Faculty Opinions recommendation of Stability of patient-specific features of altered DNA replication timing in xenografts of primary human acute lymphoblastic leukemia.

Author(s):  
Domenico Maiorano
Author(s):  
Amnon Koren ◽  
Dashiell J Massey ◽  
Alexa N Bracci

Abstract Motivation Genomic DNA replicates according to a reproducible spatiotemporal program, with some loci replicating early in S phase while others replicate late. Despite being a central cellular process, DNA replication timing studies have been limited in scale due to technical challenges. Results We present TIGER (Timing Inferred from Genome Replication), a computational approach for extracting DNA replication timing information from whole genome sequence data obtained from proliferating cell samples. The presence of replicating cells in a biological specimen leads to non-uniform representation of genomic DNA that depends on the timing of replication of different genomic loci. Replication dynamics can hence be observed in genome sequence data by analyzing DNA copy number along chromosomes while accounting for other sources of sequence coverage variation. TIGER is applicable to any species with a contiguous genome assembly and rivals the quality of experimental measurements of DNA replication timing. It provides a straightforward approach for measuring replication timing and can readily be applied at scale. Availability and Implementation TIGER is available at https://github.com/TheKorenLab/TIGER. Supplementary information Supplementary data are available at Bioinformatics online


1991 ◽  
Vol 15 (11) ◽  
pp. 1059-1066 ◽  
Author(s):  
Yasuhiko Kano ◽  
Shinobu Sakamoto ◽  
Tadashi Kasahara ◽  
Miyuki Akutsu ◽  
Yoshiharu Inoue ◽  
...  

Leukemia ◽  
2011 ◽  
Vol 26 (2) ◽  
pp. 312-322 ◽  
Author(s):  
S Stevanović ◽  
M Griffioen ◽  
B A Nijmeijer ◽  
M L J van Schie ◽  
A N Stumpf ◽  
...  

2021 ◽  
Vol 4 (8) ◽  
pp. e202101102
Author(s):  
Machika Kawamura ◽  
Satoshi Funaya ◽  
Kenta Sugie ◽  
Masataka G Suzuki ◽  
Fugaku Aoki

The pericentromeric heterochromatin of one-cell embryos forms a unique, ring-like structure around the nucleolar precursor body, which is absent in somatic cells. Here, we found that the histone H3 variants H3.1 and/or H3.2 (H3.1/H3.2) were localized asymmetrically between the male and female perinucleolar regions of the one-cell embryos; moreover, asymmetrical histone localization influenced DNA replication timing. The nuclear deposition of H3.1/3.2 in one-cell embryos was low relative to other preimplantation stages because of reduced H3.1/3.2 mRNA expression and incorporation efficiency. The forced incorporation of H3.1/3.2 into the pronuclei of one-cell embryos triggered a delay in DNA replication, leading to developmental failure. Methylation of lysine residue 27 (H3K27me3) of the deposited H3.1/3.2 in the paternal perinucleolar region caused this delay in DNA replication. These results suggest that reduced H3.1/3.2 in the paternal perinucleolar region is essential for controlled DNA replication and preimplantation development. The nuclear deposition of H3.1/3.2 is presumably maintained at a low level to avoid the detrimental effect of K27me3 methylation on DNA replication in the paternal perinucleolar region.


Cell Reports ◽  
2014 ◽  
Vol 7 (1) ◽  
pp. 62-69 ◽  
Author(s):  
Stefano Mattarocci ◽  
Maksym Shyian ◽  
Laure Lemmens ◽  
Pascal Damay ◽  
Dogus Murat Altintas ◽  
...  

2017 ◽  
Vol 29 (9) ◽  
pp. 2126-2149 ◽  
Author(s):  
Emily E. Wear ◽  
Jawon Song ◽  
Gregory J. Zynda ◽  
Chantal LeBlanc ◽  
Tae-Jin Lee ◽  
...  

Blood ◽  
1973 ◽  
Vol 41 (1) ◽  
pp. 141-154 ◽  
Author(s):  
Alvin M. Mauer ◽  
Carl F. Evert ◽  
Beatrice C. Lampkin ◽  
Nancy B. McWilliams

Abstract A model for cell kinetics of human acute lymphoblastic leukemia has been constructed with discrete modeling techniques for computer use with the GPSS/360 computer language. The model has produced results corresponding to observed biological data. It has been possible to explore mechanisms for control of the growth of the leukemic cell population. In addition to the flow of cells from the resting to the proliferative phase, two other important parts of the cell life cycle, cell death and the intracellular events after mitosis, were identified as potentially important regulatory mechanisms. Chemotherapeutic drug effects could be simulated, and in the case of vincristine an unsuspected effect was suggested. This effect of vincristine on transformation of the resting cell to an active proliferative phase has been supported by studies of vincristine effect on blast transformation of phytohemagglutinin-stimulated lymphocytes. A single cell was found to take 3½ yr to grow to a population of 1012 cells, a clinically recognizable number. Although this observation cannot be confirmed from biological studies, this time has an interesting correspondence to the peak incidence of acute lymphoblastic leukemia in childhood. It indicates that a mutational event in a single cell could account for the leukemic process in childhood acute leukemia.


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