Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation

Abstract

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis can detect protein/DNA-binding and histone-modification sites across an entire genome. Recent advances in sequencing technologies and analyses enable us to compare hundreds of samples simultaneously; such large-scale analysis has potential to reveal the high-dimensional interrelationship level for regulatory elements and annotate novel functional genomic regions de novo. Because many experimental considerations are relevant to the choice of a method in a ChIP-seq analysis, the overall design and quality management of the experiment are of critical importance. This review offers guiding principles of computation and sample preparation for ChIP-seq analyses, highlighting the validity and limitations of the state-of-the-art procedures at each step. We also discuss the latest challenges of single-cell analysis that will encourage a new era in this field.

Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks

“…Open chromatin regions are amenable to better fragmentation and therefore are preferentially represented in the digested sample. Whereas tightly packed heterochromatin is digested to a lesser extent, thereby confounding weak enrichment of true binding sites for heterochromatin markers (5). Finally, the chromatin integrity, the rate of its digestion, and strength of DNA-protein binding highly depend on the preservation and processing of the patient’s primary cancer tissue (5).…”

“…Whereas tightly packed heterochromatin is digested to a lesser extent, thereby confounding weak enrichment of true binding sites for heterochromatin markers (5). Finally, the chromatin integrity, the rate of its digestion, and strength of DNA-protein binding highly depend on the preservation and processing of the patient’s primary cancer tissue (5). Therefore, the majority of ChIP-Seq-generated data in cancer are currently limited to cell line analysis (2) and do not represent the wide heterogeneity of human malignancy that occurs on a population basis (6).…”

Sequencing on the SOLiD 5500xl System – in-depth characterization of the GC bias

“…The bias was not due to an overall bad sequencing quality of H3K9ac ChIP-seq, which actually exceeded ENCODE standards and recommendations by recent literature (of 20-40 Million reads for ChIP-seq) in sequencing depth. 9,15 Notably, sequencing depth reached saturation (Fig. S2B), and thus our experiments were clearly performed with bona fide sequencing depth for a mixed source distribution histone mark such as H3K9ac.…”

“…9 In the present study we sequenced with a depth of 40 Million reads per H3K9ac sample which exceeds the recommendation by ENCODE and those commonly found in the literature. 9,15 Our sequencing depth reached saturation, indicating that we were sequencing in a sufficient range (Fig. S2B).…”

Cloud Computing for Next-Generation Sequencing Data Analysis

“…ChIP-sequencing, also known as ChIP-seq [33,34] Existing cloud-based services can be classified into four categories or layers (see Figure 2). The first one is Infrastructure as a Service (IaaS).…”