Single-cell RNA-sequencing reveals pre-meiotic X-chromosome dosage compensation in Drosophila testis.
Single-cell RNA-sequencing reveals pre-meiotic X-chromosome dosage compensation in Drosophila testis.
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DOI：
10.1371/journal.pgen.1009728
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发表时间：
2021-08
期刊：
影响因子：
4.5
通讯作者：
Zhao L
中科院分区：
文献类型：
--
作者：
Witt E;Shao Z;Hu C;Krause HM;Zhao L
剂量补偿使XY雄性和XX雌性之间的X连锁表达相等。在雄性果蝇中，X染色体的表达水平增加了大约两倍，以补偿他们单一的X染色体。在睾丸中，剂量补偿被认为在减数分裂过程中停止；然而，所产生的转录抑制的时间和程度很难与每条染色体的整体减数分裂下调分开。为了解决这个问题，我们分析了两个黑腹果蝇品系的睾丸单细胞RNA测序(scRNA-seq)数据。我们发现有证据表明，在体细胞和减数分裂前细胞中，X染色体的转录活性与常染色体相同，而在减数分裂和减数分裂后的细胞中，X染色体的转录活性低于常染色体。在经历剂量补偿的细胞中，靠近男性特异致死染色质进入位点(CES)与X染色体转录增加相关。我们通过scRNA-seq和RNA-FISH发现大多数msl基因MLE、roX1和roX2的胚系表达水平很低或检测不到，没有胚系核roX1/2定位的证据。我们的结果表明，尽管果蝇睾丸的体细胞和减数分裂前生殖细胞存在剂量补偿，但可能有非规范因素参与了剂量补偿机制。单细胞表达模式和检测基因的丰富统计数据可以在我们的数据库中交互探索：https://zhao.labapps.rockefeller.edu/gene-expr/.雄性果蝇需要提高其单个X染色体的基因表达，才能与雌性果蝇持平，雌性果蝇有两条X染色体。在这个被称为剂量补偿的过程中，剂量补偿复合体结合到基因组染色质进入部位，并上调附近的基因表达。这一过程被认为仅限于体细胞。利用单细胞RNA-SEQ数据，我们发现果蝇睾丸中的某些生殖细胞类型显示出与常染色体相似的X染色体表达，这意味着剂量补偿活性。在这些细胞类型中，我们发现了靠近染色质进入部位的基因比远离染色质进入部位的基因表达更高的证据，这是剂量补偿的额外证据。在没有剂量补偿证据的细胞类型中，我们没有发现染色质进入位点活性的证据。有趣的是，我们发现几乎没有证据表明，使用RNA-FISH和scRNA-seq的剂量补偿复合体中的大多数基因都有表达。这表明我们观察到的减数分裂前剂量补偿可能是由非典型机制介导的。这些发现为我们对性染色体的理解提供了新的见解。
Dosage compensation equalizes X-linked expression between XY males and XX females. In male fruit flies, expression levels of the X-chromosome are increased approximately two-fold to compensate for their single X chromosome. In testis, dosage compensation is thought to cease during meiosis; however, the timing and degree of the resulting transcriptional suppression is difficult to separate from global meiotic downregulation of each chromosome. To address this, we analyzed testis single-cell RNA-sequencing (scRNA-seq) data from two Drosophila melanogaster strains. We found evidence that the X chromosome is equally transcriptionally active as autosomes in somatic and pre-meiotic cells, and less transcriptionally active than autosomes in meiotic and post-meiotic cells. In cells experiencing dosage compensation, close proximity to MSL (male-specific lethal) chromatin entry sites (CES) correlates with increased X chromosome transcription. We found low or undetectable levels of germline expression of most msl genes, mle, roX1 and roX2 via scRNA-seq and RNA-FISH, and no evidence of germline nuclear roX1/2 localization. Our results suggest that, although dosage compensation occurs in somatic and pre-meiotic germ cells in Drosophila testis, there might be non-canonical factors involved in the dosage compensation mechanism. The single-cell expression patterns and enrichment statistics of detected genes can be explored interactively in our database: https://zhao.labapps.rockefeller.edu/gene-expr/. Male flies need to boost gene expression from their single X chromosome to equal that of females, which have two X chromosomes. In this process, called dosage compensation, the dosage compensation complex binds to genomic chromatin entry sites and upregulates gene expression nearby. This process was thought to be restricted to somatic cells. Using single-cell RNA-seq data, we found that certain germ cell types in the Drosophila testis show X chromosome expression similar to that of the autosomes, implying dosage compensation activity. In these cell types, we found evidence that genes near a chromatin entry site are more highly expressed than genes farther away, which is additional evidence of dosage compensation. In cell types without evidence of dosage compensation, we saw no evidence of chromatin entry site activity. Interestingly, we found little evidence of expression of most genes from the dosage compensation complex using both RNA-FISH and scRNA-seq. This suggests that our observed pre-meiotic dosage compensation is likely to be mediated by a noncanonical mechanism. These findings add new insight into our understanding of sex chromosomes.
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影响因子：
64.5
作者：
Alekseyenko AA;Peng S;Larschan E;Gorchakov AA;Lee OK;Kharchenko P;McGrath SD;Wang CI;Mardis ER;Park PJ;Kuroda MI
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作者：
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作者：
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通讯作者：
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