BEN domain protein Elba2 can functionally substitute for linker histone H1 in Drosophila in vivo

Abstract

Metazoan linker histones are essential for development and play crucial roles in organization of chromatin, modification of epigenetic states and regulation of genetic activity. Vertebrates express multiple linker histone H1 isoforms, which may function redundantly. In contrast, H1 isoforms are not present in Dipterans, including D. melanogaster, except for an embryo-specific, distantly related dBigH1. Here we show that Drosophila BEN domain protein Elba2, which is expressed in early embryos and was hypothesized to have insulator-specific functions, can compensate for the loss of H1 in vivo. Although the Elba2 gene is not essential, its mutation causes a disruption of normal internucleosomal spacing of chromatin and reduced nuclear compaction in syncytial embryos. Elba2 protein is distributed ubiquitously in polytene chromosomes and strongly colocalizes with H1. In H1-depleted animals, ectopic expression of Elba2 rescues the increased lethality and ameliorates abnormalities of chromosome architecture and heterochromatin functions. We also demonstrate that ectopic expression of BigH1 similarly complements the deficiency of H1 protein. Thus, in organisms that do not express redundant H1 isoforms, the structural and biological functions performed by canonical linker histones in later development, may be shared in early embryos by weakly homologous proteins, such as BigH1, or even unrelated, non-homologous proteins, such as Elba2.

Nucleus Accumbens-Associated Protein 1 Binds DNA Directly through the BEN Domain in a Sequence-Specific Manner

“…Nearly complete resonance assignments were obtained for this construct using standard double and triple resonance experiments. NMR structures were generated using a combination of CYANA distance geometry calculations [ 51 , 52 , 53 ] and restrained molecular dynamics refinements in AMBER [ 54 ]. The 20 conformers with the lowest restraint violation energy were selected for the final representative ensemble and are shown in Figure 3 A and Figure S4 .…”

“…Analyses revealed the association between the BEN domains and specific DNA binding through extensive nucleotide contacts with their α helices and C-terminal loop, suggesting that the BEN domain functions in a DNA sequence-specific manner. On the other hand, recently, the Drosophila BEN-solo protein Elba2, but not Insv, was shown to rescue the deficiency of histone H1 protein in early larvae [ 53 ], supporting the sequence-recognition specificity and sequence-specific function of BEN domains.…”

“…Structure calculations for NAC1322-485 were performed using CYANA 2.1 [ 51 , 52 , 53 ]. The standard CYANA simulated annealing schedule was used with 40,000 torsion angle dynamics steps per conformer with 200 initial randomized conformers.…”

A novel TPR–BEN domain interaction mediates PICH–BEND3 association

“…BEN domains are proposed to function as adaptors to promote the assembly of higher-order chromatin, or to regulate chromatin remodeling during transcription ( 44 – 47 ). Indeed, the Drosophila melanogaster Elba2 protein has been shown to functionally substitute for histone H1 if the natural linker histone is depleted from cells ( 48 ). The structures of the insv-BEN and the Bsg25A BEN domains from Drosophila ( 33 , 34 ) have revealed that the association of BEN domains with DNA is generally accomplished through the insertion of both the loop located between the α2 and α3 helices and the long C-terminal helix into two consecutive major grooves of the nucleic acid molecule (Figure 5A ; Supplementary Figure S6A and B ).…”