Results 51 to 60 of about 2,265,648 (271)

3D chromatin architecture and transcription regulation in cancer

Journal of Hematology & Oncology, 2022
Chromatin has distinct three-dimensional (3D) architectures important in key biological processes, such as cell cycle, replication, differentiation, and transcription regulation.
Siwei Deng, Yuliang Feng, Siim Pauklin
doaj   +1 more source

Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation [PDF]

, 2017
Developmental genes in metazoan genomes are surrounded by dense clusters of conserved noncoding elements (CNEs). CNEs exhibit unexplained extreme levels of sequence conservation, with many acting as developmental long-range enhancers.
Nathan Harmston, Merkenschlager, Matthias, Matthias Merkenschlager, Tan, Ge, Harmston, N, Perry, M, Tan, G, Ing-Simmons, E, Perry, Malcolm, Boris Lenhard, Malcolm Perry, Lenhard, Boris, Elizabeth Ing-Simmons, Ge Tan, Ing-Simmons, Elizabeth, Harmston, Nathan, Merkenschlager, M, Lenhard, B   +17 more
core   +1 more source

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
openaire   +1 more source

CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains [PDF]

, 2021
Insulators play a critical role in spatiotemporal gene regulation in animals. The evolutionarily conserved CCCTC-binding factor (CTCF) is required for insulator function in mammals, but not all of its binding sites act as insulators.
Hu R., Han Y., Conte M., Zhuang X., Huang H., Juric I., Bianco S., Bintu B., Kern C., Zhu Q., Chiariello A. M., Hu M., Jussila A., Zhang Y., Nicodemi M., Yu M., Ren B., Tastemel M., Tastemel, Melodi, Jussila, A., Kern, C., Bintu, Bogdan, Zhang, Y., Bianco, S., Huang, Hui, Jussila, Adam, Ren, B., Ren, Bing, Juric, Ivan, Bintu, B., Han, Yuanyuan, Zhu, Q., Han, Y., Hu, Rong, Huang, H., Hu, M., Conte, M., Zhu, Quan, Zhuang, Xiaowei, Bianco, Simona, Yu, M., Juric, I., Conte, Mattia, Hu, Ming, Tastemel, M., Kern, Colin, Hu, R., Zhuang, X., Yu, Miao, Nicodemi, Mario, Chiariello, Andrea M, Zhang, Yanxiao, Chiariello, A.M., Nicodemi, M., Mattia Conte, Xiaowei Zhuang, Andrea M. Chiariello, Adam Jussila, Ming Hu, Bogdan Bintu, Simona Bianco, Hui Huang, Yanxiao Zhang, Colin Kern, Melodi Tastemel, Quan Zhu, Miao Yu, Yuanyuan Han, Mario Nicodemi, Rong Hu, Bing Ren, Ivan Juric   +71 more
core   +2 more sources

Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia

Nature Communications, 2019
High hyperploidy is a common feature in childhood B-cell precursor acute lymphoblastic leukemia. Here, the authors perform proteogenomic and Hi-C analyses of this leukemia and the ETV6/RUNX1 subtype and show that CTCF and cohesin expression are low in ...
Minjun Yang, Mattias Vesterlund, Ioannis Siavelis, Larissa H. Moura-Castro, Anders Castor, Thoas Fioretos, Rozbeh Jafari, Henrik Lilljebjörn, Duncan T. Odom, Linda Olsson, Naveen Ravi, Eleanor L. Woodward, Louise Harewood, Janne Lehtiö, Kajsa Paulsson   +14 more
doaj   +1 more source

Structural Fluctuations of the Chromatin Fiber within Topologically Associating Domains [PDF]

Biophysical Journal, 2016
Experiments based on chromosome conformation capture have shown that mammalian genomes are partitioned into topologically associating domains (TADs), within which the chromatin fiber preferentially interacts. TADs may provide three-dimensional scaffolds allowing genes to contact their appropriate distal regulatory DNA sequences (e.g., enhancers) and ...
G. Tiana, A. Amitai, T. Pollex, T. Piolot, D. Holcman, E. Heard, L. Giorgetti   +6 more
openaire   +4 more sources

Identifying topologically associating domains and subdomains by Gaussian Mixture model And Proportion test

, 2017
The spatial organization of the genome plays a critical role in regulating gene expression. Recent chromatin interaction mapping studies have revealed that topologically associating domains and subdomains are fundamental building blocks of the three ...
Kai Tan, Wenbao Yu, Bing He
core   +1 more source

Formation of topologically associated chromatin domains using quantum annealing. [PDF]

Sci Rep
Abstract Topologically Associating Chromatin Domains are spatially distinct chromatin regions that regulate transcription by segregating active and inactive genomic elements. Empirical studies show that their formation correlates with local patterns of epigenetic markers, yet the precise mechanisms linking 1D epigenetic landscapes to ...
Kempe T, Tabei SMA, Ansari MH.
europepmc   +4 more sources

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

RobusTAD: reference panel based annotation of nested topologically associating domains

Genome Biology
Topologically associating domains (TADs) are fundamental units of 3D genomes and play essential roles in gene regulation. Hi-C data suggests a hierarchical organization of TADs.
Yanlin Zhang, Rola Dali, Mathieu Blanchette   +2 more
doaj   +1 more source