Evidence map›Paper›PMID 41547832›Full record

ArticleNature communications2026

Af-CUT&Tag: a sensitive and antibody-free chromatin profiling method using genetically encoded tags and high-affinity binders fused to Tn5.

Xindong Wang, Xusheng Deng, Lu Qiu, Junjia Liu, Hengxiang Shen, Haoran Du, Weijie Li, Linxuan Song, Wenhui Deng, Xiaoning Dong and 5 more

Abstract read
PubMed Full text at PMC Publisher
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 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

15 authors.

Xindong Wang *State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, National Institute for Data Science in Health and Medicine Engineering, Faculty of Medicine and Life Sciences, Shenzhen Research Institute of Xiamen University, Xiamen University, Xiamen, Fujian, China.
Xusheng Deng *State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, National Institute for Data Science in Health and Medicine Engineering, Faculty of Medicine and Life Sciences, Shenzhen Research Institute of Xiamen University, Xiamen University, Xiamen, Fujian, China.
Lu QiuState Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, National Institute for Data Science in Health and Medicine Engineering, Faculty of Medicine and Life Sciences, Shenzhen Research Institute of Xiamen University, Xiamen University, Xiamen, Fujian, China.
Junjia LiuState Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, National Institute for Data Science in Health and Medicine Engineering, Faculty of Medicine and Life Sciences, Shenzhen Research Institute of Xiamen University, Xiamen University, Xiamen, Fujian, China.
Hengxiang ShenState Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, National Institute for Data Science in Health and Medicine Engineering, Faculty of Medicine and Life Sciences, Shenzhen Research Institute of Xiamen University, Xiamen University, Xiamen, Fujian, China.
Haoran DuState Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, National Institute for Data Science in Health and Medicine Engineering, Faculty of Medicine and Life Sciences, Shenzhen Research Institute of Xiamen University, Xiamen University, Xiamen, Fujian, China.
Weijie LiState Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, National Institute for Data Science in Health and Medicine Engineering, Faculty of Medicine and Life Sciences, Shenzhen Research Institute of Xiamen University, Xiamen University, Xiamen, Fujian, China.
Linxuan SongState Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, National Institute for Data Science in Health and Medicine Engineering, Faculty of Medicine and Life Sciences, Shenzhen Research Institute of Xiamen University, Xiamen University, Xiamen, Fujian, China.
Wenhui DengState Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, National Institute for Data Science in Health and Medicine Engineering, Faculty of Medicine and Life Sciences, Shenzhen Research Institute of Xiamen University, Xiamen University, Xiamen, Fujian, China.
Xiaoning DongState Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, National Institute for Data Science in Health and Medicine Engineering, Faculty of Medicine and Life Sciences, Shenzhen Research Institute of Xiamen University, Xiamen University, Xiamen, Fujian, China.
Yi HanState Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, National Institute for Data Science in Health and Medicine Engineering, Faculty of Medicine and Life Sciences, Shenzhen Research Institute of Xiamen University, Xiamen University, Xiamen, Fujian, China.
Benchao LiuState Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, National Institute for Data Science in Health and Medicine Engineering, Faculty of Medicine and Life Sciences, Shenzhen Research Institute of Xiamen University, Xiamen University, Xiamen, Fujian, China.
Jialiang HuangState Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, National Institute for Data Science in Health and Medicine Engineering, Faculty of Medicine and Life Sciences, Shenzhen Research Institute of Xiamen University, Xiamen University, Xiamen, Fujian, China.ORCID http://orcid.org/0000-0002-5218-1144
Zengpeng LiKey Laboratory of Marine Genetic Resources, State Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Fujian Collaborative Innovation Centre for Exploitation and Utilization of Marine Biological Resources, Third Institute of Oceanography Ministry of Natural Resources, Xiamen, China. lizengpeng@tio.org.cn.ORCID http://orcid.org/0009-0004-7463-0790
Yongyou ZhangState Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, School of Life Sciences, National Institute for Data Science in Health and Medicine Engineering, Faculty of Medicine and Life Sciences, Shenzhen Research Institute of Xiamen University, Xiamen University, Xiamen, Fujian, China. yongyouzhang@xmu.edu.cn.ORCID http://orcid.org/0000-0003-2413-9106

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Conventional chromatin profiling techniques are often limited by antibody availability and performance. Here, we introduce Af-CUT&Tag, a target antibody-free method that overcomes these limitations by using CRISPR-integrated peptide tags (HiBiT/ALFA-tag) recognized by engineered binders (LgBiT/NbALFA) fused to a Tn5 transposase. Af-CUT&Tag eliminates dependence on traditional target antibodies, achieving robust specificity and sensitivity with as few as 500 cells. It provides high-quality chromatin profiles, with improved signal-to-noise ratios and library quality compared with conventional antibody-based counterparts, while also enabling single-cell resolution (scAf-CUT&Tag). Applying Af-CUT&Tag to Hippo effectors (YAP1/TAZ) during liver regeneration reveals dynamic chromatin remodeling, including YAP1/TAZ-mediated control of lipid metabolism (e.g., Lpin1, Fasn) and heme clearance (Hpx, Trf). We further identify miR-122 as a critical regulator of these processes, impacting liver regeneration. The versatility of Af-CUT&Tag in cell lines, bulk tissues, and single nuclei establishes it as a powerful tool for studying gene regulation in development, disease, and regeneration.

Indexed as

ChromatinTransposasesAnimalsChromatin Assembly and DisassemblyCRISPR-Cas SystemsHumansLiver RegenerationMiceMicroRNAsTranscription FactorsChromatinMicroRNAsTranscription FactorsTransposases

Identifiers

PMID41547832
PMCPMC12914055

What Socratic 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 Socratic graph.