The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology
We report a draft assembly of the genome of Hi5 cells from the lepidopteran insect pest, Trichoplusia ni, assigning 90.6% of bases to one of 28 chromosomes and predicting 14,037 protein-coding genes. Chemoreception and detoxification gene families reveal T. ni-specific gene expansions that may explain its widespread distribution and rapid adaptation to insecticides. Transcriptome and small RNA data from thorax, ovary, testis, and the germline-derived Hi5 cell line show distinct expression profiles for 295 microRNA-and> 393 piRNA-producing loci, as well as 39 genes encoding small RNA pathway proteins. Nearly all of the W chromosome is devoted to piRNA production, and T. ni siRNAs are not 2-O-methylated. To enable use of Hi5 cells as a model system, we have established genome editing and single-cell cloning protocols. The T. ni genome provides insights into pest control and allows Hi5 cells to become a new tool for studying small RNAs ex vivo.
Workshop: Building a Registry of Candidate cis-Regulatory Elements for Human and Mouse
Many human genomes have been sequenced, yet we still lack comprehensive maps of functional genomic elements and do not fully understand how they specify cell and tissue types. Such information is critical for assessing how genomic variants affect development, ageing, and disease susceptibility. The goal of the Encyclopedia of DNA Elements (ENCODE) Project (http://www.encodeproject.org) is to discover and characterize the full repertoire of functional elements in the human and mouse genomes, and the ENCODE Project has released ten thousand experiments and introduced the ENCODE Encyclopedia, an evolving collection of annotations derived from assay-specific and integrative analyses of these experiments. At the heart of the Encyclopedia is data a new Registry of candidate cis-Regulatory Elements (ccREs), defined by a biochemical signature that uses chromatin accessibility, histone modification and transcription factor occupancy data. The Registry currently contains ~2 M human and mouse ccREs, covering hundreds of human and mouse biosamples. The ccRE landscape recapitulates the current understanding of cellular identity, tissue composition, developmental progression, and disease-associated genetic variants. Aided by a dedicated visualization engine called SCREEN (http://screen.encodeproject.org), the Registry is a resource for exploring noncoding DNA elements and their variants.
Professor Zhiping Weng
Li Weibo Chair in Biomedical Research
Director, Program in Bioinformatics and Integrative Biology
Professor, Biochemistry and Molecular Pharmacology
UMass Medical School
Dr. Zhiping Weng is Professor in Biochemistry and Molecular Pharmacology and Li Weibo Chair in Biomedical Research at University of Massachusetts Medical School. In her institutional role as Director of Program in Bioinformatics and Integrative Biology, Dr. Weng leads all aspects of research and education in the Program. She received her B.S. in Electrical Engineering from University of Science and Technology of China in 1992 and Ph.D. in Biomedical Engineering from Boston University in 1997.
Dr. Weng’s scientific research and biomedical investigations focus on genomics, epigenomics, transcriptomics, and molecular recognition. Her laboratory develops and applies cutting-edge computational and statistical methods to study biological problems with large amounts of data, e.g., gene regulation by transcriptional and post-transcriptional mechanisms and protein-protein interaction. She has developed a systematic approach to define regulatory elements in the human and mouse genomes based on a select set of predictive epigenetic signals and annotate the activities of these elements across hundreds of cell and tissue types.
Dr. Weng is a national and international leader in large-scale epigenomic sciences. She has led the Data Analysis Center of the ENCODE Consortium since 2012 and co-led the Data Analysis Center of the psychENCODE Consortium since 2015. The goals of these two consortia are to investigate the regulatory landscapes in the human genome, with ENCODE focusing on normal physiology and psychENCODE on psychiatric disorders. Dr. Weng exemplifies the next generation of computational genomicists who leverage the power of computing on big data to understanding the mysteries of the human genome.