Related Experiment Video
Updated: May 24, 2025
09:37
An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
3.3K
SHIP identifies genomic safe harbors in eukaryotic organisms using genomic general feature annotation
Matheus de Castro Leitão1,2, Letícia Sousa Cabral1, Luiza Cesca Piva2
1Department of Genetics and Morphology, University of Brasilia, Brasilia, Brazil.
Scientific Reports
|February 28, 2025
Summary
We developed SHIP, a new algorithm to systematically identify genomic safe harbors (GSHs) for stable gene expression. This tool aids in finding new sites for genetic engineering in eukaryotes.
Area of Science:
- Genomic engineering
- Synthetic biology
- Bioinformatics
Background:
- Genomic safe harbors (GSHs) are crucial for stable transgene expression but are often found empirically.
- Existing GSHs are frequently in gene-rich areas, risking expression instability.
- The need for systematic GSH identification grows with polygenic engineering.
Purpose of the Study:
- To introduce SHIP, an algorithm for systematic detection of potential GSHs in eukaryotes.
- To expand the repertoire of available GSHs for genomic engineering applications.
Main Methods:
- Developed the SHIP algorithm for identifying potential GSHs.
- Utilized Saccharomyces cerevisiae as a model organism.
- Experimentally validated five GSHs using DNA sequencing, stability assays, flow cytometry, qPCR, electron microscopy, RT-qPCR, and RNA-Seq.
Main Results:
- Successfully identified and curated five potential GSHs in Saccharomyces cerevisiae.
- Demonstrated the utility of SHIP in predicting promising GSH candidates.
Conclusions:
- SHIP is a valuable computational tool for the systematic discovery of GSHs.
- The identified GSHs provide new options for stable transgene integration in eukaryotes.
- This work facilitates experimental assessment of GSHs in annotated eukaryotic genomes.
More Related Videos
11:35Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
Published on: August 21, 2016
12.9K
09:33Author Spotlight: Finding New Therapeutic Targets for Malignant Peripheral Nerve Sheath Tumor Through Genome-Scale shRNA Screens
Published on: August 25, 2023
1.1K
Related Concept Videos
03:36Genome Annotation and Assembly
18.8K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
18.8K
02:51Multi-species Conserved Sequences
3.9K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
3.9K
01:11Genome-wide Association Studies-GWAS
12.3K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
12.3K
02:05Gene Evolution - Fast or Slow?
7.0K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
7.0K
02:54Evolutionary Relationships through Genome Comparisons
5.7K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.7K
00:58Genomic DNA in Eukaryotes
46.6K
Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
46.6K