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Assessing the translational landscape of myogenic differentiation by ribosome profiling.

de Klerk E, Fokkema IF, Thiadens KA, Goeman JJ, Palmblad M, den Dunnen JT, von Lindern M, 't Hoen PA - Nucleic Acids Res. (2015)

Bottom Line: The formation of skeletal muscles is associated with drastic changes in protein requirements known to be safeguarded by tight control of gene transcription and mRNA processing.Enrichment was also found for specific pathways known to regulate muscle biology.We identified 298 transcripts with a significant switch in TIS usage during myogenesis, which was not explained by alternative promoter usage, as profiled by DeepCAGE.

View Article: PubMed Central - PubMed

Affiliation: Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC Leiden, The Netherlands.

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(A) Percentage of reads mapped to coding and non-coding genes in myoblasts and myotubes treated with harringtoning (Har) or cycloheximide (Chx). (B) Read-length distribution of footprints mapping to protein-coding genes (top), non-coding genes (including small and long non-coding genes) or only to lincRNAs (bottom). (C) Read-length distribution of footprints mapping to Malat1, Snhg1, Rnu11 and H19. (D–G) Coverage patterns for Malat1, Snhg1, Rnu11 and H19 in harringtonin (top traces) and cycloheximide (bottom traces) treated myoblasts.
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Figure 2: (A) Percentage of reads mapped to coding and non-coding genes in myoblasts and myotubes treated with harringtoning (Har) or cycloheximide (Chx). (B) Read-length distribution of footprints mapping to protein-coding genes (top), non-coding genes (including small and long non-coding genes) or only to lincRNAs (bottom). (C) Read-length distribution of footprints mapping to Malat1, Snhg1, Rnu11 and H19. (D–G) Coverage patterns for Malat1, Snhg1, Rnu11 and H19 in harringtonin (top traces) and cycloheximide (bottom traces) treated myoblasts.

Mentions: Footprints recovered after halting translation with harringtonin or cycloheximide mainly mapped to protein coding genes (Figure 2A, Supplementary Tables S4 and S5). Reads mapping to repetitive sequences, including contamination from ribosomal and transfer RNAs, are shown separately in Supplementary Table S3.


Assessing the translational landscape of myogenic differentiation by ribosome profiling.

de Klerk E, Fokkema IF, Thiadens KA, Goeman JJ, Palmblad M, den Dunnen JT, von Lindern M, 't Hoen PA - Nucleic Acids Res. (2015)

(A) Percentage of reads mapped to coding and non-coding genes in myoblasts and myotubes treated with harringtoning (Har) or cycloheximide (Chx). (B) Read-length distribution of footprints mapping to protein-coding genes (top), non-coding genes (including small and long non-coding genes) or only to lincRNAs (bottom). (C) Read-length distribution of footprints mapping to Malat1, Snhg1, Rnu11 and H19. (D–G) Coverage patterns for Malat1, Snhg1, Rnu11 and H19 in harringtonin (top traces) and cycloheximide (bottom traces) treated myoblasts.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4482065&req=5

Figure 2: (A) Percentage of reads mapped to coding and non-coding genes in myoblasts and myotubes treated with harringtoning (Har) or cycloheximide (Chx). (B) Read-length distribution of footprints mapping to protein-coding genes (top), non-coding genes (including small and long non-coding genes) or only to lincRNAs (bottom). (C) Read-length distribution of footprints mapping to Malat1, Snhg1, Rnu11 and H19. (D–G) Coverage patterns for Malat1, Snhg1, Rnu11 and H19 in harringtonin (top traces) and cycloheximide (bottom traces) treated myoblasts.
Mentions: Footprints recovered after halting translation with harringtonin or cycloheximide mainly mapped to protein coding genes (Figure 2A, Supplementary Tables S4 and S5). Reads mapping to repetitive sequences, including contamination from ribosomal and transfer RNAs, are shown separately in Supplementary Table S3.

Bottom Line: The formation of skeletal muscles is associated with drastic changes in protein requirements known to be safeguarded by tight control of gene transcription and mRNA processing.Enrichment was also found for specific pathways known to regulate muscle biology.We identified 298 transcripts with a significant switch in TIS usage during myogenesis, which was not explained by alternative promoter usage, as profiled by DeepCAGE.

View Article: PubMed Central - PubMed

Affiliation: Department of Human Genetics, Leiden University Medical Center, Postzone S4-P, PO Box 9600, 2300 RC Leiden, The Netherlands.

Show MeSH