The 3D organization of the genome appears to be functionally relevant as it allows establishing of long-range spatial contacts between promoters and remote regulatory elements. However, most of the ...observations on the 3D genome organization have been made by conventional methods in cell population where only average characteristics of the so-called typical cell can be identified. On the other hand, FISH-based studies demonstrated that the spatial configuration of the genome varies in individual cells. However, the microscopic approaches do not allow performing a genome-wide analysis that is critical to understand better the regulatory events occurring at the level of 3D genome organization. The high throughput chromosome conformation capture protocol (Hi-C) has been modified recently to allow construction of chromatin contact frequency maps for individual cells. Using this modified protocol we constructed Hi-C maps for 20 drosophila cells (line Dm-BG3c2). In the best cell we have captured ~15% of the theoretically available contacts. This allowed constructing of the spatial contact matrices with 10 Kb resolution. Analysis of these matrices demonstrated that topologically-associating domains (TADs) do not represent a computer-generated population average, but exist in individual cells. Importantly, using a number of statistical approaches we show that the observed profile of contact chromatin domains in individual cells cannot be explained by random fluctuations. Furthermore, we show that in individual cells TADs are organized hierarchically, and that this hierarchy closely matches the hierarchy seen in population maps. Finally, we show that genomic regions that frequently harbor the contact domain borders possess specific epigenetic signatures.
Interphase chromatin in animals is constrained by interactions with the nuclear lamina (NL) - a protein mesh lining nuclear envelope and composed from lamins and lamin-associated proteins. About 30% ...of chromatin is located near the NL in a living cell forming densely packed lamina-associated domains (LADs). LADs largely overlap with topologically-associating domains (TADs) build up from repressed chromatin, and contain predominately inactive genes, thus playing a role in transcription regulation. Here, we show that the NL disruption in Drosophila leads to en mass chromatin compactisation and redistribution towards the nuclear interior. This results in an increase of contact frequency between active and repressed fractions of the genome accompanied by the transcription upregulation in LADs. A subset of TADs characterized by high level of LADs become less compact, that could be driven by the loss of interactions with the nuclear envelope as revealed by polymer modelling. These results indicate that the NL in Drosophila cells plays a role in the specific spatial positioning of the chromatin inside the nucleus, its compartmentalization and at least partially controls the packaging density and low-level transcription in LADs.
Regulation of gene transcription is a complex process controlled by many factors, including the conformation of chromatin in the nucleus. Insights into chromatin conformation on both local and global ...scales can be provided by the Hi-C (high-throughput chromosomes conformation capture) method. One of the drawbacks of Hi-C analysis and interpretation is the presence of systematic biases, such as different accessibility to enzymes, amplification, and mappability of DNA regions, which all result in different visibility of the regions. Iterative correction (IC) is one of the most popular techniques developed for the elimination of these systematic biases. IC is based on the assumption that all chromatin regions have an equal number of observed contacts in Hi-C. In other words, the IC procedure is equalizing the experimental visibility approximated by the cumulative contact frequency (CCF) for all genomic regions. However, the differences in experimental visibility might be explained by biological factors such as chromatin openness, which is characteristic of distinct chromatin states. Here we show that CCF is positively correlated with active transcription. It is associated with compartment organization, since compartment A demonstrates higher CCF and gene expression levels than compartment B. Notably, this observation holds for a wide range of species, including human, mouse, and Drosophila. Moreover, we track the CCF state for syntenic blocks between human and mouse and conclude that active state assessed by CCF is an intrinsic property of the DNA region, which is independent of local genomic and epigenomic context. Our findings establish a missing link between Hi-C normalization procedures removing CCF from the data and poorly investigated and possibly relevant biological factors contributing to CCF.
"Mirror reads" in Hi-C data Galitsyna, Aleksandra Alekseevna; Khrameeva, Ekaterina Evgenyevna; Razin, Sergey Vladimirovich ...
Genomics and computational biology,
01/2017, Volume:
3, Issue:
1
Journal Article
Open access
The detailed analysis of chromatin structure has been enabled due to rapid development of chromosome conformation capture techniques. One of the most popular and widespread variations is high ...throughput conformation capture, or Hi-C, based on paired-end sequencing. Although a standard data analysis protocol exists to process Hi-C output, some results are still controversially interpreted, for example pairs of reads that are mapped to the same strand of the same restriction fragment. Here we propose the name ”mirror reads” for these cases and investigate possible biological and methodological context of their emergence. We test multiple hypotheses of mirror reads origin, such as genome duplications, replication fork, cohesion of sister chromatids, and homologous chromosome pairing. The current work demonstrates the association of mirror reads with the presence of homologous chromosomes in the nuclei, and homologous pairing. The results support biological relevance of mirror reads.
The chromatin structure of Dictyostelium discoideum Tsoy, Olga; Galitsyna, Aleksandra; Khrameeva, Ekaterina ...
2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM),
2018-Dec.
Conference Proceeding
The principles of three-dimensional organization of chromatin are known for only few model organisms. Here we describe the structure of chromatin and gene expression in the slime mold - Dictyostelium ...discoideum, and its changes during the life cycle. The slime mold mainly exists as a unicellular amoeba, but during starvation the amoebae start to aggregate and form a multicellular fruit body for reproduction. The genome (34,21 Mb, 6 chromosomes) of D. discoideum is unusual 1: it has a high gene density, very low GC-content (22,43%) and numerous repeats.
Large-scale analysis of RNA-DNA interactions Galitsyna, Aleksandra; Zharikova, Anastasia; Logacheva, Maria ...
2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM),
2018-Dec.
Conference Proceeding
We have performed large-scale analysis of RNADNA contacts in chromatin based on our own experimental data for K562 human cells and GRID-Seq. We have devised RNA-Seq controls and validated the ...resulting interactions with known chromatin-associated RNAs. We propose a pipeline for the analysis of RNA-DNA interactions, a noise correction procedure and clustering by the distance preference approach. We have compared the obtained interactomes with DNA-DNA contacts (Hi-C) for the same cell line and report the association of contacts with active compartment A and boundaries of topologically associating domains (TADs). We have detected a fraction of chromatin-enriched RNAs and report their chromatin properties. We also describe classes of RNAs by their contact preferences with DNA.
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