Results 61 to 70 of about 1,201,498 (234)
Topologically Associated Domains Delineate Susceptibility to Somatic Hypermutation
Cell Reports, 2019 Somatic hypermutation (SHM) introduces point mutations into immunoglobulin (<i>Ig</i>) genes of activated B cells to support the process of antibody affinity maturation but also causes "off-target" mutations in other parts of the genome. We have used sensitive lentiviral SHM reporter vectors and a mutationally active human B cell line to ...
Filip Senigl +13 more
openaire +5 more sources
Deciphering the species-level structure of topologically associating domains [PDF]
, 2021 Summary Chromosome conformation capture technologies such as Hi-C have revealed a rich hierarchical structure of chromatin, with topologically associating domains (TADs) as a key organizational unit, but experimentally reported TAD architectures, currently determined separately for each cell type, are lacking for many
Rohit Singh, Bonnie Berger
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Nature Communications, 2022 Identifying structural variants (SVs) under positive selection in cancer is challenging. Here, the authors develop CSVDriver, a method that computes SV breakpoint proximity and the contribution of elements such as topologically associating domains, and ...
Alexander Martinez-Fundichely +2 more
doaj +1 more source
Genome Biology, 2021 Topologically associating domains (TADs) are the organizational units of chromosome structures. TADs can contain TADs, thus forming a hierarchy. TAD hierarchies can be inferred from Hi-C data through coding trees.
Yu Wei Zhang +2 more
doaj +1 more source
eLife, 2018 We have developed a generally adaptable, novel high-throughput Viral Chromosome Conformation Capture assay (V3C-seq) for use in trans that allows genome-wide identification of the direct interactions of a lytic virus genome with distinct regions of the ...
Kinjal Majumder +6 more
doaj +1 more source
Order and stochasticity in the folding of individual Drosophila genomes
Nature Communications, 2021 Genomes are partitioned into topologically associating domains (TADs). Here the authors present single-nucleus Hi-C maps in Drosophila at 10 kb resolution, demonstrating the presence of chromatin compartments in individual nuclei, and partitioning of the
Sergey V. Ulianov +17 more
doaj +1 more source
FEBS Letters, EarlyView.How do genomes gain new functional parts? In eukaryotes, which tend to evolve under weak selection, much of the genome is junk. Palazzo and Qiu borrow the logic of Markov chains to show how non‐functional DNA becomes functional through the appearance of intermediate states, which arise due to epistasis, buffering, and biochemical messiness, allowing ...
Alexander F. Palazzo, Yi Qiu
wiley +1 more source
RNA‐related functions of BRCA2 in transcription, replication, and genome stability
FEBS Letters, EarlyView.Beyond its role in homologous recombination, BRCA2 regulates R‐loop homeostasis, DNA–RNA hybrid resolution, RNA polymerase II dynamics, and transcriptional activation. Disruption of any of these functions can contribute to genome instability, inflammatory signaling, and tumorigenesis. BRCA2 is a central tumor suppressor protein best known for its roles
Lucia Alvaro‐Aranda +2 more
wiley +1 more source
Genome Biology, 2017 Background The human genome is hierarchically organized into local and long-range structures that help shape cell-type-specific transcription patterns.
Kevin Van Bortle +2 more
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A comparison of topologically associating domain callers over mammals at high resolution
BMC Bioinformatics, 2022 Background Topologically associating domains (TADs) are locally highly-interacting genome regions, which also play a critical role in regulating gene expression in the cell. TADs have been first identified while investigating the 3D genome structure over
Emre Sefer
doaj +1 more source