Project description:The most virulent human malaria parasite, Plasmodium falciparum, has a complex life cycle between its human host and mosquito vector. Each stage is driven by a specific transcriptional program, but with a relatively high ratio of genes to specific transcription factors, it is unclear how genes are activated or silenced at specific times. The P. falciparum genome is relatively euchromatic compared to the mammalian genome, except for specific genes that are uniquely heterochromatinized via HP1. There seems to be an association between gene activity and spatial organization; however, the molecular mechanisms behind genome organization are unclear. While P. falciparum lacks lamins and CTCF – key metazoan genome-organizing proteins – it does have all core components of the cohesin complex. In other eukaryotes, cohesin is involved in sister chromatid cohesion, transcription, and genome organization. To investigate the role of cohesin in P. falciparum, we combined genome editing, mass-spectrometry, chromatin immunoprecipitation and sequencing (ChIP-seq), and RNA sequencing to functionally characterize the cohesin subunit Structural Maintenance of Chromosomes protein 3 (SMC3). SMC3 knockdown in early stages of the intraerythrocytic developmental cycle (IDC) resulted in significant up-regulation of a subset of genes involved in erythrocyte egress and invasion, which are normally expressed at later stages. ChIP-seq of SMC3 revealed that over the IDC, enrichment at the promoter regions of these genes inversely correlates with their expression. These data suggest that SMC3 binding helps to repress specific genes until their appropriate time of expression, revealing a new mode of gene repression in P. falciparum.

2023-10-04 | PXD035225 | Pride

MicroRNA sequencing and analysis of the newt heart

Project description:MicroRNA sequencing using Ion Torrent Proton platform of the undamaged heart of the red spotted newt Notophthalmus viridescens. MicroRNAS were identified using MIRPIPE

2021-05-24 | GSE69537 | GEO

Calibrated Smc3 ChIP-seq for wild type, smc3-2R, wpl1Δ and smc3-2R wpl1Δ strains arrested in meiotic prophase I

Project description:Genome binding/occupancy profiling of the cohesin subunit Smc3 by high throughput sequencing. S. pombe is included as the calibration genome.

2022-02-04 | GSE185020 | GEO

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