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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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DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
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Pattern-based Search of Epigenomic Data Using GeNemo
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EpiAlignment: alignment with both DNA sequence and epigenomic data.

Jia Lu1, Xiaoyi Cao1, Sheng Zhong1

  • 1Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA.

Nucleic Acids Research
|May 23, 2019
PubMed
Summary
This summary is machine-generated.

EpiAlignment is a new tool for comparing DNA sequences and epigenomic data across species. It helps identify regulatory genome features beyond what sequence comparison alone can reveal.

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Area of Science:

  • Comparative epigenomics
  • Bioinformatics tools
  • Genomic regulation analysis

Background:

  • Comparative epigenomics leverages both genome and epigenome data for enhanced insights.
  • Regulatory features identified through comparative genomics surpass sequence-based comparisons.
  • The need for specialized tools to integrate and compare diverse genomic and epigenomic datasets across species is growing.

Purpose of the Study:

  • To introduce EpiAlignment, a novel web-based tool for aligning genomic regions using both DNA sequence and epigenomic data.
  • To facilitate interspecies comparison of regulatory genomic features by integrating sequence and epigenomic profiles.
  • To provide a user-friendly platform for researchers to analyze and visualize comparative epigenomic data.

Main Methods:

  • EpiAlignment utilizes a dynamic programming algorithm to compute alignment scores based on sequence and epigenome similarity.
  • The tool accepts DNA sequence and ChIP-seq derived epigenomic profiles from two species as input.
  • Pre-compiled human and mouse epigenome datasets from ENCODE and Roadmap Epigenomics consortia are available, alongside user data upload options.

Main Results:

  • EpiAlignment generates semi-global alignments of genomic regions, considering both sequence and epigenomic data.
  • The web server employs parallel computing (up to 140 threads) for efficient processing of large datasets.
  • Results are presented in interactive graphical and tabular formats for detailed visualization and analysis.

Conclusions:

  • EpiAlignment offers a powerful approach for comparative epigenomics, enhancing the discovery of regulatory genomic elements.
  • The tool simplifies the integration and analysis of sequence and epigenomic data across species.
  • EpiAlignment is accessible online, supporting researchers in advancing the understanding of genome regulation.