Pursuing gene regulation 'logic' via RNA interference and chromatin immunoprecipitation

2006 ◽  
Vol 7 (7) ◽  
pp. 692-697 ◽  
Author(s):  
Caiyi C Li ◽  
Vladimir R Ramirez-Carrozzi ◽  
Stephen T Smale
Keyword(s):  
Gene Regulation ◽  
Rna Interference ◽  
Chromatin Immunoprecipitation

scholarly journals Regulation and imaging of gene expression via an RNA interference antagonistic biomimetic probe

2017 ◽  
Vol 8 (7) ◽  
pp. 4973-4977 ◽  
Author(s):  
Kai Zhang ◽  
Xue-Jiao Yang ◽  
Wei Zhao ◽  
Ming-Chen Xu ◽  
Jing-Juan Xu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Rna Interference ◽  
Living Cells

A versatile strategy is reported which permits gene regulation and imaging in living cells via an RNA interference antagonistic probe.

scholarly journals HOXD8/DIAPH2-AS1 epigenetically regulates PAX3 and impairs HTR-8/SVneo cell function under hypoxia

2019 ◽  
Vol 39 (1) ◽  
Author(s):  
Yaling Feng ◽  
Jianxia Wang ◽  
Yue He ◽  
Heng Zhang ◽  
Minhui Jiang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Rna Interference ◽  
Chromatin Immunoprecipitation ◽  
Regulatory Network ◽  
Molecular Basis ◽  
Promoter Region ◽  
Cell Function ◽  
Down Regulation ◽  
Histone 3 ◽  
Development Data

Abstract The present study aimed to unravel the molecular basis underlying PAX3 down-regulation, known to be involved in pre-eclampsia (PE) occurrence and development. Data obtained from databases suggested that Pax3 methylation levels in the promoter region are high in the placentas of PE patients. However, the expression of methylation-adjusting enzymes, including DNMT1, LSD1, and EZH2, did not change. Since lncRNAs enhance the function of methylation-related enzymes independently of expression, we selected three lncRNAs, RP11-269F21.2, DIAPH2-AS1, and RP11-445K13.2, predicted to interact with methylation-adjusting enzymes. Two transcription factors, HOXD8 and Lhx3, predicted to regulate the expression of lncRNAs, were also selected. Using RNA interference technology, HOXD8 and Lhx3 were found to positively regulate DIAPH2-AS1 and RP11-445K13.2 in HTR-8/SVneo cells. Chromatin immunoprecipitation assays determined that DIAPH2-AS1 recruited LSD1 to histone 3, increasing DNMT1 stability at H3. The HOXD8/DIAPH2-AS1 network regulated HTR-8/SVneo cell function under hypoxia by epigenetically regulating PAX3. This regulatory network may thus be responsible for PAX3 down-regulation in the placentas of PE patients.

scholarly journals Epigenetic manipulation of gene expression

2005 ◽  
Vol 169 (6) ◽  
pp. 847-857 ◽  
Author(s):  
Rudy L. Juliano ◽  
Vidula R. Dixit ◽  
Hyunmin Kang ◽  
Tai Young Kim ◽  
Yuko Miyamoto ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Culture ◽  
Gene Regulation ◽  
Transcription Factors ◽  
Rna Interference ◽  
Antisense Oligonucleotide ◽  
Significant Progress ◽  
Direct Experience ◽  
Key Features ◽  
Epigenetic Manipulation

Cell biologists have been afforded extraordinary new opportunities for experimentation by the emergence of powerful technologies that allow the selective manipulation of gene expression. Currently, RNA interference is very much in the limelight; however, significant progress has also been made with two other approaches. Thus, antisense oligonucleotide technology is undergoing a resurgence as a result of improvements in the chemistry of these molecules, whereas designed transcription factors offer a powerful and increasingly convenient strategy for either up- or down-regulation of targeted genes. This mini-review will highlight some of the key features of these three approaches to gene regulation, as well as provide pragmatic guidance concerning their use in cell biological experimentation based on our direct experience with each of these technologies. The approaches discussed here are being intensely pursued in terms of possible therapeutic applications. However, we will restrict our comments primarily to the cell culture situation, only briefly alluding to fundamental differences between utilization in animals versus cells.

scholarly journals A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals

2012 ◽  
Vol 47 (5) ◽  
pp. 810-822 ◽  
Author(s):  
Manuel Garber ◽  
Nir Yosef ◽  
Alon Goren ◽  
Raktima Raychowdhury ◽  
Anne Thielke ◽  
...  
Keyword(s):  
Gene Regulation ◽  
High Throughput ◽  
Chromatin Immunoprecipitation

scholarly journals Specificity Principles in RNA-Guided Targeting

2016 ◽  
Author(s):  
Namita Bisaria ◽  
Inga Jarmoskaite ◽  
Daniel Herschlag
Keyword(s):  
Gene Regulation ◽  
Rna Interference ◽  
Binding Affinity ◽  
Small Rna ◽  
Kinetic Models ◽  
Specific Gene ◽  
Rational Engineering ◽  
Target Rna ◽  
Target Activity ◽  
Derived Rules

ABSTRACTRNA-guided nucleases (RGNs) provide sequence-specific gene regulation through base-pairing interactions between a small RNA guide and target RNA or DNA. RGN systems, which include CRISPR-Cas9 and RNA interference (RNAi), hold tremendous promise as programmable tools for engineering and therapeutic purposes. However, pervasive targeting of sequences that closely resemble the intended target has remained a major challenge, limiting the reliability and interpretation of RGN activity and the range of possible applications. Efforts to reduce off-target activity and enhance RGN specificity have led to a collection of empirically derived rules, which often paradoxically include decreased binding affinity of the RNA-guided nuclease to its target. Here we demonstrate that simple kinetic considerations of the targeting reaction can explain these and other literature observations. The kinetic models described provide a foundation for understanding RGN systems and a necessary physical and functional framework for their rational engineering.

scholarly journals RNA Interference in Fungi: Pathways, Functions, and Applications

2011 ◽  
Vol 10 (9) ◽  
pp. 1148-1155 ◽  
Author(s):  
Yunkun Dang ◽  
Qiuying Yang ◽  
Zhihong Xue ◽  
Yi Liu
Keyword(s):  
Gene Regulation ◽  
Rna Interference ◽  
Small Rna ◽  
Rnai Machinery ◽  
Content Type ◽  
Heterochromatin Formation ◽  
Rna Molecules ◽  
Cellular Processes ◽  
Rna Biogenesis ◽  
Core Components

ABSTRACT Small RNA molecules of about 20 to 30 nucleotides function in gene regulation and genomic defense via conserved eukaryotic RNA interference (RNAi)-related pathways. The RNAi machinery consists of three core components: Dicer, Argonaute, and RNA-dependent RNA polymerase. In fungi, the RNAi-related pathways have three major functions: genomic defense, heterochromatin formation, and gene regulation. Studies of Schizosaccharomyces pombe and Neurospora , and other fungi have uncovered surprisingly diverse small RNA biogenesis pathways, suggesting that fungi utilize RNAi-related pathways in various cellular processes to adapt to different environmental conditions. These studies also provided important insights into how RNAi functions in eukaryotic systems in general. In this review, we will discuss our current understanding of the fungal RNAi-related pathways and their functions, with a focus on filamentous fungi. We will also discuss how RNAi can be used as a tool in fungal research.

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