Results 21 to 30 of about 8,821,447 (199)

MaxComp: Predicting single-cell chromatin compartments from 3D chromosome structures.

PLoS Computational Biology
The genome is organized into distinct chromatin compartments with at least two main classes, a transcriptionally active A and an inactive B compartment, broadly corresponding to euchromatin and heterochromatin.
Yuxiang Zhan, Francesco Musella, Frank Alber   +2 more
doaj   +4 more sources

Inferring Single-Cell 3D Chromosomal Structures Based on the Lennard-Jones Potential [PDF]

International Journal of Molecular Sciences, 2021
Reconstructing three-dimensional (3D) chromosomal structures based on single-cell Hi-C data is a challenging scientific problem due to the extreme sparseness of the single-cell Hi-C data. In this research, we used the Lennard-Jones potential to reconstruct both 500 kb and high-resolution 50 kb chromosomal structures based on single-cell Hi-C data.
Zha, Mengsheng, Wang, Nan, Zhang, Chaoyang, Wang, Zheng   +3 more
openaire   +2 more sources

Manipulating the 3D organization of the largest synthetic yeast chromosome [PDF]

, 2023
Whether synthetic genomes can power life has attracted broad interest in the synthetic biology field. Here, we report de novo synthesis of the largest eukaryotic chromosome thus far, synIV, a 1,454,621-bp yeast chromosome resulting from extensive genome ...
Aizawa, Yasunori, Fanfani, Viola, Zhao, Yu, Yamashita, Hitoyoshi, Jiang, Qingwen, Lazar-Stefanita, Luciana, Deutsch, Samuel, Shen, Michael J., McCulloch, Laura H, Camellato, Brendan R., Cai, Jitong, Bader, Joel S., Goldberg, Gregory W., Zhang, Weimin, Stracquadanio, Giovanni; id_orcid, Boeke, Jef D., Xu, Zhuwei, Mitchell, Leslie A., Sun, Xiaoji, Noyes, Marcus B., Dai, Junbiao, Lobzaev, Evgenii, ?, ?, Easo, Nicole, Haase, Max A.B., Ichikawa, David M., Kurasawa, Hikaru, Lauer, Stephanie L., Lin, S. Jiaming, Zhu, Yinan, Sacasa, Maya   +30 more
core   +2 more sources

Ultra-Structural Imaging Provides 3D Organization of 46 Chromosomes of a Human Lymphocyte Prophase Nucleus [PDF]

International Journal of Molecular Sciences, 2021
Three dimensional (3D) ultra-structural imaging is an important tool for unraveling the organizational structure of individual chromosomes at various stages of the cell cycle. Performing hitherto uninvestigated ultra-structural analysis of the human genome at prophase, we used serial block-face scanning electron microscopy (SBFSEM) to understand ...
Sajid, Atiqa, Lalani, El-Nasir, Chen, Bo, Hashimoto, Teruo, Griffin, Darren K., Bhartiya, Archana, Thompson, George, Robinson, Ian K., Yusuf, Mohammed   +8 more
openaire   +3 more sources

TADs are 3D structural units of higher-order chromosome organization in Drosophila [PDF]

Science Advances, 2018
Drosophila chromosomes are organized in a series of nanocompartments that correspond to topologically associating domains.
Szabo, Quentin, Jost, Daniel, Chang, Jia-Ming, Cattoni, Diego I., Papadopoulos, Giorgio L., Bonev, Boyan, Sexton, Tom, Gurgo, Julian, Jacquier, Caroline, Nollmann, Marcelo, Bantignies, Frédéric, Cavalli, Giacomo   +11 more
openaire   +3 more sources

Heterogeneous loop model to infer 3D chromosome structures from Hi-C [PDF]

Biophysical Journal, 2019
Adapting a well-established formalism in polymer physics, we develop a minimalist approach to infer threedimensional (3D) folding of chromatin from Hi-C data. The 3D chromosome structures generated from our heterogeneous loop model (HLM) are used to visualize chromosome organizations that can substantiate the measurements from FISH ...
Liu, Lei, Kim, Min Hyeok, Hyeon, Changbong   +2 more
openaire   +2 more sources

Differences of size and shape of active and inactive X-chromosome domains in human amniotic fluid cell nuclei [PDF]

, 1993
It is a widely held belief that the inactive X-chromosome (Xi) in female cell nuclei is strongly condensed as compared to the largely decondensed active X-chromosome (Xa).
Cremer, Thomas, Stelzer, Ernst, Bischoff, A., T. Cremer, Cremer, Christoph, I. Kharboush, C. Cremer, Kharboush, I., J. Albers, E. Stelzer, Schmidt, J., A. Bischoff   +11 more
core   +1 more source

3D Analysis of chromosome architecture: advantages and limitations with SEM [PDF]

, 2005
Three-dimensional mitotic plant chromosome architecture can be investigated with the highest resolution with scanning electron microscopy compared to other microscopic techniques at present.
Formanek, H., Schroeder-Reiter, E., Wanner, Gerhard   +2 more
core   +1 more source

Use of 3D imaging for providing insights into high-order structure of mitotic chromosomes [PDF]

Chromosoma, 2018
The high-order structure of metaphase chromosomes remains still under investigation, especially the 30-nm structure that is still controversial. Advanced 3D imaging has provided useful information for our understanding of this detailed structure. It is evident that new technologies together with improved sample preparations and image analyses should be
Mohammed Yusuf, Kohei Kaneyoshi, Kiichi Fukui, Ian Robinson   +3 more
openaire   +4 more sources

Inferring chromosome radial organization from Hi-C data

BMC Bioinformatics, 2020
Background The nonrandom radial organization of eukaryotic chromosome territories (CTs) inside the nucleus plays an important role in nuclear functional compartmentalization. Increasingly, chromosome conformation capture (Hi-C) based approaches are being
Priyojit Das, Tongye Shen, Rachel Patton McCord   +2 more
doaj   +1 more source