Analysis of TGFβ1 and IL-10 Transcriptional Regulation in CTCL Cells by Chromatin Immunoprecipitation

2014 ◽  
pp. 329-341 ◽  
Author(s):  
Tzu-Pei Chang ◽  
Myra Kim ◽  
Ivana Vancurova
Keyword(s):  
Transcriptional Regulation ◽  
Chromatin Immunoprecipitation

scholarly journals Epigenetic Regulation of WNT3A Enhancer during Regeneration of Injured Cortical Neurons

2020 ◽  
Vol 21 (5) ◽  
pp. 1891
Author(s):  
Chu-Yuan Chang ◽  
Jui-Hung Hung ◽  
Liang-Wei Huang ◽  
Joye Li ◽  
Ka Shing Fung ◽  
...  
Keyword(s):  
Traumatic Brain Injury ◽  
Transcriptional Regulation ◽  
Brain Injury ◽  
Chromatin Immunoprecipitation ◽  
Cortical Neurons ◽  
Histone H3 ◽  
Neuronal Regeneration ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Topological Interaction ◽  
Potential Therapeutic Intervention

Traumatic brain injury is known to reprogram the epigenome. Chromatin immunoprecipitation-sequencing of histone H3 lysine 27 acetylation (H3K27ac) and tri-methylation of histone H3 at lysine 4 (H3K4me3) marks was performed to address the transcriptional regulation of candidate regeneration-associated genes. In this study, we identify a novel enhancer region for induced WNT3A transcription during regeneration of injured cortical neurons. We further demonstrated an increased mono-methylation of histone H3 at lysine 4 (H3K4me1) modification at this enhancer concomitant with a topological interaction between sub-regions of this enhancer and with promoter of WNT3A gene. Together, this study reports a novel mechanism for WNT3A gene transcription and reveals a potential therapeutic intervention for neuronal regeneration.

scholarly journals Identification and transcriptional regulation of the mir-218-1 alternative promoter

2020 ◽  
Author(s):  
Brenna A. Rheinheimer ◽  
Lukas Vrba ◽  
Bernard W Futscher ◽  
Ronald L Heimark
Keyword(s):  
Transcriptional Regulation ◽  
Pancreatic Ductal Adenocarcinoma ◽  
Chromatin Immunoprecipitation ◽  
Transcriptional Start Site ◽  
Regulatory Elements ◽  
Alternative Promoter ◽  
Ductal Adenocarcinoma ◽  
Start Site ◽  
Public Datasets ◽  
Intron 4

AbstractBackgroundmiRNAs are small, endogenous non-coding RNAs approximately 22 nucleotides in length that account for approximately 1% of the genome and play key regulatory roles in multiple signaling pathways. mir-218-1 is an intronic miRNA located within intron 15 of the SLIT2 gene. Public datasets showed enrichment of H3K4me3 within intron 4 of the SLIT2 gene. Therefore, we sought to determine the genomic location and transcriptional regulatory elements of the mir-218-1 candidate alternative promoter in pancreatic ductal adenocarcinoma.MethodsExpression of mir-218 was evaluated in a panel of pancreatic ductal adenocarcinoma cell lines. The mir-218-1 candidate alternative promoter was characterized by chromatin immunoprecipitation, Sequenom, and luciferase assays. Transcriptional regulation of the mir-218-1 candidate alternative promoter was assessed using chromatin immunoprecipitation and an inhibitor to NF-kB.ResultsWe found that expression of mir-218-1 does not correlate with SLIT2 expression and that mir-218-1 has a novel transcriptional start site separate from the SLIT2 promoter. This novel transcriptional start site showed transcriptional activity and was regulated by NF-kB.Conclusionsmir-218-1 is transcribed from an independent and novel transcriptional start site located within intron 4 of the SLIT2 gene in pancreatic ductal adenocarcinoma. Additionally, mir-218-1 expression is regulated by Nf-kB at this alternative transcriptional start site in pancreatic cancer.

scholarly journals A ChIP on the shoulder? Chromatin immunoprecipitation and validation strategies for ChIP antibodies

F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 235 ◽  
Author(s):  
Fiona C. Wardle ◽  
Haihan Tan
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Chromatin Immunoprecipitation ◽  
Regulation Of Gene Expression ◽  
Antigen Recognition ◽  
Validation Methods

Chromatin immunoprecipitation (ChIP) is a technique widely used in the study of epigenetics and transcriptional regulation of gene expression. However, its antibody-centric nature exposes it to similar challenges faced by other antibody-based procedures, of which the most prominent are issues of specificity and affinity in antigen recognition. As with other techniques that make use of antibodies, recent studies have shown the need for validation of ChIP antibodies in order to be sure they recognize the advertised protein or epitope. We summarize here the issues surrounding ChIP antibody usage, and highlight the toolkit of validation methods that can be employed by investigators looking to appraise these reagents.

