Mitotic bookmarking of genes: a novel dimension to epigenetic control

Abstract

Regulatory machinery is focally organized in the interphase nucleus. The information contained in these focal nuclear microenvironments must be inherited during cell division to sustain physiologically responsive gene expression in progeny cells. Recent results suggest that focal mitotic retention of phenotypic transcription factors at promoters together with histone modifications and DNA methylation--a mechanism collectively known as gene bookmarking--is a novel parameter of inherited epigenetic control that sustains cellular identity after mitosis. The epigenetic signatures imposed by bookmarking poise genes for activation or suppression following mitosis. We discuss the implications of phenotypic transcription factor retention on mitotic chromosomes in biological control and disease.

Figure 1. Distinct mechanisms control protein content of the cell during mitosis

(A) Examples of three distinct mechanisms that regulate mitotic presence of proteins are depicted. The cytoplasm is illustrated by a light blue oval, the nucleus is a blue circle, and nucleoli are red circles. Three types of nuclear proteins are shown: 1) proteins that are destined to be degraded during mitosis, 2) proteins that are displaced from mitotic chromosomes, and 3) transcription factors that are retained on target gene loci through sequence-specific protein-DNA interactions during mitosis. As cells enter mitosis, many nuclear proteins are either displaced from mitotic chromosomes to be re localized in G1 nuclei or are degraded to be re synthesized in progeny cells. Several phenotypic transcription factors are retained on mitotic chromosomes and localize to either RNA Pol I transcribed nucleolar organizing regions or RNA Pol II regulated genes involved in cell proliferation and differentiation. (B) Mitosis of a mammalian cell is depicted. Chromosomes are schematically represented in light and dark blue colors. Microtubules and spindle are drawn as green lines, while the centromeres are shown as red color circles (Metaphase).

Figure 2. Coordination of cell growth, proliferation and differentiation of mesenchymal stem cells into three distinct lineages

Mesenchymal stem cells (MSCs) can be differentiated into osteoblasts, myoblasts, or adipocytes, depending upon the available cohort of regulatory proteins, providing an example of the developmental relevance of gene bookmarking. A ribosomal DNA (rDNA) repeat that is occupied by the proliferation-promoting Myc transcription factor is illustrated. Myc upregulates rRNA transcription in non-committed, proliferating MSCs and contributes to growth potential. In response to extracellular signals, MSCs express either Runx2 when differentiated into osteoblasts, muscle regulatory factors (i.e., MyoD and myogenin) when differentiated into myoblasts, or C/EBP upon adipocyte differentiation. These phenotypic proteins occupy rDNA repeats as cells differentiate into their respective lineages and down regulate rRNA expression, concomitant with the exit of MSCs from the cell cycle, reduced cell growth and initiation of a differentiation.

Figure 3. Mitotic retention of sequence-specific transcription factors as an epigenetic mechanism for lineage maintenance in normal cells and for sustained tumor phenotype in cancer cells

Gene loci on metaphase chromosomes (blue color) are occupied by phenotypic transcription factors (green circle) for lineage maintenance through successive cell divisions in normal cells. This possibility is shown by Runx1, a hematopoietic master regulator, which associates with mitotic chromosomes (immunofluorescence; IF), occupies target genes during mitosis (Occupancy as shown by chromatin immunoprecipitation assays), and regulate their expression in interphase (as represented by Transcription, where transcripts are quantitatively measured from cells with (control) or without Runx1 (siRunx1)). In tumors, as cells undergo genomic instability and accumulate cancer mutations, it is possible that one allele (shown here as red chromosome arm) is occupied by oncogenic transcription factor (which can be a phenotypic protein, ectopically expressed in cancer cells). Successive cell divisions and acquisition of additional cancer mutations then lead to the replacement of phenotypic regulatory proteins with oncogenic transcription factors. Occupancy of target gene loci with oncogenic proteins results in a sustained tumor phenotype. This possibility is reflected by the chimeric AML1-ETO (A/E) protein that is encoded by the translocated Runx1 gene in frame with ETO gene. The oncogenic Runx1 translocation associates with mitotic chromosomes (IF), occupies target genes during mitosis (Occupancy), and regulate their expression in interphase (Transcription). Images and data are modified from Reference . Key Terms Architectural epigenetics Composite of inherited structural and functional regulatory information during mitosis that includes the cohort of regulatory and co-regulatory factors that mediate transcription and the chromatin organization of cognate gene loci.