Neurexin genes, which have been associated with certain neuropsychiatric disorders, are known to make heavy use of alternative splicing. In a recent study, scientists used the Iso-Seq method with SMRT Sequencing to better understand splice variants in neurons derived from human induced pluripotent stem cells (hiPSCs). The study, “Neuronal impact of patient-specific aberrant NRXN1α splicing,” was published in Nature Genetics. Lead authors Erin Flaherty (@erinkflaherty) and Shijia Zhu, senior author Kristen Brennand (@kristenbrennand), and collaborators at the Icahn School of Medicine at Mount Sinai and other institutions undertook the project to help shed light on disorders linked to exonic deletions in the…
Xiaochang Zhang, an assistant professor at the University of Chicago, is poised to get a powerful new data set to help his team understand the role of alternative splicing in brain development. His project, entitled “Uncovering mRNA splicing diversity in cerebral cortex development,” was selected as the winner of the 2018 Iso-Seq SMRT Grant Program. Sequencing for this project will be carried out by our Certified Service Provider RTL Genomics. We caught up with Xiaochang to learn more about his research and how SMRT Sequencing data will make a difference. Q: What’s your research focus? A: We are interested in…
Photo by John Cobb on Unsplash In eukaryotic organisms, the majority of genes are alternatively spliced to produce multiple transcript isoforms. Gene regulation through alternative splicing can dramatically increase the protein-coding potential of a genome. Therefore, understanding the functional biology of a genome requires knowing the full complement of isoforms. Microarrays and high-throughput cDNA sequencing are useful tools for studying transcriptomes, yet these technologies provide only small snippets of transcripts. Accurately reconstructing complete transcripts to study gene isoforms has been challenging [1, 2]. The Iso-Seq method produces full-length transcripts using Single Molecule, Real-Time (SMRT) Sequencing [3]. Long read lengths enable…
Photo by Forest & Kim Starr Scientists at Huazhong Agricultural University in China and collaborating institutions recently published results of an Iso-Seq analysis of allotetraploid cotton. The team’s findings are expected to be particularly useful for functional genomics, driving advances for cotton breeders as well as research biologists. “A global survey of alternative splicing in allopolyploid cotton: landscape, complexity and regulation” was published in New Phytologist by lead authors Maojun Wang and Pengcheng Wang, senior author Xianlong Zhang, and collaborators. Existing genome assemblies for polyploidy cotton were not “released with a well-annotated transcript isoform set,” the scientists write, “and so…
Photo by Paulo Costa A new paper in Scientific Reports presents results from a transcriptome analysis for Oryctolagus cuniculus. The work was done with SMRT Sequencing, which allowed scientists to discover novel transcripts and increase the diversity of known transcripts for the rabbit. “A transcriptome atlas of rabbit revealed by PacBio single-molecule long-read sequencing” comes from lead authors Shi-Yi Chen and Feilong Deng, senior author Song-Jia Lai, and collaborators at Sichuan Agricultural University. In the paper, the scientists note that an ongoing challenge in rabbit studies has been the dearth of gene-level data. “Most of the existing gene models are…