This combination of technologies enables discovery of genome-wide DNA binding sites for transcription factors and the functional activities of the promoter sequences bound by those transcription factors. “This comprehensive approach enables the comparison between binding events and transcriptional activity,” said Nathan Trinklein, Ph.D., co-founder and CEO of SwitchGear Genomics. “Characterizing the functional consequences of binding events is essential to more fully understanding the control of gene expression.”

HaloCHIP, which uses Promega HaloTag® Technology, eliminates the need for antibodies to capture protein:DNA complexes, thereby avoiding one of the major challenges of chromatin immunoprecipitation (ChIP) techniques.

“HaloCHIP allows researchers to more easily and efficiently capture genome-wide protein-DNA complexes starting with a much smaller number of cells,” stated Danette Hartzell, Senior Research Scientist at Promega Corporation. “This antibody-free method for revealing DNA binding events in combination with functional reporter assays can significantly advance gene regulation studies.”

About Promega:
Promega Corporation is a leader in providing innovative solutions and technical support to the life sciences industry. The company’s 2,000 products enable scientists worldwide to advance their knowledge in genomics, proteomics, cellular analysis, molecular diagnostics and human identification. Founded in 1978, the company is headquartered in Madison, WI, USA with branches in 14 countries and over 50 global distributors. For more information about Promega, visit www.promega.com.

About SwitchGear Genomics, Inc.:
SwitchGear Genomics Inc. is a leading provider of products for studying the regulatory elements in the human genome. The company has developed a comprehensive approach to generate new insights into gene regulatory networks and allow researchers to efficiently screen entire pathways in living cells. 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 www.switchgeargenomics.com

MENLO PARK, Calif. – October 14, 2009 – SwitchGear Genomics, Inc., a leading provider of products for studying regulatory elements in the human genome, today announced the availability of the first cost-effective, high-throughput research tools for screening transcriptional activation and repression in a number of key biological pathways. The new SwitchGear pathway sets utilize experimentally-validated luciferase reporter vectors to accurately quantify human promoter activity from complete sets of genes associated with inflammation, cholesterol biosynthesis, oncology, vascular biology, nuclear hormone receptor signaling, and many other important biological pathways.

"The SwitchGear panels of human promoter targets was selected from our genome-wide reporter collection of promoters using motif analysis and published functional genomic data sets," said Shelley Force Aldred, co-founder and President of SwitchGear Genomics, Inc. "We then performed pathway-specific inductions to create an activity profile across the set of constructs. We offer complete pathway profiling sets of constructs in high-throughput plate formats that empower researchers to efficiently profile the effects of many compounds and conditions." In addition, the company provides a smaller subset of "key responder" promoter constructs that showed a strong induction response in the experiments and which may be used as biomarkers in primary screening applications.

Researchers at the National Institutes of Health screened over 1400 compounds to test hypoxia pathway stimulation and published the results in an article entitled "Identification of Chemical Compounds that Induce HIF-1alpha Activity." The screening process, including the use of the SwitchGear Genomics hypoxia set of promoter reporter assays, differentiated between 3 hypoxia mimetics and 2 other compounds that triggered the pathway independent of HIF-1alpha, a result important for effective compound screening.

In addition to the hypoxia (HIF1a) pathway products, SwitchGear offers the following reporter assay profiling sets in both plate format and biomarker subsets: CREB, NF-kB, heat shock (HSF), p53, STAT, serum response factor (SRF), and cholesterol biosynthesis (SREBP). In addition, the company offers nuclear receptor sets for estrogen receptor, androgen receptor, and glucocorticoid receptor pathways.

About SwitchGear Genomics, Inc.:

SwitchGear Genomics, Inc. is a leading provider of products for studying regulatory elements in the human genome. The company has developed a comprehensive approach to generate new insights into gene regulatory networks and allow researchers to efficiently screen entire pathways in living cells. 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 http://www.switchgeargenomics.com.

Contact:
SwitchGear Genomics, Inc.
Brian McKelligon, 650-323-6570
Vice President, Sales and Marketing
brianm@switchgeargenomics.com

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 www.switchgeargenomics.com

Contact:
SwitchGear Genomics, Inc.
Brian McKelligon, 650-323-6570
Vice President, Sales and Marketing
brianm@switchgeargenomics.com

MENLO PARK, Calif. – December 11, 2008 – SwitchGear Genomics Inc., a leading provider of products for studying the regulatory elements in the human genome, today announced the availability of the industry’s first cost-effective high-throughput research tool for screening the transcriptional activation in the nuclear receptor and hypoxia gene pathways. The Nuclear Receptor Pathway Set™ and Hypoxia Pathway Set™ enable researchers to independently measure the impact of a stimulus on the transcriptional activation of each gene in a regulatory network.

The new SwitchGear pathway sets measure the activity of both the known and novel promoters related to nuclear receptor and hypoxia pathways. The Nuclear Receptor Pathway Set contains assay-ready luciferase reporter constructs for more than 1,000 nuclear receptor promoters and their targets. Subsets include promoter targets for PPARs, estrogen, androgen and glucocorticoid receptors. The Hypoxia Pathway Set has nearly 200 reporter constructs and provides a wide-ranging list of transcriptional promoters related to hypoxia biology, as well as promoters of genes associated with inflammation, respiration, vascular biology and novel promoters containing the hypoxia response element (HRE).

"By providing an assay-ready resource, SwitchGear enables our customers to focus not on making but using promoter reporter constructs for the comprehensive investigation of gene regulatory networks across many different experimental conditions," said Shelley Force Aldred, Ph.D., co-founder and president of SwitchGear Genomics. "The Nuclear Receptor Pathway Set and Hypoxia Pathway Set are delivered as purified transfection-ready plasmid DNAs. Customers now have the option of receiving complete sets, creating a customized subset based on our gene lists or selecting individual constructs."

