KMT2D (also known as MLL4) binds the WRAD complex, consisting of WDR5, RBBP5, ASH2L and DPY30, to form the MLL4 complex. WDR5 plays an important role in the optimal stimulation of MLL4 methyltransferase activity by the RBBP5:ASH2L heterodimer (Zhang et al. 2012).

KMT2C and KMT2D are paralogous histone methyltransferases and mainly responsible for H3K4 mono-methylation (H3K4me1) at enhancers (Lee et al. 2013). KMT2D has a partial functional redundancy with KMT2C in cells, although the phenotypes of KMT2D and KMT2C null mice suggest that MLL4 might be the dominant counterpart (Lee et al. 2013). KMT2C/D are thought to play a role in the recruitment of the acetyltransferase CBP/p300 complex, which facilitates H3K27 acetylation and RNA polymerase II's recruitment to enhancer regions (Jin et al. 2011, Wang et al. 2016, Lai et al. 2017).

Trimethylation of lysine-5 of histone H3 (H3K4) has been linked to transcriptional activation in a variety of eukaryotic species (Ruthenberg et al. 2007). Several H3K4 methyltransferases have been identified in mammals, predominantly members of the Mixed Lineage Leukemia (MLL) protein family. Five of these, KMT2A (MML1), KMT2D (MLL2), KMT2C (MLL3), KMT2B (MLL4) and SETD1A (KMT2F) have been shown to display H3K4 mono-, di- and tri-methyltransferase activity (Milne et al. 2002, Hughes et al. 2004, Cho et al. 2007, Wysocka et al. 2003). KMT2G (SETD1B) is believed to have similar activity on the basis of sequence homology (Ruthenberg et al. 2007). MLLs are a component of large multiprotein complexes that also include WDR5, RBBP5, ASH2 and DPY30, assembled to form the core MLL complex (Nakamura et al. 2002, Hughes et al. 2004, Dou et al. 2006, Tremblay et al. 2014). The WD40 domain of WDR5 recognizes and binds the histone H3 N-terminus, presenting the lysine-4 side chain for methylation by one of the catalytically active MLL family (Couture et al. 2006, Ruthenburg et al. 2006). Histone H3 recognition by WDR5 is regulated by the methylation state of the adjacent arginine (H3R2) residue. H3R2 methylation abolishes WDR5 interaction with the H3 histone tail (Couture et al. 2006); H3K4 di-/trimethylation and H3R2 methylation have an inverse relationship (Guccione et al. 2006). WHSC1L1 (KMT3F, WHISTLE), SMYD3 (KMT3E) and SETD3 are able to di-methylate H3K4 (Kim et al. 2006, Hamamoto et al. 2004, Eom et al. 2011).

Trimethylation of lysine-5 of histone H3 (H3K4) has been linked to transcriptional activation in a variety of eukaryotic species (Ruthenberg et al. 2007). Several H3K4 methyltransferases have been identified in mammals, predominantly members of the Mixed Lineage Leukemia (MLL) protein family. Five of these, KMT2A (MML1), KMT2D (MLL2), KMT2C (MLL3), KMT2B (MLL4) and SETD1A (KMT2F) have been shown to display H3K4 mono-, di- and tri-methyltransferase activity (Milne et al. 2002, Hughes et al. 2004, Cho et al. 2007, Wysocka et al. 2003). KMT2G (SETD1B) is believed to have similar activity on the basis of sequence homology (Ruthenberg et al. 2007). MLLs are a component of large multiprotein complexes that also include WDR5, RBBP5, ASH2 and DPY30, assembled to form the core MLL complex (Nakamura et al. 2002, Hughes et al. 2004, Dou et al. 2006, Tremblay et al. 2014). The WD40 domain of WDR5 recognizes and binds the histone H3 N-terminus, presenting the lysine-4 side chain for methylation by one of the catalytically active MLL family (Couture et al. 2006, Ruthenburg et al. 2006). Histone H3 recognition by WDR5 is regulated by the methylation state of the adjacent arginine (H3R2) residue. H3R2 methylation abolishes WDR5 interaction with the H3 histone tail (Couture et al. 2006); H3K4 di-/trimethylation and H3R2 methylation have an inverse relationship (Guccione et al. 2006).

