Limits...
Ancestral Chromatin Configuration Constrains Chromatin Evolution on Differentiating Sex Chromosomes in Drosophila.

Zhou Q, Bachtrog D - PLoS Genet. (2015)

Bottom Line: We show that the neo-sex chromosomes formed <1 million years ago, but nearly 60% of neo-Y linked genes have already become non-functional.Expression levels are generally lower for the neo-Y alleles relative to their neo-X homologs, and the silencing heterochromatin mark H3K9me2, but not H3K9me3, is significantly enriched on silenced neo-Y genes.Yet, neo-X genes are transcriptionally more active in males, relative to females, suggesting the evolution of incipient dosage compensation on the neo-X.

View Article: PubMed Central - PubMed

Affiliation: Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America.

ABSTRACT
Sex chromosomes evolve distinctive types of chromatin from a pair of ancestral autosomes that are usually euchromatic. In Drosophila, the dosage-compensated X becomes enriched for hyperactive chromatin in males (mediated by H4K16ac), while the Y chromosome acquires silencing heterochromatin (enriched for H3K9me2/3). Drosophila autosomes are typically mostly euchromatic but the small dot chromosome has evolved a heterochromatin-like milieu (enriched for H3K9me2/3) that permits the normal expression of dot-linked genes, but which is different from typical pericentric heterochromatin. In Drosophila busckii, the dot chromosomes have fused to the ancestral sex chromosomes, creating a pair of 'neo-sex' chromosomes. Here we collect genomic, transcriptomic and epigenomic data from D. busckii, to investigate the evolutionary trajectory of sex chromosomes from a largely heterochromatic ancestor. We show that the neo-sex chromosomes formed <1 million years ago, but nearly 60% of neo-Y linked genes have already become non-functional. Expression levels are generally lower for the neo-Y alleles relative to their neo-X homologs, and the silencing heterochromatin mark H3K9me2, but not H3K9me3, is significantly enriched on silenced neo-Y genes. Despite rampant neo-Y degeneration, we find that the neo-X is deficient for the canonical histone modification mark of dosage compensation (H4K16ac), relative to autosomes or the compensated ancestral X chromosome, possibly reflecting constraints imposed on evolving hyperactive chromatin in an originally heterochromatic environment. Yet, neo-X genes are transcriptionally more active in males, relative to females, suggesting the evolution of incipient dosage compensation on the neo-X. Our data show that Y degeneration proceeds quickly after sex chromosomes become established through genomic and epigenetic changes, and are consistent with the idea that the evolution of sex-linked chromatin is influenced by its ancestral configuration.

No MeSH data available.


Related in: MedlinePlus

Dosage compensation in male D. busckii.A. Immunostaining of male and female D. busckii polytene chromosomes with MSL-2 antibody. The neo-X / X chromosome is marked with an arrow, and the male X shows binding of MSL-2 protein. B. Comparison of normalized log2 enrichment level of H4K16ac across genes on different chromosomes. Enrichment level of H4K16ac on X-linked genes (red) is significantly higher (Wilcoxon test, P<0.001) than on any other chromosomes, while neo-sex linked genes show a significantly lower enrichment level than autosomes (green), and there is no significant difference between the neo-X (orange) and neo-Y (blue) alleles. C. Enrichment level of H4K16ac is strongly correlated between orthologous genes of D. melanogaster and D. busckii. Genes are color-coded according to chromosomal location. D-E. Metagene profiles of H4K16ac over active (D.) and silent (E.) genes. For neo-sex genes, we defined the expression status by the expression level of neo-X alleles. Note that H4K16ac is significantly more enriched at active X-linked genes, and shows a characteristic 3’ binding bias.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4482674&req=5

pgen.1005331.g005: Dosage compensation in male D. busckii.A. Immunostaining of male and female D. busckii polytene chromosomes with MSL-2 antibody. The neo-X / X chromosome is marked with an arrow, and the male X shows binding of MSL-2 protein. B. Comparison of normalized log2 enrichment level of H4K16ac across genes on different chromosomes. Enrichment level of H4K16ac on X-linked genes (red) is significantly higher (Wilcoxon test, P<0.001) than on any other chromosomes, while neo-sex linked genes show a significantly lower enrichment level than autosomes (green), and there is no significant difference between the neo-X (orange) and neo-Y (blue) alleles. C. Enrichment level of H4K16ac is strongly correlated between orthologous genes of D. melanogaster and D. busckii. Genes are color-coded according to chromosomal location. D-E. Metagene profiles of H4K16ac over active (D.) and silent (E.) genes. For neo-sex genes, we defined the expression status by the expression level of neo-X alleles. Note that H4K16ac is significantly more enriched at active X-linked genes, and shows a characteristic 3’ binding bias.

