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Joshua A Udall et al.
Frontiers in plant science, 10, 1541-1541 (2019-12-13)
One of the extraordinary aspects of plant genome evolution is variation in chromosome number, particularly that among closely related species. This is exemplified by the cotton genus (Gossypium) and its relatives, where most species and genera have a base chromosome
Dimiter Kunnev et al.
Journal of biological methods, 2(4) (2015-01-01)
Nascent strand capture and release (NSCR) is a method for isolation of short nascent strands to identify origins of DNA replication. The protocol provided involves isolation of total DNA, denaturation, size fractionation on a sucrose gradient, 5'-biotinylation of the appropriate
Takuya Hayakawa et al.
Cytogenetic and genome research, 161(8-9), 437-444 (2021-11-25)
E/L Repli-seq is a powerful tool for detecting cell type-specific replication landscapes in mammalian cells, but its potential to monitor DNA replication under replication stress awaits better understanding. Here, we used E/L Repli-seq to examine the temporal order of DNA
Lilas Courtot et al.
International journal of molecular sciences, 22(9) (2021-06-03)
DNA replication timing (RT), reflecting the temporal order of origin activation, is known as a robust and conserved cell-type specific process. Upon low replication stress, the slowing of replication forks induces well-documented RT delays associated to genetic instability, but it
Saori Takahashi et al.
Nature genetics, 51(3), 529-540 (2019-02-26)
Here, we report a single-cell DNA replication sequencing method, scRepli-seq, a genome-wide methodology that measures copy number differences between replicated and unreplicated DNA. Using scRepli-seq, we demonstrate that replication-domain organization is conserved among individual mouse embryonic stem cells (mESCs). Differentiated
Syed A Mian et al.
Nature communications, 6, 10004-10004 (2015-12-09)
Despite the recent evidence of the existence of myelodysplastic syndrome (MDS) stem cells in 5q-MDS patients, it is unclear whether haematopoietic stem cells (HSCs) could also be the initiating cells in other MDS subgroups. Here we demonstrate that SF3B1 mutation(s)
Miguel de Lucas et al.
The Plant cell, 28(10), 2616-2631 (2016-09-22)
Spatiotemporal regulation of transcription is fine-tuned at multiple levels, including chromatin compaction. Polycomb Repressive Complex 2 (PRC2) catalyzes the trimethylation of Histone 3 at lysine 27 (H3K27me3), which is the hallmark of a repressive chromatin state. Multiple PRC2 complexes have
Syuzo Kaneko et al.
Cancers, 13(9) (2021-05-01)
Although chromatin immunoprecipitation and next-generation sequencing (ChIP-seq) using formalin-fixed paraffin-embedded tissue (FFPE) has been reported, it remained elusive whether they retained accurate transcription factor binding. Here, we developed a method to identify the binding sites of the insulator transcription factor
Timour Baslan et al.
Genome research, 25(5), 714-724 (2015-04-11)
Genome-wide analysis at the level of single cells has recently emerged as a powerful tool to dissect genome heterogeneity in cancer, neurobiology, and development. To be truly transformative, single-cell approaches must affordably accommodate large numbers of single cells. This is
Hisashi Miura et al.
Nature protocols, 15(12), 4058-4100 (2020-11-25)
Replication timing (RT) domains are stable units of chromosome structure that are regulated in the context of development and disease. Conventional genome-wide RT mapping methods require many S-phase cells for either the effective enrichment of replicating DNA through bromodeoxyuridine (BrdU)
Xiang Yu et al.
Genome research, 27(7), 1238-1249 (2017-04-08)
Type II topoisomerases orchestrate proper DNA topology, and they are the targets of anti-cancer drugs that cause treatment-related leukemias with balanced translocations. Here, we develop a high-throughput sequencing technology to define TOP2 cleavage sites at single-base precision, and use the
Optimizing sparse sequencing of single cells for highly multiplex copy number profiling.
Baslan T, et al.
Genome Research, 25(5), 714-724 (2015)
Zhi Liu et al.
Cell death and differentiation, 27(10), 2843-2855 (2020-04-30)
Medullary thymic epithelial cells (mTECs) play a central role in the establishment of T cell central immunological tolerance by promiscuously expressing tissue-restricted antigens (TRAs) and presenting them to developing T cells, leading to deletion of T cells responding to self-antigens.
Dimiter Kunnev et al.
Genome research, 25(4), 558-569 (2015-03-13)
Minichromosome maintenance (MCM) proteins are loaded onto chromatin during G1-phase and define potential locations of DNA replication initiation. MCM protein deficiency results in genome instability and high rates of cancer in mouse models. Here we develop a method of nascent
Ruchi Shukla et al.
Nucleic acids research, 48(14), 7748-7766 (2020-06-26)
Mouse embryonic stem cells (mESCs) cultured with MEK/ERK and GSK3β (2i) inhibitors transition to ground state pluripotency. Gene expression changes, redistribution of histone H3K27me3 profiles and global DNA hypomethylation are hallmarks of 2i exposure, but it is unclear whether epigenetic
Isolation and sequencing of active origins of DNA replication by nascent strand capture and release (NSCR).
Kunnev D, et al.
Journal of biological methods, 2(4) (2015)
SF3B1 mutant MDS-initiating cells may arise from the haematopoietic stem cell compartment.
Mian S A, et al.
Nature Communications, 6, 10004-10004 (2015)
Raymond Lo et al.
Toxicological sciences : an official journal of the Society of Toxicology, 130(2), 349-361 (2012-08-21)
The aryl hydrocarbon receptor (AHR) and AHR nuclear translocator (ARNT) activated complex regulates genes in response to the environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). AHR has also emerged as a potential therapeutic target for the treatment of human diseases and different cancers
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