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Nascent Transcriptomics Core (NTC)

Director: Goldman, Seth, Ph.D.

Location: 45 Shattuck St, LHRRB 212, Boston, MA 02115

Summary:

The mission of the Nascent Transcriptomics Core (NTC) is to offer the community a resource for the analysis of nascent transcription, providing direct insights into gene regulation and enabling highly-sensitive identification of enhancers and long non-coding RNAs.
We offer consultation on experimental design as well as library construction services for Start-seq, PRO-seq and metabolically labeled RNA-seq (e.g. TT-seq). In addition, the NTC looks forward to expanding these offerings as we develop and optimize new RNA sequencing methods in partnership with the HMS community.
Analysis of nascent RNA, meaning RNA being actively synthesized by RNA polymerase, reveals the process of transcript elongation. This directly exposes alterations in patterns of gene expression and identifies unstable splicing intermediates or non-coding RNA transcripts that are challenging to detect by total RNA sequencing. Some applications of nascent RNA analysis include:


  • Pinpoint enhancers by sequencing 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

Affiliations:

People:

Resources:

Protocols

Services

  • Bioinformatics (only with library construction) ( Data analysis service )

    The core offers both a standard analysis package for each method as well as customized analyses. Please inquire about custom services and pricing.

  • PRO-seq (Precision Run-On) ( Material analysis service )

    Single nucleotide resolution of nascent RNA 3' ends. Used to define direct effects of experimental perturbations on the transcriptional landscape and to define enhancers.

  • Start-seq ( Material processing service )

    Isolation and sequencing of short, capped, chromatin-associated RNAs. Used to identify enhancers and profile enhancer RNA expression.

  • TT-seq ( Material processing service )

    A variant of 4-thiouridine sequencing in which the labeled RNA is captured and enriched prior to sequencing. Used to monitor RNA synthesis, co-transcriptional processing, and degradation.


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Last updated: 2019-12-19T10:13:04.455-06:00

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The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016