Ontology highlight
ABSTRACT:
PROVIDER: PRJNA961164 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24287978_1.fastq.gz | Fastqsanger.gz | |||
| SRR24287978_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
Similar Datasets
Project description:Caulanthus amplexicaulis var. amplexicaulis Transcriptome or Gene expression
| PRJNA417948 | ENA
Project description:Caulanthus amplexicaulis var. barbarae Genome sequencing
| PRJNA209542 | ENA
Project description:Caulanthus amplexicaulis var. barbarae Transcriptome or Gene expression
| PRJNA417949 | ENA
Project description:Epigenetic regulation of mutually exclusive transcription within the var gene family is important for infection and pathogenesis of the malaria parasite Plasmodium falciparum. var genes are kept transcriptionally silent via heterochromatic clusters located at the nuclear periphery; however, only a few proteins have been shown to play a direct role in var gene transcriptional regulation. Importantly, the chromatin components that contribute to var gene nuclear organization remain unknown. Here, we adapted a CRISPR-based immunoprecipitation-mass spectrometry approach for de novo identification of factors associated with specific transcriptional regulatory sequences of var genes. Tagged, catalytically inactive Cas9 (“dCas9”) was targeted to var gene promoters or introns, cross-linked, and immunoprecipitated with all DNA, proteins, and RNA associated with the targeted locus. Chromatin immunoprecipitation followed by sequencing demonstrated that genome-wide dCas9 binding was specific and robust. Proteomics analysis of dCas9-immunoprecipitates identified specific proteins for each target region, including known and novel factors such as DNA binding proteins, chromatin remodelers, and structural proteins. We also demonstrate the ability to immunoprecipitate RNA that is closely associated to the targeted locus. Our CRISPR/dCas9 study establishes a new tool for targeted purification of specific genomic loci and advances understanding of virulence gene regulation in the human malaria parasite.
2020-05-01 | GSE129397 | GEO
Project description:Malaria caused by Plasmodium falciparum involves antigenic variation on the infected red blood cells through mutually exclusive expression of var genes. The repressed var genes have a distinct genome organization where they localize as a cluster near the nuclear periphery and are bound by PfHP1 (P. falciparum Heterochromatin Protein 1). However, the mode of regulation of var genes by PfHP1 remains unclear. In this study, we show that PfHP1 undergoes liquid-liquid phase separation (LLPS) in vitro in an RNA and DNA-dependent manner. Single-molecule DNA tethering experiments further revealed that AT-rich DNA sequences act as nucleation sites for the assembly and compaction of PfHP1-mediated heterochromatinization. We have also identified point mutations in the IDRs (intrinsically disordered regions) of PfHP1 that disrupt its phase separation as well as DNA compaction in vitro. An ectopic expression of PfHP1 phase separation and DNA compaction mutants led to dispersed nuclear localization, in contrast to the punctate appearance of the wild-type protein and altered chromatin binding at var genes. These results were corroborated with DiCre/loxP based conditional expression of the same PfHP1 mutants, which also led to the de-repression of multiple var genes (as many as 54 out of 60 var genes), mimicking the phenotype of PfHP1 depletion mutants. To assess the dynamic properties of PfHP1 condensates in vivo, we performed fluorescence recovery after photobleaching (FRAP) in live parasites, which revealed rapid fluorescence recovery, supporting their liquid-like behaviour. In conclusion, our study demonstrates the role of PfHP1 mediated LLPS in formation of heterochromatin and var gene silencing; unveiling a fundamental mechanism that drives antigenic variation in P. falciparum.
2026-02-16 | GSE299944 | GEO
Project description:Comparison of small RNA fractions derived from piRNA clusters and transposon sequences in control and Su(var)3-7 null mutant.
2014-05-12 | GSE53015 | GEO
Project description:Malaria caused by Plasmodium falciparum involves antigenic variation on the infected red blood cells through mutually exclusive expression of var genes. The repressed var genes have a distinct genome organization where they localize as a cluster near the nuclear periphery and are bound by PfHP1 (P. falciparum Heterochromatin Protein 1). However, the mode of regulation of var genes by PfHP1 remains unclear. In this study, we show that PfHP1 undergoes liquid-liquid phase separation (LLPS) in vitro in an RNA and DNA-dependent manner. Single-molecule DNA tethering experiments further revealed that AT-rich DNA sequences act as nucleation sites for the assembly and compaction of PfHP1-mediated heterochromatinization. We have also identified point mutations in the IDRs (intrinsically disordered regions) of PfHP1 that disrupt its phase separation as well as DNA compaction in vitro. An ectopic expression of PfHP1 phase separation and DNA compaction mutants led to dispersed nuclear localization, in contrast to the punctate appearance of the wild-type protein and altered chromatin binding at var genes. These results were corroborated with DiCre/loxP based conditional expression of the same PfHP1 mutants, which also led to the de-repression of multiple var genes (as many as 54 out of 60 var genes), mimicking the phenotype of PfHP1 depletion mutants. To assess the dynamic properties of PfHP1 condensates in vivo, we performed fluorescence recovery after photobleaching (FRAP) in live parasites, which revealed rapid fluorescence recovery, supporting their liquid-like behaviour. In conclusion, our study demonstrates the role of PfHP1 mediated LLPS in formation of heterochromatin and var gene silencing; unveiling a fundamental mechanism that drives antigenic variation in P. Falciparum.
2026-02-16 | GSE300206 | GEO
Project description:Malaria caused by Plasmodium falciparum involves antigenic variation on the infected red blood cells through mutually exclusive expression of var genes. The repressed var genes have a distinct genome organization where they localize as a cluster near the nuclear periphery and are bound by PfHP1 (P. falciparum Heterochromatin Protein 1). However, the mode of regulation of var genes by PfHP1 remains unclear. In this study, we show that PfHP1 undergoes liquid-liquid phase separation (LLPS) in vitro in an RNA and DNA-dependent manner. Single-molecule DNA tethering experiments further revealed that AT-rich DNA sequences act as nucleation sites for the assembly and compaction of PfHP1-mediated heterochromatinization. We have also identified point mutations in the IDRs (intrinsically disordered regions) of PfHP1 that disrupt its phase separation as well as DNA compaction in vitro. An ectopic expression of PfHP1 phase separation and DNA compaction mutants led to dispersed nuclear localization, in contrast to the punctate appearance of the wild-type protein and altered chromatin binding at var genes. These results were corroborated with DiCre/loxP based conditional expression of the same PfHP1 mutants, which also led to the de-repression of multiple var genes (as many as 54 out of 60 var genes), mimicking the phenotype of PfHP1 depletion mutants. To assess the dynamic properties of PfHP1 condensates in vivo, we performed fluorescence recovery after photobleaching (FRAP) in live parasites, which revealed rapid fluorescence recovery, supporting their liquid-like behaviour. In conclusion, our study demonstrates the role of PfHP1 mediated LLPS in formation of heterochromatin and var gene silencing; unveiling a fundamental mechanism that drives antigenic variation in P. Falciparum.
2026-02-16 | GSE300368 | GEO