Replication-dependent histone genes are actively transcribed in differentiating and aging retinal neurons

In the mammalian genome, each histone family contains multiple replication-dependent paralogs, which are found in clusters where their transcription is thought to be coupled to the cell cycle. Here, we wanted to interrogate the transcriptional regulation of these paralogs during retinal development and aging. We employed deep sequencing, quantitative PCR, in situ hybridization (ISH), and microarray analysis, which revealed that replication-dependent histone genes were not only transcribed in progenitor cells but also in differentiating neurons. Specifically, by ISH analysis we found that different histone genes were actively transcribed in a subset of neurons between postnatal day 7 and 14. Interestingly, within a histone family, not all paralogs were transcribed at the same level during retinal development. For example, expression of Hist1h1b was higher embryonically, while that of Hist1h1c was higher postnatally. Finally, expression of replication-dependent histone genes was also observed in the aging retina. Moreover, transcription of replication-dependent histones was independent of rapamycin-mediated mTOR pathway inactivation. Overall, our data suggest the existence of variant nucleosomes produced by the differential expression of the replication-dependent histone genes across retinal development. Also, the expression of a subset of replication-dependent histone isotypes in senescent neurons warrants re-examining these genes as “replication-dependent.” Thus, our findings underscore the importance of understanding the transcriptional regulation of replication-dependent histone genes in the maintenance and functioning of neurons.

在哺乳动物基因组中，每个组蛋白家族均包含多个复制依赖性同源基因，这些基因在转录上被认为与细胞周期相偶联的簇中存在。本研究旨在探究这些同源基因在视网膜发育和衰老过程中的转录调控。我们采用了深度测序、定量PCR、原位杂交（ISH）和微阵列分析等技术，揭示了复制依赖性组蛋白基因不仅在前体细胞中转录，而且也在分化神经元中表达。具体而言，通过ISH分析我们发现，在出生后第7天至第14天之间，部分神经元中不同组蛋白基因处于活跃转录状态。有趣的是，在组蛋白家族内部，并非所有同源基因在视网膜发育过程中的转录水平均相同。例如，Hist1h1b的表达在胚胎期较高，而Hist1h1c的表达则在出生后较高。最终，复制依赖性组蛋白基因的表达也见于衰老的视网膜中。此外，复制依赖性组蛋白的转录与雷帕霉素介导的mTOR通路失活无关。总体而言，我们的数据表明，在视网膜发育过程中，复制依赖性组蛋白基因的差异表达产生了变异性核小体。同时，衰老神经元中复制依赖性组蛋白亚型的表达要求重新审视这些基因是否确实为“复制依赖性”。因此，我们的研究强调了理解复制依赖性组蛋白基因转录调控对于维持和神经元功能的重要性。（In the mammalian genome, each histone family contains multiple replication-dependent paralogs, which are found in clusters where their transcription is thought to be coupled to the cell cycle. Here, we wanted to interrogate the transcriptional regulation of these paralogs during retinal development and aging. We employed deep sequencing, quantitative PCR, in situ hybridization (ISH), and microarray analysis, which revealed that replication-dependent histone genes were not only transcribed in progenitor cells but also in differentiating neurons. Specifically, by ISH analysis we found that different histone genes were actively transcribed in a subset of neurons between postnatal day 7 and 14. Interestingly, within a histone family, not all paralogs were transcribed at the same level during retinal development. For example, expression of Hist1h1b was higher embryonically, while that of Hist1h1c was higher postnatally. Finally, expression of replication-dependent histone genes was also observed in the aging retina. Moreover, transcription of replication-dependent histones was independent of rapamycin-mediated mTOR pathway inactivation. Overall, our data suggest the existence of variant nucleosomes produced by the differential expression of the replication-dependent histone genes across retinal development. Also, the expression of a subset of replication-dependent histone isotypes in senescent neurons warrants re-examining these genes as “replication-dependent.” Thus, our findings underscore the importance of understanding the transcriptional regulation of replication-dependent histone genes in the maintenance and functioning of neurons.）