Molecular Development - Ribonucleic acid

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Introduction

Amphibian oocyte transcription
Epigenetics mechanisms[1]

The original "RNA family" consisted of just 3 main members; transfer RNA (tRNA), ribosomal RNA (rRNA) and messenger RNAs (mRNA). Involved in gene expression through protein translation (synthesis).


In recent years this RNA family, shown in the table below, has been expanded to include newly identified members: small nuclear RNA (snRNA) , small nucleolar RNA (snoRNA), and short regulatory RNA (piwi-associated RNA (piRNA), endogenous short-interfering RNA (endo-siRNA) and microRNA (miRNA) and now long non-coding RNA (lncRNA). Each of these new family members has a range of potential roles in development and differentiation.


Ribonucleic acid (RNA) typically consists of just 4 nucleotides: Adenine (A), Cytosine (C), Guanine (G) and Uracil (U). Note that Uracil (U) replaces Thymine (T) present in DNA. RNA is also less stable than DNA and exists as a single-stranded molecule, with secondary structure established by internal base pairing. The secondary structures often described as forming "hair-pins", "loops" and "stem-loop" structures, have a close relationship with many of the functions of these molecules.


In some species, for example the fly and frog[2], it has been shown that oocyte maternal RNA and its specific localisation has an important role in early development.


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Links: microRNA | Fly Development | Frog Development


Molecular Links: molecular | genetics | epigenetics | mitosis | meiosis | X Inactivation | Signaling | Factors | Mouse Knockout | microRNA | Mechanisms | Developmental Enhancers | Protein | Genetic Abnormal | Category:Molecular


Factor Links: AMH | hCG | BMP | sonic hedgehog | bHLH | HOX | FGF | FOX | Hippo | LIM | Nanog | NGF | Nodal | Notch | PAX | retinoic acid | SIX | Slit2/Robo1 | SOX | TBX | TGF-beta | VEGF | WNT | Category:Molecular
Mechanism Links: mitosis | cell migration | epithelial invagination | epithelial mesenchymal transition | mesenchymal epithelial transition | epithelial mesenchymal interaction | morphodynamics | tube formation | apoptosis | autophagy | axes formation | time | molecular


Some Recent Findings

  • Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes[3] "Ribosome profiling suggests that ribosomes occupy many regions of the transcriptome thought to be noncoding, including 5' UTRs and long noncoding RNAs (lncRNAs). Apparent ribosome footprints outside of protein-coding regions raise the possibility of artifacts unrelated to translation, particularly when they occupy multiple, overlapping open reading frames (ORFs). Here, we show hallmarks of translation in these footprints: copurification with the large ribosomal subunit, response to drugs targeting elongation, trinucleotide periodicity, and initiation at early AUGs. We develop a metric for distinguishing between 80S footprints and nonribosomal sources using footprint size distributions, which validates the vast majority of footprints outside of coding regions. We present evidence for polypeptide production beyond annotated genes, including the induction of immune responses following human cytomegalovirus (HCMV) infection. Translation is pervasive on cytosolic transcripts outside of conserved reading frames, and direct detection of this expanded universe of translated products enables efforts at understanding how cells manage and exploit its consequences."
  • Ribosome profiling reveals resemblance between long non-coding RNAs and 5' leaders of coding RNAs[4] "Large-scale genomics and computational approaches have identified thousands of putative long non-coding RNAs (lncRNAs). It has been controversial, however, as to what fraction of these RNAs is truly non-coding. Here, we combine ribosome profiling with a machine-learning approach to validate lncRNAs during zebrafish development in a high throughput manner. We find that dozens of proposed lncRNAs are protein-coding contaminants and that many lncRNAs have ribosome profiles that resemble the 5' leaders of coding RNAs." Zebrafish Development
More recent papers
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Search term: Ribonucleic acid Embryology