For more information on SwitchGear’s Nuclear Receptor Pathway Set and Hypoxia Pathway Set or to take advantage of the company’s current year-end promotion, please visit www.switchgeargenomics.com.

About SwitchGear Genomics, Inc.:
SwitchGear Genomics Inc. is a leading provider of products for studying the regulatory elements in the human genome. The company has developed a comprehensive approach to generate new insights into gene regulatory networks and allow researchers to efficiently screen entire pathways in living cells. 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 www.switchgeargenomics.com.

Contact:
Brian McKelligon
Vice President, Sales and Marketing
SwitchGear Genomics, Inc.
Phone: 650-323-6570
Email: brianm@switchgeargenomics.com

SOURCE: SwitchGear Genomics, Inc.

Madison, WI USA (July 24, 2007) Researchers can efficiently screen entire genetic pathways in living cells with new tools developed by SwitchGear Genomics. The product offering, which includes the first ready-to-screen libraries for high-throughput regulatory pathway research, consists of thousands of human promoters, UTRs and other regulatory elements encompassing many different disease-related pathways.

“Our philosophy at SwitchGear Genomics is that conclusions can be made with much higher confidence by integrating the data from multiple independent genome-scale experiments,” explains Shelley Force Aldred, President of SwitchGear Genomics. “These integrated data sets will explain a transcriptional regulatory network in much greater detail than if the data sets were analyzed independently of one another.”

The new tools contain Promega luciferase reporter technology. Specifically, this new offering leverages all the strengths of luciferase reporters in ease and sensitivity to provide insights into cellular signaling events following xenobiotic treatment.

“The Promega luciferase reporters, specifically the luc2P construct, offer the best characteristics in a bioluminescent reporter assay. It really delivers the strongest sensitivity, dynamic range, turnover rate and compatibility with high-throughput platforms,” says Force Aldred.

All of the regulatory elements in the libraries are cloned in a vector containing the luc2P gene, a destabilized luciferase that contains a Pro-Glu-Ser-Thr (PEST) peptide sequence for faster response time and decreased time to maximum induction.

Nathan Trinklein, PhD, CEO of SwitchGear Genomics will present the new technology at:

Drug Discovery & Development of Innovative Therapeutics World Congress
Boston, MA
Exhibit Conference Hall
August 8, 2007.

About SwitchGear Genomics
SwitchGear Genomics is based in Menlo Park, California, and was founded by scientists from Stanford University in 2005. The goal of SwitchGear Genomics is to provide custom research services and experimental tools to aid researchers in large-scale studies of transcriptional regulation. For more information about SwitchGear Genomics, visit www.switchgeargenomics.com.

About Promega
Promega Corporation is a leader in providing innovative solutions and technical support to the life sciences industry. The company’s 1,450 products enable scientists worldwide to advance their knowledge in genomics, proteomics, cellular analysis, molecular diagnostics and human identification. For more information about Promega, visit www.promega.com.

Contact:

SwitchGear Genomics
Rick Eyraud
Vice President
(650) 323-6763
info@switchgeargenomics.com

Promega
Penny Patterson
Corporate Communications
(608) 274-4330
penny.patterson@promega.com

http://genome.ucsc.edu/

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

Download the PDF from Promega »

Read the full article on Bioscience Technology »

Menlo Park, CA, April 12, 2007 –(PR.com)– SwitchGear Genomics is a biotech company based on technology developed at Stanford University that focuses on the molecular switches in the human genome that turn genes on and off. The company has just released the world’s first tool to rapidly and accurately interrogate the function of over 3,000 DNA switches that regulate cancer biology. This oncology tool enables researchers to study the activity of regulatory switches in living cancer cells. Richard Myers, Chairman of Genetics Department at Stanford University says, “SwitchGear’s novel platform directly measures the mechanisms that regulate cancer genetics. It is very exciting technology, and our lab plans to use it to provide a deeper understanding of the biology of cancer. We hope that this work will ultimately lead to new and better cancer therapeutics.”

Cancer is a genetic disease characterized by the erroneous processing of information contained in our genome. Billions of dollars have been spent in an effort to identify the genes involved in cancer. However, protein-coding genes make up a small fraction of the total genome and provide a limited view into the causes of cancer. According to Nathan Trinklein, CEO and co-founder of SwitchGear Genomics, “The DNA switches identified by SwitchGear are critical to understanding how information in the genome is processed. Cancer is a very complex disease, but one thing all cancers have in common is the inability of cells to recognize the signals to stop dividing. Many of these growth signals are contained in the DNA switches identified by SwitchGear, and researchers will now be able to analyze their function on a high-throughput scale. Our initial beta customers in pharmaceutical and academic research groups have rapidly generated very interesting data sets.”

About SwitchGear Genomics:
SwitchGear Genomics was founded by Dr. Richard Myers, Dr. Nathan Trinklein, and Dr. Shelley Force Aldred of Stanford University. SwitchGear Genomics provides novel technology to aid researchers in large-scale studies of gene regulation. The new tools and services offered by SwitchGear Genomics enables researches to gather novel data, greatly enrich existing genomic datasets, and focus on the comprehensive characterization of genetic pathways. As leaders in the fields of DNA switch identification and functional characterization, SwitchGear is in a unique position to provide the research community with an entirely new way to study the function of the human genome and ultimately develop new classes of therapeutics.

Contact:
Nathan Trinklein, Ph.D.
Co-founder, CEO
SwitchGear Genomics
Phone: 650-323-6763
Email: nathant@switchgeargenomics.com
www.switchgeargenomics.com