Molecular basis for histone H3 “K4me3-K9me3/2” methylation pattern readout by Spindlin1

Abstract

Histone recognition by ‘reader’ modules serves as a fundamental mechanism in epigenetic regulation. Previous studies have shown that Spindlin1 is a reader of histone H3K4me3 as well as “K4me3-R8me2a”, and promotes transcription of rDNA or Wnt/TCF4 target genes. Here we show that Spindlin1 also acts as a potent reader of histone H3 “K4me3-K9me3/2” bivalent methylation pattern. Calorimetric titration revealed a binding affinity of 16 nM between Spindlin1 and H3 “K4me3-K9me3” peptide, which is one to three orders of magnitude stronger than most other histone readout events at peptide level. Structural studies revealed concurrent recognition of H3K4me3 and H3K9me3/2 by aromatic pockets 2 and 1 of Spindlin1, respectively. Epigenomic profiling studies showed that Spindlin1 colocalizes with both H3K4me3 and H3K9me3 peaks in a subset of genes enriched in biological processes of transcription and its regulation. Moreover, the distribution of Spindlin1 peaks is primarily associated with H3K4me3 but not H3K9me3, which suggests that Spindlin1 is a downstream effector of H3K4me3 generated in heterochromatic regions. Collectively, our work calls attention to an intriguing function of Spindlin1 as a potent H3 “K4me3-K9me3/2” bivalent mark reader, thereby balancing gene expression and silencing in H3K9me3/2-enriched regions.

Molecular basis for SPIN·DOC-Spindlin1 engagement and its role in transcriptional inhibition

“…This work reported a transcriptional activating function of the SPIN•DOC-Spindlin1 complex through a proposed HP1-displacement mechanism. In fact, the published structural and binding studies are consistent with our current and previous results, in which SPIN•DOC-Spindlin1 engagement is fully compatible with high affinity readout of the H3 "K4me3-K9me3" mark (7). That said, the chromatin-targeting consequence of SPIN•DOC-Spindlin1 complex is determined by the occurrence of upstream marks and whether their affinity is low or high.…”

“…Spindlin1 is 262 amino acids in length and is composed of an N-terminal flexible tail and three Tudor-like repeats ( Figure 1A). The first and second Tudor domains are responsible for histone methylation readout, while the function of the third Tudor domain remains largely unknown (7,9,10,13,15). Full-length SPIN•DOC has 381 residues, most of which are flexible regions, and its middle fragment (184-240) is characteristic of K/R-rich motifs followed by a hydrophobic region ( Figure 1A, left).…”

“…These methylation marks may act alone or in combination to demarcate distinct gene expression states (e.g. "active", "repressive" or "poised") (6,7).…”

“…Spindlin1 is highly expressed in multiple cancers including colorectal cancer, cervical cancer and liposarcoma, suggesting its tumor promoter role (12,14,(22)(23)(24)(25)(26)(27). Among the three Tudor-like domains, it has been well established that the first and second Tudors participate in histone methylation readout, while the function of the third Tudor is largely unknown (7,9,10,13,15). SPIN•DOC (SPIN1 docking protein) has been identified as a Spindlin1-interacting protein and negatively regulates Spindlin1's transcriptional co-activator activity (28,29).…”

Bivalent Genes Targeting of Glioma Heterogeneity and Plasticity

“…The H3K4me3 mark is restored before the beginning of mitosis, whereas the repressive H3K27me3 mark is deposited after mitosis [ 18 ]. Other histone modifications that have also been detected in bivalent chromatin domains include the combination of H3K4me3-H3K9me3/2 and the H3K36me3-H3K27me3 marks [ 30 , 31 ]. Of importance, histone methylation depends on DNA methylation, and this crosstalk is achieved through interactions between histone and DNA methyltransferases.…”