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Updated: Jun 18, 2025

Chromatin Isolation by RNA Purification ChIRP
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Chromatin Isolation by RNA Purification ChIRP

Published on: March 25, 2012

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使用深度学习探索RNAs在染色体架构中的作用

Shuzhen Kuang1, Katherine S Pollard2,3,4

  • 1Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.

Nature communications
|July 29, 2024
PubMed
概括

染色体关联RNAs (caRNAs) 显著影响3D基因组组织. 我们的深度学习模型AkitaR揭示了新生的转录和转位的caRNAs如何影响基因组折叠,特别是在特定的细胞区域.

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Author Spotlight: Getting an A with the 3Cs: Chromosome Conformation Capture for Undergraduates09:13

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Chromatin Structure and RNA Splicing02:41

Chromatin Structure and RNA Splicing

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Chromatin Structure Regulates pre-mRNA Processing

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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Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in regulating gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
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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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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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Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
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