Evidence map›Paper›PMID 42711332›Full record

ArticleNature communications2026

Structural Characterization of Native RNA Polymerase II Transcription Complexes and Nucleosomes in Drosophila melanogaster.

Natalie L Venette-Smith, Rishi K Vishwakarma, Varun Venkatakrishnan, Roberta Dollinger, Josie Schultz, Paul Babitzke, Ganesh Anand, David S Gilmour, Jean-Paul Armache, Katsuhiko S Murakami

Abstract read
In one paragraph

Article in Nature communications, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Natalie L Venette-SmithDepartment of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
Rishi K VishwakarmaDepartment of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
Varun VenkatakrishnanDepartment of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
Roberta DollingerDepartment of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
Josie SchultzDepartment of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
Paul BabitzkeDepartment of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.ORCID 0000-0003-2481-1062
Ganesh AnandDepartment of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.ORCID 0000-0001-8995-3067
David S GilmourDepartment of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.ORCID 0000-0003-4665-6147
Jean-Paul ArmacheDepartment of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA. jza449@psu.edu.ORCID 0000-0001-9195-2282
Katsuhiko S MurakamiDepartment of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA. kum14@psu.edu.ORCID 0000-0003-2244-0501

Funding

POTENTIATED STATE OF THE HSP70 HEAT SHOCK GENER01GM047477 · NIGMS · PENNSYLVANIA STATE UNIVERSITY-UNIV PARK · PI GILMOUR, DAVID SCOTT · 1992 to 2022
$6.7M
Regulation of transcription elongationR01GM098399 · NIGMS · PENNSYLVANIA STATE UNIVERSITY, THE · PI BABITZKE, PAUL L · 2012 to 2024
$3.6M
HEI: Acquisition of a Talos Arctica G2S10OD026822 · OD · PENNSYLVANIA STATE UNIVERSITY, THE · PI HAFENSTEIN, SUSAN · 2019 to 2019
$2.0M
Post-transcription Initiation Control of Gene ExpressionR35GM153190 · NIGMS · PENNSYLVANIA STATE UNIVERSITY, THE · PI PAUL L BABITZKE · 2024 to 2026
$1.3M
Structural study of direct associations between cellular RNA polymerase and regulatory factors during the transcription cycleR35GM156623 · NIGMS · PENNSYLVANIA STATE UNIVERSITY, THE · PI Katsuhiko Murakami · 2025 to 2026
$903k
Structure of Malaria Parasite RNA polymeraseR21AI168948 · NIAID · PENNSYLVANIA STATE UNIVERSITY, THE · PI LLINAS, MANUEL, MURAKAMI, KATSUHIKO · 2022 to 2023
$435k
Molecular Mechanisms of Chromatin Remodeling and DeacetylationR35GM161751 · NIGMS · PENNSYLVANIA STATE UNIVERSITY, THE · PI Jean-Paul Armache · 2026 to 2026
$426k
NIAID NIH HHS R21 AI168948NIGMS NIH HHS R01 GM047477NIGMS NIH HHS R01 GM098399NIGMS NIH HHS R35 GM153190NIGMS NIH HHS R35 GM156623NIGMS NIH HHS R35 GM161751NIH HHS S10 OD026822U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) R35GM161751
6 · The paper itself

Abstract

Structural studies of eukaryotic RNA polymerase II (Pol II) transcription often rely on in vitro assembly, which may not fully represent native conditions. To investigate Pol II transcription in metazoan cells, we developed a method to isolate native transcription complexes from Drosophila melanogaster embryos using FLAG-tag affinity purification and Micrococcal Nuclease treatment. Cryo-EM and proteomics studies revealed diverse transcription complexes and nucleosomes, including a metazoan Rpb4/Rpb7 stalk-less Pol II elongation complex and a hexameric nucleosome lacking an H2A/H2B dimer. Notably, nucleosome is found only downstream of the nucleosome elongation complex, underscoring it as a major energy barrier and a time-consuming step during Pol II progression through chromatin. Proteomics identified co-purified factors involved in transcription initiation, elongation, and RNA modification. This study provides a framework for investigations of transcription in cells, paving the way for future studies of transient and minor complexes.

Indexed as

Drosophila melanogasterDrosophila ProteinsNucleosomesRNA Polymerase IITranscription, GeneticAnimalsChromatinCryoelectron MicroscopyEmbryo, NonmammalianHistonesProteomicsChromatinDrosophila ProteinsHistonesNucleosomesRNA Polymerase II

Identifiers

PMID42711332
PMCPMC13554098

What OpenQuestion holds

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Registered trials

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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.