Welcome to the Nascent Transcriptomics Core

The mission of the NTC is to offer the community a resource for the analysis of nascent transcription, providing new insights into gene regulation and enabling highly sensitive identification of regulatory regions such as enhancers. We offer a streamlined package of services allowing users to submit prepared cells and receive useful analyzed data. We also offer free consultations to discuss experimental and data analysis plans.

Analysis of nascent RNA--RNA that is actively being synthesized or within minutes of synthesis--can reveal changes in patterns of gene expression, transcription elongation or RNA processing and identify unstable transcripts (such as enhancer RNAs) that are challenging to detect by other RNA sequencing methods.

The core is happy to schedule consultations to help with experimental design, answer questions, and discuss data analysis. 

Applications of nascent RNA analysis include:

  • Pinpoint enhancers by identifying enhancer RNAs
  • Define long non-coding RNAs expressed in a specific cell type or condition
  • Identify sites of transcriptional initiation or pausing at single-nucleotide resolution
  • Observe unstable RNA processing intermediates, and calculate rates of RNA processing or decay

We currently offer the following services:

PRO-seq: for sensitive measurement of nascent RNA production at genes and enhancers
  • Single nucleotide resolution mapping of active RNAP across the genome
  • Analysis of polymerase pausing and productive elongation
  • Measurement of differential gene expression
  • Identification of enhancers
TT-seq:  a metabolic labeling assay using 4sU incorporation in living cells
  • Monitors newly synthesized RNA species
  • Sensitive and time resolved measurement of gene expression
  • Can inform on RNA processing intermediates from splicing and 3' end formation

If you are interested in our services, or want to find out how these methods could help your research, please fill out the consultation request from on the Project Application page or contact us directly.

The Nascent Transcriptomics Core is part of the HMS Epigenetics & Gene Dynamics Initiative