Abstract
Next-generation sequencing (NGS) technologies have enabled genome analysis of numerous economically important plants including the natural rubber tree, Hevea brasiliensis. As a result, genomic sequence data of three rubber tree clones and various types of transcriptome data such as RNA-seq, ESTs, full-length cDNAs, and isoform sequencing (Iso-seq) are currently available in the public domain. A combination of high-throughput omics approaches has led us to a deeper understanding of gene regulation. Information on the precise transcription start sites (TSSs) of genes is essential to reveal transcriptional regulation. In this chapter, we introduce the application of the CAGE (cap analysis gene expression) method for genome-wide identification of TSSs in H. brasiliensis. CAGE is a technique to obtain accurate and comprehensive TSSs throughout the genome. The data obtained from CAGE can be used to update annotation of 5′ UTRs and tissue-specific TSSs. Accurate information about TSSs also enables elucidation of gene regulatory elements in core promoters, such as TATA boxes, initiator elements (Inrs) and transcription factor-binding sites (TFBSs). By including RNA-seq and full-length cDNA data, it is also possible to generate statistics in order to discover novel genes, non-coding RNAs (ncRNAs), and antisense transcripts. In this chapter, we discuss CAGE analysis in combination with other transcriptomic data in H. brasiliensis with the ultimate aim of controlling rubber biosynthetic pathways. The CAGE data are accessible at http://rubber.riken.jp.
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Makita, Y., Kurihara, Y., Lau, NS., Kawashima, M., Othman, A.S., Matsui, M. (2020). Genome-Wide Analysis of Transcription Start Sites and Core Promoter Elements in Hevea brasiliensis. In: Matsui, M., Chow, KS. (eds) The Rubber Tree Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-030-42258-5_6
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