ASH1L

Gene

Ash1 was discovered as a gene causing an imaginal disc mutant phenotype in Drosophila. Ash1 is a member of the trithorax-group (trxG) of proteins, a group of transcriptional activators that are involved in regulating Hox gene expression and body segment identity. Drosophila Ash1 interacts with trithorax to regulate ultrabithorax expression.

The human ASH1L gene spans 227.5 kb on chromosome 1, band q22. This region is rearranged in a variety of human cancers such as leukemia, non-Hodgkin's lymphoma, and some solid tumors. The gene is expressed in multiple tissues, with highest levels in brain, kidney, and heart, as a 10.5-kb mRNA transcript. Mutations in ASH1L in humans have been associated with autism, epilepsy, and intellectual disability.

Structure

Human ASH1L protein is 2969 amino acids long with a molecular weight of 333 kDa. ASH1L has an associated with SET domain (AWS), a SET domain, a post-set domain, a bromodomain, a bromo-adjacent homology domain, and a plant homeodomain finger (PHD finger). Human and Drosophila Ash1 share 66% and 77% similarity in their SET and PHD finger domains, respectively. A bromodomain is not present in Drosophila Ash1.

The SET domain is responsible for ASH1L's histone methyltransferase (HMTase) activity. Unlike other proteins that contain a SET domain at their C terminus, ASH1L has a SET domain in the middle of the protein. The crystal structure of the human ASH1L catalytic domain, including the AWS, SET, and post-SET domains, has been solved to 2.9 angstrom resolution. The structure shows that the substrate binding pocket is blocked by a loop from the post-SET domain, and because mutation of the loop stimulates ASH1L HMTase activity, it was proposed that this loop serves a regulatory role.

Protein expression patterns and timing

ASH1L is ubiquitously expressed throughout the body. In the brain, ASH1L is expressed across brain areas and cell types, including excitatory and inhibitory neurons, astrocytes, oligodendrocytes, and microglia. ASH1L also does not appear to show specificity to any brain region. In humans, ASH1L mRNA expression levels are fairly equal across all regions of cortex. Similarly, in mice, ASH1L protein is highly expressed in the hippocampus, thalamus, hypothalamus, motor cortex, and basolateral amygdala. In humans, ASH1L expression peaks prenatally and decreases after birth, with a second peak in expression towards adulthood. In mouse, ASH1L is expressed in the developing central nervous system as early as embryonic day 8.5 and is still expressed throughout the adult mouse brain. Overall, the expression of ASH1L in the brain is spatially and temporally broad.

Function

The ASH1L protein is localized to intranuclear speckles and tight junctions, where it was hypothesized to function in adhesion-mediated signaling. ChIP analysis demonstrated that ASH1L binds to the 5'-transcribed region of actively transcribed genes. The chromatin occupancy of ASH1L mirrors that of the TrxG-related H3K4-HMTase MLL1; however, ASH1L's association with chromatin can occur independently of MLL1. While ASH1L binds to the 5'-transcribed region of housekeeping genes, it is distributed across the entire transcribed region of Hox genes. ASH1L is required for maximal expression and H3K4 methylation of HOXA6 and HOXA10.

A Hox promoter reporter construct in HeLa cells requires both MLL1 and ASH1L for activation, whereas MLL1 or ASH1L alone are not sufficient to activate transcription. The methyltransferase activity of ASH1L is not required for Hox gene activation but instead has repressive action. Knockdown of ASH1L in K562 cells causes up-regulation of the ε-globin gene and down-regulation of myelomonocytic markers GPIIb and GPIIIa, and knockdown of ASH1L in lineage marker-negative hematopoietic progenitor cells skews differentiation from myelomonocytic towards lymphoid or erythroid lineages. These results imply that ASH1L, like MLL1, facilitates myelomonocytic differentiation of hematopoietic stem cells.

The in vivo target for ASH1L's HMTase activity has been a topic of some controversy. Blobel's group found that in vitro ASH1L methylates H3K4 peptides, and the distribution of ASH1L across transcribed genes resembles that of H3K4 levels. In contrast, two other groups have found that ASH1L's HMTase activity is directed toward H3K36, using nucleosomes as substrate.

Role in human disease

There are over 100 reported pathogenic, or disease-causing, variants in the ASH1L gene. About half of the variants arise de novo, and half are inherited. Of the inherited variants, about half are maternally inherited and half are paternally inherited. Disease-causing variants may be missense, nonsense, or frameshift mutations. The missense mutations are distributed throughout the gene body without localizing to a known functional domain of ASH1L.

All affected humans are heterozygous for ASH1L mutations. A single pathogenic copy of ASH1L causes disease, which may be the result of two different genetic mechanisms: haploinsufficiency or dominant negative function. The ClinGen clinical genomics resource states that there is "Sufficient Evidence for Haploinsufficiency" in ASH1L.

The most common phenotypes, or symptoms, related to ASH1L mutations are autism spectrum disorder (ASD), epilepsy, intellectual disability, and attention deficit hyperactivity disorder (ADHD). The Simons Foundation Autism Research Initiative (SFARI) gives ASH1L a score of 1.1, indicating that ASH1L is a high confidence autism gene with the best level of evidence linking it to autism.

