ArticleProceedings of the National Academy of Sciences of the United States of America2002
In silico chromosome staining: reconstruction of Giemsa bands from the whole human genome sequence.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 42 citations in OpenAlex.
- Chromosome Bandings and Recognition.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Emergence and influence of sequence bias in evolutionarily malleable, mammalian tandem arrays.BMC biology · 2023Article
- Exploring chromatin hierarchical organization via Markov State Modelling.PLoS computational biology · 2018Article
- The Isochores as a Fundamental Level of Genome Structure and Organization: A General Overview.Journal of molecular evolution · 2017Review
- Accelerating the search for the missing proteins in the human proteome.Nature communications · 2017Review
- Integration of HIV in the Human Genome: Which Sites Are Preferential? A Genetic and Statistical Assessment.International journal of genomics · 2016Article
- Integrated small copy number variations and epigenome maps of disorders of sex development.Human genome variation · 2016Article
- Copy Number Studies in Noisy Samples.Microarrays (Basel, Switzerland) · 2013Article
- A human B cell methylome at 100-base pair resolution.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- A new platform linking chromosomal and sequence information.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2007Article
- Genome-wide sequence and functional analysis of early replicating DNA in normal human fibroblasts.BMC genomics · 2006Article
- A comparative analysis of transcribed genes in the mouse hypothalamus and neocortex reveals chromosomal clustering.Proceedings of the National Academy of Sciences of the United States of America · 2004Article
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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
Giemsa staining has been used for identifying individual human chromosomes. Giemsa-dark and -light bands generally are thought to correspond to GC-poor and GC-rich regions; however, several experiments showed that the correspondence is quite poor. To elucidate the precise relationship between GC content and Giemsa banding patterns, we developed an "in silico chromosome staining" method for reconstructing Giemsa bands computationally from the whole human genome sequence. Here we show that 850-level Giemsa bands are best correlated with the difference in GC content between a local window of 2.5 megabases and a regional window of 9.3 megabases along a chromosome. The correlations are of strong statistical significance for almost all 43 chromosomal arms. Our results clearly show that Giemsa-dark bands are locally GC-poor regions compared with the flanking regions. These findings are consistent with the model that matrix-associated regions, which are known to be AT-rich, are present more densely in Giemsa-dark bands than in -light bands.
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