dorsal/arxiv
View SchemaSpectral Analysis of Guanine and Cytosine Fluctuations of Mouse Genomic DNA
| Authors | Wentian Li, Dirk Holste |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0411017 |
| URL | https://arxiv.org/abs/q-bio/0411017 |
| DOI | 10.1142/S0219477504002087 |
| Journal | Fluctuation and Noise Letters, 4(3):L453-L464 (2004) |
Abstract
We study global fluctuations of the guanine and cytosine base content (GC%) in mouse genomic DNA using spectral analyses. Power spectra S(f) of GC% fluctuations in all nineteen autosomal and two sex chromosomes are observed to have the universal functional form S(f) \sim 1/f^alpha (alpha \approx 1) over several orders of magnitude in the frequency range 10^-7< f < 10^-5 cycle/base, corresponding to long-ranging GC% correlations at distances between 100 kb and 10 Mb. S(f) for higher frequencies (f > 10^-5 cycle/base) shows a flattened power-law function with alpha < 1 across all twenty-one chromosomes. The substitution of about 38% interspersed repeats does not affect the functional form of S(f), indicating that these are not predominantly responsible for the long-ranged multi-scale GC% fluctuations in mammalian genomes. Several biological implications of the large-scale GC% fluctuation are discussed, including neutral evolutionary history by DNA duplication, chromosomal bands, spatial distribution of transcription units (genes), replication timing, and recombination hot spots.
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"abstract": "We study global fluctuations of the guanine and cytosine base content (GC%)\nin mouse genomic DNA using spectral analyses. Power spectra S(f) of GC%\nfluctuations in all nineteen autosomal and two sex chromosomes are observed to\nhave the universal functional form S(f) \\sim 1/f^alpha (alpha \\approx 1) over\nseveral orders of magnitude in the frequency range 10^-7\u003c f \u003c 10^-5 cycle/base,\ncorresponding to long-ranging GC% correlations at distances between 100 kb and\n10 Mb. S(f) for higher frequencies (f \u003e 10^-5 cycle/base) shows a flattened\npower-law function with alpha \u003c 1 across all twenty-one chromosomes. The\nsubstitution of about 38% interspersed repeats does not affect the functional\nform of S(f), indicating that these are not predominantly responsible for the\nlong-ranged multi-scale GC% fluctuations in mammalian genomes. Several\nbiological implications of the large-scale GC% fluctuation are discussed,\nincluding neutral evolutionary history by DNA duplication, chromosomal bands,\nspatial distribution of transcription units (genes), replication timing, and\nrecombination hot spots.",
"arxiv_id": "q-bio/0411017",
"authors": [
"Wentian Li",
"Dirk Holste"
],
"categories": [
"q-bio.GN",
"q-bio.BM"
],
"doi": "10.1142/S0219477504002087",
"journal_ref": "Fluctuation and Noise Letters, 4(3):L453-L464 (2004)",
"title": "Spectral Analysis of Guanine and Cytosine Fluctuations of Mouse Genomic DNA",
"url": "https://arxiv.org/abs/q-bio/0411017"
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