MOABS: model based analysis of bisulfite sequencing data
© Sun et al.; licensee BioMed Central Ltd. 2014
Received: 12 October 2013
Accepted: 24 February 2014
Published: 24 February 2014
Bisulfite sequencing (BS-seq) is the gold standard for studying genome-wide DNA methylation. We developed MOABS to increase the speed, accuracy, statistical power and biological relevance of BS-seq data analysis. MOABS detects differential methylation with 10-fold coverage at single-CpG resolution based on a Beta-Binomial hierarchical model and is capable of processing two billion reads in 24 CPU hours. Here, using simulated and real BS-seq data, we demonstrate that MOABS outperforms other leading algorithms, such as Fisher’s exact test and BSmooth. Furthermore, MOABS analysis can be easily extended to differential 5hmC analysis using RRBS and oxBS-seq. MOABS is available at http://code.google.com/p/moabs/.
DNA methylation, an epigenetic modification affecting organization and function of the genome, plays a critical role in both normal development and disease. Until recently, the only known DNA methylation was 5-methylcytosine (5mC) at CpG dinucleotides, which is generally associated with transcriptional repression . In 2009, another form of DNA methylation termed 5-hydroxymethylcytosine (5hmC)  was found to be involved in active demethylation  and gene regulation . Understanding the functional role of DNA methylation requires knowledge of its distribution in the genome [5, 6]. Bisulfite conversion of unmethylated Cs to Ts followed by deep sequencing (BS-Seq) has emerged as the gold standard to study genome-wide DNA methylation at single-nucleotide resolution. The most popular protocols include RRBS (Reduced Representation Bisulfite Sequencing)  and WGBS (Whole Genome Bisulfite Sequencing)  for the combination of 5mc and 5hmc, oxBS-Seq (Oxidative Bisulfite Sequencing)  for 5mc and TAB-Seq (Tet-assisted Bisulfite Sequencing)  for 5hmc, respectively. After mapping BS-seq reads to the genome, the proportion of unchanged Cs is regarded as the absolute DNA methylation level. Due to random sampling nature of BS-seq, deep sequencing (e.g. >30 fold) is usually required to reduce the measurement error. Technological advances and reduced costs have seen a significant increase in interest in BS-seq among biologists. Currently, BS-seq is widely used by small laboratories to profile cell lines and animal models , as well as by large consortiums such as the NIH ENCODE, Roadmap Epigenomics, The Cancer Genome Atlas (TCGA), and European BLUEPRINT to profile thousands of cell populations. Hence, it is expected that BS-seq data will continue to grow exponentially. However, despite recent progress [7, 12–14], computational methods designed for issues specific to BS-seq are much less developed than those for other sequencing applications such as ChIP-Seq and RNA-seq.
The most fundamental aspects of BS-seq data analysis include read mapping and differential methylation detection. We previously developed one of the most widely used BS mapping programmed BSMAP . After read mapping, the most common task is the identification of differentially methylated regions (DMRs) between samples, such as disease versus normal. Based on the biological question, DMRs can range in size from a single CpG (DMC: differentially methylated CpG) to tens of millions of bases. Although several statistical methods have been applied to DMR detection , among which Fisher’s exact test p-value (FETP) method  is the most popular, several challenges remain to be addressed. 1) Statistical Power: most previous methods are very conservative in power and require deep sequencing (e.g. 30 fold). For example, Hansen  recently calculated that for single CpG methylation level “even 30× coverage yields standard error as large as 0.09”. As a compromise, many studies assumed that neighboring CpGs have similar methylation levels, thus can be combined together within a genomic region (e.g. 1 kb) to increase the statistical power . For example, BSmooth  performs local smoothing followed by t-test for DMR detection. While this strategy may be applicable in many cases, regional average analysis will unfortunately miss low-CpG-density DMRs that are abundant in the genome and critical for gene expression, such as TFBSs. Most TFBSs are small (i.e. < 50 bp) as implied by high-resolution ChIP-seq and ChIP-exo experiments  and contain few or even a single CpG(s) that are in general differentially methylated compared to surrounding ones, thus are very likely to be “overlooked” by the regional average analysis. 