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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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Global regulatory systems in bacteria enable rapid and coordinated responses to environmental changes by integrating sensory inputs with gene expression, ensuring efficient adaptation to fluctuating conditions. Key global regulatory mechanisms include regulons, two-component systems, sigma factors, and secondary messengers.Regulons and Global RegulatorsA regulon is a collection of genes and operons controlled by a common global regulator. These regulators enable bacteria to prioritize resource...
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The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
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Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...
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A Web-Based Workflow for Selecting Gene- and Tissue-Specific Enhancers
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Ensembl regulation resources.

Daniel R Zerbino1, Nathan Johnson2, Thomas Juetteman2

  • 1European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK zerbino@ebi.ac.uk.

Database : the Journal of Biological Databases and Curation
|February 19, 2016
PubMed
Summary
This summary is machine-generated.

The Ensembl project now offers comprehensive epigenomic data resources for human and mouse, including epigenetic marks and DNA methylation. This enables functional annotation of regulatory elements, advancing research in gene expression and disease.

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Area of Science:

  • Genomics and Epigenomics
  • Bioinformatics and Computational Biology

Background:

  • Advanced epigenomic techniques enable dynamic feature analysis (histone marks, DNA modifications, chromatin structure).
  • Studying epigenetic fluctuations offers insights into gene expression, cell differentiation, and disease mechanisms.

Purpose of the Study:

  • To present the Ensembl regulation data resources for epigenetic marks, transcription factor binding, and DNA methylation.
  • To provide functional annotation of regulatory elements in human and mouse genomes.

Main Methods:

  • Ensembl project collects and maintains epigenomic data for human and mouse.
  • Data includes epigenetic marks, transcription factor binding, DNA methylation, and microarray probe mappings.
  • Functional annotation of regulatory elements is generated from this data.

Main Results:

  • Ensembl regulation resources offer a centralized repository for reference epigenomes.
  • Functional annotation of regulatory elements is available for human and mouse genomes.
  • Plans are in place to expand data resources to other species.

Conclusions:

  • Ensembl provides freely accessible, queryable epigenomic data resources.
  • These resources support research in gene regulation, cell differentiation, and disease.
  • The Ensembl regulation database serves as a valuable tool for the scientific community.