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Related Concept Videos

Combinatorial Gene Control02:33

Combinatorial Gene Control

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Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
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Chromatin Packaging02:21

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Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order...
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Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...
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Epigenetics is the study of inherited changes in a cell's phenotype without changing the DNA sequences. It provides a form of memory for the differential gene expression pattern to maintain cell lineage, position-effect variegation, dosage compensation, and maintenance of chromatin structures such as telomeres and centromeres. For example, the structure and location of the centromere on chromosomes are epigenetically inherited. Its functionality is not dictated or ensured by the underlying...
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The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
Writers
The writer...
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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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Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility.

Caleb A Lareau1,2,3, Fabiana M Duarte1,2, Jennifer G Chew4

  • 1Broad Institute of MIT and Harvard, Cambridge, MA, USA.

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|June 26, 2019
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We developed a high-throughput droplet-based method for single-cell epigenome profiling, enabling massive-scale analysis of chromatin accessibility. This scalable technology reveals cell types and regulatory landscapes across millions of cells.

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Area of Science:

  • Epigenomics and Single-Cell Biology
  • Genomics and Bioinformatics
  • Molecular Biology and Genetics

Background:

  • Current single-cell epigenome mapping methods face limitations in throughput and data quality, hindering broad application.
  • Efficiently profiling chromatin accessibility at single-cell resolution is crucial for understanding cellular heterogeneity and regulatory mechanisms.

Purpose of the Study:

  • To introduce a high-quality, droplet-microfluidics-based method for single-cell chromatin accessibility profiling.
  • To demonstrate the scalability and flexibility of this droplet-based platform for large-scale epigenomic studies.

Main Methods:

  • Development of droplet single-cell assay for transposase-accessible chromatin using sequencing (dscATAC-seq) for high-throughput profiling.
  • Integration of dscATAC-seq with combinatorial indexing (dsciATAC-seq) to further enhance throughput for massive-scale single-cell studies.
  • Application of the platform to assay over 510,000 single-cell profiles from mouse brain and human bone marrow cells.

Main Results:

  • Successfully profiled chromatin accessibility in 46,653 mouse brain cells, enabling unbiased discovery of cell types and regulatory elements.
  • Analyzed 136,463 human bone marrow cells, revealing dynamic changes in cis- and trans-regulatory landscapes under different conditions.
  • Demonstrated the platform's capacity to generate over 510,000 single-cell epigenomic profiles.

Conclusions:

  • The droplet-based dscATAC-seq and dsciATAC-seq platforms offer a scalable and flexible solution for single-cell epigenome profiling.
  • This technology facilitates large-scale discovery of cell types, regulatory elements, and dynamic regulatory changes at single-cell resolution.
  • The method significantly advances the capacity for comprehensive epigenomic studies across diverse biological systems and conditions.