Back

Genome organization regulates nuclear pore complex formation and promotes differentiation during Drosophila oogenesis

Kotb, N. M.; Ulukaya, G.; Chavan, A.; Nguyen, S. C.; Proskauer, L.; Joyce, E. F.; Hasson, D.; Jagannathan, M.; Rangan, P.

2023-11-16 developmental biology
10.1101/2023.11.15.567233 bioRxiv
Show abstract

Genome organization can regulate gene expression and promote cell fate transitions. The differentiation of germline stem cells (GSCs) to oocytes in Drosophila involves changes in genome organization mediated by heterochromatin and the nuclear pore complex (NPC). Heterochromatin represses germ-cell genes during differentiation and NPCs anchor these silenced genes to the nuclear periphery, maintaining silencing to allow for oocyte development. Surprisingly, we find that genome organization also contributes to NPC formation, mediated by the transcription factor Stonewall (Stwl). As GSCs differentiate, Stwl accumulates at boundaries between silenced and active gene compartments. Stwl at these boundaries plays a pivotal role in transitioning germ-cell genes into a silenced state and activating a group of oocyte genes and Nucleoporins (Nups). The upregulation of these Nups during differentiation is crucial for NPC formation and further genome organization. Thus, crosstalk between genome architecture and NPCs is essential for successful cell fate transitions.

Matching journals

The top 5 journals account for 50% of the predicted probability mass.

1
Development
● 497 papers in training set
Top 0.4%
18.2%
Similar papers in this journal
2
eLife
● 5828 papers in training set
Top 7%
12.3%
Similar papers in this journal
3
Current Biology
○ 665 papers in training set
Top 1%
9.5%
Similar papers in this journal
4
PLOS Genetics
● 862 papers in training set
Top 1%
8.8%
Similar papers in this journal
5
Nature Communications
○ 5641 papers in training set
Top 27%
5.4%
Similar papers in this journal
50% of probability mass above
6
Proceedings of the National Academy of Sciences
● 2444 papers in training set
Top 9%
5.4%
7
Cell Reports
○ 1498 papers in training set
Top 8%
4.8%
8
iScience
○ 1154 papers in training set
Top 4%
4.3%
9
EMBO Reports
○ 263 papers in training set
Top 1%
4.0%
10
Endocrinology
● 43 papers in training set
Top 0.2%
3.2%
11
Biology of Reproduction
◐ 36 papers in training set
Top 0.3%
2.1%
12
Developmental Dynamics
○ 56 papers in training set
Top 0.3%
2.1%
13
Science Advances
● 1243 papers in training set
Top 18%
1.9%
14
Developmental Biology
○ 150 papers in training set
Top 1.0%
1.7%
15
The EMBO Journal
○ 309 papers in training set
Top 4%
1.3%
16
Scientific Reports
○ 3612 papers in training set
Top 64%
1.1%
17
Genes & Development
● 90 papers in training set
Top 1%
1.0%
18
Communications Biology
○ 993 papers in training set
Top 28%
0.9%
19
GENETICS
◐ 483 papers in training set
Top 4%
0.8%
20
Frontiers in Cell and Developmental Biology
○ 233 papers in training set
Top 5%
0.8%
21
PLOS Biology
● 486 papers in training set
Top 14%
0.6%
22
Molecular Biology of the Cell
● 311 papers in training set
Top 4%
0.6%
23
Molecular Human Reproduction
◐ 11 papers in training set
Top 0.2%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.