JUN 08, 2018 4:53 PM PDT

Visualizing Gene Activity in Single Cells

WRITTEN BY: Carmen Leitch

With labeling tools that add fluorescent tags, researchers could once see about four or five genes in a cell. Updates to that technique by scientists at Caltech will now enable the visualization of over 10,000 genes in one cell at the same time. This new method has been called intron seqFISH (sequential fluorescence in situ hybridization) and has been reported in the journal Cell.

Intron seqFISH enables 3D reconstruction of nascent transcription active sites (colored spots) in an embryonic stem cell (blue), with individual chromosomes occupying distinct spatial territories (colored differently). Here, 982 transcription active sites, corresponding to individual genes, are present in this cell. / Credit: Cai laboratory / Cell

Long Cai, research professor in biology and an affiliated faculty member of the Tianqiao and Chrissy Chen Institute for Neuroscience at Caltech led this study, which utilized introns. When genes in DNA are active, they are transcribed into RNA, an intermediary molecule the cell usually uses to make proteins. Before being made into protein, the RNA has to be modified; one edit is the removal of introns, which are non-coding regions of DNA that sit in between exons, the coding portions of genes. The investigators labeled introns because they are only around when transcription first starts. Thus, they could get a snapshot of gene activity at one moment.

In the intron seqFISH method, every intron gets a fluorescent label, which can be seen under a microscope. That indicates which genes are active and can also show how high their expression level is. In all, the researchers barcoded and visualized 10,421 genes at one time.

Previous barcoding tools have used RNA, which can show how the activity of genes changes over time. The intron labels highlighted the newly transcribed genes, the so-called nascent transcriptome. When they used the tool, the investigators were surprised by what they found; they saw that genes are transcribed on a short, oscillating course, with many genes bursting on and off over two hours.

These oscillations haven’t been observed before because of technical limitations. Intron seqFISH allowed the scientists to actually see what they measured in a single cell, ensuring it was not an artifact. Introns also don’t hang out for as long as mRNA does, so it’s easier to see them coming and going.

Introns tend to stick around the gene, so the labels also allowed the investigators to see the locations of genes in chromosomes, where the entire genome is compacted in the nucleus of cells. They saw that genes encoding for protein aren’t buried within the chromosome but are instead near the surface.

"This technique can be applied to any tissue," said Cai. "Intron seqFISH can help identify cell types and also what the cells are going to do, in addition to giving us a look at the chromosome structure in the same cells."

Learn more about the fluorescent in situ hybridization technique from the video.

Sources: AAAS/Eurekalert! Via Caltech, Cell

About the Author
  • Experienced research scientist and technical expert with authorships on over 30 peer-reviewed publications, traveler to over 70 countries, published photographer and internationally-exhibited painter, volunteer trained in disaster-response, CPR and DV counseling.
You May Also Like
NOV 09, 2021
Health & Medicine
How to Search the Cyagen Knockout Catalog Models Resource?
NOV 09, 2021
How to Search the Cyagen Knockout Catalog Models Resource?
The Cyagen Knockout Catalog Models repository provides researchers in the Americas and Europe with ready-to-use knockout ...
NOV 29, 2021
Cancer
An Amino Acid Can Improve Radiation Therapy for Metastatic Brain Cancer
NOV 29, 2021
An Amino Acid Can Improve Radiation Therapy for Metastatic Brain Cancer
There are 20 different amino acids that the human body uses to generate proteins.  Amino acids form chains called p ...
DEC 15, 2021
Microbiology
A Genetic Modification Alters Bacterial Behavior to Produce Artistic Swirls
DEC 15, 2021
A Genetic Modification Alters Bacterial Behavior to Produce Artistic Swirls
Researchers engineered a genetic circuit to make pathogenic bacteria called Myxococcus xanthus move in swirled patterns.
DEC 19, 2021
Cell & Molecular Biology
Make Edits to Whole Genes With This New Technique
DEC 19, 2021
Make Edits to Whole Genes With This New Technique
Though the CRISPR/Cas9 gene editing tool has been tweaked and modified in many ways, it typically edits relatively small ...
DEC 29, 2021
Genetics & Genomics
High-Throughput Tools Reveal New Proteins Involved in DNA Repair
DEC 29, 2021
High-Throughput Tools Reveal New Proteins Involved in DNA Repair
Our body is made up of trillions of cells, most of which contain a genome that suffers a lot of damage. That damage may ...
JAN 07, 2022
Health & Medicine
Is There a Suicide Gene?
JAN 07, 2022
Is There a Suicide Gene?
With suicide often linked to psychiatric disorders, a search for its biological underpinnings is only natural. Researche ...
Loading Comments...