero Lindholm, Allan Linneberg, Ching-Ti Liu, Stéphane Lobbens, Jian'an Luan, Valeriya Lyssenko, Satu Männistö, Olga McLeod, Julia Meyer, Evelin Mihailov, Ghazala Mirza, Thomas W Mühleisen, Martina Müller-Nurasyid, Carmen Navarro, Markus M Nöthen, Nikolay N Oskolkov, Katharine R Owen, Domenico Palli, Sonali Pechlivanis, Leena Peltonen, John RB Perry, Carl GP Platou, Michael Roden, Douglas Ruderfer, Denis Rybin, Yvonne T van der Schouw, Bengt Sennblad, Gunnar Sigurðsson, Alena Stančáková, Gerald Steinbach, Petter Storm, Konstantin Strauch, Heather M Stringham, Qi Sun, Barbara Thorand, Emmi Tikkanen, Anke Tonjes, Joseph Trakalo, Elena Tremoli, Tiinamaija Tuomi, Roman Wennauer, Steven Wiltshire, Andrew R Wood, Eleftheria Zeggini, Ian Dunham, Ewan Birney, Lorenzo Pasquali, Jorge Ferrer, Ruth JF Loos, Josée Dupuis, Jose C Florez, Eric Boerwinkle, James S Pankow, Cornelia van Duijn, Eric Sijbrands, James B Meigs, Frank B Hu, Unnur Thorsteinsdottir, Kari Stefansson, Timo A Lakka, Rainer Rauramaa, Michael Stumvoll, Nancy L Pedersen, Lars Lind, Sirkka M Keinanen-Kiukaanniemi, Eeva Korpi-Hyövälti, Timo E Saaristo, Juha Saltevo, Johanna Kuusisto, Markku Laakso, Andres Metspalu, Raimund Erbel, Karl-Heinz Jöcke, Susanne Moebus, Samuli Ripatti, Veikko Salomaa, Erik Ingelsson, Bernhard O Boehm, Richard N Bergman, Francis S Collins, Karen L Mohlke, Heikki Koistinen, Jaakko Tuomilehto, Kristian Hveem, Inger Njølstad, Panagiotis Deloukas, Peter J Donnelly, Timothy M Frayling, Andrew T Hattersley, Ulf de Faire, Anders Hamsten, Thomas Illig, Annette Peters, Stephane Cauchi, Rob Sladek, Philippe Froguel, Torben Hansen, Oluf Pedersen, Andrew D Morris, Collin NA Palmer, Sekar Kathiresan, Olle Melander, Peter M Nilsson, Leif C Groop, Inês Barroso, Claudia Langenberg, Nicholas J Wareham, Christopher A O'Callaghan, Anna L Gloyn, David Altshuler, Michael Boehnke, Tanya M Teslovich, Mark I McCarthy, Andrew P Morris, DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium
Jan 23, 2018
We performed fine mapping of 39 established type 2 diabetes (T2D) loci in 27,206 cases and 57,574 controls of European ancestry. We identified 49 distinct association signals at these loci, including five mapping in or near...
Binding Sites Case-Control Studies Chromatin Immunoprecipitation Chromosome Mapping Diabetes mellitus Type 2 Gene Expression Regulation Genetic Loci Genetic Predisposition to Disease Genome-Wide Association Study Genomics Hepatocyte Nuclear Factor 3-beta Humans Islets of Langerhans Liver Molecular Sequence Annotation Polymorphism Single Nucleotide Receptor Melatonin MT2
The endothelial transcription factor ERG promotes vascular stability and growth through Wnt/β-catenin signaling.
Graeme M Birdsey, Aarti V Shah, Neil Dufton, Louise E Reynolds, Lourdes Osuna Almagro, Youwen Yang, Irene M Aspalter, Samia T Khan, Justin C Mason, Elisabetta Dejana, Berthold Göttgens, Kairbaan Hodivala-Dilke, Holger Gerhardt, Ralf H Adams, Anna M Randi
Feb 16, 2015
Animals Antigens CD Blotting Western Cadherins Cells Cultured Chromatin Immunoprecipitation Endothelium Vascular Female Frizzled Receptors Human Umbilical Vein Endothelial Cells Humans Integrases Lung Mice Mice Transgenic Neovascularization Physiologic Oncogene Proteins Pregnancy Real-Time Polymerase Chain Reaction Signal Transduction Transcription Factors Transcriptional Regulator ERG Vascular Endothelial Growth Factor A Wnt Proteins beta Catenin
FOXM1 binds directly to non-consensus sequences in the human genome.
Deborah A Sanders, Michael V Gormally, Giovanni Marsico, Dario Beraldi, David Tannahill, Shankar Balasubramanian
Jun 24, 2015
Base Sequence Binding Sites Cell Line Chromatin Immunoprecipitation Consensus Sequence DNA Forkhead Box Protein M1 Forkhead Transcription Factors Gene Expression Regulation Genome Human HEK293 Cells HeLa Cells Humans Mutation Promoter Regions Genetic Protein Binding Protein Structure Tertiary Proteomics Sequence Analysis DNA
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