References

References

1. (2011). "Dual function of histone H3 lysine 36 methyltransferase ASH1 in regulation of Hox gene expression". PLOS ONE.
2. (September 1999). "Trithorax and ASH1 interact directly and associate with the trithorax group-responsive bxd region of the Ultrabithorax promoter". Molecular and Cellular Biology.
3. (June 2000). "huASH1 protein, a putative transcription factor encoded by a human homologue of the Drosophila ash1 gene, localizes to both nuclei and cell-cell tight junctions". Proceedings of the National Academy of Sciences of the United States of America.
4. "ASH1L_HUMAN". UniProt.
5. (March 2011). "Crystal structure of the human histone methyltransferase ASH1L catalytic domain and its implications for the regulatory mechanism". The Journal of Biological Chemistry.
6. "ASH1L protein expression summary - The Human Protein Atlas".
7. (January 2015). "Proteomics. Tissue-based map of the human proteome". Science.
8. (January 2019). "The mouse Gene Expression Database (GXD): 2019 update". Nucleic Acids Research.
9. (February 2014). "Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics". Molecular & Cellular Proteomics.
10. (November 2018). "Shared and distinct transcriptomic cell types across neocortical areas". Nature.
11. (January 2016). "Purification and Characterization of Progenitor and Mature Human Astrocytes Reveals Transcriptional and Functional Differences with Mouse". Neuron.
12. (September 2014). "An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex". The Journal of Neuroscience.
13. (April 2014). "Transcriptional landscape of the prenatal human brain". Nature.
14. (April 2022). "Counteracting epigenetic mechanisms regulate the structural development of neuronal circuitry in human neurons". Molecular Psychiatry.
15. (May 2016). "Histone methyltransferase Ash1L mediates activity-dependent repression of neurexin-1α". Scientific Reports.
16. (2018). "The Epigenetic Factor Landscape of Developing Neocortex Is Regulated by Transcription Factors Pax6→ Tbr2→ Tbr1". Frontiers in Neuroscience.
17. (January 2007). "Genome-wide atlas of gene expression in the adult mouse brain". Nature.
18. (December 2007). "Mammalian ASH1L is a histone methyltransferase that occupies the transcribed region of active genes". Molecular and Cellular Biology.
19. (August 2007). "Trithorax-group protein ASH1 methylates histone H3 lysine 36". Gene.
20. (January 2018). "Histone Lysine Methylases and Demethylases in the Landscape of Human Developmental Disorders". American Journal of Human Genetics.
21. (November 2014). "Synaptic, transcriptional and chromatin genes disrupted in autism". Nature.
22. (December 2015). "Targeted Next-Generation Sequencing Analysis of 1,000 Individuals with Intellectual Disability". Human Mutation.
23. (June 2017). "Novel MCA/ID syndrome with ASH1L mutation". American Journal of Medical Genetics. Part A.
24. (January 2019). "De novo loss-of-function variants of ASH1L are associated with an emergent neurodevelopmental disorder". European Journal of Medical Genetics.
25. (September 2021). "ASH1L mutation caused seizures and intellectual disability in twin sisters". Journal of Clinical Neuroscience.
26. (September 2015). "Molecular Diagnostic Yield of Chromosomal Microarray Analysis and Whole-Exome Sequencing in Children With Autism Spectrum Disorder". JAMA.
27. (December 2015). "De novo mutations in congenital heart disease with neurodevelopmental and other congenital anomalies". Science.
28. (May 2020). "Phenotypic and genetic spectrum of epilepsy with myoclonic atonic seizures". Epilepsia.
29. (November 2012). "Diagnostic exome sequencing in persons with severe intellectual disability". The New England Journal of Medicine.
30. (November 2016). "De novo genic mutations among a Chinese autism spectrum disorder cohort". Nature Communications.
31. (October 2020). "Large-scale targeted sequencing identifies risk genes for neurodevelopmental disorders". Nature Communications.
32. (November 2014). "The contribution of de novo coding mutations to autism spectrum disorder". Nature.
33. (April 2017). "Targeted sequencing identifies 91 neurodevelopmental-disorder risk genes with autism and developmental-disability biases". Nature Genetics.
34. (August 2019). "Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks". Cell.
35. (November 2013). "Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism". Cell.
36. (2018). "Inherited and multiple de novo mutations in autism/developmental delay risk genes suggest a multifactorial model". Molecular Autism.
37. (September 2022). "Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes". Nature Genetics.
38. (April 2017). "Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder". Nature Neuroscience.
39. (June 2015). "Excess of rare, inherited truncating mutations in autism". Nature Genetics.
40. (October 2021). "High prevalence of multilocus pathogenic variation in neurodevelopmental disorders in the Turkish population". American Journal of Human Genetics.
41. (July 2021). "Contribution of Multiple Inherited Variants to Autism Spectrum Disorder (ASD) in a Family with 3 Affected Siblings". Genes.
42. (September 2019). "Characterization of intellectual disability and autism comorbidity through gene panel sequencing". Human Mutation.
43. "ASH1L curation results".
44. "Gene: ASH1L -".