Limits...
Outline of a genome navigation system based on the properties of GA-sequences and their flanks.

Albrecht-Buehler G - PLoS ONE (2009)

Bottom Line: Introducing a new method to visualize large stretches of genomic DNA (see Appendix S1) the article reports that most GA-sequences [1] shared chains of tetra-GA-motifs and contained upstream poly(A)-segments.Although not integral parts of them, Alu-elements were found immediately upstream of all human and chimpanzee GA-sequences with an upstream poly(A)-segment.In response, the associated DNA-loop releases its nucleosomes and allows transcription of the target protein to proceed. (4) The Alu-transcripts may help control the general background of protein synthesis proportional to the number of transcriptionally active associated loops, especially in stressed cells. (5) The model offers a new mechanism of co-regulation of protein synthesis based on the shared segments of different GA-sequences.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America. g-buehler@northwestern.edu

ABSTRACT
Introducing a new method to visualize large stretches of genomic DNA (see Appendix S1) the article reports that most GA-sequences [1] shared chains of tetra-GA-motifs and contained upstream poly(A)-segments. Although not integral parts of them, Alu-elements were found immediately upstream of all human and chimpanzee GA-sequences with an upstream poly(A)-segment. The article hypothesizes that genome navigation uses these properties of GA-sequences in the following way. (1) Poly(A) binding proteins interact with the upstream poly(A)-segments and arrange adjacent GA-sequences side-by-side ('GA-ribbon'), while folding the intervening DNA sequences between them into loops ('associated DNA-loops'). (2) Genome navigation uses the GA-ribbon as a search path for specific target genes that is up to 730-fold shorter than the full-length chromosome. (3) As to the specificity of the search, each molecule of a target protein is assumed to catalyze the formation of specific oligomers from a set of transcription factors that recognize tetra-GA-motifs. Their specific combinations of tetra-GA motifs are assumed to be present in the particular GA-sequence whose associated loop contains the gene for the target protein. As long as the target protein is abundant in the cell it produces sufficient numbers of such oligomers which bind to their specific GA-sequences and, thereby, inhibit locally the transcription of the target protein in the associated loop. However, if the amount of target protein drops below a certain threshold, the resultant reduction of specific oligomers leaves the corresponding GA-sequence 'denuded'. In response, the associated DNA-loop releases its nucleosomes and allows transcription of the target protein to proceed. (4) The Alu-transcripts may help control the general background of protein synthesis proportional to the number of transcriptionally active associated loops, especially in stressed cells. (5) The model offers a new mechanism of co-regulation of protein synthesis based on the shared segments of different GA-sequences.

Show MeSH

Related in: MedlinePlus

Outline of a chromatin model that supports a fast genome navigation system.By leaping from one GA-sequence to the next along the GA-ribbon in the scanning direction while ‘reading’ the information encoded in the proteins bound to the GA sequence in the reading direction, the postulated ‘clavisomes’ (searching complexes) can efficiently find the appropriate GA-sequence on a more than 700-fold shorter search path than by crawling along the various size loops of genomic DNA. After a clavisome found its target GA-sequence and interacted with it, the nucleosomes in the associated loop are released, and the specific coding sequences in the loop are exposed to the transcription mechanisms.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2651618&req=5

pone-0004701-g006: Outline of a chromatin model that supports a fast genome navigation system.By leaping from one GA-sequence to the next along the GA-ribbon in the scanning direction while ‘reading’ the information encoded in the proteins bound to the GA sequence in the reading direction, the postulated ‘clavisomes’ (searching complexes) can efficiently find the appropriate GA-sequence on a more than 700-fold shorter search path than by crawling along the various size loops of genomic DNA. After a clavisome found its target GA-sequence and interacted with it, the nucleosomes in the associated loop are released, and the specific coding sequences in the loop are exposed to the transcription mechanisms.

Mentions: Since all pure GA-sequences of a chromosome are lined up in tandem on the same DNA strand, there is essentially only one non-disruptive way of forcing all of them into a small space, namely by placing the pure GA-sequences side-by-side while folding the intervening stretches of DNA between them into loops (See Fig. 5, Fig. 6).


