SwitchGear Genomics assay-ready 3’UTR constructs establish validity in studies that identify critical functions of microRNAs
Complete panel of 3’UTR reporter assays empowers researchers to quickly and quantitatively measure miRNA impact
MENLO PARK, Calif. – June 5, 2009 – SwitchGear Genomics Inc., a leading provider of products for studying the regulatory elements in the human genome, today announced the application of its UTR Reporter Collection™ product line in uncovering critical miRNA functions in several recent research studies.
A joint team from SwitchGear Genomics and Thermo Fisher Scientific recently published the results of a study that demonstrate key miRNA activity in mesenchymal stem cell differentiation. The study also illustrated the benefits of employing a functional profiling strategy for comprehending complex miRNA pathways.
The findings are published in the article “Functional Profiling Reveals Critical Role for miRNA in Differentiation of Human Mesenchymal Stem Cells” at http://dx.plos.org/10.1371/journal.pone.0005605.
“Current available methods focus on measuring only the levels of miRNAs within a cell type but do not identify the actual roles or targets of these miRNAs,” stated Devin Leake, Director of Research and Development for Thermo Fisher Scientific’s genomics business, which includes the Thermo Scientific Dharmacon line of microRNA products. “We conducted functional analysis of miRNAs and revealed those miRNAs that act as regulators in early hMSC differentiation.”
The team used the SwitchGear Genomics transfection-ready and sequence-verified reporter constructs to quantitatively measure the effects of miRNA mimics of interest on endogenous 3’UTRs.
“Our genome-wide collection of assay-ready 3’UTR constructs enable researchers to quickly measure miRNA function,” said Nathan Trinklein, Ph.D., co-founder and CEO of SwitchGear Genomics, “Researchers can focus on quantifying miRNA activity on transcript regulation and translational efficiency to gain insight into the actual functions of these miRNAs without having to spend time on cloning.”
In another recent article in Cancer Research, “Coordinated regulation of cell cycle transcripts by p53-inducible microRNAs, miR-192 and miR-215,” researchers describe the function of key regulatory cell cycle miRNAs. The SwitchGear reporter constructs provided the key insight that these miRNAs function as tumor suppressors and that multiple miRNA families operate in the p53 network.
Researchers at SwitchGear Genomics further conducted a study on the role of miR-122, an important regulator of cholesterol and fatty-acid metabolism in liver that has been suggested as a therapeutic target for metabolic disease. The study revealed the target UTRs that specifically responded to miR-122 in addition to the genes that it translationally repressed. The complete findings are available at http://switchgeargenomics.com/products/utr-reporter-collection/.
About SwitchGear Genomics, Inc.:
SwitchGear Genomics Inc. is a leading provider of products for studying the regulatory elements in the human genome. The company offers transfection-ready, genome-wide collections of promoter and UTR reporter constructs, empowering researchers to quantitatively measure transcriptional regulation and translational efficiency. SwitchGear was founded in March 2005 by Dr. Richard Myers, Dr. Nathan Trinklein and Dr. Shelley Force Aldred from Stanford University. For more information about SwitchGear, please visit the company’s website at switchgeargenomics.com
Contact:
SwitchGear Genomics, Inc.
Brian McKelligon, 650-323-6570
Vice President, Sales and Marketing
brianm@switchgeargenomics.com
SwitchGear genome-wide transcription start site predictions added as public track on UCSC genome browser
SwitchGear’s genome-wide predictions of transcription starts are now available as a public track on the UCSC genome browser. These are the same TSSs that are in switchDB and are now available on the UCSC site to enable comparisons with other genomic features.
Stanford Spinout SwitchGear Genomics Aims to Demystify Regulation
Source: Genome Technology
By Ciara Curtin
Genes operate under the watchful eye of their regulatory elements. But in spite of these efforts, genes can still go haywire.
Studying how these regulatory regions assert or lose their power over oncogenes might show how cancer works at the molecular level. SwitchGear Genomics, a company founded in 2005 by three Stanford University geneticists, has a new tool that allows researchers to peer into what controls the cancer genome. “We developed new approaches and new technology that actually characterizes these, what we’re calling DNA switches … in living cells in a high-throughput way,” says Nathan Trinklein, CEO and co-founder of SwitchGear Genomics. The idea is that after the cancer-regulation regions are characterized, they can be scanned to help develop new anticancer therapies.
The genome, says Trinklein, is not just genes. Non-coding regions, such as regulatory regions, are integral to a properly functioning cell. While part of the ENCODE project, Trinklein and his colleagues developed a technology that eventually helped them build SwitchGear’s new tool, the Oncology Functional Promoter Macroarray. This contains a panel of regulatory regions for known oncogenes that are spliced into vectors containing a luminescent reporter gene. The genes whose regulatory regions are contained on their panel were garnered from previous studies and gene annotations, and are involved in DNA damage, apoptosis, and cell cycle control. “This tool can be used to study, basically to characterize, cancer cells and to say which of these switches are being acted on differently in cancer cells compared to normal cells,” Trinklein says.
The tool can also be used to screen how cancer cells react to different treatments. By exposing cells in this assay to different conditions, whether a potential therapy or damage, a researcher could track how the cells’ gene transcripts change by tracing the output of the tool, as read by a luminometer. “The hope is then that you can use this as a screening tool for understanding how compounds affect cancer cells in more detailed ways,” Trinklein says. That’ll help scientists “understand if different DNA sequences might actually respond differently to certain types of cancer.”
Studying regions of gene regulation reaches beyond oncology. Not only does SwitchGear plan to tackle other conditions such as hypoxia and heart disease, the team plans to ramp up from its current small family sets to having “a genome-wide tool that will allow people to study the genome in a whole way,” says Trinklein.
http://www.genome-technology.com/issues/2_5/markers/140334-1.html
New High-Throughput Technology for Screening Transcriptional Regulatory Elements and Gene Networks
Excerpt from the article:
Here we describe the development of a new set of tools that enable detailed analysis of regulatory pathways in living cells. SwitchGear Genomics has produced a library of thousands of human promoters, UTRs and other regulatory elements contained within a state-of-the-art luciferase reporter vector, the pGL4.11[luc2P] Vector. This library combines the ability to gather highly reproducible data over a broad dynamic range with the ability to scale to hundreds or thousands of promoters in a single experiment.
Download the PDF from Promega »
Experimental Characterization Of Gene Regulatory Networks
Excerpt from the article:
The post-genome era has lead to great advances in high-throughput genomics studies. Genomic approaches such as microarray expression analyses and ChIP-chip transcription factor binding assays have provided a more comprehensive view of genetic pathways. These technologies provide valuable observational data but do not identify the functional connections within networks or explain the mechanism of gene regulation. Functional reporter assays provide an important additional layer of data for understanding mechanisms of regulation in genetic networks. Traditionally, reporter assays have been used on a very small scale to validate large-scale experiments like those described above. SwitchGear Genomics (Menlo Park, CA) has developed a novel approach that scales reporter assays to a much larger scale.
Read the full article on Bioscience Technology »