A non-parametric peak calling algorithm for DamID-Seq

PloS One
Renhua LiTingbo Jiang

Abstract

Protein-DNA interactions play a significant role in gene regulation and expression. In order to identify transcription factor binding sites (TFBS) of double sex (DSX)-an important transcription factor in sex determination, we applied the DNA adenine methylation identification (DamID) technology to the fat body tissue of Drosophila, followed by deep sequencing (DamID-Seq). One feature of DamID-Seq data is that induced adenine methylation signals are not assured to be symmetrically distributed at TFBS, which renders the existing peak calling algorithms for ChIP-Seq, including SPP and MACS, inappropriate for DamID-Seq data. This challenged us to develop a new algorithm for peak calling. A challenge in peaking calling based on sequence data is estimating the averaged behavior of background signals. We applied a bootstrap resampling method to short sequence reads in the control (Dam only). After data quality check and mapping reads to a reference genome, the peaking calling procedure compromises the following steps: 1) reads resampling; 2) reads scaling (normalization) and computing signal-to-noise fold changes; 3) filtering; 4) Calling peaks based on a statistically significant threshold. This is a non-parametric method for peak ca...Continue Reading

References

Jun 2, 2007·Science·David S JohnsonBarbara Wold
Jun 5, 2007·Nature Protocols·Maartje J VogelBas van Steensel
Sep 19, 2008·Genome Biology·Yong ZhangX Shirley Liu
Nov 26, 2008·Nature Biotechnology·Peter V KharchenkoPeter J Park
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Jul 7, 2012·Genome Research·Yuri B SchwartzVincenzo Pirrotta
Sep 8, 2012·Genome Research·Stephen G LandtMichael Snyder

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Citations

Sep 19, 2015·Wiley Interdisciplinary Reviews. Developmental Biology·Gabriel N Aughey, Tony D Southall
Oct 22, 2016·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Daniil A MaksimovStepan N Belyakin
Mar 17, 2019·Development·Gabriel N AugheyTony D Southall

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Methods Mentioned

BETA
immunoprecipitation
pull down
DamID
DamID-seq
DamID-Deq
ChIP-Seq

Software Mentioned

seq
R
Bowtie
FASTQC
DAVID
DamID
IDR
MACS
SPP

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