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Piecewise polynomial representations of genomic tracks.

ABSTRACT: Genomic data from micro-array and sequencing projects consist of associations of measured values to chromosomal coordinates. These associations can be thought of as functions in one dimension and can thus be stored, analyzed, and interpreted as piecewise-polynomial curves. We present a general framework for building piecewise polynomial representations of genome-scale signals and illustrate some of its applications via examples. We show that piecewise constant segmentation, a typical step in copy-number analyses, can be carried out within this framework for both array and (DNA) sequencing data offering advantages over existing methods in each case. Higher-order polynomial curves can be used, for example, to detect trends and/or discontinuities in transcription levels from RNA-seq data. We give a concrete application of piecewise linear functions to diagnose and quantify alignment quality at exon borders (splice sites). Our software (source and object code) for building piecewise polynomial models is available at http://sourceforge.net/projects/locsmoc/.

SUBMITTER: Tarabichi M

PROVIDER: S-EPMC3499510 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Piecewise polynomial representations of genomic tracks.

Tarabichi Maxime M Detours Vincent V Konopka Tomasz T

PloS one 20121115 11

Genomic data from micro-array and sequencing projects consist of associations of measured values to chromosomal coordinates. These associations can be thought of as functions in one dimension and can thus be stored, analyzed, and interpreted as piecewise-polynomial curves. We present a general framework for building piecewise polynomial representations of genome-scale signals and illustrate some of its applications via examples. We show that piecewise constant segmentation, a typical step in cop ...[more]

PMID: 23166601

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Project description:CHD7 is a member of the chromodomain helicase DNA binding domain family of ATP-dependent chromatin remodeling enzymes. De novo mutation of the CHD7 gene is a major cause of CHARGE syndrome, a genetic disease characterized by a complex constellation of birth defects. To gain insight to the function of CHD7, we mapped the distribution of the CHD7 protein on chromatin using the approach of chromatin immunoprecipitation on tiled microarrays (ChIP-chip). These studies were performed in human colorectal carcinoma cells, human neuroblastoma cells, and mouse embryonic stem (ES) cells before and after differentiation into neural precursor cells. The results indicate that CHD7 localizes to discrete locations along chromatin that are specific to each cell type, and that the cell-specific binding of CHD7 correlates with a subset of histone H3 methylated at lysine 4 (H3K4me). The CHD7 sites change concomitantly with H3K4me patterns during ES cell differentiation, suggesting that H3K4me is part of the epigenetic signature that defines lineage-specific association of CHD7 with specific sites on chromatin. Furthermore, the CHD7 sites are predominantly located distal to transcription start sites, most often contained within DNase hypersensitive sites, frequently conserved, and near genes expressed at relatively high levels. These features are similar to those of gene enhancer elements, raising the possibility that CHD7 functions in enhancer mediated transcription, and that the congenital anomalies in CHARGE syndrome are due to alterations in transcription of tissue-specific genes normally regulated by CHD7 during development. ChIP-chip experiments were performed for CHD7 and H3K4 mono-,di-, and trimethylation modifications in 4 cells types: human DLD1 and SH-SY5Y; mouse ES and differentiated neural precursor cells derived from mouse ES cells. Microarrays used in these experiments tiled all or subset of ENCODE regions (in mouse, analogous ENCODE regions were assayed). At least two biological replicates were performed for each CHD7 ChIP experiment; H3K4 ChIP's were performed once in each cell type.

Dataset Information

Piecewise polynomial representations of genomic tracks.

Publications

Piecewise polynomial representations of genomic tracks.

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