A Dynamic Switch in the Replication Timing of Key Regulator Genes in Embryonic Stem Cells upon Neural Induction

Perry, Pascale; Sauer, Stephan P. A.; Billon, Noëlle; Richardson, William D.; Spivakov, Mikhail; Warnes, Gary; Livesey, Frederick J.; Merkenschlager, Matthias; Fisher, Amanda G.; Azuara, Véronique

doi:10.4161/cc.3.12.1346

Cited by 91 publications

(91 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Interestingly, HBO1 HAT, similar to TIP60, is able to acetylate all four lysines in histone H4 tail, although it localizes differently from Tip60 HAT (Doyon et al, 2006), suggesting that certain HATs may be more important in replication than in other chromatin-based processes such as transcription. In addition, a correlation between histone acetylation, transcriptional competence and DNA replication timing was also found in several studies using cells with different levels of pluripotency (Vogelauer et al, 2002;Zhang et al, 2002;Lin et al, 2003;Perry et al, 2004;Azuara et al, 2006). Different chromatin-based processes including transcription, replication and DNA repair require an open chromatin structure and are mediated by TRRAPcontaining HAT complexes, indicating that these chromatin modifiers regulate distinct and often conflicting processes.…”

Section: Replicationmentioning

confidence: 64%

“…In addition, one potential leucine zipper is located at 3403-3424, and may have a role in TRRAP-DNA interaction. The N-terminus region of the protein comprises a-helical motifs known as HEAT (huntingtin, elongation factor 3, a subunit of protein phosphatase 2A and TOR1) repeats that are likely to be critical sites for protein-protein interactions (Perry et al, 2004). Eight LXXLL motifs, usually found in transcriptional coactivators (Heery et al, 1997;Torchia et al, 1997), are distributed over this region.…”

Section: Trrap Is Conserved In Evolutionmentioning

confidence: 99%

“…Although the role of chromatin modifications in replication is still poorly understood, recent studies provide evidence that post-translational chromatin modifications can control the efficiency and/or timing of replication origin activity (Vogelauer et al, 2002;Zhang et al, 2002;Kurdistani and Grunstein, 2003;Lin et al, 2003;Perry et al, 2004;Azuara et al, 2006). In yeast, histone acetylation in the vicinity of replication origin is an important determinant of replication timing and it appears that higher level of histone acetylation coincides with earlier firing of an origin (Vogelauer et al, 2002).…”

Section: Replicationmentioning

confidence: 99%

See 2 more Smart Citations

Orchestration of chromatin-based processes: mind the TRRAP

et al. 2007

View full text Add to dashboard Cite

Chromatin modifications at core histones including acetylation, methylation, phosphorylation and ubiquitination play an important role in diverse biological processes. Acetylation of specific lysine residues within the N terminus tails of core histones is arguably the most studied histone modification; however, its precise roles in different cellular processes and how it is disrupted in human diseases remain poorly understood. In the last decade, a number of histone acetyltransferases (HATs) enzymes responsible for histone acetylation, has been identified and functional studies have begun to unravel their biological functions. The activity of many HATs is dependent on HAT complexes, the multiprotein assemblies that contain one HAT catalytic subunit, adapter proteins, several other molecules of unknown function and a large protein called TRansformation/tRanscription domain-Associated Protein (TRRAP). As a common component of many HAT complexes, TRRAP appears to be responsible for the recruitment of these complexes to chromatin during transcription, replication and DNA repair. Recent studies have shed new light on the role of TRRAP in HAT complexes as well as mechanisms by which it mediates diverse cellular processes. Thus, TRRAP appears to be responsible for a concerted and context-dependent recruitment of HATs and coordination of distinct chromatin-based processes, suggesting that its deregulation may contribute to diseases. In this review, we summarize recent developments in our understanding of the function of TRRAP and TRRAP-containing HAT complexes in normal cellular processes and speculate on the mechanism underlying abnormal events that may lead to human diseases such as cancer.

