Asynchronous Replication Timing: A Mechanism for Monoallelic Choice During Development

Developmental programming is carried out by a sequence of molecular choices that epigenetically mark the genome to generate the stable cell types which make up the total organism. A number of important processes, such as genomic imprinting, selection of immune or olfactory receptors, and X-chromosome inactivation in females are dependent on the ability to stably choose one single allele in each cell. In this perspective, we propose that asynchronous replication timing (ASRT) serves as the basis for a sophisticated universal mechanism for mediating and maintaining these decisions.

Chromosomal coordination and differential structure of asynchronous replicating regions

Stochastic asynchronous replication timing (AS-RT) is a phenomenon in which the time of replication of each allele is different, and the identity of the early allele varies between cells. By taking advantage of stable clonal pre-B cell populations derived from C57BL6/Castaneous mice, we have mapped the genome-wide AS-RT loci, independently of genetic differences. These regions are characterized by differential chromatin accessibility, mono-allelic expression and include new gene families involved in specifying cell identity. By combining population level mapping with single cell FISH, our data reveal the existence of a novel regulatory program that coordinates a fixed relationship between AS-RT regions on any given chromosome, with some loci set to replicate in a parallel and others set in the anti-parallel orientation. Our results show that AS-RT is a highly regulated epigenetic mark established during early embryogenesis that may be used for facilitating the programming of mono-allelic choice throughout development.

Evaluation of Replication Mechanisms on Selected Database Systems

This paper is focused on comparing database replication over spatial data in PostgreSQL and MySQL. Database replication means solving various problems with overloading a single database server with writing and reading queries. There are many replication mechanisms that are able to handle data differently. Criteria for objective comparisons were set for testing and determining the bottleneck of the replication process. The tests were done over the real national vector spatial datasets, namely, ArcCR500, Data200, Natural Earth and Estimated Pedologic-Ecological Unit. HWMonitor Pro was used to monitor the PostgreSQL database, network and system load. Monyog was used to monitor the MySQL activity (data and SQL queries) in real-time. Both database servers were run on computers with the Microsoft Windows operating system. The results from the provided tests of both replication mechanisms led to a better understanding of these mechanisms and allowed informed decisions for future deployment. Graphs and tables include the statistical data and describe the replication mechanisms in specific situations. PostgreSQL with the Slony extension with asynchronous replication synchronized a batch of changes with a high transfer speed and high server load. MySQL with synchronous replication synchronized every change record with low impact on server performance and network bandwidth.

Reciprocal monoallelic expression of ASAR lncRNA genes controls replication timing of human chromosome 6

DNA replication occurs on mammalian chromosomes in a cell-type distinctive temporal order known as the replication timing program. We previously found that disruption of the noncanonical lncRNA genes ASAR6 and ASAR15 results in delayed replication timing and delayed mitotic chromosome condensation of human chromosome 6 and 15, respectively. ASAR6 and ASAR15 display random monoallelic expression, and display asynchronous replication between alleles that is coordinated with other random monoallelic genes on their respective chromosomes. Disruption of the expressed allele, but not the silent allele, of ASAR6 leads to delayed replication, activation of the previously silent alleles of linked monoallelic genes, and structural instability of human chromosome 6. In this report, we describe a second lncRNA gene (ASAR6-141) on human chromosome 6 that when disrupted results in delayed replication timing in cis. ASAR6-141 is subject to random monoallelic expression and asynchronous replication, and is expressed from the opposite chromosome 6 homolog as ASAR6. ASAR6-141 RNA, like ASAR6 and ASAR15 RNAs, contains a high L1 content and remains associated with the chromosome territory where it is transcribed. Three classes of cis-acting elements control proper chromosome function in mammals: origins of replication, centromeres; and telomeres, which are responsible for replication, segregation and stability of all chromosomes. Our work supports a fourth type of essential chromosomal element, “Inactivation/Stability Centers”, which express ASAR lncRNAs responsible for proper replication timing, monoallelic expression, and structural stability of each chromosome.Author summaryMammalian cells replicate their chromosomes during a highly ordered and cell type-specific program. Genetic studies have identified two long non-coding RNA genes, ASAR6 and ASAR15, as critical regulators of the replication timing program of human chromosomes 6 and 15, respectively. There are several unusual characteristics of the ASAR6 and ASAR15 RNAs that distinguish them from other long non-coding RNAs, including: being very long (>200 kb), lacking splicing of the transcripts, lacking polyadenylation, and being retained in the nucleus on the chromosomes where they are made. ASAR6 and ASAR15 also have the unusual property of being expressed from only one copy of the two genes located on homologous chromosome pairs. Using these unusual characteristics shared between ASAR6 and ASAR15, we have identified a second ASAR lncRNA gene located on human chromosome 6, which we have named ASAR6-141. ASAR6-141 is expressed from the opposite chromosome 6 homolog as ASAR6, and disruption of the expressed allele results in delayed replication of chromosome 6. ASAR6-141 RNA had previously been annotated as vlinc273. The very long intergenic non-coding (vlinc)RNAs represent a recently annotated class of RNAs that are long (>50 kb), non-spliced, and non-polyadenlyated nuclear RNAs. There are currently >2,700 vlincRNAs expressed from every chromosome, are encoded by >15% of the human genome, and with a few exceptions have no known function. Our results suggest the intriguing possibility that the vlinc class of RNAs may be functioning to control the replication timing program of all human chromosomes.

Asynchronous replication of AURKA and TP53 genes in gastric cancer patients and patients with multiple tumors

Background. The correct genome replication is essential for normal cell division to guarantee that genetic information comes changeless through the next cells generations. DNA replication is a strictly regulated and synchronous process and its disturbances could result to mutations appearances. Aberrant time of DNA replication affects on gene expression causes changes of epigenetic modifications and influences on increasing the structural rearrangements leading to enhanced genome disbalance. Replication time failure as asynchronous replication is common for cancerogeneses. The objective of our study was the assessment of asynchronous replication levels in patients with gastric cancer and patients with multiple tumors.Materials and methods. Fluorescence in situ hybridization (FISH) was used for the asynchronous replication of AURKA and TP53 genes analyses. Interphase FISH on lymphocytes of peripheral blood of 37 healthy donors, 19 patients with non-cancer gastrointestinal pathologies, 68 patients with solitary gastric cancer and 39 patients with multiple tumors having gastric cancer and other second synchronous or metachronous tumor was carried out.Results. Values of lymphocytes with asynchronous replication for AURKA were 19.8 ± 0.5 % for control group, 24.7 ± 0.4 % for non-cancer patients, 32.5 ± 0.5 % for gastric cancer patients, 39.5 ± 0.6 % for patients with multiple tumors and 17.3 ± 0.5, 19.5 ± 0.7, 26.1 ± 0.7 and 32.5 ± 0.6 % for TP53 respectively. Differences between cell populations of examined groups had statistical significance with p <0.01 for both studied gene. Also there was statistical difference between gastric cancer patients having distant metastases and gastric cancer patients without metastases for AURKA (34.4 ± 1.0 % vs. 31.7 ± 0.6 %; p = 0.02).Conclusion. High lymphocytes with asynchronous replication level in oncological patients could serve as potential marker of second tumor or possible metastatic process including the earliest stage of it.