<pubmed limit=5>Ribonucleic acid Embryology</pubmed>

RNA Classes

RNA Class Acronym Roles Examples Reviews
messenger RNA mRNA transcribed from DNA in cell nucleus and relocate to cytoplasm for translation on the ribosome Example
ribosomal RNA rRNA structural RNA that allow the assembly of ribosomal proteins in the cytoplasm into ribosomal subunits required for protein translation Example
transfer RNA tRNA carry amino acid in cell cytoplasm to ribosome PMID 24966867
small nuclear RNA snRNA involved in cell nucleus RNA splicing assemble with proteins to form small nuclear ribonucleic particles (snRNPs) PMID 23980890
small nucleolar RNA snoRNA modify other small RNAs (rRNAs and tRNAs) box C/D snoRNAs and the box H/ACA PMID 21664409 PMID 19446021
microRNA miRNA post-transcriptional regulator of gene expression PMID 25128264
endogenous short-interfering RNA endo-siRNA short regulatory RNA mainly characterised in plants PMID 22578318
piwi-associated RNA piRNA short regulatory RNA PMID 18032451 PMID 22103557
long non-coding RNA ncRNA non-coding RNA greater than 200bp in length may have different roles in signalling, protein processing and differentiation PMID 24829860

messenger RNA

(mRNA) RNA family of varying lengths transcribed from DNA in cell nucleus and relocate to cytoplasm for translation on the ribosome.

  • The initially transcribed mRNA can be further processed (spliced) with the nucleus to remove introns (non-coding sequence) from between exons (the coding sequence).
    • intron-exon-intron-exon -> exon-exon
  • Additional non-coding regions are found at either ends of the messenger RNA as untranslated regions (UTRs).
    • 5' UTR - encoded region - 3' UTR

ribosomal RNA

(rRNA) Structural RNA that allow the assembly of ribosomal proteins in the cytoplasm into ribosomal subunits required for protein translation.

transfer RNA

(tRNA) RNA family involved with specifically carrying and transferring an amino acid in the cell cytoplasm to ribosome, may have other regulatory roles.

PMID 24966867

small nuclear RNA

(snRNA) RNA family involved in cell nucleus RNA splicing assemble and along with proteins form small nuclear ribonucleic particles (snRNPs).

PMID 23980890

small nucleolar RNA

(snoRNA) This family of RNAs modify other small RNAs (rRNAs and tRNAs) and fall into 2 main classes; box C/D snoRNAs and the box H/ACA.

PMID 21664409 PMID 19446021

microRNA

(miRNA ) Large family of short RNAs involved in post-transcriptional regulators of gene expression.

  • short hairpin RNA (shRNA) has a role in RNA interference (RNAi)
  • RNA interference (RNAi) is post-transcriptional gene silencing by means of sequence-specific mRNA degradation.
    • Note that RNAi has now been developed as a research technique to specifically carry out gene silencing in cells, tissues and embryos.

PMID 25128264

endogenous short-interfering RNA

(endo-siRNA) A family of short regulatory RNA mainly characterised in plants.

  • see also short hairpin RNA (shRNA).

PMID 22578318 ===piwi-associated RNA (piRNA) short regulatory RNA PMID 18032451 PMID 22103557

long non-coding RNA

(ncRNA) Family of non-coding RNA greater than 200bp in length may have different roles in signalling, protein processing and differentiation.

PMID 24829860


Links: Molecular Development


Epigenetics

Epigenetics as the name implies, is the inheritance mechanisms that lie outside the DNA sequence of our genes.

One of the initial discoveries was the effects of DNA methylation upon gene expression and then modifications of nucleosomal histones.

This DNA methylation, usually associated with 5-methylcytosine (m5C), leads to transcriptional silencing in vertebrates.

Links: Epigenetics
Epigenetics mechanisms

References

  1. <pubmed>16688142</pubmed>
  2. <pubmed>10064610</pubmed>
  3. <pubmed>25159147</pubmed>
  4. <pubmed>23698349</pubmed>


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Cite this page: Hill, M.A. (2019, August 21) Embryology Molecular Development - Ribonucleic acid. Retrieved from https://embryology.med.unsw.edu.au/embryology/index.php/Molecular_Development_-_Ribonucleic_acid

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© Dr Mark Hill 2019, UNSW Embryology ISBN: 978 0 7334 2609 4 - UNSW CRICOS Provider Code No. 00098G