Sense of time (temporal sense) is believed to be processed by various brain regions in a complex manner, among which the basal ganglia, including the striatum and subthalamic nucleus (STN), play ...central roles. However, the precise mechanism for processing sense of time has not been clarified. To examine the role of the STN in temporal processing of the sense of time by directly manipulating STN function by switching a deep brain stimulation (DBS) device On/Off in 28 patients with Parkinson's disease undergoing STN-DBS therapy. The test session was performed approximately 20 min after switching the DBS device from On to Off or from Off to On. Temporal sense processing was assessed in three different tasks (time reproduction, time production, and bisection). In the three temporal cognitive tasks, switching STN-DBS to Off caused shorter durations to be produced compared with the switching to the On condition in the time production task. In contrast, no effect of STN-DBS was observed in the time bisection or time reproduction tasks. These findings suggest that the STN is involved in the representation process of time duration and that the role of the STN in the sense of time may be limited to the exteriorization of memories formed by experience.
The rotigotine transdermal patch (RTP) is a dopamine agonist used to treat Parkinson’s disease (PD). Some PD patients cannot continue RTP treatment due to application site reactions. We explored ...sites for RTP where application site reactions are less severe than those in the six approved application sites. Thirty PD patients (12 men, mean age = 76 years) who underwent RTP at the approved sites and had some application site reactions were enrolled in this study. When applying the RTP to the approved application sites for more than four weeks (pre-RTP) and then on the shin for the following four weeks (post-RTP), skin reactions, itching evaluated using the skin irritation score, motor symptoms, clinical global impressions scale, and plasma rotigotine concentration were examined. The mean visual analogue scale and skin irritation score in the post-RTP group were significantly lower than those in the pre-RTP group. The mean Movement Disorder Society-Unified Parkinson’s Disease Rating Scale part III score in the post-RTP group was slightly but significantly lower than that in the pre-RTP group. Plasma rotigotine concentration in the post-RTP group was slightly but significantly lower than that in the pre-RTP group. These results indicate that the shin can be a useful application site for RTP.
Transcription through the nucleosome Kujirai, Tomoya; Kurumizaka, Hitoshi
Current opinion in structural biology,
April 2020, 2020-Apr, 2020-04-00, 20200401, Volume:
61
Journal Article
Peer reviewed
Open access
•Dynamic changes in the nucleosome structure take place when RNA polymerase II transcribes through a nucleosome.•Nucleosome reassembly may be mediated by the template looping and/or proteins with ...acidic, intrinsically disordered regions.•Transcription elongation factors, histone chaperones, and chromatin remodeling factors regulate transcription on chromatin.
Eukaryotic genomic DNA is wrapped around the histone octamer and forms the nucleosome, which is the basic unit of chromatin. Nevertheless, eukaryotic RNA polymerases transcribe the DNA that is tightly bound to the histone core in the nucleosome. For transcription to proceed on the nucleosome, the RNA polymerases must overcome the tight contacts between histones and DNA during transcription elongation. Here, we review the structural and biochemical studies of the transcription mechanism on the nucleosome, and focus on recent information to understand how RNA polymerases transcribe the genomic DNA in chromatin.
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•Histone variants play vital roles in the epigenetic regulation of eukaryotic chromatin.•Histone variants confer structural and physical diversities to the nucleosome core ...particle.•Up to 50% amino acid sequence differences are found between histone variants and canonical histones.
Chromatin compacts genomic DNA in eukaryotes. The primary chromatin unit is the nucleosome core particle, composed of four pairs of the core histones, H2A, H2B, H3, and H4, and 145–147 base pairs of DNA. Since replication, recombination, repair, and transcription take place in chromatin, the structure and dynamics of the nucleosome must be versatile. These nucleosome characteristics underlie the epigenetic regulation of genomic DNA. In higher eukaryotes, many histone variants have been identified as non-allelic isoforms, which confer nucleosome diversity. In this article, we review the manifold types of nucleosomes produced by histone variants, which play important roles in the epigenetic regulation of chromatin.
Genomic DNA forms chromatin, in which the nucleosome is the repeating unit. The mechanism by which RNA polymerase II (RNAPII) transcribes the nucleosomal DNA remains unclear. Here we report the ...cryo-electron microscopy structures of RNAPII-nucleosome complexes in which RNAPII pauses at the superhelical locations SHL(-6), SHL(-5), SHL(-2), and SHL(-1) of the nucleosome. RNAPII pauses at the major histone-DNA contact sites, and the nucleosome interactions with the RNAPII subunits stabilize the pause. These structures reveal snapshots of nucleosomal transcription, in which RNAPII gradually tears DNA from the histone surface while preserving the histone octamer. The nucleosomes in the SHL(-1) complexes are bound to a "foreign" DNA segment, which might explain the histone transfer mechanism. These results provide the foundations for understanding chromatin transcription and epigenetic regulation.
