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Precise Maps of 5′ Ends & 3′ Ends

End-Seq

High Resolution Maps of the 5’ & 3’ UTR landscape

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Technology Overview

Precise mapping of transcription start sites (TSS) and polyadenylation sites (PAS) is critical to understand gene regulation and transcript diversity. Alternate TSS and PAS usage can either include or exclude key regulatory elements found in the untranslated regions (UTRs) at the ends of transcripts, ultimately having a profound impact on the molecular and cellular physiology of cells. Regulatory elements in 5′ and 3′ UTRs have been implicated in human disease and can function as therapeutic targets.

The End-Seq technology enables mapping of the 5′ ends and 3′ ends of transcripts by sequencing from the TSS and PAS, respectively, revealing the complete UTR landscape of expressed transcripts. 5′ and 3′ End-Seq enrich for transcript ends to detect known and novel TSS and PAS at single nucleotide resolution.

Technology Highlights

Technology Highlights

Enrich for TSS and PAS to define 5′ and 3′ UTR Landscape

  • End-Seq enriches the sample for reads at transcript ends requiring lower sequencing depths
  • Greater depth of coverage around the PAS and TSS allows for more precise detection of known and novel polyA and transcription start sites

Genome-Wide End Calling at Single Nucleotide Resolution

  • Precise definition of transcription start sites and poly-adenylation sites at single nucleotide resolution
  • End-Seq correctly identifies TSS and PAS for shorter isoforms expressed in the same sample with longer isoforms

High Confidence TSS and PAS

  • Defined read cliffs in 5’ End-Seq and 3’ End-Seq data allow application of the PureCLIP peak calling algorithm to call single nucleotide end positions near annotated TSS and PAS
  • 3′ End-Seq increases the confidence of detected PAS by removing any PAS reads caused by internal A-rich genomic regions

Enrich for TSS and PAS to define 5′ and 3′ UTR Landscape

  • End-Seq enriches the sample for reads at transcript ends requiring lower sequencing depths
  • Greater depth of coverage around the PAS and TSS allows for more precise detection of known and novel polyA and transcription start sites

Genome-Wide End Calling at Single Nucleotide Resolution

  • Precise definition of transcription start sites and poly-adenylation sites at single nucleotide resolution
  • End-Seq correctly identifies TSS and PAS for shorter isoforms expressed in the same sample with longer isoforms

High Confidence TSS and PAS

  • Defined read cliffs in 5’ End-Seq and 3’ End-Seq data allow application of the PureCLIP peak calling algorithm to call single nucleotide end positions near annotated TSS and PAS
  • 3′ End-Seq increases the confidence of detected PAS by removing any PAS reads caused by internal A-rich genomic regions

“End-Seq assays are an invaluable part of our target assessment process at Ribometrix. The data are robust and often reveal novel 5’ and 3’ ends that aren’t reflected in public databases. Having this knowledge significantly influences strategic decisions around target selection in our RNA-targeting drug development process.”


Matt Smola, Ph.D., Associate Director.
Ribometrix

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Explore the solutions that build on our cutting edge 5′ & 3′ End-Seq technology.

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End-Seq™ Resources

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2023

5′ End-Seq Data Sheet
5′ End-Seq facilitates active transcript end detection, enrichment and mapping, and identifies known and novel transcription start sites at single nucleotide resolution in only 2 days.

2023

3′ End-Seq Data Sheet
3′ End-Seq is a technology for defining 3′ ends of transcripts by sequencing from the PAS. 3′ End-Seq can identify high confidence, known and novel PAS at single nucleotide resolution in 2 days

2023

3′ End-Seq Protocol
See the full 3′ End-Seq protocol

2023

5′ End-Seq Protocol
See the full 5′ End-Seq protocol