scholarly journals A complete protocol for genome-scale analysis of replication timing in mammalian cells

2010 ◽  
Author(s):  
Tyrone Ryba ◽  
Dana Battaglia ◽  
Benjamin Pope ◽  
Ichiro Hiratani ◽  
David Gilbert
Keyword(s):  
Mammalian Cells ◽  
Replication Timing ◽  
Scale Analysis ◽  
Genome Scale

scholarly journals Genome-scale analysis of replication timing: from bench to bioinformatics

2011 ◽  
Vol 6 (6) ◽  
pp. 870-895 ◽  
Author(s):  
Tyrone Ryba ◽  
Dana Battaglia ◽  
Benjamin D Pope ◽  
Ichiro Hiratani ◽  
David M Gilbert
Keyword(s):  
Replication Timing ◽  
Scale Analysis ◽  
Genome Scale

scholarly journals The Protective Role of Dormant Origins in Response to Replicative Stress

2018 ◽  
Vol 19 (11) ◽  
pp. 3569 ◽  
Author(s):  
Lilas Courtot ◽  
Jean-Sébastien Hoffmann ◽  
Valérie Bergoglio
Keyword(s):  
Dna Replication ◽  
Mammalian Cells ◽  
Genome Stability ◽  
Replication Timing ◽  
Protective Role ◽  
Entire Genome ◽  
Replicative Stress ◽  
A Cell ◽  
The Many

Genome stability requires tight regulation of DNA replication to ensure that the entire genome of the cell is duplicated once and only once per cell cycle. In mammalian cells, origin activation is controlled in space and time by a cell-specific and robust program called replication timing. About 100,000 potential replication origins form on the chromatin in the gap 1 (G1) phase but only 20–30% of them are active during the DNA replication of a given cell in the synthesis (S) phase. When the progress of replication forks is slowed by exogenous or endogenous impediments, the cell must activate some of the inactive or “dormant” origins to complete replication on time. Thus, the many origins that may be activated are probably key to protect the genome against replication stress. This review aims to discuss the role of these dormant origins as safeguards of the human genome during replicative stress.

Mapping replication timing domains genome wide in single mammalian cells with single-cell DNA replication sequencing

2020 ◽  
Vol 15 (12) ◽  
pp. 4058-4100
Author(s):  
Hisashi Miura ◽  
Saori Takahashi ◽  
Takahiro Shibata ◽  
Koji Nagao ◽  
Chikashi Obuse ◽  
...  
Keyword(s):  
Dna Replication ◽  
Single Cell ◽  
Mammalian Cells ◽  
Replication Timing ◽  
Genome Wide

Integrated Genome-Scale Analysis and Northern Blot Detection of Retrotransposon siRNAs Across Plant Species

2020 ◽  
pp. 387-411
Author(s):  
Marcel Böhrer ◽  
Bart Rymen ◽  
Christophe Himber ◽  
Aude Gerbaud ◽  
David Pflieger ◽  
...  
Keyword(s):  
Plant Species ◽  
Northern Blot ◽  
Scale Analysis ◽  
Genome Scale

scholarly journals Genome-scale analysis of evolutionary rate and selection in a fast-expanding Spanish cluster of HIV-1 subtype F1

2018 ◽  
Vol 66 ◽  
pp. 43-47 ◽  
Author(s):  
Juan Á. Patiño-Galindo ◽  
Francisco Domínguez ◽  
María T. Cuevas ◽  
Elena Delgado ◽  
Mónica Sánchez ◽  
...  
Keyword(s):  
Evolutionary Rate ◽  
Scale Analysis ◽  
Genome Scale ◽  
Hiv 1

Identification and validation of tumor environment phenotypes in lung adenocarcinoma by integrative genome-scale analysis

2020 ◽  
Vol 69 (7) ◽  
pp. 1293-1305
Author(s):  
Guoshu Bi ◽  
Zhencong Chen ◽  
Xiaodong Yang ◽  
Jiaqi Liang ◽  
Zhengyang Hu ◽  
...  
Keyword(s):  
Lung Adenocarcinoma ◽  
Scale Analysis ◽  
Tumor Environment ◽  
Genome Scale

scholarly journals Genome-Scale Analysis Identifies Novel Transcript-Variants in Esophageal Adenocarcinoma

2020 ◽  
Vol 10 (3) ◽  
pp. 652-654.e17
Author(s):  
B.P.D. Purkayastha ◽  
E.R. Chan ◽  
D. Ravillah ◽  
L. Ravi ◽  
R. Gupta ◽  
...  
Keyword(s):  
Esophageal Adenocarcinoma ◽  
Scale Analysis ◽  
Novel Transcript ◽  
Transcript Variants ◽  
Genome Scale
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