Limits...
Comparative Genomics Reveals Chd1 as a Determinant of Nucleosome Spacing in Vivo.

Hughes AL, Rando OJ - G3 (Bethesda) (2015)

Bottom Line: In contrast, the K. lactis gene encoding the ATP-dependent remodeler Chd1 was found to direct longer internucleosomal spacing in S. cerevisiae, establishing that this remodeler is partially responsible for the relatively long internucleosomal spacing observed in K. lactis.By analyzing several chimeric proteins, we find that sequence differences that contribute to the spacing activity of this remodeler are dispersed throughout the coding sequence, but that the strongest spacing effect is linked to the understudied N-terminal end of Chd1.Taken together, our data find a role for sequence evolution of a chromatin remodeler in establishing quantitative aspects of the chromatin landscape in a species-specific manner.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605.

No MeSH data available.


Isw1a and Hho1 are not responsible for nucleosome spacing differences between S. cerevisiae and K. lactis. (A) Genome-wide nucleosome mapping data are shown for all S. cerevisiae genes, aligned by the transcription start site (TSS). Data are shown for wild-type yeast, yeast lacking the HHO1 gene, and hho1Δ yeast expressing the HHO1 ortholog from K. lactis. (B) As in (A), but for double mutations in ISW1 and IOC3. For all nucleosome mapping data in this figure and below, the y-axis shows normalized nucleosome occupancy, with a value of 1 being the genome-wide average occupancy of MNase-Seq reads. Note that data for BY4741 here are from an underdigested MNase sample, resulting in differences in nucleosome occupancy, but no effect on linker lengths.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4555225&req=5

fig1: Isw1a and Hho1 are not responsible for nucleosome spacing differences between S. cerevisiae and K. lactis. (A) Genome-wide nucleosome mapping data are shown for all S. cerevisiae genes, aligned by the transcription start site (TSS). Data are shown for wild-type yeast, yeast lacking the HHO1 gene, and hho1Δ yeast expressing the HHO1 ortholog from K. lactis. (B) As in (A), but for double mutations in ISW1 and IOC3. For all nucleosome mapping data in this figure and below, the y-axis shows normalized nucleosome occupancy, with a value of 1 being the genome-wide average occupancy of MNase-Seq reads. Note that data for BY4741 here are from an underdigested MNase sample, resulting in differences in nucleosome occupancy, but no effect on linker lengths.

Mentions: Genome-wide nucleosome mapping in S. cerevisiae strains lacking these factors, or carrying the K. lactis orthologs, revealed no effect of histone H1 or of the Isw1a complex in establishment of nucleosome spacing in vivo (Figure 1). For Isw1, we generated deletion and swap strains for the ATPase subunit Isw1 in combination with Ioc3 (which binds Isw1 to form the Isw1a complex). Deletion of either the Isw1a complex or histone H1 does not have a general effect on chromatin structure, particularly with regard to internucleosomal spacing. Swap strains carrying the K. lactis orthologs of these factors do not exhibit increased nucleosome spacing as assayed by genome-wide nucleosome mapping, suggesting that sequence differences in these proteins are not responsible for the difference in average linker length between these species (or that the K. lactis orthologs are not functional in S. cerevisiae; see Discussion).


Comparative Genomics Reveals Chd1 as a Determinant of Nucleosome Spacing in Vivo.

Hughes AL, Rando OJ - G3 (Bethesda) (2015)

Isw1a and Hho1 are not responsible for nucleosome spacing differences between S. cerevisiae and K. lactis. (A) Genome-wide nucleosome mapping data are shown for all S. cerevisiae genes, aligned by the transcription start site (TSS). Data are shown for wild-type yeast, yeast lacking the HHO1 gene, and hho1Δ yeast expressing the HHO1 ortholog from K. lactis. (B) As in (A), but for double mutations in ISW1 and IOC3. For all nucleosome mapping data in this figure and below, the y-axis shows normalized nucleosome occupancy, with a value of 1 being the genome-wide average occupancy of MNase-Seq reads. Note that data for BY4741 here are from an underdigested MNase sample, resulting in differences in nucleosome occupancy, but no effect on linker lengths.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4555225&req=5

fig1: Isw1a and Hho1 are not responsible for nucleosome spacing differences between S. cerevisiae and K. lactis. (A) Genome-wide nucleosome mapping data are shown for all S. cerevisiae genes, aligned by the transcription start site (TSS). Data are shown for wild-type yeast, yeast lacking the HHO1 gene, and hho1Δ yeast expressing the HHO1 ortholog from K. lactis. (B) As in (A), but for double mutations in ISW1 and IOC3. For all nucleosome mapping data in this figure and below, the y-axis shows normalized nucleosome occupancy, with a value of 1 being the genome-wide average occupancy of MNase-Seq reads. Note that data for BY4741 here are from an underdigested MNase sample, resulting in differences in nucleosome occupancy, but no effect on linker lengths.
Mentions: Genome-wide nucleosome mapping in S. cerevisiae strains lacking these factors, or carrying the K. lactis orthologs, revealed no effect of histone H1 or of the Isw1a complex in establishment of nucleosome spacing in vivo (Figure 1). For Isw1, we generated deletion and swap strains for the ATPase subunit Isw1 in combination with Ioc3 (which binds Isw1 to form the Isw1a complex). Deletion of either the Isw1a complex or histone H1 does not have a general effect on chromatin structure, particularly with regard to internucleosomal spacing. Swap strains carrying the K. lactis orthologs of these factors do not exhibit increased nucleosome spacing as assayed by genome-wide nucleosome mapping, suggesting that sequence differences in these proteins are not responsible for the difference in average linker length between these species (or that the K. lactis orthologs are not functional in S. cerevisiae; see Discussion).

Bottom Line: In contrast, the K. lactis gene encoding the ATP-dependent remodeler Chd1 was found to direct longer internucleosomal spacing in S. cerevisiae, establishing that this remodeler is partially responsible for the relatively long internucleosomal spacing observed in K. lactis.By analyzing several chimeric proteins, we find that sequence differences that contribute to the spacing activity of this remodeler are dispersed throughout the coding sequence, but that the strongest spacing effect is linked to the understudied N-terminal end of Chd1.Taken together, our data find a role for sequence evolution of a chromatin remodeler in establishing quantitative aspects of the chromatin landscape in a species-specific manner.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605.

No MeSH data available.