Long Reads Capture Simultaneous Enhancer-Promoter Methylation Status for Cell-type Deconvolution

Margalit, S.; Abramson, Y.; Sharim, H.; Manber, Z.; Bhattacharya, S.; Chen, Y. W.; Vilain, E.; Barseghyan, H.; Elkon, R.; Sharan, R.; Ebenstein, Y.

doi:10.1101/2021.01.28.428654

bioRxiv · 10.1101/2021.01.28.428654

Long Reads Capture Simultaneous Enhancer-Promoter Methylation Status for Cell-type Deconvolution

Margalit, S.·Abramson, Y.·Sharim, H.·Manber, Z.·Bhattacharya, S.·Chen, Y. W.·Vilain, E.·Barseghyan, H.·Elkon, R.·Sharan, R.·Ebenstein, Y.

View original source ↗Export metadata ↓

Abstract

MotivationWhile promoter methylation is associated with reinforcing fundamental tissue identities, the methylation status of distant enhancers was shown by genome-wide association studies to be a powerful determinant of cell-state and cancer. With recent availability of long-reads that report on the methylation status of enhancer-promoter pairs on the same molecule, we hypothesized that probing these pairs on the single-molecule level may serve the basis for detection of rare cancerous transformations in a given cell population. We explore various analysis approaches for deconvolving cell-type mixtures based on their genome-wide enhancer-promoter methylation profiles. ResultsTo evaluate our hypothesis we examine long-read optical methylome data for the GM12787 cell line and myoblast cell lines from two donors. We identified over 100,000 enhancer-promoter pairs that co-exist on at least 30 individual DNA molecules per pair. We developed a detailed methodology for mixture deconvolution and applied it to estimate the proportional cell compositions in synthetic mixtures based on analyzing their enhancer-promoter pairwise methylation. We found our methodology to lead to very accurate estimates, outperforming our promoter-based deconvolutions. Moreover, we show that it can be generalized from deconvolving different cell types to subtle scenarios where one wishes to deconvolve different cell populations of the same cell-type. AvailabilityThe code used in this work to analyze single-molecule Bionano Genomics optical maps is available via the GitHub repository https://github.com/ebensteinLab/Single_molecule_methylation_in_EP. Contactuv@post.tau.ac.il (Y.E), roded@tauex.tau.ac.il (R.S)

Source connections

Published article ↗

Explore related subjects

bioinformatics Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Margalit, S., Abramson, Y., Sharim, H., Manber, Z., Bhattacharya, S., Chen, Y. W., Vilain, E., Barseghyan, H., Elkon, R., Sharan, R., Ebenstein, Y.. 2021-01-29. Long Reads Capture Simultaneous Enhancer-Promoter Methylation Status for Cell-type Deconvolution. https://doi.org/10.1101/2021.01.28.428654

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

StableProt: Structure-Aware Deep Learning for Protein Thermostability (Tm) and Environmental Adaptation (OGT) Prediction

Predicting protein melting temperature (Tm) and organismal optimal growth temperature (OGT) is essential for enzyme engineering, biocatalyst design, and metagenomic bioprospecting, yet computational prediction faces several fundamental bottlenecks: sequence-only representations miss tertiary packing; dual-task coupling induces destructive gradient conflict; natural database skew (>87% mesophiles) drives mesophilic collapse; and existing tools produce uncalibrated point predictions. To address these challenges, we present StableProt, a structure-aware framework that couples amino acid sequences with Foldseek 3Di structural tokens via a frozen SaProt backbone to capture 3D contacts. Disjoint heads condition thermodynamic stability on ecological context without gradient conflict, while targeted 14% mesophilic subsampling expands thermophile representation to eliminate mesophilic collapse. Calibrated ensemble modeling reduces calibration error to 1.92%, providing dependable 95% confidence intervals. Evaluating models across 10{degrees}C temperature intervals reveals severe baseline collapse at thermal extremes, whereas StableProt maintains robust accuracy across regimes. On ProThermDB and zero-shot FireProtDB, StableProt achieves state-of-the-art probabilistic accuracy (CRPS = 4.52{degrees}C and 8.71{degrees}C) while recovering 92.0% of hyperthermophiles ([≥]80{degrees}C), and in prospective validation, its calibrated intervals capture both enzyme stability (75.3% coverage) and host environmental growth temperatures (78.1% coverage). StableProt is freely accessible as an interactive web server at https://stableprot.dixitlab.org/.

bioinformatics↗

bioRxiv2026

RoDPAA: A Robust Dissimilarity-Based Principal Angle Analysis Framework for Multi-View Microbiome Data Integration

Multiview microbiome studies profile the same participants across body sites or molecular layers, but integration is hampered by sparse, compositional data, modest sample sizes and methods that recognize only exact sharing. We present RoDPAA (Robust Dissimilarity-based Principal Angle Analysis), a framework that represents each view through any data-appropriate dissimilarity, such as Bray--Curtis, without log-ratio transformation or likelihood assumptions. RoDPAA aligns view-specific signal subspaces through principal angles, captures complete and partial sharing, and tests by permutation how many components are shared, using only eigendecomposition and little tuning. In Gaussian simulations, RoDPAA matched JIVE and MOFA given true ranks, ran faster and alone recovered the shared dimension in every replicate. In two inflammatory bowel disease (IBD) cohorts with sparse, zero-inflated data, Bray--Curtis-based RoDPAA recovered shared structure that was stable to prevalence filtering, whereas log-ratio-based alternatives were not. Its leading microbiome--metabolome factors, learned without disease labels, were the only ones associated with IBD.

bioinformatics↗

bioRxiv2026

Deducing splicing events from transcript sets with splicelogic

Long-read RNA sequencing captures a greater proportion of full-length transcripts, enabling more accurate isoform identification, discovery of novel isoforms, and more precise differential transcript usage analysis. However, comparing transcripts, whether between conditions or between sets such as novel and annotated isoforms, yields complex isoform changes that are hard to manipulate, summarize, and visualize. This is compounded by vertical integration of some tools, where downstream analysis depends on the specific output of a particular upstream tool. To address this gap, we have developed splicelogic, an R/Bioconductor package that makes transcript-set comparisons biologically interpretable by turning them into discrete splicing events, such as exon skipping, alternative splice sites, intron retention, and alternative transcription start and end sites. We designed splicelogic to integrate easily with existing RNA-seq workflows and tools. The splicelogic functions are modular, readable, and extensible, making it easy for users to adapt core logic to their own custom scientific questions or novel splicing definitions. By obtaining interpretable splicing events from transcript changes, splicelogic enables downstream analyses, including annotation of RNA-binding protein recognition sites, alongside summary statistics and visualization. The splicelogic package is publicly available and distributed through Bioconductor.

bioinformatics↗