2) Biological Significance: previous methods use p-value for statistical significance of DMR. This p-value metric only tells whether a region is differentially methylated, but does not directly measure the magnitude of the methylation difference. A similar problem also exists in gene expression profiling, where the p-value does not directly measure the expression fold-change . Since sequencing depth in BS-seq experiments can fluctuate by an order of magnitude in different loci, a very small methylation difference, although not biologically meaningful, can easily return a significant p-value if the underlying sequencing depth is deep enough. On the other hand, the nominal methylation difference, i.e. direct subtraction of two methylation ratios, suffers significantly from the random sampling error such that a large difference with low sequencing depth is not likely to be statistically meaningful. 3) Biological Variation is an essential feature of DNA methylation , and should be handled carefully to detect reproducible DMRs that represent the common characteristics of the sample group. However, most previous methods fail to account for biological variation between replicates, and simply pool the raw data from replicates for DMR detection. Some of the resulting DMRs may have significant differences at the mean level but might not be reproducible between replicates, and hence are “false-positives”. To our knowledge, BSmooth  is the first replicate-aware program that accounted for biological variation using a modified t-test.
In response to these challenges, we developed a powerful differential methylation analysis algorithm termed MOABS: Model-based Analysis of Bisulfite Sequencing data. Its source code is available as Additional file 1. MOABS uses a Beta-Binomial hierarchical model to capture both sampling and biological variations, and accordingly adjusts observed nominal methylation difference by sequencing depth and sample reproducibility. The resulting credible methylation difference (CDIF) is a single metric that combines both biological and statistical significance of differential methylation. Using both simulated and real whole-genome BS-seq data from mouse brain tissues and stem cells, we demonstrate the superior performance of MOABS over other leading methods, especially at low sequencing depth. Furthermore, one practical challenge is that BS-seq data analysis is usually computational intensive, and requires multiple steps. We therefore seamlessly integrate several major BS-seq processing procedures into MOABS, including read mapping, methylation ratio calling, identification of hypo- or hyper- methylated regions from one sample, and differential methylation from multiple samples. MOABS is implemented in C++ with highly efficient numerical algorithms, and thus is at least 10 times faster than other popular packages. For example, it takes only 24 CPU hours to detect differential methylation from 2 billion aligned reads. Together, MOABS provides a comprehensive, accurate, efficient and user-friendly solution for analyzing large-scale BS-seq data.
Results and discussion
Beta-Binomial hierarchical model for both sampling and biological variations
For a single CpG locus in the j-th biological replicate of condition i, we denote the number of total reads, the number of methylated reads and methylation ratio as n ij , k ij and p ij , respectively. For a typical two group comparison, i = 1,2 and j = 1, 2, …, N, where N is the number of replicates in each condition. The n ij and k ij are observations from experiments, while the p ij is unknown with k ij /n ij as its nominal estimation. Given p ij and n ij , the number of methylated reads k ij is characterized by the sampling variation from sequencing and can be modeled by a Binomial distribution: k ij ~ Binomial(n ij , p ij ). The posterior distribution of the methylation ratio p ij will then follow a Beta distribution Beta(α ij , β ij ) and can be estimated using an Empirical Bayes approach. The prior distribution will be estimated from the whole genome, in which most CpGs are either fully methylated or fully un-methylated, resulting in a bimodal distribution. The Empirical Bayes approach will automatically incorporate such bimodal information in the methylation ratio estimation and hence increases the power of our analysis.
Credible methylation difference (CDIF) is a single metric for both statistical and biological significance of differential methylation
In practice, CDIF represents the conservative estimation of the true methylation difference, i.e. for 97.5% of chance the absolute value of true methylation difference is greater than or equal to that of CDIF. The CDIF value will be assigned to 0 is there is no significant difference. Constructed in this way, the CDIF value, if greater than the resolution defined as min(1/n1, 1/n2), guarantees a significant p-value from Fisher’s exact test, and at the same time represents the magnitude of methylation difference. The sequencing depth will largely influence CDIF, since bigger n i will make a smaller 95% CI of the methylation difference, normally resulting in greater CDIF value.
