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Related Concept Videos

Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

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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...
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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...
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Overview of Transposition and Recombination02:13

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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...
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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...
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Alternative RNA Splicing02:18

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Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
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Related Experiment Video

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Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites
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Long-Read Sequencing Identifies the First Retrotransposon Insertion and Resolves Structural Variants Causing

Belén de la Morena-Barrio1, Jonathan Stephens2,3, María Eugenia de la Morena-Barrio1

  • 1Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Universidad de Murcia, Murcia, Spain.

Thrombosis and Haemostasis
|June 28, 2022
PubMed
Summary

Long-read sequencing successfully identified complex structural variants (SVs) causing inherited antithrombin deficiency (ATD). This advanced method revealed novel retroelement insertions, improving diagnosis for rare thrombotic disorders.

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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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Area of Science:

  • Genetics
  • Genomics
  • Molecular Biology

Background:

  • Inherited antithrombin deficiency (ATD) is a critical genetic disorder linked to thrombotic events.
  • Causal variants in SERPINC1 gene are identified in most ATD cases, primarily single-nucleotide variants and indels.
  • Detecting structural variants (SVs) in SERPINC1 is challenging due to its repetitive nature.

Purpose of the Study:

  • To identify and characterize disease-associated SVs in patients with inherited antithrombin deficiency.
  • To investigate the molecular mechanisms underlying ATD, particularly in cases with previously unknown genetic defects.
  • To evaluate the utility of long-read whole-genome sequencing for resolving complex genetic variants in ATD.

Main Methods:

  • Long-read whole-genome sequencing was performed on 19 patients with type I ATD.
  • A specialized analysis workflow was developed to detect and characterize SVs.
  • Novel SVs and retroelement insertions were confirmed using de novo assembly, PCR, and sequencing.

Main Results:

  • The study successfully identified all eight previously detected SVs and a complex rearrangement misclassified as a deletion.
  • A novel 2.4 kb SINE-VNTR-Alu retroelement insertion was identified as the cause of ATD in two cases.
  • Breakpoint analysis revealed repetitive elements and microhomologies, suggesting a common replication-based mechanism for SV formation.

Conclusions:

  • Long-read sequencing is a powerful tool for identifying and characterizing complex SVs in inherited antithrombin deficiency.
  • This technology enhances the understanding of molecular mechanisms in rare genetic disorders.
  • The findings expand the known genetic causes of ATD and highlight retrotransposon insertions as a significant factor.