Single-molecule imaging is a useful technique to reveal the structural property and dynamics of biomolecules in living cells. Although the imaging technology is often used to understand molecular mechanisms in living systems, special techniques and advanced knowledge are required. In this review, we describe a basic principle of singlemolecule imaging under a fluorescence microscope and highlight its application to single RNA imaging in living cells.
Transposition of transposons, the selfish mobile DNA elements, often destabilizes the genome and so organisms with sexual reproduction system have acquired, through evolution, machineries to repress transposons in the germline. One such machinery is RNA silencing mediated by PIWI-interacting RNAs (piRNAs). piRNAs repress transposons at both transcriptional and post-transcriptional levels. Recent studies using Drosophila as a model system have shed light on the mechanisms underlying piRNA-mediated silencing pathway. In this article, we will summarize basic knowledge and recent findings regarding piRNA-mediated transcriptional transposon silencing in Drosophila.
Genome DNA is organized into chromatin together with histones, and then, chromatin is arranged spatially within the nucleus in a highly organized manner. Genome functions, including transcription, DNA replication, and DNA repair, are governed by this hierarchical organization of chromatin and the nucleus. As candidates for evolutionarily conserved molecules involved in both chromatin and nuclear organization, the actin family, consisting of conventional actin and actin-related proteins (Arps), has been researched. The Arps share evolutionarily and structurally features with actin and are classified into ten subfamilies from Arp1 to Arp10, and Arp subfamilies 4, 5, 6, 7, 8, and 9 are localized predominantly in the nucleus. These nuclear Arps have been found in chromatin remodeling and modification complexes as functionally essential components, mostly, together with actin. In addition, nuclear actin and Arps were shown to be involved in nuclear organization. These observations suggest that actin family members have important roles in functional organization of chromatin and the nucleus.
Genome editing technology enables pinpoint modification of the vast ocean of genomic DNA sequence. Genomic DNA consists of approximately three billion base pairs in mammals. It had seemed almost impossible to edit a specific region in such a huge genome, but an emerging novel technique using site-specific nucleases, such as zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9, heralds a new era. In this article, we review the basics and applications of genome editing technologies.
Epigenetics refers to a collection of phenomena and mechanisms that define stably heritable phenotypes that result from changes to chromosomes without alterations in DNA sequence. One phenomenon that illustrates the importance of epigenetics is cellular differentiation. A multicellular organism consists of diverse types of cells that share an identical genotype. Despite their identical genotype, the cells in body have distinct cellular phenotypes and functions that are attributable to the difference between their gene expression profiles. The molecular mechanisms underlying these epigenetic phenomena involve a range of chemical modifications of chromatin including DNA methylation and covalent modification of histone proteins. Here we describe the mechanism how chemical modifications of chromatin are regulated.
Chromatin accommodates genomic DNA within the nucleus. Nucleosomes, which are the fundamental unit of chromatin, are composed of four histones, H2A, H2B, H3, and H4, as protein components. DNA is then wrapped around a histone octamer, containing two of each histone, H2A, H2B, H3, and H4. Histone isoforms called variants have been identified, and their tissue/cell type-specific expression and specific incorporation at certain chromatin regions have been found. These suggest that histone variants may play essential roles in the formation of functional chromosome architectures and chromatin domains, which functions as the epigenetic regulator of genomic DNA. Here, we present current results on the structural and functional analyses of various nucleosomes containing histone variants.