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Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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...
Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

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 addition of a...
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
Regulation of the Unfolded Protein Response01:31

Regulation of the Unfolded Protein Response

Inositol-requiring kinase one or IRE1 is the most conserved eukaryotic unfolded protein response (UPR) receptor. It is a type I transmembrane protein kinase receptor with a distinctive site-specific RNase activity. As the binding mechanics of the misfolded proteins with the N-terminal domain of IRE-1 are unclear, three binding models — direct, indirect, and allosteric -- are proposed for receptor activation. Nevertheless, it is known that once a misfolded protein associates with IRE1, it...

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Related Experiment Video

Updated: Jun 30, 2026

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFR&#945;+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis
12:29

Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis

Published on: April 16, 2018

PyPeakRankR: Reproducible Peak-Level Feature Extraction for Regulatory Element Ranking.

Saroja Somasundaram, Nelson J Johansen, Trygve E Bakken

    Arxiv
    |June 29, 2026
    PubMed
    Summary
    This summary is machine-generated.

    PyPeakRankR is a new Python package that helps scientists prioritize regulatory elements identified by ATAC-seq. It extracts key features, enabling reproducible analysis and efficient functional validation of genomic regions.

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    Prediction and Validation of Gene Regulatory Elements Activated During Retinoic Acid Induced Embryonic Stem Cell Differentiation
    09:07

    Prediction and Validation of Gene Regulatory Elements Activated During Retinoic Acid Induced Embryonic Stem Cell Differentiation

    Published on: June 21, 2016

    Area of Science:

    • Genomics
    • Computational Biology
    • Bioinformatics

    Background:

    • High-throughput assays like ATAC-seq generate numerous candidate regulatory elements (peaks).
    • A standardized method is lacking for prioritizing these peaks for functional validation based on diverse quantitative features.

    Purpose of the Study:

    • To introduce PyPeakRankR, an open-source Python package for extracting and assembling peak-level features.
    • To enable reproducible prioritization of regulatory elements for functional studies.

    Main Methods:

    • PyPeakRankR extracts features including BigWig signal, GC content, conservation scores, and cell-type specificity.
    • It generates a reproducible peak-by-feature matrix in a TSV file.
    • The package offers a command-line interface and Python API, supporting cross-assembly scoring.

    Main Results:

    • PyPeakRankR successfully separates feature extraction from downstream ranking for transparent benchmarking.
    • Validated in the BICCN challenge, its predecessor ranked top 3 for enhancer prediction.
    • Used in a basal ganglia study, it helped identify enhancer-AAV tools with high cell-type specificity.

    Conclusions:

    • PyPeakRankR provides a standardized, efficient, and reproducible tool for prioritizing regulatory elements from ATAC-seq data.
    • Its validated performance aids in identifying functional genomic regions for biological research.