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Related Concept Videos

Transcription01:10

Transcription

155.8K
Overview
Transcription is the process of synthesizing RNA from a DNA sequence by RNA polymerase. It is the first step in producing a protein from a gene sequence. Additionally, many other proteins and regulatory sequences are involved in the proper synthesis of messenger RNA (mRNA). Regulation of transcription is responsible for the differentiation of all the different types of cells and often for the proper cellular response to environmental signals.
Transcription Can Produce Different Kinds...
155.8K
Eukaryotic Transcription Inhibitors01:52

Eukaryotic Transcription Inhibitors

10.9K
Certain biochemical processes, such as embryonic development and cell growth regulation, depend on the repression of specific genes. DNA binding proteins known as eukaryotic transcription inhibitors regulate the repression of gene expression in eukaryotes. The presence of these inhibitors at the required location and time in the cell is triggered by the presence of hormones and additional signals from other cells.
Eukaryotic transcription inhibitors usually contain two distinct domains, a...
10.9K
Transcription Factors02:16

Transcription Factors

82.3K
Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
82.3K
Master Transcription Regulators02:23

Master Transcription Regulators

7.7K
Master transcription regulators are regulatory proteins that are predominantly responsible for regulating the expression of multiple genes. Often these genes work in concert to drive a  complex process. Activation of a master transcription regulator can lead to a cascade of transcriptional activation necessary for that outcome. These regulators can directly bind to the regulatory sequences of the various genes involved, or they can indirectly regulate transcription by binding to regulatory...
7.7K
Eukaryotic Transcription Activators02:42

Eukaryotic Transcription Activators

12.6K
Transcription activators are proteins that promote the transcription of genes from DNA to RNA. In most cases, these proteins contain two separate domains ‒ a domain that binds to DNA and a domain for activating transcription; however, in some cases, a single domain is responsible for both binding and activation of transcription, as seen in the glucocorticoid receptor and MyoD.
The binding domains are capable of recognizing and interacting with regulatory sequences on the DNA. These...
12.6K
Transcription Attenuation in Prokaryotes02:42

Transcription Attenuation in Prokaryotes

18.2K
Transcriptional attenuation occurs when RNA transcription is prematurely terminated due to the formation of a terminator mRNA hairpin structure.  Bacteria use these hairpins to regulate the transcription process and control the synthesis of several amino acids including histidine, lysine, threonine, and phenylalanine. Transcription attenuation takes place in the non-coding regions of mRNA.
There are several different mechanisms used to attenuate transcription. In ribosome mediated...
18.2K

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Related Experiment Video

Updated: Jan 23, 2026

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms
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Effect of de novo transcriptome assembly on transcript quantification.

Ping-Han Hsieh1, Yen-Jen Oyang1,2, Chien-Yu Chen3,4

  • 1Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 10617, Taiwan.

Scientific Reports
|June 6, 2019
PubMed
Summary
This summary is machine-generated.

De novo transcriptome assembly quality significantly impacts gene expression quantification accuracy. Assembly completeness affects abundance estimation, with quantifiers over-estimating collapsed genes and under-estimating duplicated genes.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Transcriptomics

Background:

  • Accurate transcript expression quantification is crucial for understanding cellular functions.
  • De novo transcriptome assembly is necessary for organisms lacking a reference genome.
  • Assembly errors can lead to unreliable gene expression estimates.

Purpose of the Study:

  • To investigate the impact of de novo transcriptome assembly quality on gene expression quantification.
  • To analyze how assembly errors like over-extended and incomplete contigs affect abundance estimation.
  • To evaluate quantifier behavior with sequence ambiguity and its effect on quantification accuracy.

Main Methods:

  • Examined the effect of assembly completeness on contig abundance estimation.
  • Investigated quantifier performance with sequence ambiguity (e.g., family-collapse, duplicated contigs).
  • Analyzed read proportion of estimated abundance (RPEA) for detecting under-estimation in duplicated contigs.
  • Compared quantification accuracy at the sequence and connected component levels.

Main Results:

  • Assembly completeness strongly impacts abundance estimation accuracy.
  • Quantifiers tend to over-estimate expression for family-collapse contigs.
  • Quantifiers tend to under-estimate expression for duplicated contigs.
  • Read proportion of estimated abundance (RPEA) can help detect under-estimation of duplicated contigs.
  • Quantification at the connected component level shows higher accuracy than at the sequence level.

Conclusions:

  • De novo transcriptome assembly quality is critical for reliable gene expression quantification.
  • Understanding assembly errors is key to improving quantification accuracy.
  • Connected component-level analysis offers a more robust approach for quantification in the absence of a reference transcriptome.