Genpathway’s TranscriptionPath™ assays identify and quantify the genomic DNA sequences undergoing active transcription within cells. TranscriptionPath incorporates the chromatin immunoprecipitation (ChIP) technique to isolate and analyze complexes that comprise DNA and transcription machinery proteins. Purification of DNA from the complexes results in the “transcriptome” for any sample, but at the DNA level. The DNA is analyzed using one or a combination of Genpathway’s analysis modes, including Query- Mode™, which tests specific genes or genomic regions for transcription using quantitative PCR (Q-PCR); or DiscoveryMode™, Expanded Discovery™, or ChIP-on-Chip/Tiling™, analysis modes that discover transcribed sequences across the genome.

TranscriptionPath—A Novel, Improved Method to Directly Measure Transcription

TranscriptionPath measures the process of transcription— the primary level at which compounds and other treatments exert their effects within cells. Changes in gene transcription can be detected within a few minutes—a capability that RNA profiling cannot provide. TranscriptionPath determines when genes are activated or repressed and identifies the primary targets of compounds versus secondary and later targets. Absolute transcription levels are determined, including baseline levels, that can be compared across genes, cells, treatments, experiments, and time. Because Genpathway’s assays measure DNA, which is far more stable than RNA, the transcription complexes analyzed are much more durable in cells and tissues and the results are more reproducible. Analysis is carried out independent of other genes such as housekeeping (HK) genes, and does not automatically require normalization to HK genes.

Advantages of TranscriptionPath in Analyzing Gene Expression

Genpathway’s direct transcription assays are accurate, sensitive, quantitative, and highly reproducible. Repeat experiments involving cells and animals treated months apart show essentially identical changes in transcription. Because RNA degrades but transcription complexes are stable, tissue held under suboptimal conditions—for example, at room temperature for hours or at -70°C for years—can be assayed. Tissues that contain high levels of RNase (such as pancreas) and unseparated whole blood can be assayed.

TranscriptionPath Analyzes a Different Endpoint than RNA

When investigators refer to RNA profiling as “transcription profiling,” they are often using RNA as a surrogate for transcription. However, RNA profiling measures the level of accumulated RNA within a cell, which can be affected by multiple cellular processes and thus does not necessarily reflect levels of transcription. RNA profiling, particularly using microarrays, can also produce variable results due to inherent instability of RNA and differences between analysis programs. For these and other reasons, RNA profiling requires validation with a more independent and quantitative analysis method. Among other applications, TranscriptionPath offers researchers an independent way to validate or clarify their RNA profiling results.

Applications of TranscriptionPath

The types of applications are extensive:

Genpathway Offers Complete ChIP Assay Services

Genpathway’s transcription-based assays include TranscriptionPath™, which directly analyzes the process of transcription; and FactorPath™, which directly analyzes how genes are regulated by transcription factors and co-regulating factors. In many cases, a combination of these two types of assays that correlates changes in gene transcription and regulation will provide the most valuable information. Genpathway offers both types of assays as a service with any of four analysis modes, with a focus on high-quality data, rapid turnaround, and cost-effectiveness. Customers supply the samples to be tested—cells that have been briefly fixed, or frozen tissue—along with assay-specific information.