Related Experiment Video

Updated: Aug 11, 2026

Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells
13:07

Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells

Published on: January 30, 2019

Reverse transcriptase template switching and false alternative transcripts

Julie Cocquet1, Allen Chong, Guanglan Zhang

  • 1INSERM U709, Hôpital Cochin, Pavillon Baudelocque, 123 Bd de Port Royal, 75014 Paris, France.

Genomics
|February 7, 2006
PubMed

Insights

Reverse transcriptase (RT) template switching can create artificial deletions in cDNA, mimicking alternative transcripts. Researchers confirmed these artifacts in human splice sites, highlighting the need for careful transcript annotation.

Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Reverse transcriptase (RT) exhibits template-switching behavior, dependent on sequence homology.
  • This RT propensity can lead to artificially deleted cDNA sequences.
  • Such artifacts may be misinterpreted as genuine alternative transcripts in eukaryotic gene studies.

Purpose of the Study:

  • To investigate the occurrence of RT template-switching artifacts in cDNA databases.
  • To assess the prevalence of these artifacts within human splice site data.
  • To provide guidance for accurate alternative transcript annotation.

Main Methods:

  • Scanning a collection of human splice sites from the Information for the Coordinates of Exons (ICE) database.
  • Experimental validation of identified template-switching events.
  • Analysis of sequence characteristics associated with artifact formation, such as direct repeats.

Main Results:

  • Confirmed several instances of template-switching artifacts at the experimental level.
  • Artifacts constitute a notable fraction of sequences with noncanonical splice signals.
  • These artifacts are relatively rare within the overall cDNA database context.

Conclusions:

  • Template-switching artifacts can be experimentally confirmed and are present in cDNA databases.
  • Careful consideration of RT properties (e.g., thermostability) and sequence features (e.g., direct repeats) is crucial for accurate alternative transcript annotation.
  • Distinguishing true alternative splicing from RT-induced artifacts is essential for reliable genomic data interpretation.

More Related Videos

Reverse Genetics to Engineer Positive-Sense RNA Virus Variants15:49

Reverse Genetics to Engineer Positive-Sense RNA Virus Variants

Published on: June 9, 2022

Detection of Human Immunodeficiency Virus Type 1 (HIV-1) Antisense Protein (ASP) RNA Transcripts in Patients by Strand-Specific RT-PCR08:01

Detection of Human Immunodeficiency Virus Type 1 (HIV-1) Antisense Protein (ASP) RNA Transcripts in Patients by Strand-Specific RT-PCR

Published on: November 27, 2019

Related Concept Videos

Viruses with RNA Genomes01:29

Viruses with RNA Genomes

RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...
LTR Retrotransposons03:08

LTR Retrotransposons

LTR retrotransposons are class I transposable elements with long terminal repeats flanking an internal coding region. These elements are less abundant in mammals compared to other class I transposable elements. About 8 percent of human genomic DNA comprises LTR retrotransposons. Some of the common examples of LTR retrotransposons are Ty elements in yeast and Copia elements in Drosophila.
The internal coding region of LTR retrotransposons and their mechanism of transposition closely resembles a...
Translesion DNA Polymerases02:10

Translesion DNA Polymerases

Translesion (TLS) polymerases rescue stalled DNA polymerases at sites of damaged bases by replacing the replicative polymerase and installing a nucleotide across the damaged site. Doing so, TLS allows additional time for the cell to repair the damage before resuming regular DNA replication.
TLS polymerases are found in all three domains of life - archaea, bacteria, and eukaryotes. Of the different classes of TLS polymerases, members of the Y family are fitted with specialized structures that...
Overview of Transposition and Recombination02:13

Overview of Transposition and Recombination

Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
Leaky Scanning02:28

Leaky Scanning

During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R stands for...
Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...