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Related Concept Videos

General Transcription Factors01:30

General Transcription Factors

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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...
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Cis-regulatory Sequences02:02

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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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...
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Genome Annotation and Assembly

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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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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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Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences
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Maize and millet transcription factors annotated using comparative genomic and transcriptomic data.

Jinn-Jy Lin, Chun-Ping Yu, Yao-Ming Chang

  • 1Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan. whli@sinica.edu.tw.

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Summary

This study comprehensively annotated transcription factors (TFs) and transcription coregulators (TCs) in maize and foxtail millet, identifying new families and C4-related genes to advance understanding of gene regulation and photosynthesis.

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Area of Science:

  • Plant molecular biology
  • Genomics
  • Bioinformatics

Background:

  • Transcription factors (TFs) bind DNA to regulate gene expression.
  • Transcription coregulators (TCs) modulate gene expression via interactions.
  • Identifying and classifying TFs and TCs is crucial for understanding gene regulation.

Purpose of the Study:

  • To perform a genome-wide annotation and classification of TFs and TCs in maize and foxtail millet.
  • To identify novel TF and TC families and analyze their evolutionary and functional aspects.
  • To investigate tissue-specific expression patterns and identify potential C4-related genes.

Main Methods:

  • Genome-wide annotation of TFs and TCs in maize (Zea mays) and foxtail millet (Setaria italica).
  • Classification of identified genes into families.
  • Comparative analysis with homologous genes in Arabidopsis and rice.
  • Gene expression analysis using RNA-seq and microarray data.
  • Identification of pseudogenes and transposable elements.

Main Results:

  • Comprehensive genome-wide annotation of TFs and TCs in maize and foxtail millet.
  • Identification of numerous new TF and TC families, including 9 new maize TF families.
  • Detection of pseudogenes and transposable elements in existing databases.
  • Identification of tissue-specific TFs and TCs and potential C4-related genes.

Conclusions:

  • Expanded TF and TC annotations in maize and millet with supporting genomic and expression data.
  • Identified TFs and TCs with tissue-specific expression patterns.
  • Facilitates research into gene regulation, tissue morphogenesis, and C4 photosynthesis in these species.