n silico characterization of a rare disease that affects the dynamics and function of linker histone H1

Turunç, Serhan
Uça, Merve
Dimitrov, Stefan
Angelov, Dimitar
Kale, Seyit
The eukaryotic genome is wrapped in nucleosomes to form chromatin. Nucleosomes contain 147 bp of DNA wrapped ~1.65 times around a histone octamer comprising two copies each of the core histones H2A, H2B, H3, and H4. In higher eukaryotes, a fifth histone, known as the linker histone H1, binds the nucleosome core particle and the linker DNA between nucleosomes so as to facilitate the delicate folding of the chromatin fiber into higher order three-dimensional structure. H1 is a tripartite protein composed of a folded central region sandwiched between a short N-terminal domain and a long, highly positively charged C-terminal domain (CTD). The long unstructured carboxy-terminal domain (CTD) of linker histone is poorly conserved among subtypes and species. In mammals, 11 H1 variants have been identified, including seven somatic H1s and four germ-cell-specific H1s. Linker histone H1.4, which belongs to the somatic subtypes of family H1, plays a crucial role in the maintenance of the stable higher-order structure of chromatin. In late 2019, germline frameshift mutations involving the CTD of H1.4, were causally linked to an as-yet poorly defined syndrome, later called the Rahman syndrome (RS). In affected individuals, characteristic phenotypes include intellectual disability, skeletal and cardiac anomalies. All disease-causing mutations are located in a small region in the CTD tail and generally lead to a shorter protein with a highly negatively charged C-terminal tail. Motivated by this fact, we hypothesize that the chromatin domains harboring the RS H1.4 mutant could exhibit a less condensed and differently organized structure, which could disrupt the delicate architecture and function of chromatin. To understand how the Rahman syndrome (RS) mutant Histone H1.4 affects nucleosome dynamics, we performed atomistic molecular simulations of the WT (wild type) - as well as the RS mutant H1.4 bound nucleosome core particles at the sub-microsecond timescale. Because the complete CTD is too large for atomistic-level simulations, we incorporated a ~30 amino acid segment close to the globular domain known to be critical for the compaction function of H1. Among all RS patients, we chose the very first patient, “patient #1”, because of the early positioning of the frameshift mutation in the genotype and the dramatic net charge reversal of the CTD. Indeed, we found that the H1.4 of patient #1 could not only not fold the linker DNA strands but it was actually destabilizing them in comparison to the WT as well as a “tailless” mutant that lacks the CTD altogether. In all surviving RS patients, there is a small shared region at the terminus of the mutated CTD tail which is elusive in terms of its cytotoxic role as well as potential loss- or gain of function in the cell. To characterize this region in detail, we performed accelerated atomistic simulations of the isolated shared mutant CTD segment as well as its WT counterpart. In these simulations, also known as metadynamics, we encourage the disordered protein to visit rare and novel structural configurations more frequently than it would normally do under ambient equilibrium conditions. We found that the mutant segment is distinctly more compact in comparison to its WT counterpart, which could be potentially implicated in the binding of de novo intra-nuclear partners. In conclusion, rare diseases are not rare in the increasingly crowded world population, especially for Turkey, as a Mediterranean country. The findings of this study will not only give us information about the Rahman syndrome but also provide important findings about the 3D chromatin architecture mechanism, which is still a mystery in the epigenetics field. In the near future, we will apply EuroHPC for extra computing time. It will accelerate the analysis of complete Rahman syndrome CTD simulations. In this project, in cellulo and in vitro experiments are still a work in progress in parallel with our in silico research. The combination of these studies is expected not only to shed light on the mechanism of Rahman syndrome but could also be used as an example of a “workflow” for rare disease studies.


