The chromatin landscape of Drosophila: comparisons between species, sexes, and chromosomes
The chromatin landscape of Drosophila: comparisons between species, sexes, and chromosomes
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DOI：
10.1101/gr.172155.114
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发表时间：
2014-07-01
期刊：
影响因子：
7
通讯作者：
Bachtrog, Doris
中科院分区：
文献类型：
--
作者：
Brown, Emily J.;Bachtrog, Doris
染色质景观是基因调控的关键，但人们对它在性别或物种之间的差异知之甚少。在这里，我们研究了性染色体年轻的物种米兰达果蝇的性别特异性染色质景观，并将其与黑腹果蝇进行了比较。我们分析了米兰达线虫雌雄幼虫的六种组蛋白修饰(H3K4me1、H3K4me3、H3K36me3、H4K16ac、H3K27me3和H3K9me2)，并定义了七种具有生物学意义的染色质状态，它们对转录和沉默基因、重复元件、管家和组织特异性基因显示了不同的富集性。活跃和抑制染色质状态的全基因组分布在男性和女性之间是不同的。在雄性中，由于半合子X的剂量补偿，相对于雌性，活性染色质在X上丰富。此外，与雌性相比，雄性基因组中较小部分的常染色质处于抑制染色质状态。然而，性别特定的染色质状态似乎不能解释基因的性别偏见表达。总体而言，雄性和雌性D.Miranda之间对染色质状态的保守与D.Miranda和D.Blackogaster之间的保守相当，后者在30年前出现了分歧。活性染色质状态在物种间高度保守，而异染色质则表现出非常低的保守水平。染色质图谱的差异导致了物种之间的表达差异，在两个物种中，类似于26%的不同染色质状态的基因表现出物种特异性或物种偏见的表达，大约是零预期的三倍。我们的数据表明，男性的异形性染色体(即一个高转录的X和一个失活的Y)可能有助于活跃和抑制染色质标记在染色体和性别之间的全球重新分配。
The chromatin landscape is key for gene regulation, but little is known about how it differs between sexes or between species. Here, we study the sex-specific chromatin landscape of Drosophila miranda, a species with young sex chromosomes, and compare it with Drosophila melanogaster. We analyze six histone modifications in male and female larvae of D. miranda (H3K4me1, H3K4me3, H3K36me3, H4K16ac, H3K27me3, and H3K9me2), and define seven biologically meaningful chromatin states that show different enrichments for transcribed and silent genes, repetitive elements, housekeeping, and tissue-specific genes. The genome-wide distribution of both active and repressive chromatin states differs between males and females. In males, active chromatin is enriched on the X, relative to females, due to dosage compensation of the hemizygous X. Furthermore, a smaller fraction of the euchromatic portion of the genome is in a repressive chromatin state in males relative to females. However, sex-specific chromatin states appear not to explain sex-biased expression of genes. Overall, conservation of chromatin states between male and female D. miranda is comparable to conservation between D. miranda and D. melanogaster, which diverged >30MY ago. Active chromatin states are more highly conserved across species, while heterochromatin shows very low levels of conservation. Divergence in chromatin profiles contributes to expression divergence between species, with similar to 26% of genes in different chromatin states in the two species showing species-specific or species-biased expression, an enrichment of approximately threefold over null expectation. Our data suggest that heteromorphic sex chromosomes in males (that is, a hypertranscribed X and an inactivated Y) may contribute to global redistribution of active and repressive chromatin marks between chromosomes and sexes.