SMYD3 (KMT3E) and PRDM9 (KMT8B) are able to tri-methylate H3K4 (Hamamoto et al. 2004, Hayashi et al. 2005, Koh-Stenta et al. 2014).

Tri-methylation of lysine-5 of histone H3 (H3K4) has been linked to transcriptional activation in a variety of eukaryotic species (Ruthenberg et al. 2007). Several H3K4 methyltransferases have been identified in mammals, predominantly members of the Mixed Lineage Leukemia (MLL) protein family. Five of these, KMT2A (MML1), KMT2D (MLL2), KMT2C (MLL3), KMT2B (MLL4) and SETD1A (KMT2F) have been shown to display H3K4 mono-, di- and tri-methyltransferase activity (Milne et al. 2002, Hughes et al. 2004, Cho et al. 2007, Wysocka et al. 2003). KMT2G (SETD1B) is believed to have similar activity on the basis of sequence homology (Ruthenberg et al. 2007). MLLs are a component of large multiprotein complexes that also include WDR5, RBBP5, ASH2 and DPY30, assembled to form the core MLL complex (Nakamura et al. 2002, Hughes et al. 2004, Dou et al. 2006, Tremblay et al. 2014). The WD40 domain of WDR5 recognizes and binds the histone H3 N-terminus, presenting the lysine-4 side chain for methylation by one of the catalytically active MLL family (Couture et al. 2006, Ruthenburg et al. 2006). Histone H3 recognition by WDR5 is regulated by the methylation state of adjacent arginine (H3R2) residue. H3R2 methylation abolishes WDR5 interaction with the H3 histone tail (Couture et al. 2006); H3K4 di-/trimethylation and H3R2 methylation have an inverse relationship (Guccione et al. 2006).

SETD7 (KMT7, SET9, SET7/9) is an H3K4 mono-methytransferase (Wang et al. 2001, Xiao et al. 2003, Hu & Zhang 2006) that can also methylate a wide range of non-histone proteins (Dhayalan et al. 2011). SETD3 can mono- and di-methylate H3K4 and H3K36 (Eom et al. 2011).

WDR5 is a component of six mammalian histone methyltransferase KMT2 complexes: Mixed Lineage Leukemia (MLL) 1-4, SET1A, and SET1B. All KMT2 complexes consist of a histone methyltransferase (KMT2A, KMT2B, KMT2C, KMT2D, SETD1A, or SETD1B, respectively) and the WRAD subcomplex composed of WDR5, RBBP5, ASH2L, and DPY30. The WRAD complex regulates the enzymatic activity of histone methyltransferases and enables their recruitment to chromatin. Additional transcription cofactors associate with each KMT2 histone methyltransferase complex, enabling their functional diversification. For a detailed overview, please refer to Cho et al. 2007, Song et al. 2008, Takahashi et al. 2011, Couture and Skiniotis 2013, van Nuland et al. 2013, Klonou et al. 2021.

The KMT2 complexes are evolutionarily conserved. While a single SET1/COMPASS complex is present in yeast, three distinct complexes are present in Drosophila: trithorax (Trx), trithorax-related (Trr), and Set1. In mammals, due to gene duplication, two Trx-like complexes (one with KMT2A and another with KMT2B as the catalytic subunit), as well as two Trr-like complexes (one with KMT2C and another with KMT2D as the catalytic subunit), and two Set1-like complexes (one with SETD1A and another with SETD1B as the catalytic subunit) are formed. For review, please refer to Rao and Dou 2015.

