Replication timing properties, of the humanHPRT locus on active, inactive and reactivated X chromosomes

1997 ◽  
Vol 23 (2) ◽  
pp. 97-109 ◽  
Author(s):  
Prem S. Subramanian ◽  
A. Craig Chinault
Keyword(s):  
Replication Timing ◽  
X Chromosomes ◽  
Timing Properties

scholarly journals Delayed DNA replication in haploid human embryonic stem cells

2021 ◽  
Author(s):  
Matthew M. Edwards ◽  
Michael V. Zuccaro ◽  
Ido Sagi ◽  
Qiliang Ding ◽  
Dan Vershkov ◽  
...  
Keyword(s):  
Stem Cells ◽  
Dna Replication ◽  
Embryonic Stem Cells ◽  
X Chromosome ◽  
Human Embryonic Stem Cells ◽  
Embryonic Stem ◽  
Replication Timing ◽  
Genetic System ◽  
X Chromosomes ◽  
Genomic Regions

Haploid human embryonic stem cells (ESCs) provide a powerful genetic system but diploidize at high rates. We hypothesized that diploidization results from aberrant DNA replication. To test this, we profiled DNA replication timing in isogenic haploid and diploid ESCs. The greatest difference was the earlier replication of the X Chromosome in haploids, consistent with the lack of X-Chromosome inactivation. We also identified 21 autosomal regions that had delayed replication in haploids, extending beyond the normal S phase and into G2/M. Haploid-delays comprised a unique set of quiescent genomic regions that are also underreplicated in polyploid placental cells. The same delays were observed in female ESCs with two active X Chromosomes, suggesting that increased X-Chromosome dosage may cause delayed autosomal replication. We propose that incomplete replication at the onset of mitosis could prevent cell division and result in re-entry into the cell cycle and whole genome duplication.

Imprint switching for non-random X-chromosome inactivation during mouse oocyte growth

Development ◽  
2000 ◽  
Vol 127 (14) ◽  
pp. 3101-3105 ◽  
Author(s):  
T. Tada ◽  
Y. Obata ◽  
M. Tada ◽  
Y. Goto ◽  
N. Nakatsuji ◽  
...  
Keyword(s):  
X Chromosome ◽  
Replication Timing ◽  
X Chromosome Inactivation ◽  
Chromosome Inactivation ◽  
Nuclear Transplantation ◽  
Chromosome X ◽  
Oocyte Growth ◽  
X Chromosomes ◽  
Embryonic Tissues ◽  
Extraembryonic Tissues

In mammals, X-chromosome inactivation occurs in all female cells, leaving only a single active X chromosome. This serves to equalise the dosage of X-linked genes in male and female cells. In the mouse, the paternally derived X chromosome (X(P)) is imprinted and preferentially inactivated in the extraembryonic tissues whereas in the embryonic tissues inactivation is random. To investigate how X(P) is chosen as an inactivated X chromosome in the extraembryonic cells, we have produced experimental embryos by serial nuclear transplantation from non-growing (ng) oocytes and fully grown (fg) oocytes, in which the X chromosomes are marked with (1) an X-linked lacZ reporter gene to assay X-chromosome activity, or (2) the Rb(X.9)6H translocation as a cytogenetic marker for studying replication timing. In the extraembryonic tissues of these ng/fg embryos, the maternal X chromosome (X(M)) derived from the ng oocyte was preferentially inactivated whereas that from the fg oocyte remained active. However, in the embryonic tissues, X inactivation was random. This suggests that (1) a maternal imprint is set on the X(M) during oocyte growth, (2) the maternal imprint serves to render the X(M) resistant to inactivation in the extraembryonic tissues and (3) the X(M) derived from an ng oocyte resembles a normal X(P).

scholarly journals Signatures of replication timing, recombination, and sex in the spectrum of rare variants on the human X chromosome and autosomes

2019 ◽  
Vol 116 (36) ◽  
pp. 17916-17924 ◽  
Author(s):  
Ipsita Agarwal ◽  
Molly Przeworski
Keyword(s):  
X Chromosome ◽  
Rare Variants ◽  
Low Frequency ◽  
Replication Timing ◽  
Double Strand Breaks ◽  
X Chromosomes ◽  
Strand Breaks ◽  
Biochemical Processes ◽  
Males And Females ◽  
Mutational Processes

The sources of human germline mutations are poorly understood. Part of the difficulty is that mutations occur very rarely, and so direct pedigree-based approaches remain limited in the numbers that they can examine. To address this problem, we consider the spectrum of low-frequency variants in a dataset (Genome Aggregation Database, gnomAD) of 13,860 human X chromosomes and autosomes. X-autosome differences are reflective of germline sex differences and have been used extensively to learn about male versus female mutational processes; what is less appreciated is that they also reflect chromosome-level biochemical features that differ between the X and autosomes. We tease these components apart by comparing the mutation spectrum in multiple genomic compartments on the autosomes and between the X and autosomes. In so doing, we are able to ascribe specific mutation patterns to replication timing and recombination and to identify differences in the types of mutations that accrue in males and females. In particular, we identify C > G as a mutagenic signature of male meiotic double-strand breaks on the X, which may result from late repair. Our results show how biochemical processes of damage and repair in the germline interact with sex-specific life history traits to shape mutation patterns on both the X chromosome and autosomes.

scholarly journals Replication Timing Properties within the Mouse Distal Chromosome 7 Imprinting Cluster

