Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells

Abstract

Duplication of the genome in mammalian cells occurs in a defined temporal order referred to as its replication-timing (RT) program. RT changes dynamically during development, regulated in units of 400-800 kb referred to as replication domains (RDs). Changes in RT are generally coordinated with transcriptional competence and changes in subnuclear position. We generated genome-wide RT profiles for 26 distinct human cell types, including embryonic stem cell (hESC)-derived, primary cells and established cell lines representing intermediate stages of endoderm, mesoderm, ectoderm, and neural crest (NC) development. We identified clusters of RDs that replicate at unique times in each stage (RT signatures) and confirmed global consolidation of the genome into larger synchronously replicating segments during differentiation. Surprisingly, transcriptome data revealed that the well-accepted correlation between early replication and transcriptional activity was restricted to RT-constitutive genes, whereas two-thirds of the genes that switched RT during differentiation were strongly expressed when late replicating in one or more cell types. Closer inspection revealed that transcription of this class of genes was frequently restricted to the lineage in which the RT switch occurred, but was induced prior to a late-to-early RT switch and/or down-regulated after an early-to-late RT switch. Analysis of transcriptional regulatory networks showed that this class of genes contains strong regulators of genes that were only expressed when early replicating. These results provide intriguing new insight into the complex relationship between transcription and RT regulation during human development.

Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq

“…In human cells, this process typically lasts 8–10 hours 1 . Different regions of the genome replicate at different times during S phase, following a defined replication timing (RT) program 2–8 . The reader is referred to many recent reviews of RT in mammalian cells and its association with mutation rates 9 , chromatin and transcription 10–15 .…”

DNA replication origins—where do we begin?

“…Although still highly correlated on the megabase scale, at increased resolution, it is possible to find a significant number of smaller changes in replication timing that are developmentally regulated (Rivera-Mulia et al 2015) or linked to the underlying genotype (Koren et al 2014). For example, replication timing changes that occur during differentiation of mESCs typically involve the consolidation of smaller neighboring replication domains (Hiratani et al 2008).…”

Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips

“…Replication timing is associated with multiple different genomic and epigenetic features, including gene expression, chromatin accessibility, and the spatial organization of chromatin in the nucleus. In metazoans, replication timing is considered a functional readout of the many factors affecting large-scale chromatin structure (Rivera-Mulia et al, 2015;Rivera-Mulia and Gilbert, 2016). Recalling that the spatial arrangement of replication activities in maize nuclei is quite different from human cells (Bass et al, 2015;Savadel and Bass, 2017), it will be of particular interest to examine the extent to which maize replication timing is regulated by large-scale features such as chromatin domains, as opposed to local features such as hypersensitive sites.…”

“…To accomplish this task, higher eukaryotes organize the process both temporally and spatially so that replication initiates at multiple loci, or origins, distributed throughout the genome, with different origins becoming active at different times during S phase (Masai et al, 2010). In most higher eukaryotes, there is an association between early replication and euchromatic, transcriptionally active chromatin (Hatton et al, 1988;Hiratani et al, 2008;Lee et al, 2010;Ryba et al, 2010), though there are classes of genes that have a much weaker association with replication time and are developmentally regulated in humans and mice (Hiratani et al, 2008;Rivera-Mulia et al, 2015). Conversely, there is also a long established association between late replication and classical heterochromatin (Lima-de-Faria and Jaworska, 1968;Pryor et al, 1980), although there are a few exceptions (Kim et al, 2003).…”