We believe CDIF is a better metric to capture the methylation difference than statistical p-value or nominal methylation difference. Three CpG examples are shown in Figure 1c. According to p-value 1.4e-10, CpG #3 is the most significant one. However, this significant p-value, which is largely driven by the high sequencing depth, does not correctly represent the actual biological difference of 0.3, which is the smallest among three CpGs. On the other hand, if we use nominal difference, CpG #2 would be the most significant. However, its low sequencing depth makes this high nominal difference unreliable. CDIF is able to penalize the nominal difference according to its statistical significance and ranks CpG #1 as the most significant followed by CpGs #2 and #3, although CpG #1 does not have the most significant p-value or nominal difference. Taken together, CDIF reaches a well balance between statistical and biological significance and gives a more stable and biological meaningful interpretation and ranking of differential methylation.
Functions and performance of the MOABS pipeline
All the modules are wrapped in a single master script such that users can specify the input BS-seq reads and run all the modules one by one automatically. The MOABS pipeline is developed using C++ with highly efficient numerical algorithms, native multiple-threading and cluster support so that multiple jobs can run in parallel on different computing nodes. Several mathematical and computational optimizations have made MOABS pipeline extremely efficient. For example, it takes only one hour on 24 CPUs (IBM power7 4 Ghz) to detect differential methylation for approximately 30 million CpGs in the human genome based on 2 billion aligned reads. MOABS is significantly faster than other software. For example, a benchmark (Additional file 2: Table S1) based on public BS-seq data in mouse hematopoietic stem cell (HSC)  reveals that MOABS is roughly 3.3, 1.7, and 1.4 times faster than BSmooth in bisulfite mapping, methylation call and differential methylation analysis, respectively. In summary, MOABS is a comprehensive, accurate, efficient and user-friendly solution for analyzing large-scale BS-seq data.
Simulated BS-seq data reveals the superior performance of MOABS
MOABS improves the detection of allele specific DNA methylation
The 32 known DMRs can be easily detected by both MOABS and FETP mainly because they have large methylation differences and high read depth (54-fold in DMR regions), which is consistent with our simulation study. However, deep bisulfite sequencing of the mammalian genome is still quite expensive. This reality motivated us to test to what extent these known DMRs can still be recovered at a lower sequencing depth. The same previous procedure was applied to compare all three methods. The number of recovered known DMRs at 5% FDR is plotted at each sequencing depth from random sampling (Figure 4b). We observe that the lower sequencing depth, the greater performance difference between MOABS and FETP. For example, when the depth is at 11-fold, MOABS recovers roughly 90% of known DMRs, while FETP only detects 78% of DMRs. When the depth is further lowed to 3.1-fold, MOABS can still recover roughly 70% of known DMRs, while FETP detects 44% DMRs. Interestingly, BSmooth’s performance is largely independent of sequencing depth, probably because it was designed mainly for low sequencing depth. Indeed, at a low depth of 3.1-fold, BSmooth outperforms FETP. However, at sequencing depth higher than 3.1-fold, BSmooth has a lower sensitivity than the other two methods. Collectively, we conclude that MOABS is superior in DMR detection, especially at low sequencing depth.
MOABS reliably reveals differential methylation underlying TFBSs
We then used TFBSs to evaluate DMC detection assuming tissue-specific TF binding is associated with tissue-specific hypo-methylation. For a fair comparison, we calculated FDR for each method based on a method-specific null distribution obtained through permutation of read sample labels. At FDR of 5%, MOABS, FETP and BSmooth predicted 32,867, 32,047 and 18,021 differentially methylated TFBSs respectively (Figure 5c). We also used a method similar to Gene Set Enrichment Analysis (GSEA ) to test enrichment of TFBS moving down the lists of DMCs ranked by different methods. MOABS shows the highest enrichment score (Figure 5d) of TFBS. For example, with the same 4,000 most significant DMCs, MOABS recovers 1,000 TFBSs while FETP only predicts ~600 TFBSs (i.e., 40% less).
