Advancing crop genomics from lab to fieldPurugganan, Michael D.; Jackson, Scott A.
doi: 10.1038/s41588-021-00866-3pmid: 33958781
Crop genomics remains a key element in ensuring scientific progress to secure global food security. It has been two decades since the sequence of the first plant genome, that of Arabidopsis thaliana, was released, and soon after that the draft sequencing of the rice genome was completed. Since then, the genomes of more than 100 crops have been sequenced, plant genome research has expanded across multiple fronts and the next few years promise to bring further advances spurred by the advent of new technologies and approaches. We are likely to see continued innovations in crop genome sequencing, genetic mapping and the acquisition of multiple levels of biological data. There will be exciting opportunities to integrate genome-scale information across multiple scales of biological organization, leading to advances in our mechanistic understanding of crop biological processes, which will, in turn, provide greater impetus for translation of laboratory results to the field.
Engineering three-dimensional genome foldingZhang, Di; Lam, Jessica; Blobel, Gerd A.
doi: 10.1038/s41588-021-00860-9pmid: 33958782
Animal genomes are partitioned and folded at various scales that contribute distinctly to nuclear processes. While structural features have been disrupted either globally or at select loci in loss-of-function studies, gain-of-function studies that probe the role of genome architecture have lagged behind. Here we examine recent advances in experimentally creating chromatin loops, contact domains, boundaries and compartments. Furthermore, we explore parallels between this emerging theme and natural evolution of mammalian genomes with increasing architectural complexity. Finally, we provide a perspective on how insights arising from recent gain-of-function studies may inform future endeavors toward engineering the three-dimensional genome.
Transcription-dependent domain-scale three-dimensional genome organization in the dinoflagellate Breviolum minutumMarinov, Georgi K.; Trevino, Alexandro E.; Xiang, Tingting; Kundaje, Anshul; Grossman, Arthur R.; Greenleaf, William J.
doi: 10.1038/s41588-021-00848-5pmid: 33927397
Dinoflagellate chromosomes represent a unique evolutionary experiment, as they exist in a permanently condensed, liquid crystalline state; are not packaged by histones; and contain genes organized into tandem gene arrays, with minimal transcriptional regulation. We analyze the three-dimensional genome of Breviolum minutum, and find large topological domains (dinoflagellate topologically associating domains, which we term ‘dinoTADs’) without chromatin loops, which are demarcated by convergent gene array boundaries. Transcriptional inhibition disrupts dinoTADs, implicating transcription-induced supercoiling as the primary topological force in dinoflagellates.
Genetic and spatial organization of the unusual chromosomes of the dinoflagellate Symbiodinium microadriaticumNand, Ankita; Zhan, Ye; Salazar, Octavio R.; Aranda, Manuel; Voolstra, Christian R.; Dekker, Job
doi: 10.1038/s41588-021-00841-ypmid: 33927399
Dinoflagellates are main primary producers in the oceans, the cause of algal blooms and endosymbionts of marine invertebrates. Much remains to be understood about their biology, including their peculiar crystalline chromosomes. We assembled 94 chromosome-scale scaffolds of the genome of the coral endosymbiont Symbiodinium microadriaticum and analyzed their organization. Genes are enriched towards the ends of chromosomes and are arranged in alternating unidirectional blocks. Some chromosomes are enriched for genes involved in specific biological processes. The chromosomes fold as linear rods and each is composed of a series of structural domains separated by boundaries. Domain boundaries are positioned at sites where transcription of two gene blocks converges and disappear when cells are treated with chemicals that block transcription, indicating correlations between gene orientation, transcription and chromosome folding. The description of the genetic and spatial organization of the S. microadriaticum genome provides a foundation for deeper exploration of the extraordinary biology of dinoflagellates and their chromosomes.