Histone Marks-Dependent Effect on Alternative Splicing: New Perspectives for Targeted Splicing Modulation in Cancer?

Abstract

Alternative splicing (AS) is a tightly regulated mechanism that generates the complex human proteome from a small number of genes. Cis-regulatory RNA motifs in exons and introns control AS, recruiting positive and negative trans-acting splicing regulators. At a higher level, chromatin affects splicing events. Growing evidence indicates that the popular histone code hypothesis can be extended to RNA-level processes, such as AS. In addition to nucleosome positioning, which can generate transcriptional barriers to shape the final splicing outcome, histone post-translational modifications can contribute to the detailed regulation of single exon inclusion/exclusion. A histone-based system can identify alternatively spliced chromatin stretches, affecting RNAPII elongation locally or recruiting splicing components via adaptor complexes. In tumor cells, several mechanisms trigger misregulated AS events and produce cancer-associated transcripts. On a genome-wide level, aberrant AS can be the consequence of dysfunctional epigenetic splicing code, including altered enrichment in histone post-translational modifications. This review describes the main findings related to the effect of histone modifications and variants on splicing outcome and how a dysfunctional epigenetic splicing code triggers aberrant AS in cancer. In addition, it highlights recent advances in programmable DNA-targeting technologies and their possible application for AS targeted epigenetic modulation.

Keywords: alternative splicing; cancer transcript variants; epigenome editing; histone post-translational modifications; histone-code.

Figure 1

Two non-exclusive models describe how transcription and alternative splicing are functionally coupled. Left: In the context of the Kinetic Coupling Model, the rate of transcriptional elongation, influenced by different histone PTMs, affects AS outcome. At high RNA polymerase II (RNA Pol II) elongation rates, there is a brief temporal window in which weak (purple) and strong (pink) splice sites (SS) compete for the recruitment of the splicing machinery, resulting in the skipping of the weaker exon (purple rectangle). On the contrary, exon inclusion is favored by RNA Pol II slowing down or pausing, which facilitates the recognition of the weak SS before the strong SS is synthesized. Right: According to the Chromatin-Adaptor Model, histone-PTMs changes along the gene (marked in different colors) determine the recruitment of specific adaptor proteins, which, in turn, recruit splicing factors and the transcription machinery, hence influencing AS decisions. Created with BioRender.com.

Figure 2

Genes undergoing alternative splicing produce functionally alternative products that can have dramatic effects on physiological processes and, consequently, can participate in the development or progression of cancer. The model represents how intragenic histone PTMs can drive distinct AS outcomes associated with common cancer hallmarks, such as genome instability, reduced cell death and differentiation, enhanced proliferation, metabolic reprogramming, and induced cell migration/invasion. Created with BioRender.com.

Figure 3

Overview of targeted epigenetic editing tools for localized modification of histone post-translational modifications. (a) CRISPR-dCas9 can target specific genomic locations by exploiting complementarity with a guide RNA. (b) Zinc Finger proteins can recognize 3 bps of DNA and the fusion of 6 ZFs can identify specific 18 bps sequences. (c) TALE domains can recognize a single-base pair and the fusion of several repeats distinguishes a specific locus. Created with BioRender.com.