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Related Concept Videos

Chromatin Position Affects Gene Expression02:35

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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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In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
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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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In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.
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The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
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Investigation of the Transcriptional Role of a RUNX1 Intronic Silencer by CRISPR/Cas9 Ribonucleoprotein in Acute Myeloid Leukemia Cells
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Dynamic Runx1 chromatin boundaries affect gene expression in hematopoietic development.

Dominic D G Owens1,2, Giorgio Anselmi1, A Marieke Oudelaar1,3

  • 1MRC Molecular Hematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.

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|February 10, 2022
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Dynamic changes in chromatin structure, including sub-TAD formation, are crucial for regulating the RUNX1 gene during hematopoietic development and gene expression.

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Area of Science:

  • Genomics
  • Developmental Biology
  • Epigenetics

Background:

  • RUNX1 is a key transcription factor for blood development, often altered in leukemia.
  • Runx1 gene expression is complex, controlled by two promoters and enhancers.
  • Understanding Runx1's regulation is vital for developmental hematopoiesis research.

Purpose of the Study:

  • To investigate the 3D chromatin conformation dynamics of the Runx1 gene during mouse embryonic stem cell differentiation.
  • To elucidate the role of enhancer-promoter interactions and topological domains in Runx1 gene regulation.

Main Methods:

  • Analysis of 3D chromatin conformation using mouse embryonic stem cell differentiation cultures.
  • Assessing chromatin accessibility, enhancer-promoter interactions, and CTCF-CTCF interactions.
  • Investigating the impact of CTCF site deletion on chromatin structure and gene expression.

Main Results:

  • Runx1 resides in a large topologically associating domain (TAD).
  • Chromatin accessibility and enhancer-promoter interactions increase during differentiation, correlating with Runx1 expression.
  • Tissue-specific sub-TADs form over Runx1, linked to dynamic enhancer-promoter interactions and promoter demethylation.
  • Deletion of CTCF sites at sub-TAD boundaries partially disrupts domain structure and delays hematopoietic development.

Conclusions:

  • Dynamic sub-TAD boundaries are essential for establishing TAD structure and coordinating gene expression of large developmental genes like Runx1.
  • Chromatin conformation changes play a critical role in the precise spatiotemporal regulation of Runx1 during hematopoietic development.