Publications by authors named "C Simoes-Pires"
Article Synopsis
- The study explores how Toxoplasma gondii, an intracellular parasite, influences the gene expression and chromatin state of human fibroblasts.
- It highlights a significant activation of host genes that can either protect the host or benefit the parasite, revealing a complex interaction between the two.
- The research combines genomic data from both host and parasite, leading to new insights into T. gondii’s genome, including a novel TATA box motif and the identification of transcription factors that impact both host and parasite physiology.
The CRISPR-Cas9 system can be modified to perform "epigenetic editing" by utilizing the catalytically inactive (dead) Cas9 (dCas9) to recruit regulatory proteins to specific genomic locations. In prior studies, epigenetic editing with multimers of the transactivator VP16 and guide RNAs (gRNAs) was found to cause adverse cellular responses. These side effects may confound studies inducing new cellular properties, especially if the cellular responses are maintained through cell divisions-an epigenetic regulatory property.
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- Scientists usually find it hard to use CRISPR to edit DNA in certain human cells called lymphoblastoid cell lines because it's tough to get the DNA into those cells.
- This new method allows for easier and more effective editing of DNA without creating extra pieces of unwanted DNA (called 'scarless' editing), achieving a better success rate than before.
- Because this protocol doesn't need complex virus-based techniques, it makes it simpler to use these cells for studying genetics in populations.
Functional variants in the genome are usually identified by their association with local gene expression, DNA methylation or chromatin states. DNA sequence motif analysis and chromatin immunoprecipitation studies have provided indirect support for the hypothesis that functional variants alter transcription factor binding to exert their effects. In this study, we provide direct evidence that functional variants can alter transcription factor binding.
View Article and Find Full Text PDFCurrent approaches to detect and characterize mosaic chromosomal aneuploidy are limited by sensitivity, efficiency, cost, or the need to culture cells. We describe the mosaic aneuploidy detection by massively parallel sequencing (MAD-seq) capture assay and the analytical approach that allow low (<10%) levels of mosaicism for chromosomal aneuploidy or regional loss of heterozygosity to be detected, assigned to a meiotic or mitotic origin, and quantified as a proportion of the cells in the sample. We show results from a multi-ethnic MAD-seq (meMAD-seq) capture design that works equally well in populations of diverse racial and ethnic origins and how the analytical approach can be applied to exome or whole-genome sequencing data, revealing previously unrecognized aneuploidy or copy number neutral loss of heterozygosity in samples studied by the 1000 Genomes Project, cell lines from public repositories, and one of the Illumina Platinum Genomes samples.
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