All KMT2 complexes methylate lysine K5 of histone H3 (K4 in mature histone H3 peptides, as the initiator methionine is removed), which is associated with transcriptional activation. Different KMT2 complexes preferentially monomethylate, dimethylate, or trimethylate H3K4, depending on the presence of accessory subunits, transcriptional co-factors, and posttranslational modifications. The catalytic activity of KMT2 complexes may differ between endogenous complexes and complexes reconstituted in vitro by mammalian proteins expressed and produced in bacterial or insect cells. The KMT2A and KMT2B complexes preferentially methylate H3K4 at a limited number of target gene promoters, while KMT2C and KMT2D complexes preferentially methylate H3K4 at a limited number of target gene enhancers. SETD1A and SETD1B complexes are responsible for the bulk of cellular H3K4 methylation and show less target specificity. For overview, please refer to Patel et al. 2009, Wang et al. 2009, Rao and Dou 2015.

In both Drosophila and vertebrates, KMT2 complexes control the expression of evolutionarily conserved Hox genes which serve as master regulators of embryonic patterning (reviewed in Soshnikova and Duboule 2009).

Germline mutations in human KMT2 complexes are the underlying cause of several chromatinopathies. Germline loss-of-function (LOF) mutations in KMT2A cause Weideman-Steiner syndrome, a rare autosomal-dominant disorder characterized by intellectual disability, developmental delay, pre- and post-natal growth delay, hypertrichosis, short stature, hypotonia, distinctive facial features, skeletal abnormalities, feeding problems and behavioral difficulties (reviewed in Castiglioni et al. 2022). Germline LOF mutations in KMT2B cause dystonia-28 (DYT28) and intellectual developmental, autosomal dominant disorder-68 (MRD68). DYT28 is an autosomal dominant neurologic disorder characterized by onset of progressive dystonia in the first decade of life (reviewed in Zech et al. 2019), while MRD68 is an autosomal dominant disorder characterized by developmental delay/intellectual disability, microcephaly, poor growth, feeding difficulties, and dysmorphic features (Cif et al. 2020). Germline LOF mutations in KMT2C cause Kleefstra syndrome-2 (KLEFS2), an autosomal dominant neurodevelopmental disorder characterized by delayed psychomotor development, variable intellectual disability, and mild dysmorphic features (reviewed in Lavery et al. 2020). Germline LOF mutations in KMT2D cause Kabuki syndrome 1, a congenital mental retardation syndrome with postnatal dwarfism, a facial dysmorphism and skeletal abnormalities (reviewed in Lavery et al. 2020). Germline LOF mutations in SETD1A cause early-onset epilepsy with or without developmental delay (EPEDD), an autosomal dominant neurologic disorder (Yu et al. 2019), and neurodevelopmental disorder with speech impairment and dysmorphic facies (NEDSID) (Kummeling et al. 2021). Germline LOF mutations in SETD1B cause intellectual developmental disorder with seizures and language delay (IDDSELD) (Roston et al. 2021).

Somatic mutations in KMT2 genes contribute to cancer development. They were first discovered in Mixed Lineage Leukemia (MLL), characterized by chromosomal translocations that involve the KMT2A gene locus on chromosome 11 (chromosomal band 11q23) and result in the expression of fusion proteins with oncogenic properties. Besides gene fusions, other types of KMT2A mutations are also present in blood cancers (most frequently in high-grade B-cell lymphoma, T-cell lymphoblastic leukemia, and acute myeloid leukemia) and solid tumors (most often reported in lung adenocarcinoma, colon adenocarcinoma, and bladder urothelial carcinoma). Somatic cancer mutations in other KMT2 genes (KMT2B, KMT2C, KMT2D, SETD1A and SETD1B) are less characterized but most frequently affect the catalytic SET domain and show different distributions between different cancer types. For review, please refer to Rao and Dou 2015, Castiglioni et al. 2022. Several anti-cancer therapeutics are being developed that affect the association of KMT2 enzymes with components of the WRAD complex, in particular WDR5 (reviewed in Vedadi et al. 2017; Siladi et al. 2022).

WDR5 is also a component of three histone acetyltransferase complexes, GCN5-ATAC, PCAF-ATAC, and MOF/KAT8-NSL. The role of WDR5 in epigenetic regulation of gene expression through histone acetylation is under investigation (reviewed in Guarnaccia and Tansey 2018).

