Evidence map›Paper›PMID 38014330›Full record

ArticlebioRxiv : the preprint server for biology2023

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

Noor M Kotb, Gulay Ulukaya, Ankita Chavan, Son C Nguyen, Lydia Proskauer, Eric Joyce, Dan Hasson, Madhav Jagannathan, Prashanth Rangan

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed, 2 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

9 authors at 6 institutions in 3 countries.

Noor M KotbDepartment of Biomedical Sciences/Wadsworth Center, University at Albany SUNY, Albany, NY 12202.
Gulay UlukayaDepartment of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029.
Ankita ChavanDepartment of Biology, Institute of Biochemistry, ETH Zurich, 8092 Zurich.
Son C NguyenDepartment of Genetics, University of Pennsylvania, Philadelphia, PA 19104.
Lydia ProskauerDepartment of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12202.
Eric JoyceDepartment of Genetics, University of Pennsylvania, Philadelphia, PA 19104.
Dan HassonDepartment of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029.
Madhav JagannathanDepartment of Biology, Institute of Biochemistry, ETH Zurich, 8092 Zurich.
Prashanth RanganDepartment of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029.
ETH Zurich · CHInstitute of Bioinformatics and Systems Biology · DEUniversity of Pennsylvania · USAmherst College · USIcahn School of Medicine at Mount Sinai · USWadsworth Center · US

Funding

Conduits: Mount Sinai Health System Translational Science HubUL1TR004419 · NCATS · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI Rosalind J Wright · 2022 to 2026
$46.4M
THE TISCH CANCER INSTITUTE - CANCER CENTER SUPPORT GRANTP30CA196521 · NCI · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI Ramon E Parsons · 2015 to 2026
$35.4M
Regulation of stem cell differentiation during Drosophila oogenesisR01GM111779 · NIGMS · STATE UNIVERSITY OF NEW YORK AT ALBANY · PI RANGAN, PRASHANTH · 2014 to 2022
$2.7M
Big Omics Data Engine 2 SupercomputerS10OD026880 · OD · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI KOVATCH, PATRICIA · 2019 to 2019
$2.0M
Role of RNA degradation in germline stem cell to oocyte transitionR01GM135628 · NIGMS · STATE UNIVERSITY OF NEW YORK AT ALBANY · PI RANGAN, PRASHANTH · 2020 to 2023
$1.3M
Cellular rejuvenation during oogenesisR56AG082906 · NIA · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI CAPELSON, MAYA, RANGAN, PRASHANTH · 2023 to 2023
$387k
NCATS NIH HHS UL1 TR004419NCI NIH HHS P30 CA196521NIA NIH HHS R56 AG082906NIGMS NIH HHS R01 GM111779NIGMS NIH HHS R01 GM135628NIH HHS S10 OD026880
6 · The paper itself

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.

Indexed as

differentiationgenome organizationheterochromatinlaminNPCNucleoporins

Identifiers

PMID38014330
PMCPMC10680722
OpenAlexW4388724121

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.