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Ribosomal RNA Synthesis02:53

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Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
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The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
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Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
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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.
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Transcriptome-wide profiling of multiple RNA modifications simultaneously at single-base resolution.

Vahid Khoddami1,2,3, Archana Yerra2,3, Timothy L Mosbruger4

  • 1Department of Cell Biology, Harvard Medical School, Boston, MA 02115.

Proceedings of the National Academy of Sciences of the United States of America
|March 16, 2019
PubMed
Summary
This summary is machine-generated.

Researchers developed RBS-Seq, a new method to simultaneously detect multiple RNA modifications at single-base resolution. This technique accurately maps N6-methyladenosine (m1A), pseudouridine (Ψ), and 5-methylcytosine (m5C) modifications across the transcriptome.

Keywords:
RNA methylationRNA modificationm1Amethyl adenosinepseudouridine

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Area of Science:

  • Epitranscriptomics
  • Molecular Biology
  • Genomics

Background:

  • RNA modifications are crucial for RNA function, stability, and cellular fate.
  • Current methods lack the ability to profile multiple RNA modifications simultaneously at single-base resolution.
  • Accurate profiling of RNA modifications is essential for understanding cellular status.

Purpose of the Study:

  • To develop a novel method for simultaneous, high-resolution, transcriptome-wide profiling of multiple RNA modifications.
  • To enable the detection of N6-methyladenosine (m1A), pseudouridine (Ψ), and 5-methylcytosine (m5C) modifications concurrently.
  • To facilitate covariation studies by mapping multiple modifications within the same RNA molecule.

Main Methods:

  • Developed RBS-Seq, a modification of RNA bisulfite sequencing.
  • RBS-Seq enables sensitive and simultaneous detection of m5C, Ψ, and m1A at single-base resolution.
  • m5C and m1A are detected via base mismatches, while Ψ is identified by a 1-2 base deletion signature.

Main Results:

  • RBS-Seq accurately maps m5C, Ψ, and m1A modifications transcriptome-wide.
  • Identified known modification sites in tRNAs and rRNAs, and discovered hundreds of new sites in noncoding RNAs and mRNAs.
  • Results suggest significantly fewer m5C sites and absence of substantial m1A in mRNAs compared to previous studies.

Conclusions:

  • RBS-Seq provides a powerful tool for high-precision mapping of multiple RNA modifications.
  • The method enables sensitive detection and covariation studies of epitranscriptomic marks.
  • Refined datasets and approaches will advance future epitranscriptome research.