Evidence map›Paper›PMID 41720075›Full record

ArticleMolecular cell2026

Cell-free genomics reveals fundamental regulatory principles of the Mycobacterium tuberculosis transcription cycle.

Ruby Froom, Michael B Wolfe, Kelly N Eckartt, Rachel A Mooney, Madeleine Delbeau, Mirjana Lilic, Alexis Jaramillo Cartagena, Jeremy M Rock, Seth A Darst, Robert Landick and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Molecular cell, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. RNAP-seq:bioRxiv : the preprint server for biology · 2026
    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

11 authors.

Ruby FroomLaboratory of Molecular Pathogenesis, The Rockefeller University, New York, NY 10065, USA; Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA. Electronic address: rfroom01@rockefeller.edu.
Michael B WolfeDepartment of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
Kelly N EckarttLaboratory of Molecular Pathogenesis, The Rockefeller University, New York, NY 10065, USA.
Rachel A MooneyDepartment of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
Madeleine DelbeauLaboratory of Molecular Pathogenesis, The Rockefeller University, New York, NY 10065, USA.
Mirjana LilicLaboratory of Molecular Pathogenesis, The Rockefeller University, New York, NY 10065, USA.
Alexis Jaramillo CartagenaLaboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA.
Jeremy M RockLaboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA.
Seth A DarstLaboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA.
Robert LandickDepartment of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA. Electronic address: rlandick@wisc.edu.
Elizabeth A CampbellLaboratory of Molecular Pathogenesis, The Rockefeller University, New York, NY 10065, USA. Electronic address: campbee@rockefeller.edu.

Funding

STRUCTURE/FUNCTION OF TRANSCRIPTION COMPLEX RNA HAIRPINSR01GM038660 · NIGMS · WASHINGTON UNIVERSITY · PI Robert Landick · 1992 to 2026
$12.2M
Structural and functional studies of the mycobacterial transcription cycleR35GM151879 · NIGMS · ROCKEFELLER UNIVERSITY · PI ELIZABETH A CAMPBELL · 2024 to 2026
$1.4M
NIGMS NIH HHS R01 GM038660NIGMS NIH HHS R35 GM151879
6 · The paper itself

Abstract

Tiers of gene regulation govern cellular life. The intrinsic activities of RNA polymerase (RNAP) constitute a primary tier, while direct modulation by accessory transcription factors (TFs) constitutes a secondary tier. Cellular signaling cascades and feedback loops generate tertiary and higher-order tiers. Dissecting gene regulation requires distinguishing direct TF targets at the genome scale from indirect network effects. A major obstacle is the lack of tools to interrogate transcription machineries from difficult-to-culture microbes-such as pathogens, commensals, and environmental species-at the genome scale. Here, we introduce cell-free genomics (CFG), an empirical approach that identifies the direct targets of RNAP and TFs and systematizes their transcriptional effects. We demonstrate the efficacy of CFG by characterizing global and essential transcription initiation (CRP and holo-WhiB1) and elongation-termination factors (NusA and NusG) from the deadly pathogen, Mycobacterium tuberculosis. CFG expands our understanding of transcription principles and is broadly extensible to other perturbations and diverse species.

Indexed as

Bacterial ProteinsGene Expression Regulation, BacterialGenomicsMycobacterium tuberculosisTranscription, GeneticCell-Free SystemDNA-Directed RNA PolymerasesTranscription FactorsBacterial ProteinsDNA-Directed RNA PolymerasesTranscription Factorscell-free genomicsgenome-scale transcriptionMycobacterium tuberculosisRNA polymerasetranscription factorstranscription regulation

Identifiers

PMID41720075
PMCPMC13173409

What OpenQuestion holds

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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.