Herein we present several strategies for testing the function of cis-regulatory elements using the PhiC31 integrase system. Firstly, we present two different strategies to analyze the activity of candidate enhancer elements. Targeted integration of candidate enhancers into the same genomic location circumvents the variability-associated random integration and position effects. This method is suitable for testing of candidate enhancers identified through computational or other analyses a priori. Secondly, we present methodology for targeted integration of BACs into the same genomic location(s). By using additional reporters integrated into a BAC, this enables experimental testing whether cis-regulatory elements are functional in the sequence inserted in the BAC.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1007/978-1-4939-3771-4_6 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Genome-wide analysis of sugar transporter gene family in and , expression profiling and identification of transcription factors.
Front Plant Sci
January 2025
State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Sugarcane Biology, Guangxi University, Guangxi, China.
Sugar, the primary product of photosynthesis, is a vital requirement for cell activities. Allocation of sugar from source to sink tissues is facilitated by sugar transporters (ST). These STs belong to the Major Facilitator Superfamily (MFS), the largest family of STs in plants.
View Article and Find Full Text PDFUncovering the chromatin-mediated transcriptional regulatory network governing cold stress responses in fish immune cells.
J Genet Genomics
January 2025
Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 201306, China; Marine Biomedical Science and Technology Innovation Platform of Lin-gang Special Area, Shanghai 201306, China. Electronic address:
Temperature fluctuations challenge ectothermic species, particularly tropical fish dependent on external temperatures for physiological regulation. However, the molecular mechanisms through which low-temperature stress impacts immune responses in these species, especially in relation to chromatin accessibility and epigenetic regulation, remain poorly understood. In this study, we investigate chromatin and transcriptional changes in the head kidney and thymus tissues of Nile tilapia (Oreochromis niloticus), a tropical fish of significant economic importance, under cold stress.
View Article and Find Full Text PDFGenome wide identification of MATE and ALMT gene family in lentil (Lens culinaris Medikus) and expression profiling under Al stress condition.
BMC Plant Biol
January 2025
Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
Background: The membrane transporters viz. multidrug and toxic compound extrusion (MATE) and aluminum-activated malate transporter (ALMT) are associated with aluminum (Al) tolerance by accelerating secretion of organic acids, which can influence nutrient availability and stress response. However, such transporter families have not yet been reported in lentil under Al stress condition.
View Article and Find Full Text PDFMultiscale footprints reveal the organization of cis-regulatory elements.
Nature
January 2025
Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Cis-regulatory elements (CREs) control gene expression and are dynamic in their structure and function, reflecting changes in the composition of diverse effector proteins over time. However, methods for measuring the organization of effector proteins at CREs across the genome are limited, hampering efforts to connect CRE structure to their function in cell fate and disease. Here we developed PRINT, a computational method that identifies footprints of DNA-protein interactions from bulk and single-cell chromatin accessibility data across multiple scales of protein size.
View Article and Find Full Text PDFRegulatory non-coding somatic mutations as drivers of neuroblastoma.
Br J Cancer
January 2025
University of Naples Federico II, Department of Molecular Medicine and Medical Biotechnology, Naples, Italy.
Background: Emerging evidence suggests that non-coding somatic single nucleotide variants (SNVs) in cis-regulatory elements (CREs) contribute to cancer by disrupting gene expression networks. However, the role of non-coding SNVs in cancer, particularly neuroblastoma, remains largely unclear.
Methods: SNVs effect on CREs activity was evaluated by luciferase assays.
Want AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!