Chromatin loop anchors predict transcript and exon usage.

Publisher: Oxford University Press Country of Publication: England NLM ID: 100912837 Publication Model: Print Cited Medium: Internet ISSN: 1477-4054 (Electronic) Linking ISSN: 14675463 NLM ISO Abbreviation: Brief Bioinform Subsets: MEDLINE

Publication: Oxford : Oxford University Press
Original Publication: London ; Birmingham, AL : H. Stewart Publications, [2000-

Exons* ; Transcription, Genetic*; Chromatin/*genetics ; Chromatin Assembly and Disassembly/*genetics ; Computational Biology/*methods; DNA Methylation ; Epigenesis, Genetic ; Epigenomics/methods ; Gene Expression Regulation ; Histones/metabolism ; Models, Biological ; Reproducibility of Results

Epigenomics and transcriptomics data from high-throughput sequencing techniques such as RNA-seq and ChIP-seq have been successfully applied in predicting gene transcript expression. However, the locations of chromatin loops in the genome identified by techniques such as Chromatin Interaction Analysis with Paired End Tag sequencing (ChIA-PET) have never been used for prediction tasks. Here, we developed machine learning models to investigate if ChIA-PET could contribute to transcript and exon usage prediction. In doing so, we used a large set of transcription factors as well as ChIA-PET data. We developed different Gradient Boosting Trees models according to the different tasks with the integrated datasets from three cell lines, including GM12878, HeLaS3 and K562. We validated the models via 10-fold cross validation, chromosome-split validation and cross-cell validation. Our results show that both transcript and splicing-derived exon usage can be effectively predicted with at least 0.7512 and 0.7459 of accuracy, respectively, on all cell lines from all kinds of validations. Examining the predictive features, we found that RNA Polymerase II ChIA-PET was one of the most important features in both transcript and exon usage prediction, suggesting that chromatin loop anchors are predictive of both transcript and exon usage.
(© The Author(s) 2021. Published by Oxford University Press.)

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Keywords: ChIA-PET; alternative splicing; chromatin loop anchors; exon usage; gene expression; histone modifications; machine learning; transcript

0 (Chromatin)
0 (Histones)

Date Created: 20210715 Date Completed: 20220311 Latest Revision: 20220311

20231215

PMC8575016

10.1093/bib/bbab254

34263910