Evidence map›Paper›PMID 38869785›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2024

MNase-Seq Analysis for Identifying Stress-Altered Nucleosome Occupancy in Plants.

Caleb Watkins, Karyn L Willyerd, Chi-Ping Liao, Donald R Ruhl, Charles Chen

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2024. 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. 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

5 authors.

Caleb WatkinsDepartment of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, USA.
Karyn L WillyerdDepartment of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, USA.
Chi-Ping LiaoDepartment of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, USA.
Donald R RuhlDepartment of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, USA.
Charles ChenDepartment of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, USA. Charles.chen@okstate.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Nucleosome occupancy plays an important role in chromatin compaction, affecting biological processes by hampering the binding of cis-acting elements such as transcription factors, RNA polymerase machinery, and coregulatory. Accessible regions allow for cis-acting elements to bind DNA and regulate transcription. Here, we detail our protocol to profile nucleosome occupancy and chromatin structure dynamics under drought stress at the genome-wide scale using micrococcal nuclease (MNase) digestion. Combining variable MNase concentration treatments and high-throughput sequencing, we investigate the changes in the overall chromatin state using bread wheat samples from an exemplary drought experiment.

Indexed as

High-Throughput Nucleotide SequencingMicrococcal NucleaseNucleosomesStress, PhysiologicalTriticumChromatinDroughtsGene Expression Regulation, PlantPlantsChromatinMicrococcal NucleaseNucleosomesChromatin structural variationMNase digestionMNase-seqNucleosome occupancy

Identifiers

PMID38869785

What OpenQuestion holds

Textmetadata
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.