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Identification of differentially expressed non-coding RNAs in embryonic stem cell neural differentiation.

Skreka K, Schafferer S, Nat IR, Zywicki M, Salti A, Apostolova G, Griehl M, Rederstorff M, Dechant G, Hüttenhofer A - Nucleic Acids Res. (2012)

Bottom Line: By high-throughput sequencing and transcriptional profiling we identified several novel miRNAs to be involved in ES cell differentiation, as well as seven small nucleolar RNAs.In addition, expression of 7SL, 7SK and vault-2 RNAs was significantly up-regulated during ES cell differentiation.Additionally, these novel intraRNAs and interRNAs were not only found to be differentially expressed in stem-cell derivatives, but also in primary cultures of hippocampal neurons and astrocytes, strengthening their potential function in neural ES cell differentiation.

View Article: PubMed Central - PubMed

Affiliation: Division of Genomics and RNomics, Biocenter, Medical University Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria.

ABSTRACT
Protein-coding genes, guiding differentiation of ES cells into neural cells, have extensively been studied in the past. However, for the class of ncRNAs only the involvement of some specific microRNAs (miRNAs) has been described. Thus, to characterize the entire small non-coding RNA (ncRNA) transcriptome, involved in the differentiation of mouse ES cells into neural cells, we have generated three specialized ribonucleo-protein particle (RNP)-derived cDNA libraries, i.e. from pluripotent ES cells, neural progenitors and differentiated neural cells, respectively. By high-throughput sequencing and transcriptional profiling we identified several novel miRNAs to be involved in ES cell differentiation, as well as seven small nucleolar RNAs. In addition, expression of 7SL, 7SK and vault-2 RNAs was significantly up-regulated during ES cell differentiation. About half of ncRNA sequences from the three cDNA libraries mapped to intergenic or intragenic regions, designated as interRNAs and intraRNAs, respectively. Thereby, novel ncRNA candidates exhibited a predominant size of 18-30 nt, thus resembling miRNA species, but, with few exceptions, lacking canonical miRNA features. Additionally, these novel intraRNAs and interRNAs were not only found to be differentially expressed in stem-cell derivatives, but also in primary cultures of hippocampal neurons and astrocytes, strengthening their potential function in neural ES cell differentiation.

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Length distribution and abundance of contigs from the three RNP libraries. NcRNAs were clustered in unique contigs; the consensus sequence was employed to determine the absolute abundance versus the length of respective ncRNAs (contigs exhibiting a size >99 nt are rare and are therefore not shown).
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gks311-F4: Length distribution and abundance of contigs from the three RNP libraries. NcRNAs were clustered in unique contigs; the consensus sequence was employed to determine the absolute abundance versus the length of respective ncRNAs (contigs exhibiting a size >99 nt are rare and are therefore not shown).

Mentions: Analysis of the length distribution of novel and known ncRNA candidates from the three cDNA libraries showed a bias towards 18–30 nt sized ncRNA species in all three cDNA libraries (Figure 4). Thereby, in the NP library the 18–30 nt peak is ∼2-fold larger compared to ES and N/G libraries. A second, smaller peak of ncRNA sequences appears at RNAs sized 45–47 nt which increases at the N/G stage; a third potential peak, sized 71–78 nt, is also observed (Figure 4).Figure 4.


Identification of differentially expressed non-coding RNAs in embryonic stem cell neural differentiation.

Skreka K, Schafferer S, Nat IR, Zywicki M, Salti A, Apostolova G, Griehl M, Rederstorff M, Dechant G, Hüttenhofer A - Nucleic Acids Res. (2012)

Length distribution and abundance of contigs from the three RNP libraries. NcRNAs were clustered in unique contigs; the consensus sequence was employed to determine the absolute abundance versus the length of respective ncRNAs (contigs exhibiting a size >99 nt are rare and are therefore not shown).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3401476&req=5

gks311-F4: Length distribution and abundance of contigs from the three RNP libraries. NcRNAs were clustered in unique contigs; the consensus sequence was employed to determine the absolute abundance versus the length of respective ncRNAs (contigs exhibiting a size >99 nt are rare and are therefore not shown).
Mentions: Analysis of the length distribution of novel and known ncRNA candidates from the three cDNA libraries showed a bias towards 18–30 nt sized ncRNA species in all three cDNA libraries (Figure 4). Thereby, in the NP library the 18–30 nt peak is ∼2-fold larger compared to ES and N/G libraries. A second, smaller peak of ncRNA sequences appears at RNAs sized 45–47 nt which increases at the N/G stage; a third potential peak, sized 71–78 nt, is also observed (Figure 4).Figure 4.

Bottom Line: By high-throughput sequencing and transcriptional profiling we identified several novel miRNAs to be involved in ES cell differentiation, as well as seven small nucleolar RNAs.In addition, expression of 7SL, 7SK and vault-2 RNAs was significantly up-regulated during ES cell differentiation.Additionally, these novel intraRNAs and interRNAs were not only found to be differentially expressed in stem-cell derivatives, but also in primary cultures of hippocampal neurons and astrocytes, strengthening their potential function in neural ES cell differentiation.

View Article: PubMed Central - PubMed

Affiliation: Division of Genomics and RNomics, Biocenter, Medical University Innsbruck, Innrain 80/82, A-6020 Innsbruck, Austria.

ABSTRACT
Protein-coding genes, guiding differentiation of ES cells into neural cells, have extensively been studied in the past. However, for the class of ncRNAs only the involvement of some specific microRNAs (miRNAs) has been described. Thus, to characterize the entire small non-coding RNA (ncRNA) transcriptome, involved in the differentiation of mouse ES cells into neural cells, we have generated three specialized ribonucleo-protein particle (RNP)-derived cDNA libraries, i.e. from pluripotent ES cells, neural progenitors and differentiated neural cells, respectively. By high-throughput sequencing and transcriptional profiling we identified several novel miRNAs to be involved in ES cell differentiation, as well as seven small nucleolar RNAs. In addition, expression of 7SL, 7SK and vault-2 RNAs was significantly up-regulated during ES cell differentiation. About half of ncRNA sequences from the three cDNA libraries mapped to intergenic or intragenic regions, designated as interRNAs and intraRNAs, respectively. Thereby, novel ncRNA candidates exhibited a predominant size of 18-30 nt, thus resembling miRNA species, but, with few exceptions, lacking canonical miRNA features. Additionally, these novel intraRNAs and interRNAs were not only found to be differentially expressed in stem-cell derivatives, but also in primary cultures of hippocampal neurons and astrocytes, strengthening their potential function in neural ES cell differentiation.

Show MeSH
Related in: MedlinePlus