In this instance, the sequencing depth is sufficient to enable MOABS and FETP to recover very similar number of TFBSs. However, when we randomly sampled reads to a depth of 4-fold, MOABS recovered many more TFBS (15,349) than FETP (7,520) and BSmooth (4,028) (Figure 5e). Again, at this low sequencing depth, MOABS not only recovers 2–3 fold more TFBSs, but also exhibit more significant score of TFBS enrichment in the most significant DMCs. In both high and low sequencing depths, BSmooth recovers fewer TFBSs mainly because its smoothing function easily ignores small region with a few CpGs. Together, using tissue specific in vivo TFBSs, we demonstrate that MOABS can better recover differential methylation in small regulatory regions with a few CpGs, especially at low sequencing depth (e.g. 4-fold).
MOABS detects differential 5hmc in ES cells using RRBS and oxBS-Seq
When applied to RRBS and oxBS-seq data derived from ES cell lines with different passages , MOABS reported 299 genes with decreased 5hmc and 125 genes with increased 5hmc (Additional file 6: Table S3) in promoters in the later passage P20, which is consistent with the mass spectrometry data  that shows overall reduced 5hmc in later passage. This result implies that the epigenetic stability of ES cells is impacted by prolonged in vitro culture. This is an important issue for both the safety and efficacy of stem cell-derived tissues in cell-replacement therapies as well as the appropriate interpretation of experimental models. Mono-allelic gene expression, including genomic imprinting, is primarily regulated through epigenetic mechanisms and thus can serve as a useful model of epigenetic stability. As expected, our analysis identified five imprinted genes with decreased 5hmc: Plagl1, Sfmbt2, Gpr1, Kcnq1 and Kcnq1ot1, as well as one imprinted gene with increased 5hmc, Pcdha4-g.
The role of 5hmc in disease remains unclear. A recent study suggests that genome-wide loss of 5hmc is an epigenetic feature of neurodegenerative Huntington’s disease . The authors identified 559 genes with decreased 5hmc in the diseased mice compared to healthy controls. A considerable fraction of these disease-specific genes were uncovered in our differential 5hmc analysis in ES cells. This included 26 of 299 and 11 of 125 genes (overlapping p-value < 8e-5) with decreased and increased 5hmc, respectively. These results suggest that one potential consequence of decreased epigenetic stability over time in ES cells is the acquisition of pathological epimutations.
The observed bias toward loss of 5hmc in ES cells upon long-term culture may also suggest stem cell properties, such as pluripotency, are affected. Ficz and colleagues  showed that knockdown of Tet1/Tet2 in mouse ES cells down regulates epigenetic reprogramming and pluripotency-related genes such as Esrrb, Klf2, Tcl1, Zfp42, Dppa3, Ecat1 and Prdm14. Decreased expression was concomitant with both decreased 5hmC and increased 5mC at the gene promoters. In our differential 5hmc analysis in ES cells, we observed decreased 5hmc at three of these genes: Ecat1, Esrrb, and Zfp42. Together, we conclude that MOABS can be used effectively to infer differential 5hmc using RRBS and oxBS-Seq.
While progress in next-generation sequencing allows increasingly affordable BS-seq experiments, the resulting data generated poses significant and unique bioinformatics challenges. The lack of efficient computational methods is the major bottleneck that prevents a broad adoption of such powerful technologies. In response to this challenge, we developed MAOBS, an accurate, comprehensive, efficient, and user-friendly pipeline for BS-seq data analysis. The MOABS analysis is novel and significant in two major aspects: 1) MOABS CDIF value provides an innovative strategy to combine statistical p-value and biological difference into a single metric, which will bring biological relevance to the interpretation of the DNA methylation data. 2) MOABS does not sacrifice resolution with low sequencing depth. By relying on the Beta-Binomial Hierarchical Model and Empirical Bayes approach, MOABS has enough power to detect single-CpG-resolution differential methylation in low-CpG-density regulatory regions, such as TFBSs, with as low as 10-fold. The low-depth BS-seq experimental design enables remarkable cost reduction per sample. In Figure 3 simulated data, we showed that MOABS achieved roughly 80% sensitivity with 5% FDR at 10-fold sequencing depth. In Figure 4b real data, we showed that as sequencing depth decreased to 11-fold by sampling, MOABS recovered roughly 90% of known DMRs. The MOABS sensitivity starts to drop dramatically when sequencing depth is further reduced. Based on the above two observations, we would recommend low-depth (e.g. 10-fold) BS-seq on more biological samples with the same limited budget, which in most scenarios will provide greater biological insights than high-depth BS-seq on fewer samples.
