Remodeling of nuclear landscapes during human myelopoietic cell differentiation maintains co-aligned active and inactive nuclear compartments

Abstract

BackgroundPrevious studies of higher order chromatin organization in nuclei of mammalian species revealed both structural consistency and species-specific differences between cell lines and during early embryonic development. Here, we extended our studies to nuclear landscapes in the human myelopoietic lineage representing a somatic cell differentiation system. Our longterm goal is a search for structural features of nuclei, which are restricted to certain cell types/species, as compared to features, which are evolutionary highly conserved, arguing for their basic functional roles in nuclear organization.ResultsCommon human hematopoietic progenitors, myeloid precursor cells, differentiated monocytes and granulocytes analyzed by super-resolution fluorescence microscopy and electron microscopy revealed profound differences with respect to global chromatin arrangements, the nuclear space occupied by the interchromatin compartment and the distribution of nuclear pores. In contrast, we noted a consistent organization in all cell types with regard to two co-aligned networks, an active (ANC) and an inactive (INC) nuclear compartment delineated by functionally relevant hallmarks. The ANC is enriched in active RNA polymerase II, splicing speckles and histone signatures for transcriptionally competent chromatin (H3K4me3), whereas the INC carries marks for repressed chromatin (H3K9me3).ConclusionsOur findings substantiate the conservation of the recently published ANC-INC network model of mammalian nuclear organization during human myelopoiesis irrespective of profound changes of the global nuclear architecture observed during this differentiation process. According to this model, two spatially co-aligned and functionally interacting active and inactive nuclear compartments (ANC and INC) pervade the nuclear space.Electronic supplementary materialThe online version of this article (doi:10.1186/s13072-015-0038-0) contains supplementary material, which is available to authorized users.

Nuclear compartmentalization, dynamics, and function of regulatory DNA sequences

“…Color heat maps delineating for example, seven DAPI intensity classes in nuclear SIM sections ( Figure C,D) show a multilayered shell‐like chromatin organization of CDCs with compact chromatin (classes 5‐7) typically located in their interior, surrounded by a decondensed peripheral layer (classes 2‐3), and lined by the IC (IC = class 1). Quantitative 3D mapping of numerous “active” and “inactive” nuclear marks, such as different histone signatures, RNAPII, nascent RNA, and splicing speckles on chromatin compaction classified images and their quantitative assignment to a given chromatin compaction class revealed a significantly distinct distribution of “active” and “inactive” marks ( Figure D ). “Active” marks are highly enriched in classes 1‐3, whereas “repressive” marks are enriched in classes 5‐7, class 4 is considered as an intermediate zone (for review, see Reference ).…”

“…Quantitative 3D mapping of numerous “active” and “inactive” nuclear marks, such as different histone signatures, RNAPII, nascent RNA, and splicing speckles on chromatin compaction classified images and their quantitative assignment to a given chromatin compaction class revealed a significantly distinct distribution of “active” and “inactive” marks ( Figure D ). “Active” marks are highly enriched in classes 1‐3, whereas “repressive” marks are enriched in classes 5‐7, class 4 is considered as an intermediate zone (for review, see Reference ). This organization suggested an active and an inactive nuclear compartment (termed ANC and INC) that forms two spatially co‐aligned and functionally interacting networks (Figure D).…”

Super-Resolution Microscopy in Studying the Structure and Function of the Cell Nucleus

“…For example, there are reports on the reorganization of the cell nucleus structure during myelopoiesis in humans [50], neurogenesis in mice [51], in cells of early embryos and cloned bovine cells [52, 53], and in the cell cycle of yeast [54]. Such studies are often descriptive, because very little is known about the mechanisms of fine nuclear structure formation.…”

Distinct and shared three‐dimensional chromosome organization patterns in lymphocytes, monoclonal gammopathy of undetermined significance and multiple myeloma

“…The organization of chromatin and chromosomes in the nucleus influences gene expression and nuclear function . Several studies indicate that interphase positioning of CTs may not only be tissue‐specific, but is subject to changes during differentiation …”