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Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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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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Cis-regulatory Sequences02:02

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Transcription Factors02:16

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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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Eukaryotic Transcription Inhibitors01:52

Eukaryotic Transcription Inhibitors

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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.
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Master Transcription Regulators02:23

Master Transcription Regulators

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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...
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Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
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High-throughput Screening for Chemical Modulators of Post-transcriptionally Regulated Genes
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POSTAR2: deciphering the post-transcriptional regulatory logics.

Yumin Zhu1,2, Gang Xu1, Yucheng T Yang3

  • 1MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.

Nucleic Acids Research
|September 22, 2018
PubMed
Summary

POSTAR2 enhances RNA regulation studies by integrating over 1200 CLIP-seq datasets and a new Translatome module. This resource aids research into RNA-binding proteins and the cellular translational landscape.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Post-transcriptional regulation of RNA is fundamental to cellular processes.
  • Functional genomic data on RNA regulation is rapidly expanding.
  • Databases are crucial for organizing and accessing this growing information.

Purpose of the Study:

  • To update and expand the POSTAR2 database with new datasets and features.
  • To provide a comprehensive resource for studying post-transcriptional regulation and RNA translation.
  • To improve data visualization and accessibility for researchers.

Main Methods:

  • Incorporated approximately 500 new CLIP-seq datasets, totaling over 1200, across six species.
  • Added a 'Translatome' module utilizing Ribo-seq data, encompassing millions of open reading frames (ORFs).
  • Updated and unified existing post-transcriptional regulation and variation data, merging CLIPdb into POSTAR2.

Main Results:

  • POSTAR2 now hosts an extensive collection of protein-RNA interaction data.
  • The Translatome module offers insights into the translational landscape.
  • Enhanced web interfaces facilitate multi-layer visualization of regulatory interactions.

Conclusions:

  • The updated POSTAR2 database serves as a valuable tool for investigating RNA-binding protein regulation.
  • It supports the exploration of the translational landscape and its coordination with RNA regulation.
  • POSTAR2 facilitates a deeper understanding of complex post-transcriptional regulatory networks.