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Reprogramming of the non-coding transcriptome during brain development.

Valadkhan S, Nilsen TW - J. Biol. (2010)

Bottom Line: A recent global analysis of gene expression during the differentiation of neuronal stem cells to neurons and oligodendrocytes indicates a complex pattern of changes in the expression of both protein-coding transcripts and long non-protein-coding RNAs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106, USA. saba.valadkhan@case.edu

ABSTRACT
A recent global analysis of gene expression during the differentiation of neuronal stem cells to neurons and oligodendrocytes indicates a complex pattern of changes in the expression of both protein-coding transcripts and long non-protein-coding RNAs.

Show MeSH
Genomic position of lncRNAs may offer clues to their function. The positional relationship of the lncRNAs (thin arrows) compared to the transcript they regulate (thick arrow) is shown. Serrated lines indicate the long distance between the intergenic lncRNAs and the nearest known transcript, which they may or may not regulate. The three major functional mechanisms employed by currently characterized lncRNAs are listed to the right, and the likelihood that each strategy is used is shown by: - (unlikely to be used), + (likely to be used) or ++ (very likely to be used) signs.
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Figure 1: Genomic position of lncRNAs may offer clues to their function. The positional relationship of the lncRNAs (thin arrows) compared to the transcript they regulate (thick arrow) is shown. Serrated lines indicate the long distance between the intergenic lncRNAs and the nearest known transcript, which they may or may not regulate. The three major functional mechanisms employed by currently characterized lncRNAs are listed to the right, and the likelihood that each strategy is used is shown by: - (unlikely to be used), + (likely to be used) or ++ (very likely to be used) signs.

Mentions: While the above data suggest that the expression pattern of lncRNAs is at least as complex as that of mRNAs, a crucial question is the functional significance of the observed changes in lncRNA expression. To date, the molecular mechanism of function of the majority of lncRNAs remains unknown. However, the most informative clues to their possible mode of function come from their genomic position in relation to other transcripts. In many of the studied examples, lncRNAs have been found within transcriptionally complex loci where their expression, directly or indirectly, influences their neighboring genes [2-4]. An lncRNA may partially or completely overlap another gene in the sense or antisense direction, or it can be located in the close vicinity of another gene in the converging or diverging sense or antisense orientation without overlapping it (Figure 1). Depending on the exact position, the lncRNA transcript may affect the neighboring gene through formation of double-stranded RNA, or cause transcriptional interference or alter the local chromatin structure merely by being transcribed. There are also several known examples of intergenic lncRNAs, transcripts that are located far away from other known transcripts and that are likely to exert their cellular function, if any, in trans, through mechanisms yet to be elucidated.


Reprogramming of the non-coding transcriptome during brain development.

Valadkhan S, Nilsen TW - J. Biol. (2010)

Genomic position of lncRNAs may offer clues to their function. The positional relationship of the lncRNAs (thin arrows) compared to the transcript they regulate (thick arrow) is shown. Serrated lines indicate the long distance between the intergenic lncRNAs and the nearest known transcript, which they may or may not regulate. The three major functional mechanisms employed by currently characterized lncRNAs are listed to the right, and the likelihood that each strategy is used is shown by: - (unlikely to be used), + (likely to be used) or ++ (very likely to be used) signs.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2871522&req=5

Figure 1: Genomic position of lncRNAs may offer clues to their function. The positional relationship of the lncRNAs (thin arrows) compared to the transcript they regulate (thick arrow) is shown. Serrated lines indicate the long distance between the intergenic lncRNAs and the nearest known transcript, which they may or may not regulate. The three major functional mechanisms employed by currently characterized lncRNAs are listed to the right, and the likelihood that each strategy is used is shown by: - (unlikely to be used), + (likely to be used) or ++ (very likely to be used) signs.
Mentions: While the above data suggest that the expression pattern of lncRNAs is at least as complex as that of mRNAs, a crucial question is the functional significance of the observed changes in lncRNA expression. To date, the molecular mechanism of function of the majority of lncRNAs remains unknown. However, the most informative clues to their possible mode of function come from their genomic position in relation to other transcripts. In many of the studied examples, lncRNAs have been found within transcriptionally complex loci where their expression, directly or indirectly, influences their neighboring genes [2-4]. An lncRNA may partially or completely overlap another gene in the sense or antisense direction, or it can be located in the close vicinity of another gene in the converging or diverging sense or antisense orientation without overlapping it (Figure 1). Depending on the exact position, the lncRNA transcript may affect the neighboring gene through formation of double-stranded RNA, or cause transcriptional interference or alter the local chromatin structure merely by being transcribed. There are also several known examples of intergenic lncRNAs, transcripts that are located far away from other known transcripts and that are likely to exert their cellular function, if any, in trans, through mechanisms yet to be elucidated.

Bottom Line: A recent global analysis of gene expression during the differentiation of neuronal stem cells to neurons and oligodendrocytes indicates a complex pattern of changes in the expression of both protein-coding transcripts and long non-protein-coding RNAs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106, USA. saba.valadkhan@case.edu

ABSTRACT
A recent global analysis of gene expression during the differentiation of neuronal stem cells to neurons and oligodendrocytes indicates a complex pattern of changes in the expression of both protein-coding transcripts and long non-protein-coding RNAs.

Show MeSH