Chromatin immunoprecipitation followed by sequencing(ChIP-seq)is increasingly being used for genome-wide profiling of transcriptional regulation,as this technique enables dissection of the gene regulatory networks.With input as control,a variety of statistical methods have been proposed for identifying the enriched regions in the genome,i.e.,the transcriptional factor binding sites and chromatin modifications.However,when there are no controls,whether peak calling is still reliable awaits systematic evaluations.To address this question,we used a Bayesian framework approach to show the effectiveness of peak calling without controls(PCWC).Using several different types of ChIP-seq data,we demonstrated the relatively high accuracy of PCWC with less than a 5%false discovery rate(FDR).Compared with previously published methods,e.g.,the model-based analysis of ChIP-seq(MACS),PCWC is reliable with lower FDR.Furthermore,to interpret the biological significance of the called peaks,in combination with microarray gene expression data,gene ontology annotation and subsequent motif discovery,our results indicate PCWC possesses a high efficiency.Additionally,using in silico data,only a small number of peaks were identified,suggesting the significantly low FDR for PCWC.
Pseudogenes are genomic remnants of ancient protein-coding genes which have lost their coding potentials through evolution.Although broadly existed,pseudogenes used to be considered as junk or relics of genomes which have not drawn enough attentions of biologists until recent years.With the broad applications of high-throughput experimental techniques,growing lines of evidence have strongly suggested that some pseudogenes possess special functions,including regulating parental gene expression and participating in the regulation of many biological processes.In this review,we summarize some basic features of pseudogenes and their functions in regulating development and diseases.All of these observations indicate that pseudogenes are not purely dead fossils of genomes,but warrant further exploration in their distribution,expression regulation and functions.A new nomenclature is desirable for the currently called 'pseudogenes' to better describe their functions.