Copy Number Variation (CNV) is a common issue in many disease related bisulfite sequencing. The sequencing depth is normally higher or lower in high (or low) copy-number regions and this depth bias has an impact on our CDIF calculation. To correct this bias, we have included a separate script ‘redepth.pl’ in the MOABS package. Users can select their favorite CNV detection tools , such as CNV-Seq, Control-FREEC and VarScan, to predict the CNV region from genome sequencing or bisulfite sequencing. Nearly all these tools output a bed file of CNV regions with predicted copy number based on a p-value cutoff. The script ‘redepth.pl’ manipulates the read alignment BAM files according to the CNV prediction. If a read is located in a CNV region with a predicted copy number of X in a diploid genome, the read will have a probability of 2/X to be kept in the new BAM files. Reads in the non-CNV regions will keep unchanged. This process will result in CNV bias free BAM files for downstream analysis.
Large-scale case–control epigenome-wide association study (EWAS) is a powerful strategy to identify disease-associated epigenetic biomarkers. Currently, most studies use Illumina bisulfite arrays (e.g. 450 K) mainly due to the cost constraint. MOABS in theory can also be applied to such studies when EWAS bisulfite sequencing data are publicly available.
In summary, as DNA methylation is increasingly recognized as a key regulator of genomic function, deciphering its genome-wide distribution using BS-seq in numerous samples and conditions will continue to be a major research interest. MOABS significantly increase the speed, accuracy, statistical power and biological relevance of the BS-seq data analysis. We believe that MOABS’s superior performance will greatly facilitate the study of epigenetic regulation in numerous biological systems and disease models.
Materials and methods
The major portions of the methods for the model are described here. In the Additional file 7, we provide more details and additional methods to make the model complete.
Distribution for difference of two Binomial proportions
where α = k + α0, β = n-k + β0, if Be(α0, β0) is priori distribution for p. We also give formulas to numerically calculate the confidence interval for the single Binomial proportional p under observed (n, k).
The methylation ratio difference at a defined genomic locus from two biological samples is the difference of two Binomial proportions p1-p2. Many methods have been proposed to estimate the confidence interval p1-p2 of and their merits have been subject to decades of considerable debate [22, 33–38]. No comprehensive comparison of currently available methods is available. This motivated us to turn to the direct and exact numerical calculation of confidence interval from Bayesian perspective.
where f i (p i ) ≡ f(p i ; n i , k i ). Boundary conditions like the proportional area condition, minimal length condition can be applied to get unique solutions for (a, b).
Distribution for difference of difference
where f i (p i ) ≡ f(p i ; n i , k i ).
where f(t) and f′(t′) are the distributions of 5hmc ratio for sample S and S′ respectively. After distribution of difference of 5hmc ratio between two samples is obtained, similarly confidence interval, credible difference and similarity test p-value can be calculated.
Distribution for measurements with replicates
where the expression inside log is the probability P(k i ; n i , α, β) defined in equation (5) and B (α, β)is the Beta function.
Differentially methylated cytosine
Differentially methylated region
Fisher’s exact test P-value
Transcription factor binding site.
We are grateful to Wei Xie for sharing the mouse methylome data, and Grant A. Challen for critical reading of this manuscript. This work was supported by CPRIT RP110471-C3 and NIH R01HG007538 (to WL).
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