The temporal order of DNA replication [replication timing (RT)] is correlated with chromatin modifications and three-dimensional genome architecture; however, causal links have not been established, largely because of an inability to manipulate the global RT program. We show that loss of RIF1 causes near-complete elimination of the RT program by increasing heterogeneity between individual cells. RT changes are coupled with widespread alterations in chromatin modifications and genome compartmentalization. Conditional depletion of RIF1 causes replication-dependent disruption of histone modifications and alterations in genome architecture. These effects were magnified with successive cycles of altered RT. These results support models in which the timing of chromatin replication and thus assembly plays a key role in maintaining the global epigenetic state.

5 6DNA is replicated in a defined temporal order termed the replication timing (RT) program. RT is 2 7 spatially segregated in the nucleus with early/late replication corresponding to Hi-C A/B 2 8 chromatin compartments, respectively. Early replication is also associated with active histone 2 9 modifications and transcriptional permissiveness. However, the mechanistic interplay between 3 0 RT, chromatin state, and genome compartmentalization is largely unknown. Here we report that 3 1RT is central to epigenome maintenance and compartmentalization in both human embryonic 3 2 stem cells (hESCs) and cancer cell line HCT116. Knockout (KO) of the conserved RT control 3 3 factor RIF1, rather than causing discrete RT switches as previously suspected, lead to 3 4 dramatically increased cell to cell heterogeneity of RT genome wide, despite RIF1's enrichment 3 5 in late replicating chromatin. RIF1 KO hESCs have a nearly random RT program, unlike all prior 3 6 RIF1 KO cells, including HCT116, which show localized alterations. Regions that retain RT, 3 7 which are prevalent in HCT116 but rare in hESCs, consist of large H3K9me3 domains revealing 3 8 two independent mechanisms of RT regulation that are used to different extents in different cell 3 9 types. RIF1 KO results in a striking genome wide downregulation of H3K27ac peaks and 4 0 enrichment of H3K9me3 at large domains that remain late replicating, while H3K27me3 and 4 1H3K4me3 are re-distributed genome wide in a cell type specific manner. These histone 4 2 modification changes coincided with global reorganization of genome compartments, 4 3 transcription changes and a genome wide strengthening of TAD structures. Inducible 4 4 degradation of RIF1 revealed that disruption of RT is upstream of genome compartmentalization 4 5 changes. Our findings demonstrate that disruption of RT leads to widespread epigenetic mis-4 6 regulation, supporting previously speculative models in which the timing of chromatin assembly 4 7 at the replication fork plays a key role in maintaining the global epigenetic state, which in turn 4 8 5 8 chromatin correspond to A-and B-compartments respectively as defined by high throughput 5 9chromatin conformation capture (Hi-C) (2). Despite these close correlations, the mechanistic link 6 0 between RT and the accurate maintenance of chromatin through cell cycles remains elusive. 1Prior work has shown that histones and their modifications are both recycled from parental 6 2 chromatin and added and modified de novo after passage of the replication fork with different 6 3 chromatin states showing differing dynamics of reassembly (3, 4). It has long been 6 4 hypothesized that RT influences chromatin maintenance. Indeed, microinjection of plasmids into 6 5 mammalian nuclei revealed that plasmids replicated in early S phase were decorated with 6 6 acetylated histones, while those replicated later in S phase were devoid of acetylated histones 6 7 (5). However, there is still no direct evidence implicating RT in epigenetic state maintenance, 6 8 largely due to t...

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Polymorphic integrations of endogenous retroviruses (ERVs) have been previously detected in mouse and human genomes. While most are inert, a subset can influence the activity of the host genes. However, the molecular mechanism underlying how such elements affect the epigenome and transcriptome and their roles in driving intra-specific variation remain unclear. Here, by utilizing wildtype murine embryonic stem cells (mESCs) derived from distinct genetic backgrounds, we discover a polymorphic MMERGLN (GLN) element capable of regulating H3K27ac enrichment and transcription of neighboring loci. We demonstrate that this polymorphic element can enhance the neighboring Klhdc4 gene expression in cis, which alters the activity of downstream stress response genes. These results suggest that the polymorphic ERV-derived cis-regulatory element contributes to differential phenotypes from stimuli between mouse strains. Moreover, we identify thousands of potential polymorphic ERVs in mESCs, a subset of which show an association between proviral activity and nearby chromatin states and transcription. Overall, our findings elucidate the mechanism of how polymorphic ERVs can shape the epigenome and transcriptional networks that give rise to phenotypic divergence between individuals.

