QuickBiology News

In human genes, more than 95% of multi-exon genes undergo pre-mRNA alternative splicing. “One gene, more spliced isoforms” ------ this strategy is the most important contributor to protein diversity. However, researchers debate that in the transcriptome, ~ 30% genes have antisense transcripts, big parts of isoforms may be just mis-spliced, they are degraded through NMD (Nonsense-mediated Decay), cannot produce proteins. Read More

Single-cell analysis has been becoming popular for understanding the patterns of genomic or transcriptomic variations in complex organs. Quick Biology has given lots of examples that how single cell sequencing technology accelerates researchers’ work. Most single cell platforms are droplet-based methods. In recent Genome Research, Li and his colleagues from Cold Spring Harbor developed a new assay, called BAG-seq. Read More

In life science, single cell resolution at molecular level is growing in popularity. Science Journal reviews recent advances into how single cell genomics is being used to develop personalized phenotyping strategies that cross subcellular, cellular, and tissue scales to link our genome to our cumulative cellular phenotypes. By single cell strategy, we not only catalog our human cell types, but we can also track how a cell develops, differentiate. Read More

GWAS (Genome-wide association study) is an approach to associate genetic variants with traits (such as human height, or even diseases). However, every cell in your body has the same DNA. It is a challenge of using GWAS to identify which type of tissue or cell types associated with certain diseases. In recent Nature communications, Researchers in Broad and MIT performed massively parallel single-cell RNA sequencing in two platforms: droplet-based microfluidics and nanowell-based Seq-well.Read More

The nervous system exhibits the most extensive usage of pre-mRNA alternative transcript isoforms. However, it remains debated as to what extent pre-mRNA alternative splicing events detected by RNA-seq are indeed recruited for translation to produce proteins. Ribosome-seq uses specialized messenger RNA sequencing to determine which mRNAs are being actively translated (Fig. 1), it only targets mRNA protected by the ribosome during the process of decoding by translation.
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Characterization of host cell response of viral infection is of great interest. Deep insights into molecular signatures of specific cell subsets to viral infection will provide potential antiviral therapies. In recent Nature communications, Researchers in Germany used Herpesvirus (HSV) infection as a virus-host model, performed single-cell RNA-sequencing of HSV-1 infected primary fibroblasts at different infection time points.Read More

Population stratification is the presence of a systematic difference in allele frequencies between subpopulations in a population, which possibly due to different ancestry, especially in the context of association studies (https://en.wikipedia.org/wiki/Population_stratification). Precision Medicine must rely on these structured data, analyze the health of patient populations, then make clinical decisions.Read More

The Cancer Genome Atlas (TCGA) Program has sequenced over 20, 000 cancers of 33 cancer types (https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga), and revealed many mutational signatures underlying the biological process. However, cancers are end stages of an evolutionary process, which commonly arise through the accumulation of several driver mutations that engender a series of cancer cell clonal expansions. Read More

Unlike next-generation sequencing (specifically, Illumina Sequencing by Synthesis Technology), new third-generation sequencing is being developed to overcome limitations such as amplification biases, short reads (reads size < 300 bp). Oxford Nanopore Technology uses nanopore-based sequencing to detect changes in current as a single strand of nucleic acid sequence transverses a pore protein. Read More

Tumor heterogeneity is the critical factor harboring resistance mechanisms. During drug treatment, the evolutionary pressure drives outgrowth of distinct tumor subclones, which finally results in acquired resistance of current targeted therapies.Read More