CoChat
Sign Up
Cited by 64

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

Selective regulation of biological processes by vitamin D based on the spatio-temporal cistrome of its receptor

Neme, Antonio, Seuter, Sabine, Carlberg, Carsten·2017·Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
DOI 10.1016/j.bbagrm.2017.07.002
Open this paper in CoChat — free account

Abstract

The transcription factor vitamin D receptor (VDR) is the exclusive nuclear target of the biologically active form of vitamin D (1,25(OH) 2 D 3 ). In THP-1 human monocytes we obtained a highly accurate VDR cistrome after 2 and 24h ligand stimulation comprising >11,600 genomic loci, 78% of which were detected exclusively after 24h. In contrast, a group of 510 persistent VDR sites occurred at all conditions and some 2100 VDR loci were only transiently occupied. Machine learning and statistical analysis as well as a comparison with the re-analyzed B cell VDR cistrome indicated a subgroup of 339 highly conserved persistent VDR sites that were suited best for describing vitamin D-triggered gene regulatory scenarios. The 1,25(OH) 2 D 3 -dependent transcriptome of THP-1 cells comprised 587 genes, 311 of which were primary targets with main functions in the immune system. More than 97% of the latter genes were located within 1,25(OH) 2 D 3 -modulated topologically associated domains (TADs). The number of persistent and transient VDR sites was found to be the main discriminator for sorting these TADs into five classes carrying vitamin D target genes involved in distinct biological processes. In conclusion, specific regulation of biological processes by vitamin D depends on differences in time-dependent VDR binding.

Overview

Integrity signals

Registry

Crossref · 10.1016/j.bbagrm.2017.07.002

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Verification

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

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?

  • In THP-1 cells, ChIP-seq detected 11,657 VDR binding sites, only 510 of which were occupied under all conditions; 2109 transient VDR-binding sites existed, and the majority of binding sites (9038) were only observed after 24 h ligand stimulation.

    “In THP‐1 cells, ChIP‐seq detected 11,657 VDR binding sites (Neme et al., 2017), although only 510 were occupied under all conditions. In addition to these persistent binding sites, 2109 transient VDR‐binding sites were found to exist. The majority of binding sites (9038) were only observed after 24 h ligand stimulation.”

    From The evolution of human skin pigmentation: A changing medley of vitamins, genetic variability, and UV radiation during human expansion (2023) · cites this paper as Neme et al., 2017