Mentions: To evaluate the mechanism of dosage compensation in D. busckii, we utilized both bioinformatics and experimental approaches. First, we annotated the intact open reading frames and gene expression patterns of the key MSL complex proteins and non-coding RNAs, as well as the POF protein and a duplicated copy of POF found in D. busckii. Transcriptome profiling revealed that MSL-2, POF, roX-1 and roX-2 non-coding RNA all exhibit male-biased expression patterns (S9 Fig), similar to their orthologs in D. melanogaster. We further performed immunostaining with a new D. melanogaster MSL-2 antibody, and find weak but male-specific staining of the X chromosome in D. busckii (Fig 5A). In D. melanogaster, the MSL complex catalyzes the deposition of the activating histone mark H4K16ac, and ChIP-seq profiling in D. busckii clearly reveals that H4K16ac is significantly enriched on the ancestral male X relative to autosomes and the neo-sex chromosomes (Wilcoxon test, P<2.2e-16, Fig 5B). This is consistent with MSL-dependent dosage compensation in D. busckii, and orthologous X-linked genes show a significant correlation in their enrichment levels of H4K16ac between larvae samples of D. busckii and D. melanogaster (Spearman’s rank correlation coefficient: 0.36, P<2.2e-16; Fig 5C), suggesting that a similar set of genes is being targeted by the dosage compensation complex on the X in both species. Finally, our metagene analysis of the H4K16ac mark reveals a distinctive 3’ bias specifically over active X-linked gene bodies (Fig 5D), consistent with the pattern mediated by the MSL complex in D. melanogaster [46,48]. Taken together, these results suggest that D. busckii shares the same mechanism of dosage compensation for the ancestral X chromosome as D. melanogaster, despite their distant phylogenetic relationship (Fig 2) and their different sex chromosome karyotype.


Ancestral Chromatin Configuration Constrains Chromatin Evolution on Differentiating Sex Chromosomes in Drosophila.

Zhou Q, Bachtrog D - PLoS Genet. (2015)

Dosage compensation in male D. busckii.A. Immunostaining of male and female D. busckii polytene chromosomes with MSL-2 antibody. The neo-X / X chromosome is marked with an arrow, and the male X shows binding of MSL-2 protein. B. Comparison of normalized log2 enrichment level of H4K16ac across genes on different chromosomes. Enrichment level of H4K16ac on X-linked genes (red) is significantly higher (Wilcoxon test, P<0.001) than on any other chromosomes, while neo-sex linked genes show a significantly lower enrichment level than autosomes (green), and there is no significant difference between the neo-X (orange) and neo-Y (blue) alleles. C. Enrichment level of H4K16ac is strongly correlated between orthologous genes of D. melanogaster and D. busckii. Genes are color-coded according to chromosomal location. D-E. Metagene profiles of H4K16ac over active (D.) and silent (E.) genes. For neo-sex genes, we defined the expression status by the expression level of neo-X alleles. Note that H4K16ac is significantly more enriched at active X-linked genes, and shows a characteristic 3’ binding bias.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4482674&req=5