show abstract

Section: Replicationmentioning

confidence: 64%

Section: Trrap Is Conserved In Evolutionmentioning

confidence: 99%

Section: Replicationmentioning

confidence: 99%

See 1 more Smart Citation

Orchestration of chromatin-based processes: mind the TRRAP

et al. 2007

View full text Add to dashboard Cite

show abstract

“…However, ES cell-specific genes change their position during differentiation-e.g., in humans the NANOG gene relocates from a more peripheral positioning in ES cells to a more central position in B cells-and the OCT4 gene loops out from its chromosome territory in ES cells (Wiblin et al 2005). This also correlates with an early replication timing of these genes in ES cells compared with a later one in differentiated cells (Perry et al 2004). In mouse ES cells "bivalent chromatin domains" of large regions of active and repressive histone modifications exist.…”

Section: Es Cellsmentioning

confidence: 90%

Dynamics and interplay of nuclear architecture, genome organization, and gene expression

Schneider¹,

Grosschedl²

2007

Genes Dev.

364

313

View full text Add to dashboard Cite

The organization of the genome in the nucleus of a eukaryotic cell is fairly complex and dynamic. Various features of the nuclear architecture, including compartmentalization of molecular machines and the spatial arrangement of genomic sequences, help to carry out and regulate nuclear processes, such as DNA replication, DNA repair, gene transcription, RNA processing, and mRNA transport. Compartmentalized multiprotein complexes undergo extensive modifications or exchange of protein subunits, allowing for an exquisite dynamics of structural components and functional processes of the nucleus. The architecture of the interphase nucleus is linked to the spatial arrangement of genes and gene clusters, the structure of chromatin, and the accessibility of regulatory DNA elements. In this review, we discuss recent studies that have provided exciting insight into the interplay between nuclear architecture, genome organization, and gene expression.

show abstract

“…In contrast, genes that are associated with maintenance of pluripotency in stem cells shift to a later replication status after commitment. 9 Examples are also seen in imprinted and other monoallelically-expressed genes where the active alleles replicate earlier than the inactive alleles. 10 This relationship does not hold in all genomic regions, since a highly transcribed and late-replicating region was recently identified on chromosome 22.…”

Section: Abbreviationsmentioning

confidence: 99%

Replication Timing Profile Reflects the Distinct Functional and Genomic Features of the MHC Class II Region

Takousis

Johonnett²,

Williamson³

et al. 2007

Cell Cycle

Self Cite

View full text Add to dashboard Cite

The timing of DNA replication generally correlates with transcription, gene density and sequence composition. How is the timing affected if a genomic region has a combination of features that individually correlate with either early or late replication? The major histocompatibility complex (MHC) class II region is an AT-rich isochore that would be expected to replicate late, but it also contains coordinately regulated genes that are highly expressed in antigen-presenting cells and are strongly inducible in other cell types. Using cytological and biochemical assays, we find that the entire MHC replicates within the first half of S-phase, and that the class II region replicates slightly later than the adjacent regions irrespective of gene expression. These data suggest that despite ATrichness, an early-to-middle replication time in the class II region is defined by an open chromatin conformation that allows rapid transcriptional activation as a defence against pathogens.

show abstract

A Dynamic Switch in the Replication Timing of Key Regulator Genes in Embryonic Stem Cells upon Neural Induction

Abstract: BrdU 5'-bromodeoxyuridine EB embryoid bodies ES cells embryonic stem cells LIF leukaemia inhibitory factor H3K4 histone H3 lysine 4 H3K9 histone H3 lysine 9 H4K20 histone H4 lysine 20 RA retinoic acid

Cited by 91 publications

References 40 publications

Orchestration of chromatin-based processes: mind the TRRAP

Orchestration of chromatin-based processes: mind the TRRAP

Dynamics and interplay of nuclear architecture, genome organization, and gene expression

Replication Timing Profile Reflects the Distinct Functional and Genomic Features of the MHC Class II Region

Contact Info

Product

Resources

About