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Related Concept Videos

Nucleoid01:24

Nucleoid

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The nucleoid represents a structurally and functionally distinct region within prokaryotic cells, where the cell's DNA and associated proteins are housed. Unlike eukaryotic cells, prokaryotes lack a membrane-bound nucleus, and the nucleoid facilitates the organization and accessibility of the genetic material within this constraint. The DNA in most bacteria and archaea exists as a single, circular, double-stranded molecule that is highly compacted through supercoiling and interactions with...
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Ribosome Profiling02:24

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
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Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

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Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences  access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area. 
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The Nucleolus02:55

The Nucleolus

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The nucleolus is the most prominent substructure of the nucleus. When it was first discovered, it was considered to be an isolated organelle that forms fibrils and granules. In 1931, the relationship between the nucleolus and chromosomes was first described by Heitz. He observed that the appearance and size of nucleolus varies depending on the stage of the cell cycle. He also noticed constricted regions on different chromosomes clustered together at definite cell cycle stages. These regions,...
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Genomic DNA in Prokaryotes00:46

Genomic DNA in Prokaryotes

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The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
Genomic Diversity in Bacteria
Although bacterial genomes are much...
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Structure of a Gene01:30

Structure of a Gene

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A gene is the fundamental unit of heredity. Every individual has two copies of each gene, one inherited from each parent. Although most people contain the same genes, there is a small fraction that is slightly different amongst people. A gene with a small difference in its sequence of DNA bases forms different alleles, contributing to different phenotypes.
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Related Experiment Video

Updated: Feb 24, 2026

High-Resolution Mapping of Protein-DNA Interactions in Mouse Stem Cell-Derived Neurons using Chromatin Immunoprecipitation-Exonuclease ChIP-Exo
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High-Resolution Mapping of Protein-DNA Interactions in Mouse Stem Cell-Derived Neurons using Chromatin Immunoprecipitation-Exonuclease ChIP-Exo

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Nucleoid-Associated Proteins: Genome Level Occupancy and Expression Analysis.

Parul Singh1,2, Aswin Sai Narain Seshasayee3

  • 1National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, 560065, Karnataka, India. singh.parul686@gmail.com.

Methods in Molecular Biology (Clifton, N.J.)
|August 27, 2017
PubMed
Summary
This summary is machine-generated.

Chromatin Immunoprecipitation sequencing (ChIP-Seq) identifies DNA binding protein locations. Combining ChIP-Seq with transcriptome data reveals direct and indirect effects on gene expression in E. coli.

Keywords:
ChIP-SeqGTFMACSNAPRegulation of transcription initiationZ-score

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Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis
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Related Experiment Videos

Last Updated: Feb 24, 2026

High-Resolution Mapping of Protein-DNA Interactions in Mouse Stem Cell-Derived Neurons using Chromatin Immunoprecipitation-Exonuclease ChIP-Exo
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High-Resolution Mapping of Protein-DNA Interactions in Mouse Stem Cell-Derived Neurons using Chromatin Immunoprecipitation-Exonuclease ChIP-Exo

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Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis
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Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

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

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Area of Science:

  • Molecular Biology
  • Genomics
  • Microbiology

Background:

  • Chromatin Immunoprecipitation sequencing (ChIP-Seq) identifies genome-wide DNA binding protein targets in vivo.
  • Transcriptome experiments assess the impact of DNA binding proteins on gene expression.
  • Integrating these datasets allows for the dissection of direct and indirect regulatory effects.

Purpose of the Study:

  • To demonstrate the application of ChIP-Seq and transcriptome analysis to study Nucleoid Associated Proteins (NAPs) and Global Transcription Factors (GTFs).
  • To infer binding properties and transcriptional effects of specific NAPs (Fis, HNS) and a GTF (CRP) in Escherichia coli K12 MG1655.
  • To highlight the complex interplay between DNA-protein interactions and gene expression regulation.

Main Methods:

  • Genome-wide identification of DNA binding protein targets using Chromatin Immunoprecipitation sequencing (ChIP-Seq).
  • Assessment of gene expression changes using transcriptome experiments.
  • Integration of ChIP-Seq and transcriptome data to analyze direct and indirect regulatory roles.
  • Application of these techniques to study Fis, HNS, and CRP in Escherichia coli.

Main Results:

  • ChIP-Seq successfully identified genomic binding regions for NAPs Fis and HNS, and GTF CRP in E. coli.
  • Transcriptome data provided insights into the gene expression changes influenced by these proteins.
  • The combined data revealed complex regulatory relationships, underscoring combinatorial control in gene expression.

Conclusions:

  • ChIP-Seq coupled with transcriptome analysis is a powerful approach to dissecting DNA-protein interactions and their effects on gene expression.
  • The study elucidates the roles of NAPs and GTFs in regulating gene expression in E. coli.
  • Findings contribute to understanding the intricate mechanisms of combinatorial gene regulation in prokaryotes.