CLIP and RNA electrophoretic mobility shift assays suggest a direct interaction between MSI1 and MCPH1_L
To test the possibility of MSI1 controlling the expression of MPCH1, an RNA immunoprecipitation, which maps interactions between RNA and other proteins, was conducted along with a CLIP and RNA mobility shift assays, which are also used to detect protein and RNA interactions. The scientists found that MSI1 can act as an activator or inhibitor of the MPHC1 locus.
We find MSI1 to be abundant in neural precursors of the ventricular and subventricular zones of the human embryonic brain, but absent from mature neurons
An immunohistochemistry assay was conducted on a human embryonic brain 10 and 12 weeks after conception. The tissue was stained with antibodies against MSI1 and neuron-specific beta-III tubulin along with DNA. The scientists found that MSI1 is high in ventricular and subventricular precursors, but not found in mature neurons, which is evidence for the ZIKV attack of brain cells in the womb.
Consistently, in ZIKV-infected cells, MSI1 colocalized with double-stranded RNA (dsRNA), a viral replication intermediate, as visualized by confocal and stimulated emission depletion (STED) super-resolution microscopy (Fig. 1, F and G)
An immunofluorescence assay run of PE243 infected cells allowed scientists to detect MSI1, dsRNA and DNA with the use of confocal microscopy and STED (uses fluorescence to overcome any diffraction that may be seen in the confocal microscopy) super resolution microscopy. The results were finding MSI1 and dsRNA near each other in the cell.
Two sites were conserved between PE243 and the Ugandan MR766 strains (sites 1 and 2), whereas the third (site 3) was found only in the Asian-lineage strains including PE243 (Fig. 1A and fig. S1, A and B)
The 3' UTR (untranslated region) of PE243 (the Brazilian ZIKV strain) was used in an RNA pull-down assay. The biotinylated (covalently bound to biotin) PE2443 RNA was incubated with cell extracts. Finally, a Western blot was run to conclude the two conserved with the Ugandan MR677 strain and one with the Asian strain.
Affymetrix Genome-Wide Human SNP 6.0 Array
Genomic arrays are used to select for specific genes. In this study, a genomic array consisting of 1.8 million genetic markers including single nucleotide polymorphisms (SNPs) was used. The array displays genetic variation within SNPs. Affymetrix Genome-Wide Human SNP 6.0 Array was conducted to detect various markers such as SNPs to perform association studies, especially in larger samples. The array was conducted on 31 tibetan individuals to analyze alleles with a strong positive selection.
genome-wide regression analysis
A regression in which the gene of interest is selected against genes that are not important to the study.
stepwise linear regression
A method of regressing variables while removing those that aren’t important.
empirical significance level
An empirical research is a research that uses observations that are verifiable rather than theories. The level of significance in an empirical research is the probability of rejecting the null hypothesis.
integrated haplotype score
The measurement of the extended haplotype homozygosity (EHH) at a given SNP along the original allele relative to the derived allele. Like the cross population extended haplotype homozygosity, integrated haplotype score detects natural selection, even when the sample size is limited.
cross-population extended haplotype homozygosity (XP-EHH)
A comparison statistic test to determine the amount of homozygosity within two populations. Simonson et al., conducted a cross population extended haplotype homozygosity to compare the homozygosity between the Tibetan population, who live on highlands and Han Chinese (CHB) and Japanese (JPT), who live on lowlands. By comparing between the populations that live in different environments, alleles that have increased in frequency, sometimes upto fixation, can be pinpointed. Cross population extended haplotype homozygosity was used to identify six of the 10 genes that were selected from the 240 genes.
Gene Ontology
Gene Ontology is an initiative that aims to address different concepts and vocabularies aimed to describe the functions of a gene and its products. Gene ontology studies genes based in three major categories: biological component, molecular functions and cellular compartments.
priori functional candidate loci
An approach focusing on associations between gene variations within the gene of interest and phenotypes. The loci is selected based on priori or independent knowledge of the gene’s function and impact. Based on the known functions of the genes, candidate loci were selected for additional studies such as genome-wide scanning. Gene Ontology project was conducted to select for a priori functional candidate loci. Various categories, such as detection of oxygen, NO metabolic process, oxygen sensor activity, oxygen binding, oxygen transport, response to hypoxia, response to oxygen levels and vasodilation were used to define a functional candidate loci.
a genome-wide scan
An approach that scans markers of the entire set of DNA to find genetic variation associated with an adaptation or disease. Simonson et al., used genome-wide scan to identify genes that were positively selected for high altitude adaptations. By scanning through the entire set of DNA, genes were categorized into three groups: functional candidates, XP-EHH candidates and iHS candidates. The set of functional candidates consists of genes that are related to physiological traits of hypoxia. The XP-EHH and iHS consist of genes in in the top 1% of the sample