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 31

  1. Verstuyf, 2010, Vitamin D: a pleiotropic hormone, Kidney Int., 78, 140, 10.1038/ki.2010.17 · DOI
  2. Feldman, 2014, The role of vitamin D in reducing cancer risk and progression, Nat. Rev. Cancer, 14, 342, 10.1038/nrc3691 · DOI
  3. Carlberg, 2014, The physiology of vitamin D-far more than calcium and bone, Front. Physiol., 5, 335, 10.3389/fphys.2014.00335 · DOI
  4. Haussler, 2008, Vitamin D receptor: molecular signaling and actions of nutritional ligands in disease prevention, Nutr. Rev., 66, S98, 10.1111/j.1753-4887.2008.00093.x · DOI
  5. Umesono, 1991, Direct repeats as selective response elements for the thyroid hormone, retinoic acid, and vitamin D3 receptors, Cell, 65, 1255, 10.1016/0092-8674(91)90020-Y · DOI
  6. Carlberg, 1993, Two nuclear signalling pathways for vitamin D, Nature, 361, 657, 10.1038/361657a0 · DOI
  7. Ramagopalan, 2010, A ChIP-seq defined genome-wide map of vitamin D receptor binding: associations with disease and evolution, Genome Res., 20, 1352, 10.1101/gr.107920.110 · DOI
  8. Heikkinen, 2011, Nuclear hormone 1α,25-dihydroxyvitamin D3 elicits a genome-wide shift in the locations of VDR chromatin occupancy, Nucleic Acids Res., 39, 9181, 10.1093/nar/gkr654 · DOI
  9. Tuoresmäki, 2014, Patterns of genome-wide VDR locations, PLoS One, 9, 10.1371/journal.pone.0096105 · DOI
  10. Meyer, 2012, VDR/RXR and TCF4/beta-catenin cistromes in colonic cells of colorectal tumor origin: impact on c-FOS and c-MYC gene expression, Mol. Endocrinol., 26, 37, 10.1210/me.2011-1109 · DOI
  11. Seuter, 2016, Epigenome-wide effects of vitamin D and their impact on the transcriptome of human monocytes involve CTCF, Nucleic Acids Res., 44, 4090, 10.1093/nar/gkv1519 · DOI
  12. Phillips, 2009, CTCF: master weaver of the genome, Cell, 137, 1194, 10.1016/j.cell.2009.06.001 · DOI
  13. Ghirlando, 2016, CTCF: making the right connections, Genes Dev., 30, 881, 10.1101/gad.277863.116 · DOI
  14. Ali, 2016, Insulators and domains of gene expression, Curr. Opin. Genet. Dev., 37, 17, 10.1016/j.gde.2015.11.009 · DOI
  15. Dixon, 2012, Topological domains in mammalian genomes identified by analysis of chromatin interactions, Nature, 485, 376, 10.1038/nature11082 · DOI · Paper page
  16. Neme, 2016, Vitamin D-dependent chromatin association of CTCF in human monocytes, Biochim. Biophys. Acta, 1859, 1380, 10.1016/j.bbagrm.2016.08.008 · DOI
  17. ENCODE-Project-Consortium, 2012, An integrated encyclopedia of DNA elements in the human genome, Nature, 489, 57, 10.1038/nature11247 · DOI · Paper page
  18. Tsuchiya, 1980, Establishment and characterization of a human acute monocytic leukemia cell line (THP-1), Int. J. Cancer, 26, 171, 10.1002/ijc.2910260208 · DOI
  19. Matilainen, 2010, Primary effect of 1α,25(OH)2D3 on IL-10 expression in monocytes is short-term down-regulation, Biochim. Biophys. Acta, 1803, 1276, 10.1016/j.bbamcr.2010.07.009 · DOI
  20. Gynther, 2011, Mechanism of 1α,25-dihydroxyvitamin D3-dependent repression of interleukin-12B, Biochim. Biophys. Acta, 1813, 810, 10.1016/j.bbamcr.2011.01.037 · DOI
  21. Seuter, 2013, Chromatin acetylation at transcription start sites and vitamin D receptor binding regions relates to effects of 1α,25-dihydroxyvitamin D3 and histone deacetylase inhibitors on gene expression, Nucleic Acids Res., 41, 110, 10.1093/nar/gks959 · DOI
  22. Zhang, 2012, ChIA-PET analysis of transcriptional chromatin interactions, Methods, 58, 289, 10.1016/j.ymeth.2012.08.009 · DOI
  23. Langmead, 2009, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol., 10, R25, 10.1186/gb-2009-10-3-r25 · DOI · Paper page
  24. Li, 2009, The sequence alignment/map format and SAMtools, Bioinformatics, 25, 2078, 10.1093/bioinformatics/btp352 · DOI · Paper page
  25. Robinson, 2011, Integrative genomics viewer, Nat. Biotechnol., 29, 24, 10.1038/nbt.1754 · DOI · Paper page
  26. Zhang, 2008, Model-based analysis of ChIP-Seq (MACS), Genome Biol., 9, R137, 10.1186/gb-2008-9-9-r137 · DOI · Paper page
  27. Heinz, 2010, Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities, Mol. Cell, 38, 576, 10.1016/j.molcel.2010.05.004 · DOI · Paper page
  28. Dobin, 2013, STAR: ultrafast universal RNA-seq aligner, Bioinformatics, 29, 15, 10.1093/bioinformatics/bts635 · DOI · Paper page
  29. Love, 2014, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol., 15, 550, 10.1186/s13059-014-0550-8 · DOI · Paper page
  30. Eden, 2009, GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists, BMC Bioinf., 10, 48, 10.1186/1471-2105-10-48 · DOI · Paper page
  31. Seuter, 2017, Epigenomic PU.1-VDR crosstalk modulates vitamin D signaling, Biochim. Biophys. Acta, 1860, 405, 10.1016/j.bbagrm.2017.02.005 · DOI

Cited by

Sorted by citations

Metadata

Authors
Neme, A., Seuter, S., & Carlberg, C.
Venue
Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
Publisher
Elsevier BV
Published
2017-09
Volume
1860
Issue
9
Pages
952-961
ISSN
1874-9399
DOI
10.1016/j.bbagrm.2017.07.002
Cited by
64
References
1
Language
en
Licence
www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Funders
Academy of Finland (267067)

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