Results 41 to 50 of about 104,409 (252)

Models incorporating chromatin modification data identify functionally important p53 binding sites

, 2013
Genome-wide prediction of transcription factor binding sites is notoriously difficult. We have developed and applied a logistic regression approach for prediction of binding sites for the p53 transcription factor that incorporates sequence information ...
Barker, Daniel, Iggo, Richard Derek, Lim, Ji-Hyun   +2 more
core   +1 more source

Subtype‐specific enhancer RNAs define transcriptional regulators and prognosis in breast cancers

Molecular Oncology, EarlyView.
This study employed machine learning methodologies to perform the subtype‐specific classification of RNA‐seq data sets, which are mapped on enhancers from TCGA‐derived breast cancer patients. Their integration with gene expression (referred to as ProxCReAM eRNAs) and chromatin accessibility profiles has the potential to identify lineage‐specific and ...
Aamena Y. Patel, Peyman Zarrineh, Nathnael T. Tuffa, Jigar H. Sheth, Sumitra Mohan, Mudassar Iqbal, Sankari Nagarajan   +6 more
wiley   +1 more source

Reactivity of human AGO2 monoclonal antibody 11A9 with the SWI/SNF complex: A case study for rigorously defining antibody selectivity

Scientific Reports, 2017
In this study, we originally aimed to characterize the potential role of Argonaute 2 (AGO2) in the nucleus, a key protein of the miRNA machinery. We combined Chromatin Immunoprecipitation (ChIP) with high throughput sequencing (ChIP-seq) and quantitative
Roderick A. P. M. van Eijl, Teun van den Brand, Luan N. Nguyen, Klaas W. Mulder   +3 more
doaj   +1 more source

Genome-wide Interrogation of Protein-DNA Interactions in Mammalian Cells Using ChIPmentation

STAR Protocols, 2020
Summary: Mapping the genomic locations of chromatin-associated proteins, such as transcription factors and histone modifications, is key to understanding the mechanisms of transcriptional regulation.
Wei Xu, Ying Ye, Andrew D. Sharrocks, Wensheng Zhang, Xi Chen   +4 more
doaj   +1 more source

Profiling of promoter occupancy by PPARalpha in human hepatoma cells via ChIP-chip analysis

, 2010
The transcription factor peroxisome proliferator-activated receptor alpha (PPARalpha) is an important regulator of hepatic lipid metabolism. While PPARalpha is known to activate transcription of numerous genes, no comprehensive picture of PPARalpha ...
Degenhardt, Tatjana, de Groot, Philip, Merja Heinäniemi, Väisänen, Sami, de Groot, P.J., Carlberg, Carsten, Carsten Carlberg, de Vries, Sacco C, Müller, M.R., David L. M. van der Meer, Vries, Sacco, de, Philip J. de Groot, van der Meer, D.L., Degenhardt, T., Kersten, Sander, de Vries, Sacco, Heinaniemi, M., Vries, S.C., de, Kersten, A.H., Müller, Michael, Carlberg, C., Meer, D.L., van der, Sander Kersten, Michael Müller, Meer, D.L.M., van der, Groot, Philip, de, de Vries, S.C., Väisänen, S., Sami Väisänen, van der Meer, David L M, Groot, P.J., de, Heinäniemi, Merja, van der Meer, D.L.M., de Groot, Philip J, Tatjana Degenhardt, Sacco C. de Vries   +35 more
core   +1 more source

CCDC80 suppresses high‐grade serous ovarian cancer migration via negative regulation of B7‐H3

Molecular Oncology, EarlyView.
PAX8 is a lineage‐specific master regulator of transcription in high‐grade serous ovarian cancer (HGSC) progression. We show for the first time that PAX8 facilitates proliferation and metastasis by repressing the cell autonomous tumor suppressor CCDC80 and inducing B7‐H3 expression.
Aya Saleh, Nitzan Medina‐Itzhaki, Milena Chekov, Eden Gal‐Swisa, Roba Gabesh‐Wahabi, Inbar Savyon, Inna Naroditsky, Hilary A. Kenny, Basem Fares, Lina Korsensky, Einav Girsh, Liron Berger, Ruth Perets   +12 more
wiley   +1 more source

Genome-wide histone modification profiling of inner cell mass and trophectoderm of bovine blastocysts by RAT-ChIP.

PLoS ONE, 2019
Chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-seq) has revolutionized our understanding of chromatin-related biological processes.
Tõnis Org, Kati Hensen, Rita Kreevan, Elina Mark, Olav Sarv, Reidar Andreson, Ülle Jaakma, Andres Salumets, Ants Kurg   +8 more
doaj   +1 more source

Loss of IGF‐1R impairs DNA‐PKcs recruitment to chromatin leading to defective end‐joining

Molecular Oncology, EarlyView.
IGF‐1R promotes radioresistance by facilitating DNA‐PKcs recruitment to chromatin, enabling non‐homologous end‐joining (NHEJ) repair of double‐strand breaks. Inhibition or loss of IGF‐1R disrupts this recruitment to damage sites, driving compensatory reliance on microhomology‐mediated end‐joining (MMEJ) repair.
Matthew O. Ellis, Jack V. Mills, Wojciech Niedzwiedz, Valentine M. Macaulay   +3 more
wiley   +1 more source

Chromatin Immunoprecipitation Experiments from Whole Drosophila Embryos or Larval Imaginal Discs

Bio-Protocol, 2017
Chromatin Immunoprecipitation coupled either to qPCR (qChIP) or high-throughput sequencing (ChIP-Seq) has been extensively used in the last decades to identify the DNA binding sites of transcription factors or the localization of various histone marks ...
Vincent Loubiere, Anna Delest, Bernd Schuettengruber, Anne-Marie Martinez, Giacomo Cavalli   +4 more
doaj   +1 more source

Identifying transcription factors controlling the basal expression of human MRP4 highlights a substantial role for Sp1

FEBS Open Bio, EarlyView.
The MRP4 transporter exports several drugs and signaling molecules. Here, we identified key promoter elements regulating basal MRP4 expression. Using reporter assays, we defined a conserved region with essential Sp1 and contributory Ets sites, which controlled basal MRP4 expression.
Debora Singer, Angelique Kragl, Katrin Ziems, Juliane Glaubitz, Sophie Grammbauer, Susanne Hildebrandt, Mladen V. Tzvetkov, Gabriele Jedlitschky   +7 more
wiley   +1 more source