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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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Genome Annotation and Assembly03:36

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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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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Protein Networks02:26

Protein Networks

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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.1K
Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

7.5K
Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein....
7.5K
Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

1.1K
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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Related Experiment Video

Updated: Sep 23, 2025

Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers
03:37

Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers

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Annotating regulatory elements by heterogeneous network embedding.

Yurun Lu1,2, Zhanying Feng1,2, Songmao Zhang1

  • 1CEMS, NCMIS, HCMS, MADIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China.

Bioinformatics (Oxford, England)
|May 13, 2022
PubMed
Summary
This summary is machine-generated.

We developed RE-GOA, a novel method using natural language processing to annotate regulatory elements (REs) and their functions. This approach improves upon existing methods for gene regulation analysis.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Regulatory elements (REs) control gene expression through complex networks.
  • Current methods for RE annotation are costly and labor-intensive.

Purpose of the Study:

  • To develop a systematic Gene Ontology Annotation method for Regulatory Elements (RE-GOA).
  • To leverage natural language processing and network embedding for RE annotation.

Main Methods:

  • Assembled a heterogeneous network integrating regulation, protein-protein interactions, and Gene Ontology (GO) terms.
  • Performed network embedding to associate REs with GO terms in a low-dimensional vector space.

Main Results:

  • RE-GOA outperforms existing methods in annotating transcription factor binding sites (ChIP-seq).
  • Demonstrated effectiveness in functional enrichment analysis of ATAC-seq data.
  • Showcased utility in revealing genetic correlations from GWAS summary statistics.

Conclusions:

  • RE-GOA offers a powerful and efficient approach for regulatory element annotation.
  • The method advances understanding of gene regulation and genetic associations.