pgen.1005331.g005: Dosage compensation in male D. busckii.A. Immunostaining of male and female D. busckii polytene chromosomes with MSL-2 antibody. The neo-X / X chromosome is marked with an arrow, and the male X shows binding of MSL-2 protein. B. Comparison of normalized log2 enrichment level of H4K16ac across genes on different chromosomes. Enrichment level of H4K16ac on X-linked genes (red) is significantly higher (Wilcoxon test, P<0.001) than on any other chromosomes, while neo-sex linked genes show a significantly lower enrichment level than autosomes (green), and there is no significant difference between the neo-X (orange) and neo-Y (blue) alleles. C. Enrichment level of H4K16ac is strongly correlated between orthologous genes of D. melanogaster and D. busckii. Genes are color-coded according to chromosomal location. D-E. Metagene profiles of H4K16ac over active (D.) and silent (E.) genes. For neo-sex genes, we defined the expression status by the expression level of neo-X alleles. Note that H4K16ac is significantly more enriched at active X-linked genes, and shows a characteristic 3’ binding bias.
Mentions: To evaluate the mechanism of dosage compensation in D. busckii, we utilized both bioinformatics and experimental approaches. First, we annotated the intact open reading frames and gene expression patterns of the key MSL complex proteins and non-coding RNAs, as well as the POF protein and a duplicated copy of POF found in D. busckii. Transcriptome profiling revealed that MSL-2, POF, roX-1 and roX-2 non-coding RNA all exhibit male-biased expression patterns (S9 Fig), similar to their orthologs in D. melanogaster. We further performed immunostaining with a new D. melanogaster MSL-2 antibody, and find weak but male-specific staining of the X chromosome in D. busckii (Fig 5A). In D. melanogaster, the MSL complex catalyzes the deposition of the activating histone mark H4K16ac, and ChIP-seq profiling in D. busckii clearly reveals that H4K16ac is significantly enriched on the ancestral male X relative to autosomes and the neo-sex chromosomes (Wilcoxon test, P<2.2e-16, Fig 5B). This is consistent with MSL-dependent dosage compensation in D. busckii, and orthologous X-linked genes show a significant correlation in their enrichment levels of H4K16ac between larvae samples of D. busckii and D. melanogaster (Spearman’s rank correlation coefficient: 0.36, P<2.2e-16; Fig 5C), suggesting that a similar set of genes is being targeted by the dosage compensation complex on the X in both species. Finally, our metagene analysis of the H4K16ac mark reveals a distinctive 3’ bias specifically over active X-linked gene bodies (Fig 5D), consistent with the pattern mediated by the MSL complex in D. melanogaster [46,48]. Taken together, these results suggest that D. busckii shares the same mechanism of dosage compensation for the ancestral X chromosome as D. melanogaster, despite their distant phylogenetic relationship (Fig 2) and their different sex chromosome karyotype.

Bottom Line: We show that the neo-sex chromosomes formed <1 million years ago, but nearly 60% of neo-Y linked genes have already become non-functional.Expression levels are generally lower for the neo-Y alleles relative to their neo-X homologs, and the silencing heterochromatin mark H3K9me2, but not H3K9me3, is significantly enriched on silenced neo-Y genes.Yet, neo-X genes are transcriptionally more active in males, relative to females, suggesting the evolution of incipient dosage compensation on the neo-X.

View Article: PubMed Central - PubMed

Affiliation: Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America.

ABSTRACT
Sex chromosomes evolve distinctive types of chromatin from a pair of ancestral autosomes that are usually euchromatic. In Drosophila, the dosage-compensated X becomes enriched for hyperactive chromatin in males (mediated by H4K16ac), while the Y chromosome acquires silencing heterochromatin (enriched for H3K9me2/3). Drosophila autosomes are typically mostly euchromatic but the small dot chromosome has evolved a heterochromatin-like milieu (enriched for H3K9me2/3) that permits the normal expression of dot-linked genes, but which is different from typical pericentric heterochromatin. In Drosophila busckii, the dot chromosomes have fused to the ancestral sex chromosomes, creating a pair of 'neo-sex' chromosomes. Here we collect genomic, transcriptomic and epigenomic data from D. busckii, to investigate the evolutionary trajectory of sex chromosomes from a largely heterochromatic ancestor. We show that the neo-sex chromosomes formed <1 million years ago, but nearly 60% of neo-Y linked genes have already become non-functional. Expression levels are generally lower for the neo-Y alleles relative to their neo-X homologs, and the silencing heterochromatin mark H3K9me2, but not H3K9me3, is significantly enriched on silenced neo-Y genes. Despite rampant neo-Y degeneration, we find that the neo-X is deficient for the canonical histone modification mark of dosage compensation (H4K16ac), relative to autosomes or the compensated ancestral X chromosome, possibly reflecting constraints imposed on evolving hyperactive chromatin in an originally heterochromatic environment. Yet, neo-X genes are transcriptionally more active in males, relative to females, suggesting the evolution of incipient dosage compensation on the neo-X. Our data show that Y degeneration proceeds quickly after sex chromosomes become established through genomic and epigenetic changes, and are consistent with the idea that the evolution of sex-linked chromatin is influenced by its ancestral configuration.

No MeSH data available.


Related in: MedlinePlus