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Related Concept Videos

Transcription Factors02:16

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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Transcription Elongation Factors02:35

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Transcription elongation is a dynamic process that alters depending upon the sequence heterogeneity of the DNA being transcribed. Hence, it is not surprising that the elongation complex's composition also varies along the way while transcribing a gene.
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Eukaryotic Transcription Activators02:42

Eukaryotic Transcription Activators

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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.
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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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Prokaryotic Transcriptional Activators and Repressors01:58

Prokaryotic Transcriptional Activators and Repressors

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The organization of prokaryotic genes in their genome is notably different from that of eukaryotes. Prokaryotic genes are organized, such that the genes for proteins involved in the same biochemical process or function are located together in groups. This group of genes, along with their regulatory elements, are collectively known as an operon. The functional genes in an operon are transcribed together to give a single strand of mRNA known as polycistronic mRNA.
Transcription of prokaryotic...
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ATAC-Seq Optimization for Cancer Epigenetics Research
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Detecting Differential Transcription Factor Activity from ATAC-Seq Data.

Ignacio J Tripodi1,2, Mary A Allen3, Robin D Dowell4,5,6

  • 1Computer Science, University of Colorado, Boulder, CO 80305, USA. ignacio.tripodi@colorado.edu.

Molecules (Basel, Switzerland)
|May 12, 2018
PubMed
Summary
This summary is machine-generated.

This study introduces a simple method to identify key transcription factors (TFs) affected by cellular changes using chromatin accessibility data. This approach aids in understanding TF roles in diseases, even with limited biological samples.

Keywords:
ATAC-seqDAStkDNase I cleavageRNA-seqmotifopen chromatinperturbationtranscription factor

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Transcription factors (TFs) regulate gene expression and are crucial in cellular functions and disease pathogenesis.
  • Non-coding single nucleotide polymorphisms can impact TF activity by altering protein structure or DNA binding.
  • Understanding TF activity is vital for disease research and therapeutic development.

Purpose of the Study:

  • To present a novel, rapid method for identifying key transcription factors altered by cellular perturbations.
  • To demonstrate the utility of chromatin accessibility data in pinpointing affected TFs.
  • To provide a tool for TF activity analysis, especially when biological samples are scarce.

Main Methods:

  • Review of high-throughput approaches for studying transcription factor activity.
  • Analysis of genome-wide chromatin accessibility data (ATAC-seq) to map TF recognition motifs.
  • Correlation of TF motif profiles with open chromatin regions to identify perturbed TFs.

Main Results:

  • The genome-wide profile of TF recognition motifs relative to open chromatin regions effectively identifies key TFs affected by perturbations.
  • The developed method is simple, quick to implement, and suitable for experiments with limited biological samples.
  • Demonstrated the power of ATAC-seq data in inferring TF activity changes.

Conclusions:

  • This method offers a straightforward way to determine altered transcription factor activity in various biological contexts.
  • It has the potential to be widely applied in drug discovery and disease research to understand TF roles.
  • Facilitates the study of TF perturbations in conditions with limited sample availability.