Cargando…

Tracing the molecular basis of transcriptional dynamics in noisy data by using an experiment-based mathematical model

Changes in transcription factor levels, epigenetic status, splicing kinetics and mRNA degradation can each contribute to changes in the mRNA dynamics of a gene. We present a novel method to identify which of these processes is changed in cells in response to external signals or as a result of a dise...

Descripción completa

Detalles Bibliográficos
Autores principales:	Rybakova, Katja N., Tomaszewska, Aleksandra, van Mourik, Simon, Blom, Joke, Westerhoff, Hans V., Carlberg, Carsten, Bruggeman, Frank J.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2015
Materias:	Gene regulation, Chromatin and Epigenetics
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4288170/ https://www.ncbi.nlm.nih.gov/pubmed/25477385 http://dx.doi.org/10.1093/nar/gku1272

Ejemplares similares

Chromatin acetylation at transcription start sites and vitamin D receptor binding regions relates to effects of 1α,25-dihydroxyvitamin D(3) and histone deacetylase inhibitors on gene expression
por: Seuter, Sabine, et al.
Publicado: (2013)

Epigenome-wide effects of vitamin D and their impact on the transcriptome of human monocytes involve CTCF
por: Seuter, Sabine, et al.
Publicado: (2016)

Dataset integration identifies transcriptional regulation of microRNA genes by PPARγ in differentiating mouse 3T3-L1 adipocytes
por: John, Elisabeth, et al.
Publicado: (2012)

Cyclical regulation of the insulin-like growth factor binding protein 3 gene in response to 1α,25-dihydroxyvitamin D(3)
por: Malinen, Marjo, et al.
Publicado: (2011)

Nuclear hormone 1α,25-dihydroxyvitamin D(3) elicits a genome-wide shift in the locations of VDR chromatin occupancy
por: Heikkinen, Sami, et al.
Publicado: (2011)

Structural basis of specific DNA binding by the transcription factor ZBTB24
por: Ren, Ren, et al.
Publicado: (2019)

Molecular basis for lethal cross-talk between two unrelated bacterial transcription factors - the regulatory protein of a restriction-modification system and the repressor of a defective prophage
por: Wisniewska, Aleksandra, et al.
Publicado: (2022)

Structural and mechanistic basis of anti-termination of Rho-dependent transcription termination by bacteriophage P4 capsid protein Psu
por: Ranjan, Amitabh, et al.
Publicado: (2013)

Structural basis for Klf4 recognition of methylated DNA
por: Liu, Yiwei, et al.
Publicado: (2014)

Profiling of promoter occupancy by PPARα in human hepatoma cells via ChIP-chip analysis
por: van der Meer, David L. M., et al.
Publicado: (2010)

Chromosome intermingling—the physical basis of chromosome organization in differentiated cells
por: Maharana, Shovamayee, et al.
Publicado: (2016)

Structural basis of the specific interaction of SMRT corepressor with histone deacetylase 4
por: Park, Suk-Youl, et al.
Publicado: (2018)

Molecular basis for the methylation specificity of ATXR5 for histone H3
por: Bergamin, Elisa, et al.
Publicado: (2017)

Distinctive structural basis for DNA recognition by the fission yeast Zn(2)Cys(6) transcription factor Pho7 and its role in phosphate homeostasis
por: Garg, Angad, et al.
Publicado: (2018)

Epigenetic control of a VDR-governed feed-forward loop that regulates p21((waf1/cip1)) expression and function in non-malignant prostate cells
por: Thorne, James L., et al.
Publicado: (2011)

Structural basis for effects of CpA modifications on C/EBPβ binding of DNA
por: Yang, Jie, et al.
Publicado: (2019)

Structural basis for preferential binding of human TCF4 to DNA containing 5-carboxylcytosine
por: Yang, Jie, et al.
Publicado: (2019)

Molecular basis of crosstalk in nuclear receptors: heterodimerization between PXR and CAR and the implication in gene regulation
por: Bwayi, Monicah N, et al.
Publicado: (2022)

Structural basis of SETD6-mediated regulation of the NF-kB network via methyl-lysine signaling
por: Chang, Yanqi, et al.
Publicado: (2011)

Excision of thymine and 5-hydroxymethyluracil by the MBD4 DNA glycosylase domain: structural basis and implications for active DNA demethylation
por: Hashimoto, Hideharu, et al.
Publicado: (2012)

Tagetitoxin inhibits transcription by stabilizing pre-translocated state of the elongation complex
por: Yuzenkova, Yulia, et al.
Publicado: (2013)

Excision of 5-hydroxymethyluracil and 5-carboxylcytosine by the thymine DNA glycosylase domain: its structural basis and implications for active DNA demethylation
por: Hashimoto, Hideharu, et al.
Publicado: (2012)

Non-perfectly matching small RNAs can induce stable and heritable epigenetic modifications and can be used as molecular markers to trace the origin and fate of silencing RNAs
por: Fei, Yue, et al.
Publicado: (2021)

Structural and functional characterization of a cell cycle associated HDAC1/2 complex reveals the structural basis for complex assembly and nucleosome targeting
por: Itoh, Toshimasa, et al.
Publicado: (2015)

Hypoxia-induced transcriptional stress is mediated by ROS-induced R-loops
por: Ma, Tiffany S, et al.
Publicado: (2023)

Multiplex Eukaryotic Transcription (In)activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism
por: Rybakova, Katja N., et al.
Publicado: (2015)

Octamer-dependent transcription in T cells is mediated by NFAT and NF-κB
por: Mueller, Kerstin, et al.
Publicado: (2013)

Requirement of TFIIH kinase subunit Mat1 for RNA Pol II C-terminal domain Ser5 phosphorylation, transcription and mRNA turnover
por: Helenius, Katja, et al.
Publicado: (2011)

Transcriptome analyses of cells carrying the Type II Csp231I restriction–modification system reveal cross-talk between two unrelated transcription factors: C protein and the Rac prophage repressor
por: Negri, Alessandro, et al.
Publicado: (2019)

Coactivators enable glucocorticoid receptor recruitment to fine-tune estrogen receptor transcriptional responses
por: Bolt, Michael J., et al.
Publicado: (2013)

FUS/TLS contributes to replication-dependent histone gene expression by interaction with U7 snRNPs and histone-specific transcription factors
por: Raczynska, Katarzyna Dorota, et al.
Publicado: (2015)

Extensive remodeling of DC function by rapid maturation-induced transcriptional silencing
por: Seguín-Estévez, Queralt, et al.
Publicado: (2014)

Genome-wide assessment of differential roles for p300 and CBP in transcription regulation
por: Ramos, Yolande F. M., et al.
Publicado: (2010)

Integrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes
por: Mokry, Michal, et al.
Publicado: (2012)

Transcription profiling during the cell cycle shows that a subset of Polycomb-targeted genes is upregulated during DNA replication
por: Peña-Diaz, Javier, et al.
Publicado: (2013)

Snail1 transcription factor controls telomere transcription and integrity
por: Mazzolini, Rocco, et al.
Publicado: (2018)

Transcription-coupled changes to chromatin underpin gene silencing by transcriptional interference
por: Ard, Ryan, et al.
Publicado: (2016)

Displacement of the transcription factor B reader domain during transcription initiation
por: Dexl, Stefan, et al.
Publicado: (2018)

Estrogen-induced transcription at individual alleles is independent of receptor level and active conformation but can be modulated by coactivators activity
por: Stossi, Fabio, et al.
Publicado: (2020)

Local states of chromatin compaction at transcription start sites control transcription levels
por: Ishihara, Satoru, et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_boo9l9hpbo38i8g9r6jkniac7k