The Drosophila Fab-7 boundary modulates Abd-B gene activity by guiding an inversion of collinear chromatin organization and alternate promoter use DOI Creative Commons
Laura Moniot-Perron, Benoît Moindrot, Line Manceau

et al.

Cell Reports, Journal Year: 2023, Volume and Issue: 42(1), P. 111967 - 111967

Published: Jan. 1, 2023

Hox genes encode transcription factors that specify segmental identities along the anteroposterior body axis. These are organized in clusters, where their order corresponds to activity axis, a feature known as collinearity. In Drosophila, BX-C cluster contains three most posterior genes, collinear activation incorporates progressive changes histone modifications, chromatin architecture, and use of boundary elements cis-regulatory regions. To dissect functional hierarchies, we compare organization cell lines larvae, with focus on Abd-B gene. Our work establishes importance Fab-7 for insulation between 3D domains carrying different modifications. Interestingly, detect non-canonical inversion dynamics at Abd-B, domain active modifications progressively decreasing size. This dynamic differentially activates alternative promoters gene, thereby expanding possibilities fine-tuning transcriptional output.

Language: Английский

Regulatory landscape of enhancer-mediated transcriptional activation DOI
Koji Kawasaki, Takashi Fukaya

Trends in Cell Biology, Journal Year: 2024, Volume and Issue: 34(10), P. 826 - 837

Published: Feb. 13, 2024

Language: Английский

Citations

10
Principles of long-range gene regulation DOI Creative Commons
Sanyami Zunjarrao, Maria Cristina Gambetta

Current Opinion in Genetics & Development, Journal Year: 2025, Volume and Issue: 91, P. 102323 - 102323

Published: Feb. 13, 2025

Transcription from gene promoters occurs in specific spatiotemporal patterns multicellular organisms, controlled by genomic regulatory elements. The communication between a element and promoter requires certain degree of physical proximity them; hence, most regulation locally the genome. However, recent discoveries have revealed long-range strategies that enhance interactions elements overcoming distances them linear These new findings challenge traditional view how expression are controlled. This review examines recently reported Drosophila mammals, offering insights into their mechanisms evolution.

Language: Английский

Citations

2
Hi-GDT: A Hi-C-based 3D gene domain analysis tool for analyzing local chromatin contacts in plants DOI Creative Commons
Hongwoo Lee, Pil Joon Seo

GigaScience, Journal Year: 2025, Volume and Issue: 14

Published: Jan. 1, 2025

Three-dimensional (3D) chromatin organization is emerging as a key factor in gene regulation eukaryotes. Recent studies using high-resolution Hi-C analysis have explored fine-scale local contact domains plants, exemplified by the basic established at accessible border regions Arabidopsis (Arabidopsis thaliana). However, we lack effective tools to identify these and examine their structural dynamics. We developed Hi-C-based 3D Gene Domain Tool (Hi-GDT) with particular focus on borders. Hi-GDT successfully identifies domains, including single-gene multigene high reproducibility. can also be used discover that are differentially organized association differences expression between tissue types, genotypes, or response environmental stimuli. valuable tool for identifying genes regulated dynamic conformational changes, expanding our understanding of functional relevance plants. publicly available https://github.com/CDL-HongwooLee/Hi-GDT.

Language: Английский

Citations

1
M1BP cooperates with CP190 to activate transcription at TAD borders and promote chromatin insulator activity DOI Creative Commons
Indira Bag, Shue Chen, Leah F. Rosin

et al.

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: July 7, 2021

Abstract Genome organization is driven by forces affecting transcriptional state, but the relationship between transcription and genome architecture remains unclear. Here, we identified Drosophila factor Motif 1 Binding Protein (M1BP) in physical association with gypsy chromatin insulator core complex, including universal protein CP190. M1BP required for enhancer-blocking barrier activities of as well its proper nuclear localization. Genome-wide, specifically colocalizes CP190 at 1-containing promoters, which are enriched topologically associating domain (TAD) borders. facilitates binding many shared sites vice versa. Both factors promote 1-dependent gene expression near TAD borders genome-wide. Finally, loss reduces accessibility increases both inter- intra-TAD local compaction. Our results reveal functional interaction to activate mediate insulator-dependent organization.

