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Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

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The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
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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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One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
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RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
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Transcriptional attenuation occurs when RNA transcription is prematurely terminated due to the formation of a terminator mRNA hairpin structure.  Bacteria use these hairpins to regulate the transcription process and control the synthesis of several amino acids including histidine, lysine, threonine, and phenylalanine. Transcription attenuation takes place in the non-coding regions of mRNA.
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Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
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Related Experiment Video

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5' tRNA halves are highly expressed in the primate hippocampus and might sequence-specifically regulate gene

Julia Jehn1, Jana Treml1, Svenja Wulsch1

  • 1Institute of Organismic and Molecular Evolution iOME, Anthropology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany.

RNA (New York, N.Y.)
|March 8, 2020
PubMed
Summary

tRNA-derived small RNAs (tsRNAs) are not degradation products but regulate gene expression. This study reveals 5' tRNA halves (5' tRHs) in primate brains and uncovers novel sequence-specific gene silencing and stabilization mechanisms.

Keywords:
gene regulationk-mer mappingsmall noncoding RNAstRNA fragmentstarget identificationtarget prediction

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • Mature tRNA fragments, previously considered non-functional, are now recognized as tRNA-derived small RNAs (tsRNAs).
  • tsRNAs participate in various cellular processes, but their regulatory mechanisms and expression profiles remain largely unexplored.
  • Understanding tsRNA function is crucial for deciphering novel gene regulation pathways.

Purpose of the Study:

  • To investigate the expression profiles of tsRNAs across different species and tissues.
  • To elucidate the molecular mechanisms by which 5' tRNA halves (5' tRHs) regulate gene expression.
  • To identify novel gene targets and regulatory rules for 5' tRHs.

Main Methods:

  • Comparative analysis of tsRNA expression in various species and tissues, with a focus on primate hippocampus.
  • Experimental manipulation of 5' tRH levels in human cells using synthetic mimics and antisense RNAs.
  • RNA sequencing (RNA-seq) to identify differentially expressed transcripts.
  • A novel k-mer mapping approach to determine tsRNA targeting rules.

Main Results:

  • High expression of 5' tRHs was observed, particularly in the primate hippocampus.
  • Sequence-specific gene silencing by 5' tRHs was demonstrated, with target sites located in the CDS or 3' UTR.
  • A novel regulatory mechanism, distinct from miRNA-like seed matching, was suggested.
  • Some 5' tRHs were found to stabilize mRNAs, indicating a dual role in gene regulation.

Conclusions:

  • tsRNAs, especially 5' tRHs, play significant roles in gene regulation beyond simple degradation.
  • The targeting mechanism of 5' tRHs is sequence-specific and differs from canonical miRNA pathways.
  • 5' tRHs can act as both gene silencers and stabilizers, highlighting their complex regulatory functions.