The function of WDR5-containing histone modifying complexes is currently depicted in the following Reactome pathways: "Transcriptional regulation of granulopoiesis" (MLL1 complex), "Transcriptional regulation by RUNX1" (MLL1 complex), "Activation of anterior HOX genes in hindbrain development during early embryogenesis" (MLL3 complex and MLL4 complex), "TCF dependent signaling in response to WNT" (MLL4 complex), and "Chromatin organization" (MLL1 complex, MLL2 complex, MLL3 complex, MLL4 complex, SET1A complex, SET1B complex, GCN5-ATAC complex, PCAF-ATAC complex, and MOF/KAT8-NSL complex). Please note that there is an inconsistency in naming of MLL2 and MLL4 complexes in the literature and in Reactome pathways, as MLL2 and MLL4 have been used as synonyms for both KMT2B and KMT2D, depending on whether the numbering of MLLs referred to order of cloning or whether it referred to similarity to founding MLL1 (MLL, KMT2A) enzyme. The current UniProt standard is for MLL2 to be used as the preferred synonym of KMT2B, and for MLL4 to be used as the preferred synonym of KMT2D.

Hox genes encode proteins that contain the DNA-binding homeobox motif and control early patterning of segments in the embryo as well as later events in development (reviewed in Rezsohazy et al. 2015). Mammals have 39 Hox genes arrayed in 4 linear clusters, with each cluster containing 9 to 11 genes. Based on homologies, the genes have been assigned to 13 paralogous groups. The nomenclature of Hox genes uses a letter to indicate the cluster and a number to indicate the paralog group. For example, HOXA4 is the gene in cluster A that is most similar with genes of paralog group 4 from other clusters.
One of the most striking aspects of mammalian Hox gene function is the mechanism of their activation during embryogenesis: the order of genes in a cluster correlates with the timing and location of their activation such that genes at the 3' end of a cluster are activated first and genes at the 5' end of a cluster are activated last. (5' and 3' refer to the transcriptional orientation of the genes in the cluster.) Because development of segments of the embryo proceeds from anterior to posterior this means that the anterior boundaries of expression of 3' genes are more anterior (rostral) and the anterior boundaries of expression of 5' genes are more posterior (caudal). Expression of HOX genes initiates in the posterior primitive streak at the beginning of gastrulation at approximately E7.5 in mouse. As gastrulation proceeds, further 5' genes are sequentially activated and they too undergo the same chromatin changes and migration. After formation of the axis of the embryo, similar waves of activation of HOXA and HOXD clusters occur in developing limbs beginning at about E9. Retinoids, especially all trans retinoic acid (atRA), participate in initiating the process via retinoid receptors. Other factors such as FGFs and Wnt, also regulate Hox expression. After activation, Hox genes participate in maintaining their own expression (autoregulation), activating later, 5' Hox genes, and repressing prior, 3' Hox genes (crossregulation). Differentiation of embryonal carcinoma cells and embryonic stem cells in response to retinoic acid is used to model the process in vitro (reviewed in Gudas et al. 2013).
Activation of Hox genes is accompanied by a change from bivalent chromatin to euchromatin (reviewed in Soshnikova and Duboule 2009). Bivalent chromatin has extensive methylation of lysine-9 on histone H3 (H3K9me3), a repressive mark, with interspersed punctate regions of methylation of lysine-4 on histone H3 (H3K4me2, H3K4me3), an activating mark. Euchromatization initiates at the 3' ends of clusters and proceeds towards the 5' ends, with the euchromatin migrating to an active region of the nucleus (reviewed in Montavon and Duboule 2013). This change in chromatin reflects a loss of H3K27me3 and a gain of H3K4me2,3. Polycomb repressive complexes bind H3K27me3 and are responsible for maintenance of repression, KDM6A and KDM6B histone demethylases remove H3K27me3, and members of the trithorax family of histone methylases (KMT2A, KMT2C, KMT2D) methylate H3K4.

Histone-lysine N-methyltransferase subclass 2