ArticleBMC genomics2013
Spatial compartmentalization at the nuclear periphery characterized by genome-wide mapping.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 34 citations in OpenAlex.
- Many roads lead to a plant cistrome: mapping and interpreting transcription factor binding in plants.Genome biology · 2026Review
- Comparison of genome architecture at two stages of male germline cell differentiation in Drosophila.Nucleic acids research · 2022Article
- Genomic loci mispositioning in Tmem120a knockout mice yields latent lipodystrophy.Nature communications · 2022Article
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- The Role of Nucleoporin Elys in Nuclear Pore Complex Assembly and Regulation of Genome Architecture.International journal of molecular sciences · 2020Review
- Optimization of DamID for use in primary cultures of mouse hepatocytes.Methods (San Diego, Calif.) · 2019Article
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- The large fraction of heterochromatin in Drosophila neurons is bound by both B-type lamin and HP1a.Epigenetics & chromatin · 2018Article
- Mechanisms of allelic and clinical heterogeneity of lamin A/C phenotypes.Physiological genomics · 2018Review
- Nucleoporin 107, 62 and 153 mediate Kcnq1ot1 imprinted domain regulation in extraembryonic endoderm stem cells.Nature communications · 2018Article
- Implications of CpG islands on chromosomal architectures and modes of global gene regulation.Nucleic acids research · 2018Article
- Identifying Novel Transcriptional and Epigenetic Features of Nuclear Lamina-associated Genes.Scientific reports · 2017Article
- Data analysis algorithm for DamID-seq profiling of chromatin proteins in Drosophila melanogaster.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2016Article
- Tissue-Specific Gene Repositioning by Muscle Nuclear Membrane Proteins Enhances Repression of Critical Developmental Genes during Myogenesis.Molecular cell · 2016Article
- Identification of Tox chromatin binding properties and downstream targets by DamID-Seq.Genomics data · 2016Article
- DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments.Journal of visualized experiments : JoVE · 2016Article
- Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2.BMC genomics · 2015Article
- damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets.Bioinformatics (Oxford, England) · 2015Article
- Tox: a multifunctional transcription factor and novel regulator of mammalian corticogenesis.The EMBO journal · 2015Article
- Getting Down to Specifics: Profiling Gene Expression and Protein-DNA Interactions in a Cell Type-Specific Manner.Advances in genetics · 2015Review
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHow gene positioning to the nuclear periphery regulates transcription remains largely unclear. By cell imaging, we have previously observed the differential compartmentalization of transcription factors and histone modifications at the nuclear periphery in mouse C2C12 myoblasts. Here, we aim to identify DNA sequences associated with the nuclear lamina (NL) and examine this compartmentalization at the genome-wide level.
resultsWe have integrated high throughput DNA sequencing into the DNA adenine methyltransferase identification (DamID) assay, and have identified ~15, 000 sequencing-based Lamina-Associated Domains (sLADs) in mouse 3T3 fibroblasts and C2C12 myoblasts. These genomic regions range from a few kb to over 1 Mb and cover ~30% of the genome, and are spatially proximal to the NL. Active histone modifications such as H3K4me2/3, H3K9Ac and H3K36me3 are distributed predominantly out of sLADs, consistent with observations from cell imaging that they are localized away from the nuclear periphery. Genomic regions around transcription start sites of expressed sLAD genes display reduced association with the NL; additionally, expressed sLAD genes possess lower levels of active histone modifications than expressed non-sLAD genes.
conclusionsOur work has shown that genomic regions associated with the NL are characterized by the paucity of active histone modifications in mammalian cells, and has revealed novel connections between subnuclear gene positioning, histone modifications and gene expression.
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