During pregnancy the maternal–fetal interface plays vital roles in fetal development. Its disruption is frequently found in pregnancy complications. Recent studies show increased incidences of adverse pregnancy outcomes in patients with COVID-19; however, the mechanism remains unclear. Here we analysed the molecular impacts of SARS-CoV-2 infection on the maternal–fetal interface. Generating bulk and single-nucleus transcriptomic and epigenomic profiles from patients with COVID-19 and control samples, we discovered aberrant immune activation and angiogenesis patterns in distinct cells from patients. Surprisingly, retrotransposons were also dysregulated in specific cell types. Notably, reduced enhancer activities of LTR8B elements were functionally linked to the downregulation of pregnancy-specific glycoprotein genes in syncytiotrophoblasts. Our findings revealed that SARS-CoV-2 infection induced substantial changes to the epigenome and transcriptome at the maternal–fetal interface, which may be associated with pregnancy complications.

Transposable elements (TEs) are mobile genetic elements that can randomly integrate into other genomic sites. They have successfully replicated and now occupy around 40% of the total DNA sequence in humans. TEs in the genome have a complex relationship with the host cell, being both potentially deleterious and advantageous at the same time. Only a tiny minority of TEs are still capable of transposition, yet their fossilized sequence fragments are thought to be involved in various molecular processes, such as gene transcriptional activity, RNA stability and subcellular localization, and chromosomal architecture. TEs have also been implicated in biological processes, although it is often hard to reveal cause from correlation due to formidable technical issues in analyzing TEs. In this review, we compare and contrast two views of TE activity: one in the pluripotent state, where TEs are broadly beneficial, or at least mechanistically useful, and a second state in human disease, where TEs are uniformly considered harmful.

During pregnancy, the maternal-fetal interface plays vital roles in fetal development. Its disruption is frequently found in pregnancy complications. Recent works show increased incidences of adverse pregnancy outcomes in COVID-19 patients; however, the mechanism remains unclear. Here, we analyzed the molecular impacts of SARS-CoV-2 infection on the maternal-fetal interface. Generating bulk and single-nucleus transcriptomic and epigenomic profiles from COVID-19 patients and control samples, we discovered aberrant immune activation and angiogenesis patterns in patients. Surprisingly, retrotransposons were dysregulated in specific cell types. Notably, reduced enhancer activities of LTR8B elements were functionally linked to the downregulation of Pregnancy-Specific Glycoprotein genes in syncytiotrophoblasts. Our findings revealed that SARS-CoV-2 infection induced significant changes to the epigenome and transcriptome at the maternal-fetal interface, which may be associated with pregnancy complications.

The chlorine-based organometallic halide perovskite (Cl-OHP) film with a (001)-preferred orientation and good crystallization has been synthesized by a hybrid sequential deposition process. The photoluminescence and absorption spectra of the Cl-OHP film in the blue light region have been investigated at operating temperatures ranging from 10 to 350 K. The Cl-OHP film shows a strong exciton-related emission of which the exciton binding energies at low temperature and high temperature are 136 meV and 41 meV, respectively. It is found that the blueshift from excitonic luminescence is initially observed at temperature below 175 K, and then, the redshift occurs from 175 to 350 K. Meanwhile, the bandgap of the Cl-OHP film widens with the increase in operating temperature. The nonmonotonous shifts on the emission peak energy are attributed to the competition between the Stokes effect and bandgap widening. This should contribute to the understanding of photophysical processes in Cl-OHP materials and devices.