Related Experiment Video
Updated: Mar 9, 2026
10:46
Dissection of Enhancer Function Using Multiplex CRISPR-based Enhancer Interference in Cell Lines
Published on: June 2, 2018
9.9K
Copy number alterations unmasked as enhancer hijackers
Rameen Beroukhim1, Xiaoyang Zhang1, Matthew Meyerson1
1Dana-Farber Cancer Institute, the Broad Institute of Harvard and MIT, and Harvard Medical School, Boston, Massachusetts, USA.
Nature Genetics
|December 29, 2016
Summary
This study introduces a new analytical framework to understand how DNA copy number alterations, driven by genomic rearrangements, contribute to cancer. It shifts focus from gene dosage to the underlying structural variations in DNA.
Area of Science:
- Genomics
- Cancer Biology
- Bioinformatics
Background:
- DNA copy number alterations (CNAs) are crucial in disease, particularly cancer.
- Current research primarily focuses on gene dosage effects of CNAs.
- The role of genomic rearrangements underlying CNAs in oncogenesis is often overlooked.
Purpose of the Study:
- To develop and present an innovative analytical framework.
- To analyze copy number alterations (CNAs) driven by genomic rearrangements.
- To understand the oncogenic mechanisms of these specific CNAs.
Main Methods:
- Development of a novel analytical framework.
- Application of the framework to identify and characterize CNAs arising from genomic rearrangements.
- Integration of genomic structural variation analysis with copy number profiling.
Main Results:
- The study successfully implemented a new framework for analyzing CNAs.
- Identified specific copy number alterations predominantly caused by underlying genomic rearrangements.
- Provided insights into the oncogenic potential of these rearrangement-driven CNAs.
Conclusions:
- The proposed analytical framework offers a new perspective on CNA analysis.
- Genomic rearrangements play a critical, often underestimated, role in driving oncogenic CNAs.
- This approach enhances our understanding of cancer development and potential therapeutic targets.
Related Concept Videos
02:26Comparing Copy Number Variations and SNPs
19.0K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
19.0K
01:06Induced Pluripotent Stem Cells
5.8K
Stem cells are undifferentiated cells that divide and produce different cell types. Ordinarily, cells that have differentiated into a specific cell type are terminally differentiated; however, scientists have found a way to reprogram these mature cells so that they dedifferentiate and return to an unspecialized, proliferative state. These cells are pluripotent like embryonic stem cells—able to produce all cell types—and are called induced pluripotent stem cells (iPSCs).
Somatic...
Somatic...
5.8K
02:46Genome Copying Errors
5.3K
DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their survival. Therefore, the copying errors are checked and repaired at three levels.
5.3K
01:37Epigenetic Regulation
4.0K
Epigenetic changes alter the physical structure of the DNA without changing the genetic sequence and often regulate whether genes are turned on or off. This regulation ensures that each cell produces only proteins necessary for its function. For example, proteins that promote bone growth are not produced in muscle cells. Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
X-chromosome...
X-chromosome...
4.0K
02:32Position-effect Variegation
7.2K
In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.
7.2K
02:08Gene Conversion
10.8K
Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
10.8K