2002 ◽  
Vol 66 (5) ◽  
pp. 1046-1051 ◽  
Author(s):  
Kazuhiro KAGOTANI ◽  
Shin-ichiro TAKEBAYASHI ◽  
Atsushi KOHDA ◽  
Hiroshi TAGUCHI ◽  
Martina PAULSEN ◽  
...  
Keyword(s):  
Replication Timing ◽  
Chromosome 7 ◽  
Distal Chromosome ◽  
Timing Properties

scholarly journals Delayed DNA replication in haploid human embryonic stem cells

2021 ◽  
Author(s):  
Matthew Micheal Edwards ◽  
Michael V. Zuccaro ◽  
Ido Sagi ◽  
Qiliang Ding ◽  
Dan Vershkov ◽  
...  
Keyword(s):  
Stem Cells ◽  
Dna Replication ◽  
Embryonic Stem Cells ◽  
X Chromosome ◽  
Human Embryonic Stem Cells ◽  
Embryonic Stem ◽  
Replication Timing ◽  
Genetic System ◽  
X Chromosomes ◽  
Genomic Regions

Haploid human embryonic stem cells (ESCs) provide a powerful genetic system but diploidize at high rates. We hypothesized that diploidization results from aberrant DNA replication. To test this, we profiled DNA replication timing in isogenic haploid and diploid ESCs. The greatest difference was the earlier replication of the X chromosome in haploids, consistent with the lack of X chromosome inactivation. Surprisingly, we also identified 21 autosomal regions that had dramatically delayed replication in haploids, extending beyond the normal S phase and into G2/M. Haploid-delays comprised a unique set of quiescent genomic regions that are also under-replicated in polyploid placental cells. The same delays were observed in female ESCs with two active X chromosomes, suggesting that increased X chromosome dosage may cause delayed autosomal replication. We propose that incomplete replication at the onset of mitosis could prevent cell division and result in re-entry into the cell cycle and whole genome duplication.

scholarly journals Late Replication of the Inactive X Chromosome Is Independent of the Compactness of Chromosome Territory in Human Pluripotent Stem Cells

Acta Naturae ◽  
2013 ◽  
Vol 5 (2) ◽  
pp. 54-61
Author(s):  
A. V. Panova ◽  
E. D. Nekrasov ◽  
M. A. Lagarkova ◽  
S. L. Kiselev ◽  
A. N. Bogomazova
Keyword(s):  
Stem Cells ◽  
X Chromosome ◽  
Pluripotent Stem Cells ◽  
Replication Timing ◽  
Chromosome Territory ◽  
Late Replication ◽  
Facultative Heterochromatin ◽  
X Chromosomes ◽  
Inactive X Chromosome ◽  
The Status

Dosage compensation of the X chromosomes in mammals is performed via the formation of facultative heterochromatin on extra X chromosomes in female somatic cells. Facultative heterochromatin of the inactivated X (Xi), as well as constitutive heterochromatin, replicates late during the S-phase. It is generally accepted that Xi is always more compact in the interphase nucleus. The dense chromosomal folding has been proposed to define the late replication of Xi. In contrast to mouse pluripotent stem cells (PSCs), the status of X chromosome inactivation in human PSCs may vary significantly. Fluorescence in situ hybridization with a whole X-chromosome-specific DNA probe revealed that late-replicating Xi may occupy either compact or dispersed territory in human PSCs. Thus, the late replication of the Xi does not depend on the compactness of chromosome territory in human PSCs. However, the Xi reactivation and the synchronization in the replication timing of X chromosomes upon reprogramming are necessarily accompanied by the expansion of X chromosome territory.

Replication asynchrony and differential condensation of X chromosomes in female platypus (Ornithorhynchus anatinus)

2009 ◽  
Vol 21 (8) ◽  
pp. 952 ◽  
Author(s):  
Kristen K. K. Ho ◽  
Janine E. Deakin ◽  
Megan L. Wright ◽  
Jennifer A. Marshall Graves ◽  
Frank Grützner
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Dosage Compensation ◽  
Gene Expression Analysis ◽  
Chromatin Condensation ◽  
Replication Timing ◽  
X Chromosomes ◽  
Asynchronous Replication ◽  
Y Chromosomes ◽  
Ornithorhynchus Anatinus

A common theme in the evolution of sex chromosomes is the massive loss of genes on the sex-specific chromosome (Y or W), leading to a gene imbalance between males (XY) and females (XX) in a male heterogametic species, or between ZZ and ZW in a female heterogametic species. Different mechanisms have evolved to compensate for this difference in dosage of X-borne genes between sexes. In therian mammals, one of the X chromosomes is inactivated, whereas bird dosage compensation is partial and gene-specific. In therian mammals, hallmarks of the inactive X are monoallelic gene expression, late DNA replication and chromatin condensation. Platypuses have five pairs of X chromosomes in females and five X and five Y chromosomes in males. Gene expression analysis suggests a more bird-like partial and gene-specific dosage compensation mechanism. We investigated replication timing and chromosome condensation of three of the five X chromosomes in female platypus. Our data suggest asynchronous replication of X-specific regions on X1, X3 and X5 but show significantly different condensation between homologues for X3 only, and not for X1 or X5. We discuss these results in relation to recent gene expression analysis of X-linked genes, which together give us insights into possible mechanisms of dosage compensation in platypus.

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