Results 41 to 50 of about 1,018,957 (214)

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, Vlada V. Zakharova, Aleksandra A. Galitsyna, Pavel I. Kos, Kirill E. Polovnikov, Ilya M. Flyamer, Elena A. Mikhaleva, Ekaterina E. Khrameeva, Diego Germini, Mariya D. Logacheva, Alexey A. Gavrilov, Alexander S. Gorsky, Sergey K. Nechaev, Mikhail S. Gelfand, Yegor S. Vassetzky, Alexander V. Chertovich, Yuri Y. Shevelyov, Sergey V. Razin   +17 more
doaj   +1 more source

Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells. [PDF]

Nat Genet, 2019
Chromatin architecture has been implicated in cell type-specific gene regulatory programs, yet how chromatin remodels during development remains to be fully elucidated.
Zhang Y, Li T, Preissl S, Amaral ML, Grinstein JD, Farah EN, Destici E, Qiu Y, Hu R, Lee AY, Chee S, Ma K, Ye Z, Zhu Q, Huang H, Fang R, Yu L, Izpisua Belmonte JC, Wu J, Evans SM, Chi NC, Ren B.   +21 more
europepmc   +2 more sources

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

Parvovirus minute virus of mice interacts with sites of cellular DNA damage to establish and amplify its lytic infection

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, Juexin Wang, Maria Boftsi, Matthew S Fuller, Jordan E Rede, Trupti Joshi, David J Pintel   +6 more
doaj   +1 more source

DeTOKI identifies and characterizes the dynamics of chromatin TAD-like domains in a single cell

Genome Biology, 2021
Topologically associating domains (TAD) are a key structure of the 3D mammalian genomes. However, the prevalence and dynamics of TAD-like domains in single cells remain elusive.
Xiao Li, Guangjie Zeng, Angsheng Li, Zhihua Zhang   +3 more
doaj   +1 more source

Form and function of topologically associating genomic domains in budding yeast

, 2017
Significance In metazoans, topological domains are regions in the genome that more frequently associate with themselves than with neighboring regions. These domains are important for regulating transcription and replication.
Devon Chandler-Brown, Aaron F. Straight, Ferhat Ay, Zhijun Duan, Umut Eser, William Stafford Noble, Jan M. Skotheim   +6 more
core   +1 more source

From junk to function — How weak selection in eukaryotes builds new parts and drives genomic complexity

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

Finding Topologically Associating Domains [PDF]

, 2015
In this thesis, we propose a new method for finding Topologically Associating Domains, which are contiguous segments of chromatin, ranging in size from thousands to millions of base pairs.
Grytten, Ivar
core  

Topological organization and dynamic regulation of human tRNA genes during macrophage differentiation

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, Douglas H. Phanstiel, Michael P. Snyder   +2 more
doaj   +1 more source

Membrane composition and thermodynamic identity as boundaries of life for synthetic cell research

FEBS Letters, EarlyView.
What makes a cell a cell? The boundary of a living cell is not just a wall. Read as a Markov blanket, the membrane separates internal from external states, generating identity and non‐equilibrium order. Can this identity be rebuilt from scratch in a synthetic cell?
Caterina Presutti, Bert Poolman
wiley   +1 more source