RT-PCR amplification of a Rhizopus oryzae lactate dehydrogenase gene fragment
Hakki, EE; Akkaya, Mahinur (Elsevier BV, 2001-02-01)
No amino acid or DNA sequence information in sequence databases was found for a fungal lactate dehydrogenase (LDH) isozyme. Highly conserved regions in the lactate dehydrogenase enzymes of all taxonomies are found to be beta alpha beta nucleotide binding and substrate binding sites, also catalysis/active site. The conserved regions were selected as PCR primer target regions. The degenerate primers were designed according to the codon usage, determined by analyzing a number of different genes of Rhizopus spe...
APOBEC3B expression in drug resistant MCF-7 breast cancer cell lines
Onguru, Onder; Yalcin, Serap; Rosemblit, Cinthia; Zhang, Paul J.; Kilic, Selim; Gündüz, Ufuk (2016-04-01)
APOBEC3B belongs to a protein family of cytidine deaminases that can insert mutations in DNA and RNA as a result of their ability to deaminate cytidine to uridine. It has been shown that APOBEC3B-catalysed deamination provides a chronic source of DNA damage in breast cancers. We investigated APOBEC3B expression in four drug resistant breast cancer cell lines (Doxorubicin, Etoposide, Paclitaxel and Docetaxel resistant MCF-7 cell lines) using a novel RNA in situ hybridization technology (RNAscope) and compare...
Semi-automatic segmentation of mitochondria on electron microscopy images using kalman filtering approach
Mohammadi Alamdari, Aynaz; Mumcuoğlu, Ünal Erkan; Department of Medical Informatics (2016)
Mitochondria are membrane bound organelles found in most eukaryotic cells. Mitochondria provide cell’s energy; hence they are called ‘power houses of the cell’. The structure of mitochondria can be illustrated in an electron micrograph. This structure has two membranes: inner and outer. There is a gap between these two membranes, called inter-membrane space. Folds of inner membrane inside the mitochondria form the cristae. To study the relation between mitochondria’s physical structure and its function, ele...
Molecular dynamics simulations and coupled nucleotide substitution experiments indicate the nature of A center dot A base pairing and a putative structure of the coralyne-induced homo-adenine duplex
Joung, In Suk; Persil Çetinkol, Özgül; HUD, Nicholas V.; Cheatham, Thomas E. (Oxford University Press (OUP), 2009-12-01)
Coralyne is an alkaloid drug that binds homo-adenine DNA (and RNA) oligonucleotides more tightly than it does Watson-Crick DNA. Hud's laboratory has shown that poly(dA) in the presence of coralyne forms an anti-parallel duplex, however attempts to determine the structure by NMR spectroscopy and X-ray crystallography have been unsuccessful. Assuming adenine-adenine hydrogen bonding between the two poly(dA) strands, we constructed 40 hypothetical homo-(dA) anti-parallel duplexes and docked coralyne into the s...
Real-Time PCR Investigation of the Dynamic Expression of Three "RNA Processing and Modification" Genes of Phanerochaete chrysosporium Exposed to Lead
Tekın, Elif; İçgen, Bülent; Özcengiz, Gülay (Springer Science and Business Media LLC, 2013-01-01)
The expression of three ribosome binding proteins namely; polyadenylate-binding protein, splicing factor RNPS1 and ATP-dependent RNA helicase of Phanerochaete chrysosporium exposed to lead were analyzed by real-time PCR. The mRNA level of splicing factor RNPS1 showed 2.7 (p < 0.05), 2.6 (p < 0.05) and 4.9-fold (p < 0.001) increase when the cells were exposed to 25, 50 and 100 mu M lead, respectively. 50 and 100 mu M lead exposure resulted in almost 2-fold (p < 0.01and p < 0.05, respectively) increase in the...
Citation Formats
S. Turunç, M. Uça, S. Dimitrov, D. Angelov, and S. Kale, “n silico characterization of a rare disease that affects the dynamics and function of linker histone H1,” Erdemli, Mersin, TÜRKİYE, 2022, p. 3012, Accessed: 00, 2023. [Online]. Available: https://hibit2022.ims.metu.edu.tr.