Discovery of MLL1 binding units, their localization to CpG Islands, and their potential function in mitotic chromatin

Abstract

BackgroundMixed Lineage Leukemia 1 (MLL1) is a mammalian ortholog of the Drosophila Trithorax. In Drosophila, Trithorax complexes transmit the memory of active genes to daughter cells through interactions with Trithorax Response Elements (TREs). However, despite their functional importance, nothing is known about sequence features that may act as TREs in mammalian genomic DNA.ResultsBy analyzing results of reported DNA binding assays, we identified several CpG rich motifs as potential MLL1 binding units (defined as morphemes). We find that these morphemes are dispersed within a relatively large collection of human promoter sequences and appear densely packed near transcription start sites of protein-coding genes. Genome wide analyses localized frequent morpheme occurrences to CpG islands. In the human HOX loci, the morphemes are spread across CpG islands and in some cases tail into the surrounding shores and shelves of the islands. By analyzing results of chromatin immunoprecipitation assays, we found a connection between morpheme occurrences, CpG islands, and chromatin segments reported to be associated with MLL1. Furthermore, we found a correspondence of reported MLL1-driven “bookmarked” regions in chromatin to frequent occurrences of MLL1 morphemes in CpG islands.ConclusionOur results implicate the MLL1 morphemes in sequence-features that define the mammalian TREs and provide a novel function for CpG islands. Apparently, our findings offer the first evidence for existence of potential TREs in mammalian genomic DNA and the first evidence for a connection between CpG islands and gene-bookmarking by MLL1 to transmit the memory of highly active genes during mitosis. Our results further suggest a role for overlapping morphemes in producing closely packed and multiple MLL1 binding events in genomic DNA so that MLL1 molecules could interact and reside simultaneously on extended potential transcriptional maintenance elements in human chromosomes to transmit the memory of highly active genes during mitosis.

Impact of the MLL1 morphemes on codon utilization and preservation in CpG Islands

“…The MLL1 morphemes consist of the following sequences: CGCG, CGACG/CGTCG; CGCCG/CGGCG; CGCGCG; CGTGCG/CGCACG; CGCCCG/CGGGCG; CGGACG/CGTCCG; CGTACG; complementary sequences are shown in 5′ to 3’ direction. These sequences are interchangeably referred to as MLL1 sites, binding units, or morphemes: the smallest “words” in DNA that selectively bind MLL1 . In a DNA segment, morpheme occurrences may overlap at CG producing a short or a long block of consecutive morphemes.…”

“…For example: DNA compaction may enforce rules for structural features that would facilitate nucleosome formation . Creation and maintenance of open chromatin structures may involve specific DNA sequence elements spread in promoters as well is exons of genes . Regulation of gene expression may favor dual‐use for codons "duons", sequences that would simultaneously specify a codon for amino acids and transcription factor recognition sites .…”

“…MLL1 contributes to the regulation of several genes in the four human HOX loci , which contain 39 genes with major roles in the development of the central nervous system, axial skeleton, gastrointestinal and urogenital tracts . Several genes in these loci include overlaps of the various MLL1 morphemes . Furthermore, the genes that encode HOXD13 and HOXA13 include tracts of repeated GGC/CCG, produced from overlapping morphemes (Figures and ); Significantly, expansion of these repeats causes limb malformations, synpolydactyly, and hand‐foot‐genital syndrome …”

“…At the onset of mitosis, MLL1 associates with gene promoters in a manner favoring genes that were highly transcribed during interphase . The MLL1 morphemes in CGIs have been implicated in gene bookmarking events by serving as Trithorax Response Elements (TREs) in the human chromosomes . Furthermore, MLL1 is the central component in multiprotein complexes that catalyze trimethylation of lysine 4 in histone H3 producing H3K4me3, marks that create chromatin structures that could support or be poised for transcription .…”

Development and Use of Assay Conditions Suited to Screening for and Profiling of SET-Domain-Targeted Inhibitors of the MLL/SET1 Family of Lysine Methyltransferases

“…On the other hand, and this need not conflict with the idea just mentioned, MLL1 may play a more widespread role in global H3K4 methylation than is generally suggested. 69,70 An ongoing concern for drug discovery efforts involving high-throughput screening of large compound collections are promiscuous inhibitors or nuisance compounds, 71,72 which by various mechanisms, such as chemical assay interference 73 or compound aggregation-based effects, 74 show up repeatedly, across multiple target classes, as false-positive hits. 75 A different but related concern is that hit compounds exhibit leadlike properties; that is, they have physical and chemical properties suitable for the downstream analytical and chemical modification procedures employed in the further steps of drug development.…”