scholarly journals Regulation of endothelial hemoglobin alpha expression by Kruppel-like factors

2017 ◽  
Vol 22 (5) ◽  
pp. 363-369 ◽  
Author(s):  
Panjamaporn Sangwung ◽  
Guangjin Zhou ◽  
Yuan Lu ◽  
Xudong Liao ◽  
Benlian Wang ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Transcriptional Regulation ◽  
Chromatin Immunoprecipitation ◽  
Binding Sites ◽  
Vascular Tone ◽  
Opposite Effect ◽  
Reporter Assays ◽  
And Function

Hemoglobin subunit alpha (HBA) expression in endothelial cells (ECs) has recently been shown to control vascular tone and function. We sought to elucidate the transcriptional regulation of HBA expression in the EC. Gain of KLF2 or KLF4 function studies led to significant induction of HBA in ECs. An opposite effect was observed in ECs isolated from animals with endothelial-specific ablation of Klf2, Klf4 or both. Promoter reporter assays demonstrated that KLF2/KLF4 transactivated the hemoglobin alpha promoter, an effect that was abrogated following mutation of all four putative KLF-binding sites. Fine promoter mutational studies localized three out of four KLF-binding sites (sites 2, 3, and 4) as critical for the transactivation of the HBA promoter by KLF2/KLF4. Chromatin immunoprecipitation studies showed that KLF4 bound to the HBA promoter in ECs. Thus, KLF2 and KLF4 serve as important regulators that promote HBA expression in the endothelium.

TRCirc: a resource for transcriptional regulation information of circRNAs

2018 ◽  
Vol 20 (6) ◽  
pp. 2327-2333 ◽  
Author(s):  
Zhidong Tang ◽  
Xuecang Li ◽  
Jianmei Zhao ◽  
Fengcui Qian ◽  
Chenchen Feng ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Chromatin Immunoprecipitation ◽  
Cell Types ◽  
Circular Rnas ◽  
Rna Seq ◽  
Current Version ◽  
Genomic Technologies ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Efficient Retrieval ◽  
User Friendly

Abstract In recent years, high-throughput genomic technologies like chromatin immunoprecipitation sequencing (ChIp-seq) and transcriptome sequencing (RNA-seq) have been becoming both more refined and less expensive, making them more accessible. Many circular RNAs (circRNAs) that originate from back-spliced exons have been identified in various cell lines across different species. However, the regulatory mechanism for transcription of circRNAs remains unclear. Therefore, there is an urgent need to construct a database detailing the transcriptional regulation of circRNAs. TRCirc (http://www.licpathway.net/TRCirc) provides a resource for efficient retrieval, browsing and visualization of transcriptional regulation information of circRNAs. The current version of TRCirc documents 92 375 circRNAs and 161 transcription factors (TFs) from more than 100 cell types and together represent more than 765 000 TF–circRNA regulatory relationships. Furthermore, TRCirc provides other regulatory information about transcription of circRNAs, including their expression, methylation levels, H3K27ac signals in regulation regions and super-enhancers associated with circRNAs. TRCirc provides a convenient, user-friendly interface to search, browse and visualize detailed information about these circRNAs.

scholarly journals BRD2 regulation of sigma-2 receptor expression upon cytosolic cholesterol deprivation

2019 ◽  
Author(s):  
Hongtao Shen ◽  
Jing Li ◽  
Xiujie Xie ◽  
Huan Yang ◽  
Mengxue Zhang ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Transcription Factors ◽  
Fatty Acid ◽  
Chromatin Immunoprecipitation ◽  
Acid Metabolism ◽  
Gene Promoter ◽  
Cholesterol Homeostasis ◽  
Receptor Expression ◽  
Antipsychotic Treatment ◽  
Protein Levels

AbstractTraditionally a pharmacologic target for antipsychotic treatment, the sigma-2 receptor (S2R) was recently implicated in cholesterol homeostasis. Here we investigated the transcriptional regulation of S2R by the Bromo/ExtraTerminal epigenetic reader family (BETs, including BRD2, 3, 4) upon cholesterol perturbation.Cytosolic cholesterol deprivation was induced using an export blocker of lysosomal cholesterol in ARPE19 cells. This condition upregulated mRNA and protein levels of S2R, and of SREBP2 but not SREBP1, transcription factors key to cholesterol/fatty acid metabolism. Silencing BRD2 but not BRD4 (though widely deemed as a master regulator) or BRD3 prevented S2R upregulation induced by cholesterol deprivation. Silencing SREBP2 but not SREBP1 diminished S2R expression. Furthermore, BRD2 co-immunoprecipitated with the SREBP2 transcription-active N-terminal domain, and chromatin immunoprecipitation-qPCR showed a BRD2 occupancy at the S2R gene promoter.In summary, this study reveals a novel BRD2/SREBP2 cooperative regulation of S2R transcription in response to cytosolic cholesterol deprivation, thus shedding new light on epigenetic control of cholesterol biology.

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