Language: Английский

Citations

52
Function and Evolution of the Loop Extrusion Machinery in Animals DOI Open Access
Evelyn Kabirova, Artem Nurislamov, Artem Shadskiy

et al.

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(5), P. 5017 - 5017

Published: March 6, 2023

Structural maintenance of chromosomes (SMC) complexes are essential proteins found in genomes all cellular organisms. Essential functions these proteins, such as mitotic chromosome formation and sister chromatid cohesion, were discovered a long time ago. Recent advances chromatin biology showed that SMC involved many other genomic processes, acting active motors extruding DNA, which leads to the loops. Some loops formed by highly cell type developmental stage specific, SMC-mediated DNA required for VDJ recombination B-cell progenitors, or dosage compensation Caenorhabditis elegans X-chromosome inactivation mice. In this review, we focus on extrusion-based mechanisms common multiple types species. We will first describe an anatomy their accessory proteins. Next, provide biochemical details extrusion process. follow sections describing role gene regulation, repair, topology.

Language: Английский

Citations

22
RNA polymerases reshape chromatin architecture and couple transcription on individual fibers DOI
Thomas W. Tullius, R. Stefan Isaac, Danilo Dubocanin

et al.

Molecular Cell, Journal Year: 2024, Volume and Issue: 84(17), P. 3209 - 3222.e5

Published: Aug. 26, 2024

Language: Английский

Citations

8
Cooperative insulation of regulatory domains by CTCF-dependent physical insulation and promoter competition DOI Creative Commons

Thais Ealo,

Víctor Sánchez-Gaya, Patricia Respuela

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Aug. 23, 2024

Abstract The specificity of gene expression during development requires the insulation regulatory domains to avoid inappropriate enhancer-gene interactions. In vertebrates, this insulator function is mostly attributed clusters CTCF sites located at topologically associating domain (TAD) boundaries. However, TAD boundaries allow some physical crosstalk across domains, which odds with specific and precise developmental genes. Here we show that genes nearby cooperatively foster robust domains. By genetically dissecting a couple representative loci in mouse embryonic stem cells, prevent undesirable contacts ( i.e . insulation), while preferentially contribute through non-structural mechanisms involving promoter competition rather than enhancer blocking. Overall, our work provides important insights into turn might help interpreting pathological consequences certain structural variants.

Language: Английский

Citations

7
Mechanisms of enhancer-promoter communication and chromosomal architecture in mammals and Drosophila DOI Creative Commons
Olga Kyrchanova, Oleg V. Bylino, Pavel Georgiev

et al.

Frontiers in Genetics, Journal Year: 2022, Volume and Issue: 13

Published: Dec. 1, 2022

The spatial organization of chromosomes is involved in regulating the majority intranuclear processes higher eukaryotes, including gene expression. Drosophila was used as a model to discover many transcription factors whose homologs play key role regulation expression mammals. According modern views, cohesin complex mostly determines architecture mammalian by forming chromatin loops on anchors created CTCF DNA-binding architectural protein. chromosome poorly understood Drosophila, and merely one proteins with proven potential organize specific long-range interactions between regulatory elements genome. review compares mechanisms responsible for mammals Drosophila.

Language: Английский

Citations

25
The scales, mechanisms, and dynamics of the genome architecture DOI Creative Commons
Ludvig Lizana, Yuri B. Schwartz

Science Advances, Journal Year: 2024, Volume and Issue: 10(15)

Published: April 10, 2024

Even when split into several chromosomes, DNA molecules that make up our genome are too long to fit the cell nuclei unless massively folded. Such folding must accommodate need for timely access selected parts of by transcription factors, RNA polymerases, and replication machinery. Here, we review current understanding inside interphase nuclei. We consider resulting architecture at three scales with a particular focus on intermediate (meso) scale summarize insights gained from recent experimental observations diverse computational models.

Language: Английский

Citations

6
Factors that determine cell type–specific CTCF binding in health and disease DOI
Catherine Do, Jane A. Skok

Current Opinion in Genetics & Development, Journal Year: 2024, Volume and Issue: 88, P. 102244 - 102244

Published: Aug. 14, 2024

Language: Английский

Citations

6