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Translation Efficiency Test Using Polysome Profiles Under Heat Stress08:39

Translation Efficiency Test Using Polysome Profiles Under Heat Stress

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The protocol presented here involves polysomal profiling to isolate translatome, mRNAs associated with ribosomes, into non-polysomal and polysomal RNAs from Arabidopsis through sucrose density gradient centrifugation. This method demonstrates the translation efficiency of heat-stressed...
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Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling12:57

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Translational regulation plays an important role in the control of protein abundance. Here, we describe a high-throughput method for quantitative analysis of translation in the budding yeast Saccharomyces...
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Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions10:16

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DNA regulatory elements, such as enhancers, control gene expression by physically contacting target gene promoters, often through long-range chromosomal interactions spanning large genomic distances. Promoter Capture Hi-C (PCHi-C) identifies significant interactions between promoters and distal regions, enabling the assignment of potential regulatory sequences to their target...
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Genomics02:02

Genomics

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Egg Microinjection and Efficient Mating for Genome Editing in the Firebrat Thermobia domestica06:08

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We provide a detailed protocol for rearing, microinjection of eggs and for efficient mating of the firebrat Thermobia domestica to generate and maintain mutant strains after genome...
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Here, we describe a simple technique intended for the efficient generation of genetically modified mice called CRISPR RNP Electroporation of Zygotes (CRISPR-EZ). This method delivers editing reagents by electroporation into embryos at an efficiency approaching 100%. This protocol is effective for point mutations, small genomic insertions, and deletions in mammalian...
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Related Experiment Video

Updated: Jan 19, 2026

Author Spotlight: Polysome Profiling Protocol for Studying Translational Regulation in Arabidopsis Under Heat Stress
08:39

Author Spotlight: Polysome Profiling Protocol for Studying Translational Regulation in Arabidopsis Under Heat Stress

Published on: October 11, 2024

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Efficient merging of genome profile alignments.

André Hennig1, Kay Nieselt1

  • 1Center for Bioinformatics (ZBIT), Integrative Transcriptomics, Eberhard Karls University of Tübingen, Tübingen, Germany.

Bioinformatics (Oxford, England)
|September 13, 2019
PubMed
Summary

Genome Profile Alignment (GPA) dramatically speeds up whole-genome alignment (WGA) by aligning WGA profiles, reducing computation time from months to hours for large datasets.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Current whole-genome alignment (WGA) methods lack scalability for large datasets.
  • Profile alignment methods improve computational efficiency but struggle with genomic rearrangements in WGAs.
  • Existing tools cannot align or extend WGA profiles, limiting large-scale analyses.

Purpose of the Study:

  • To introduce Genome Profile Alignment (GPA), a novel approach for scalable WGA.
  • To enable the alignment and extension of WGA profiles for efficient large-scale genome comparisons.
  • To significantly reduce the computational time required for generating large-scale WGAs.

Main Methods:

  • GPA utilizes existing whole-genome aligners to compute smaller aligned genome sets.

More Related Videos

Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling
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Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions

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Related Experiment Videos

Last Updated: Jan 19, 2026

Author Spotlight: Polysome Profiling Protocol for Studying Translational Regulation in Arabidopsis Under Heat Stress
08:39

Author Spotlight: Polysome Profiling Protocol for Studying Translational Regulation in Arabidopsis Under Heat Stress

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Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling
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Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling

Published on: December 21, 2017

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Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions

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  • A divide-and-conquer strategy combines these sets into a comprehensive WGA.
  • The SuperGenome data structure facilitates coordinate system transfer for profile alignment.

    • Main Results:

    • GPA generates large-scale WGAs significantly faster than conventional methods, reducing runtime from months to hours.
    • The approach maintains high alignment quality, comparable to traditional methods.
    • Demonstrated scalability on bacterial datasets comprising hundreds of genomes.

    Conclusions:

    • GPA offers a scalable and efficient solution for large-scale whole-genome alignment.
    • The method overcomes limitations of existing profile alignment techniques for WGAs.
    • GPA enables faster and more accessible comparative genomics research.