ArticleGenome research2011
Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers, 1 of them a synthesis that pooled it.
What it found
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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.
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Who cites it
26 citing papers in PubMed, 1 synthesis or guideline pooled it, 49 citations in OpenAlex.
- HSC commitment-associated epigenetic signature is prognostic in acute myeloid leukemia.The Journal of clinical investigation · 2014Pooled it
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- The topography of nullomer-emerging mutations and their relevance to human disease.Computational and structural biotechnology journal · 2025Article
- Sex-specific DNA-replication in the early mammalian embryo.Nature communications · 2024Article
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- Family-effects in the epigenomic response of red blood cells to a challenge test in the European sea bass (Dicentrarchus labrax, L.).BMC genomics · 2021Article
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- In silico APC/C substrate discovery reveals cell cycle-dependent degradation of UHRF1 and other chromatin regulators.PLoS biology · 2020Article
- Rapid Irreversible Transcriptional Reprogramming in Human Stem Cells Accompanied by Discordance between Replication Timing and Chromatin Compartment.Stem cell reports · 2019Article
- Retargeting of macroH2A following mitosis to cytogenetic-scale heterochromatic domains.The Journal of cell biology · 2019Article
- Replication timing and epigenome remodelling are associated with the nature of chromosomal rearrangements in cancer.Nature communications · 2019Article
- The Protective Role of Dormant Origins in Response to Replicative Stress.International journal of molecular sciences · 2018Review
- Selective modulation of local linkages between active transcription and oxidative demethylation activity shapes cardiomyocyte-specific gene-body epigenetic status in mice.BMC genomics · 2018Article
- SMITE: an R/Bioconductor package that identifies network modules by integrating genomic and epigenomic information.BMC bioinformatics · 2017Article
- Differential Analysis of Genetic, Epigenetic, and Cytogenetic Abnormalities in AML.International journal of genomics · 2017Article
- Post-conversion targeted capture of modified cytosines in mammalian and plant genomes.Nucleic acids research · 2015Article
- Genome-wide assays that identify and quantify modified cytosines in human disease studies.Epigenetics & chromatin · 2015Review
- DNA demethylation by 5-aza-2'-deoxycytidine is imprinted, targeted to euchromatin, and has limited transcriptional consequences.Epigenetics & chromatin · 2015Article
- Pancreatic cancer patient survival correlates with DNA methylation of pancreas development genes.PloS one · 2015Article
- How might epigenetic dysregulation in early embryonic life contribute to autism spectrum disorder?Epigenomics · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
16 authors at 2 institutions in 1 country.
Funding
Abstract
Heterochromatin is believed to be associated with increased levels of cytosine methylation. With the recent availability of genome-wide, high-resolution molecular data reflecting chromatin organization and methylation, such relationships can be explored systematically. As well-defined surrogates for heterochromatin, we tested the relationship between DNA replication timing and DNase hypersensitivity with cytosine methylation in two human cell types, unexpectedly finding the later-replicating, more heterochromatic regions to be less methylated than early replicating regions. When we integrated gene-expression data into the study, we found that regions of increased gene expression were earlier replicating, as previously identified, and that transcription-targeted cytosine methylation in gene bodies contributes to the positive correlation with early replication. A self-organizing map (SOM) approach was able to identify genomic regions with early replication and increased methylation, but lacking annotated transcripts, loci missed in simple two variable analyses, possibly encoding unrecognized intergenic transcripts. We conclude that the relationship of cytosine methylation with heterochromatin is not simple and depends on whether the genomic context is tandemly repetitive sequences often found near centromeres, which are known to be heterochromatic and methylated, or the remaining majority of the genome, where cytosine methylation is targeted preferentially to the transcriptionally active, euchromatic compartment of the genome.
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Registered trials
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.