Outline of a genome navigation system based on the properties of GA-sequences and their flanks.

Albrecht-Buehler G - PLoS ONE (2009)

Outline of a chromatin model that supports a fast genome navigation system.By leaping from one GA-sequence to the next along the GA-ribbon in the scanning direction while ‘reading’ the information encoded in the proteins bound to the GA sequence in the reading direction, the postulated ‘clavisomes’ (searching complexes) can efficiently find the appropriate GA-sequence on a more than 700-fold shorter search path than by crawling along the various size loops of genomic DNA. After a clavisome found its target GA-sequence and interacted with it, the nucleosomes in the associated loop are released, and the specific coding sequences in the loop are exposed to the transcription mechanisms.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2651618&req=5

pone-0004701-g006: Outline of a chromatin model that supports a fast genome navigation system.By leaping from one GA-sequence to the next along the GA-ribbon in the scanning direction while ‘reading’ the information encoded in the proteins bound to the GA sequence in the reading direction, the postulated ‘clavisomes’ (searching complexes) can efficiently find the appropriate GA-sequence on a more than 700-fold shorter search path than by crawling along the various size loops of genomic DNA. After a clavisome found its target GA-sequence and interacted with it, the nucleosomes in the associated loop are released, and the specific coding sequences in the loop are exposed to the transcription mechanisms.
Mentions: Since all pure GA-sequences of a chromosome are lined up in tandem on the same DNA strand, there is essentially only one non-disruptive way of forcing all of them into a small space, namely by placing the pure GA-sequences side-by-side while folding the intervening stretches of DNA between them into loops (See Fig. 5, Fig. 6).

Bottom Line: Introducing a new method to visualize large stretches of genomic DNA (see Appendix S1) the article reports that most GA-sequences [1] shared chains of tetra-GA-motifs and contained upstream poly(A)-segments.Although not integral parts of them, Alu-elements were found immediately upstream of all human and chimpanzee GA-sequences with an upstream poly(A)-segment.In response, the associated DNA-loop releases its nucleosomes and allows transcription of the target protein to proceed. (4) The Alu-transcripts may help control the general background of protein synthesis proportional to the number of transcriptionally active associated loops, especially in stressed cells. (5) The model offers a new mechanism of co-regulation of protein synthesis based on the shared segments of different GA-sequences.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America. g-buehler@northwestern.edu

ABSTRACT
Introducing a new method to visualize large stretches of genomic DNA (see Appendix S1) the article reports that most GA-sequences [1] shared chains of tetra-GA-motifs and contained upstream poly(A)-segments. Although not integral parts of them, Alu-elements were found immediately upstream of all human and chimpanzee GA-sequences with an upstream poly(A)-segment. The article hypothesizes that genome navigation uses these properties of GA-sequences in the following way. (1) Poly(A) binding proteins interact with the upstream poly(A)-segments and arrange adjacent GA-sequences side-by-side ('GA-ribbon'), while folding the intervening DNA sequences between them into loops ('associated DNA-loops'). (2) Genome navigation uses the GA-ribbon as a search path for specific target genes that is up to 730-fold shorter than the full-length chromosome. (3) As to the specificity of the search, each molecule of a target protein is assumed to catalyze the formation of specific oligomers from a set of transcription factors that recognize tetra-GA-motifs. Their specific combinations of tetra-GA motifs are assumed to be present in the particular GA-sequence whose associated loop contains the gene for the target protein. As long as the target protein is abundant in the cell it produces sufficient numbers of such oligomers which bind to their specific GA-sequences and, thereby, inhibit locally the transcription of the target protein in the associated loop. However, if the amount of target protein drops below a certain threshold, the resultant reduction of specific oligomers leaves the corresponding GA-sequence 'denuded'. In response, the associated DNA-loop releases its nucleosomes and allows transcription of the target protein to proceed. (4) The Alu-transcripts may help control the general background of protein synthesis proportional to the number of transcriptionally active associated loops, especially in stressed cells. (5) The model offers a new mechanism of co-regulation of protein synthesis based on the shared segments of different GA-sequences.

Show MeSH
Related in: MedlinePlus