Evidence map›Paper›PMID 41896479›Full record

ArticleNature biotechnology2026

Mapping cis-regulatory mutations at scale in sorghum enables modulation of gene expression.

Evan D Groover, David Ding, Flora Z Wang, Gonzalo Benegas, Joseph Rivera, Shahar Schwartz, Stephen Chen, Michael F Moubarak, Viktoriya Georgieva, Peggy G Lemaux and 4 more

Abstract read
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In one paragraph

Article in Nature biotechnology, 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. Review
  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

14 authors.

Evan D Groover *Innovative Genomics Institute, University of California, Berkeley, CA, USA.
David Ding *Innovative Genomics Institute, University of California, Berkeley, CA, USA.
Flora Z WangInnovative Genomics Institute, University of California, Berkeley, CA, USA.ORCID http://orcid.org/0009-0006-2874-0942
Gonzalo BenegasDepartment of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA.
Joseph RiveraInnovative Genomics Institute, University of California, Berkeley, CA, USA.
Shahar SchwartzInnovative Genomics Institute, University of California, Berkeley, CA, USA.
Stephen ChenInnovative Genomics Institute, University of California, Berkeley, CA, USA.
Michael F MoubarakInnovative Genomics Institute, University of California, Berkeley, CA, USA.
Viktoriya GeorgievaInnovative Genomics Institute, University of California, Berkeley, CA, USA.ORCID http://orcid.org/0009-0001-5843-726X
Peggy G LemauxInnovative Genomics Institute, University of California, Berkeley, CA, USA.
Brian J StaskawiczInnovative Genomics Institute, University of California, Berkeley, CA, USA.
Krishna K NiyogiInnovative Genomics Institute, University of California, Berkeley, CA, USA.ORCID http://orcid.org/0000-0001-7229-2071
Yun S SongInnovative Genomics Institute, University of California, Berkeley, CA, USA.ORCID http://orcid.org/0000-0002-0734-9868
David F SavageInnovative Genomics Institute, University of California, Berkeley, CA, USA. dsavage@berkeley.edu.ORCID http://orcid.org/0000-0003-0042-2257

Funding

National Science Foundation (NSF) 2305833
6 · The paper itself

Abstract

Precise modulation of gene expression through cis-regulatory editing holds promise for nontransgenic crop improvement. However, the sequence-to-function relationships that govern plant promoter activity remain poorly understood. Here we develop a massively parallel reporter assay in Sorghum bicolor to systematically measure the effects of >30,000 mutations spanning deletions, substitutions and motif insertions accessible through CRISPR editing across entire native promoters and 5' untranslated regions of 3 photosynthesis genes: PsbS, Raf1 and SBPase. We find that gene expression is most tunable within a ~500-bp core promoter region. The mutational effects are reproducible across biological replicates and predictive of protein output. Within these regions, we identify compact deletions and motif insertions that strongly increase protein production (>30-fold relative to wild type), outperforming transgenic enhancer elements. Mutation-effect relationships are gene specific, highlighting the need for tailored regulatory maps. Our results establish a high-throughput strategy for cis-regulatory fine-mapping that may enable crop improvements through minimal, precise and nontransgenic gene edits.

Identifiers

PMID41896479

What OpenQuestion holds

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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.