Cited by 87Single-cell and spatial transcriptomicsLiver physiology and pathologyGenomics and Chromatin Dynamics

Single-nucleus RNA-seq2 reveals functional crosstalk between liver zonation and ploidy

Open access
Richter, M. L., Deligiannis, I. K., Yin, K., Danese, A., Lleshi, E., Coupland, P., Vallejos, C. A., Matchett, K. P. +3 more·2021·Nature Communications

Published version of a preprint

Abstract

Single-cell RNA-seq reveals the role of pathogenic cell populations in development and progression of chronic diseases. In order to expand our knowledge on cellular heterogeneity, we have developed a single-nucleus RNA-seq2 method tailored for the comprehensive analysis of the nuclear transcriptome from frozen tissues, allowing the dissection of all cell types present in the liver, regardless of cell size or cellular fragility. We use this approach to characterize the transcriptional profile of individual hepatocytes with different levels of ploidy, and have discovered that ploidy states are associated with different metabolic potential, and gene expression in tetraploid mononucleated hepatocytes is conditioned by their position within the hepatic lobule. Our work reveals a remarkable crosstalk between gene dosage and spatial distribution of hepatocytes.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/s41467-021-24543-5

Cites

142 of 143 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • A single-nucleus RNA sequencing study found differences between 2n and 4n hepatocytes with regards to their expression of genes associated with metabolism, which shows crosstalk with the hepatocyte's position within the lobule.

    “Recently, a single-nucleus RNA sequencing study found differences between 2n and 4n hepatocytes with regards to their expression of genes associated with metabolism, which shows crosstalk with the hepatocyte’s position within the lobule.40”

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Cited by

Sorted by citations

Authors
Richter, M. L., Deligiannis, I. K., Yin, K., Danese, A., Lleshi, E., Coupland, P., Vallejos, C. A., Matchett, K. P., Henderson, N. C., Colome-Tatche, M., & Martinez-Jimenez, C. P.
Affiliations
  • Helmholtz Munich (DE)
  • University of Cambridge (GB)
  • Western General Hospital (GB)
  • Centre for Inflammation Research (GB)
Venue
Nature Communications
Published
2021-07-12
Volume
12
Issue
1
Pages
4264-4264
ISSN
2041-1723 (ISSN-L)
OpenAlex
W3180187472
Cited by
75
References
141
Citations by year
2026: 8 · 2025: 16 · 2024: 9 · 2023: 21 · 2022: 17 · 2021: 4
FWCI
5.02
Type
journal article
Language
en
Open access
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
  • PuSH - Publication Server of Helmholtz Zentrum München (submittedVersion, cc-by)
  • Apollo (University of Cambridge) (submittedVersion, cc-by)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • mediaTUM – the media and publications repository of the Technical University Munich (Technical University Munich) (submittedVersion, other-oa)
  • Site cant be reached (submittedVersion, cc-by)
  • Repository of Digital Objects for Teaching Research and Culture (University of Valencia) (submittedVersion, other-oa)
  • Apollo
  • Apollo (cc-by)
Funders
  • Deutsches Krebsforschungszentrum
  • Wellcome Trust (219542/Z/19/Z, 219542/Z/19/Z, WT098051, 219542, WT 098051)
  • Cancer Research UK (WT098051)
  • University of Edinburgh
  • European Association for the Study of the Liver
  • Cancer Research UK Cambridge Institute, University of Cambridge
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
  • Health Sciences › Medicine › Hepatology › Liver physiology and pathology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords
nuclear transcriptome, hepatocyte ploidy, liver zonation, hepatic lobule, gene dosage, cellular heterogeneity
MeSH terms
Animals, Cell Nucleus, Chronic Disease, Frozen Sections, Gene Expression Regulation, Liver, Liver Diseases, Mice, Inbred C57BL, Ploidies, Regeneration, Stem Cells, Transcription Factors, Transcription, Genetic, Biomarkers, Sequence Analysis, RNA, Gene Expression Profiling, Hepatocytes, Mice, Single-Cell Analysis, Gene Ontology

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review