Highly structured homolog pairing reflects functional organization of the Drosophila genome
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ABSTRACT:
PROVIDER: PRJNA496497 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8058300_1.fastq.gz | Fastqsanger.gz | |||
| SRR8058300_2.fastq.gz | Fastqsanger.gz | |||
| SRR8058291_1.fastq.gz | Fastqsanger.gz | |||
| SRR8058291_2.fastq.gz | Fastqsanger.gz | |||
| SRR8058301_1.fastq.gz | Fastqsanger.gz |
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Project description:Trans-homolog interactions encompass potent regulatory functions, which have been studied extensively in Drosophila, where homologs are paired in somatic cells and pairing-dependent gene regulation, or transvection, is well-documented. Nevertheless, the structure of pairing and whether its functional impact is genome-wide have eluded analysis. Accordingly, we generated a diploid cell line from divergent parents and applied haplotype-resolved Hi-C, discovering that homologs pair relatively precisely genome-wide in addition to establishing trans-homolog domains and compartments. We also elucidated the structure of pairing with unprecedented detail, documenting significant variation across the genome. In particular, we characterized two forms: tight pairing, consisting of contiguous small domains, and loose pairing, consisting of single larger domains. Strikingly, active genomic regions (A-type compartments, active chromatin, expressed genes) correlated with tight pairing, suggesting that pairing has a functional role genome-wide. Finally, using RNAi and haplotype-resolved Hi-C, we show that disruption of pairing-promoting factors results in global changes in pairing.
2018-10-16 | GSE121256 | GEO
Project description:Trans-homolog interactions have been studied extensively in Drosophila, where homologs are paired in somatic cells and transvection is prevalent. Nevertheless, the detailed structure of pairing and its functional impact have not been thoroughly investigated. Accordingly, we generated a diploid cell line from divergent parents and applied haplotype-resolved Hi-C, showing that homologs pair with varying precision genome-wide, in addition to establishing trans-homolog domains and compartments. We also elucidate the structure of pairing with unprecedented detail, observing significant variation across the genome and revealing at least two forms of pairing: tight pairing, spanning contiguous small domains, and loose pairing, consisting of single larger domains. Strikingly, active genomic regions (A-type compartments, active chromatin, expressed genes) correlated with tight pairing, suggesting that pairing has a functional implication genome-wide. Finally, using RNAi and haplotype-resolved Hi-C, we show that disruption of pairing-promoting factors results in global changes in pairing, including the disruption of some interaction peaks.
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Project description:Genome organization involves cis and trans chromosomal interactions, both implicated in gene regulation, development, and disease. Here, we focused on trans interactions in Drosophila, where homologous chromosomes are paired in somatic cells from embryogenesis through adulthood. We first addressed the long-standing question of whether pairing extends genome-wide and, to this end, developed a haplotype-resolved Hi-C approach that uses a new strategy to minimize homolog misassignment and thus robustly distinguish trans-homolog from cis contacts. This approach revealed striking genome-wide pairing in Drosophila embryos. Moreover, we discovered pairing to be surprisingly structured, with trans-homolog domains and interaction peaks, many coinciding with the positions of analogous cis features. We also found a significant correlation between pairing and the chromatin accessibility mediated by the pioneer factor Zelda. Our findings reveal a complex, highly structured organization underlying homolog pairing, first discovered more than a century ago.
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Project description:Two different models have been proposed to explain how the endpoints of chromatin looped domains (“TADs”) in eukaryotic chromosomes are determined. In the first a cohesin complex extrudes a loop until it encounters a boundary element roadblock, generating a stem-loop (and an unanchored loop). In this model, boundaries are functionally autonomous: they have an intrinsic ability to halt the movement of incoming cohesin complexes that is independent of the properties of neighboring boundaries. In the second, loops are generated by boundary:boundary pairing. In this model, boundaries are functionally non-autonomous, and their ability to form a loop depends upon how well they match with their neighbors. Moreover, unlike the loop-extrusion model, pairing interactions can generate both stem-loops and circle-loops. We have used a combination of Micro-C to analyze how TADs are organized and experimental manipulations of the even-skipped TAD boundary, homie, to test the predictions of the “loop-extrusion” and the “boundary-pairing” models. Our findings are incompatible with the loop-extrusion model and instead suggest that endpoints of TADs in flies are determined by a mechanism in which boundary elements physically pair with their neighbors, either head-to-head, or head-to-tail.
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Project description:Determinants of chromosome organization: Loop extrusion or boundary:boundary pairing?
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Project description:During meiosis, chromosomes undergo extensive changes in structure and intranuclear positioning. How these chromosome organization changes occur and how they influence meiosis-specific chromosome events are not fully understood. Using Hi-C, we characterized chromosome architecture throughout mouse spermatogenesis at high temporal resolution. Our study revealed an intimate link between chromosome organization features and homolog pairing and alignment. We found that the meiotic chromosomes progressively reshape from TAD-like domains into linearly arranged loop arrays during prophase I. The transcriptionally active and inactive genomic regions exhibit distinct dynamics of loop growth, resulting in alternating domains consisting of shorter and longer chromosome loops. Such a domanial organization along meiotic chromosome axes is tightly correlated with the strength and precision of inter-homolog alignment. We further showed that a significant fraction of chromosomes near chromosome ends exhibit elevated inter-chromosomal association upon entering zygotene stage, while also exhibiting a higher degree of inter-homolog alignment. Using a mouse model defective in LINC complex component SUN1, we demonstrated that the prominent alignment of chromosome ends is dependent on the association of telomeres with the mechano-transducing LINC complex, but not the tethering of telomeres to the nuclear periphery. Taken together, our results suggest the 3D chromosome organization may provide a structural framework for the regulation of meiotic chromosome processes in higher eukaryotes.
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Project description:The spatial organization of chromosomes within interphase nuclei is important for gene expression and epigenetic inheritance. Although the extent of physical interaction between chromosomes and their degree of compaction varies during development and between different cell-types, it is unclear how regulation of chromosome interactions and compaction relate to spatial organization of genomes. Drosophila is an excellent model system for studying chromosomal interactions including homolog pairing. Recent work has shown that condensin II governs both interphase chromosome compaction and homolog pairing and condensin II activity is controlled by the turnover of its regulatory subunit Cap-H2. Specifically, Cap-H2 is a target of the SCFSlimb E3 ubiquitin-ligase which down-regulates Cap-H2 in order to maintain homologous chromosome pairing, chromosome length and proper nuclear organization. Here, we identify Casein Kinase I alpha (CK1?) as an additional negative-regulator of Cap-H2. CK1?-depletion stabilizes Cap-H2 protein and results in an accumulation of Cap-H2 on chromosomes. Similar to Slimb mutation, CK1? depletion in cultured cells, larval salivary gland, and nurse cells results in several condensin II-dependent phenotypes including dispersal of centromeres, interphase chromosome compaction, and chromosome unpairing. Moreover, CK1? loss-of-function mutations dominantly suppress condensin II mutant phenotypes in vivo. Thus, CK1? facilitates Cap-H2 destruction and modulates nuclear organization by attenuating chromatin localized Cap-H2 protein.
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