Nuclear compartments: an incomplete primer to nuclear compartments, bodies, and genome organization relative to nuclear architecture
AS Belmont - Cold Spring Harbor perspectives in biology, 2022 - cshperspectives.cshlp.org
This work reviews nuclear compartments, defined broadly to include distinct nuclear
structures, bodies, and chromosome domains. It first summarizes original cytological …
structures, bodies, and chromosome domains. It first summarizes original cytological …
Macromolecular crowding: Sensing without a sensor
All living cells are crowded with macromolecules. Crowding can directly modulate
biochemical reactions to various degrees depending on the sizes, shapes, and binding …
biochemical reactions to various degrees depending on the sizes, shapes, and binding …
RNA polymerase II is required for spatial chromatin reorganization following exit from mitosis
Mammalian chromosomes are three-dimensional entities shaped by converging and
opposing forces. Mitotic cell division induces marked chromosome condensation, but …
opposing forces. Mitotic cell division induces marked chromosome condensation, but …
[HTML][HTML] Radiation-induced DNA damage and repair effects on 3D genome organization
The three-dimensional structure of chromosomes plays an important role in gene expression
regulation and also influences the repair of radiation-induced DNA damage. Genomic …
regulation and also influences the repair of radiation-induced DNA damage. Genomic …
Suppression of liquid–liquid phase separation by 1, 6-hexanediol partially compromises the 3D genome organization in living cells
SV Ulianov, AK Velichko, MD Magnitov… - Nucleic acids …, 2021 - academic.oup.com
Liquid–liquid phase separation (LLPS) contributes to the spatial and functional segregation
of molecular processes within the cell nucleus. However, the role played by LLPS in …
of molecular processes within the cell nucleus. However, the role played by LLPS in …
[HTML][HTML] Hyperosmotic stress alters the RNA polymerase II interactome and induces readthrough transcription despite widespread transcriptional repression
NA Rosa-Mercado, JT Zimmer, M Apostolidi, J Rinehart… - Molecular cell, 2021 - cell.com
Stress-induced readthrough transcription results in the synthesis of downstream-of-gene
(DoG)-containing transcripts. The mechanisms underlying DoG formation during cellular …
(DoG)-containing transcripts. The mechanisms underlying DoG formation during cellular …
Sequence-based modeling of three-dimensional genome architecture from kilobase to chromosome scale
J Zhou - Nature genetics, 2022 - nature.com
To learn how genomic sequence influences multiscale three-dimensional (3D) genome
architecture, this manuscript presents a sequence-based deep-learning approach, Orca, that …
architecture, this manuscript presents a sequence-based deep-learning approach, Orca, that …
LRRC8A-containing chloride channel is crucial for cell volume recovery and survival under hypertonic conditions
Regulation of cell volume is essential for tissue homeostasis and cell viability. In response to
hypertonic stress, cells need rapid electrolyte influx to compensate water loss and to prevent …
hypertonic stress, cells need rapid electrolyte influx to compensate water loss and to prevent …
Who let the DoGs out?–biogenesis of stress-induced readthrough transcripts
NA Rosa-Mercado, JA Steitz - Trends in biochemical sciences, 2022 - cell.com
Readthrough transcription caused by inefficient 3′-end cleavage of nascent mRNAs has
emerged as a hallmark of the mammalian cellular stress response and results in the …
emerged as a hallmark of the mammalian cellular stress response and results in the …
[HTML][HTML] Mechanistic drivers of chromatin organization into compartments
HL Harris, MJ Rowley - Current Opinion in Genetics & Development, 2024 - Elsevier
Highlights•Recent work indicates that chromatin compartments can finely segregate
genomic intervals that are 1–2 kb in size.•Evidence both supports and refutes several …
genomic intervals that are 1–2 kb in size.•Evidence both supports and refutes several …