Structural basis for the inhibition of cGAS by nucleosomes Kujirai, Tomoya; Zierhut, Christian; Takizawa, Yoshimasa ...
Science (American Association for the Advancement of Science),
10/2020, Volume:
370, Issue:
6515
Journal Article
Peer reviewed
Open access
The cyclic guanosine monophosphate-adenosine monophosphate synthase (cGAS) senses invasion of pathogenic DNA and stimulates inflammatory signaling, autophagy, and apoptosis. Organization of host DNA ...into nucleosomes was proposed to limit cGAS autoinduction, but the underlying mechanism was unknown. Here, we report the structural basis for this inhibition. In the cryo-electron microscopy structure of the human cGAS-nucleosome core particle (NCP) complex, two cGAS monomers bridge two NCPs by binding the acidic patch of the histone H2A-H2B dimer and nucleosomal DNA. In this configuration, all three known cGAS DNA binding sites, required for cGAS activation, are repurposed or become inaccessible, and cGAS dimerization, another prerequisite for activation, is inhibited. Mutating key residues linking cGAS and the acidic patch alleviates nucleosomal inhibition. This study establishes a structural framework for why cGAS is silenced on chromatinized self-DNA.
RNA polymerase II (RNAPII) transcribes chromosomal DNA that contains multiple nucleosomes. The nucleosome forms transcriptional barriers, and nucleosomal transcription requires several additional ...factors in vivo. We demonstrate that the transcription elongation factors Elf1 and Spt4/5 cooperatively lower the barriers and increase the RNAPII processivity in the nucleosome. The cryo-electron microscopy structures of the nucleosome-transcribing RNAPII elongation complexes (ECs) reveal that Elf1 and Spt4/5 reshape the EC downstream edge and intervene between RNAPII and the nucleosome. They facilitate RNAPII progression through superhelical location SHL(-1) by adjusting the nucleosome in favor of the forward progression. They suppress pausing at SHL(-5) by preventing the stable RNAPII-nucleosome interaction. Thus, the EC overcomes the nucleosomal barriers while providing a platform for various chromatin functions.
Mixed anionic materials such as oxyhydrides and oxynitrides have recently attracted significant attention due to their unique properties, such as fast hydride ion conduction, enhanced ferroelectrics, ...and catalytic activity. However, high temperature (≥800 °C) and/or complicated processes are required for the synthesis of these compounds. Here we report that a novel perovskite oxynitride-hydride, BaCeO3–x N y H z , can be directly synthesized by the reaction of CeO2 with Ba(NH2)2 at low temperatures (300–600 °C). BaCeO3–x N y H z , with and without transition metal nanoparticles, functions as an efficient catalyst for ammonia synthesis through the lattice N3– and H– ion-mediated Mars–van Krevelen mechanism, while ammonia synthesis occurs over conventional catalysts through a Langmuir–Hinshelwood mechanism with high energy barriers (85–121 kJ mol–1). As a consequence, the unique reaction mechanism leads to enhancement of the activity of BaCeO3-based catalysts by a factor of 8–218 and lowers the activation energy (46–62 kJ mol–1) for ammonia synthesis. Furthermore, isotopic experiments reveal that this catalyst shifts the rate-determining step for ammonia synthesis from N2 dissociation to N–H bond formation.
During gene transcription, RNA polymerase II (RNAPII) traverses nucleosomes in chromatin, but the mechanism has remained elusive. Using cryo–electron microscopy, we obtained structures of the RNAPII ...elongation complex (EC) passing through a nucleosome in the presence of the transcription elongation factors Spt6, Spn1, Elf1, Spt4/5, and Paf1C and the histone chaperone FACT (facilitates chromatin transcription). The structures show snapshots of EC progression on DNA mediating downstream nucleosome disassembly, followed by its reassembly upstream of the EC, which is facilitated by FACT. FACT dynamically adapts to successively occurring subnucleosome intermediates, forming an interface with the EC. Spt6, Spt4/5, and Paf1C form a “cradle” at the EC DNA-exit site and support the upstream nucleosome reassembly. These structures explain the mechanism by which the EC traverses nucleosomes while maintaining the chromatin structure and epigenetic information.
A passage through nucleosomes
In the eukaryotic cell nucleus, genomic DNA is wrapped around histones to form nucleosomes, which are the basic units of the beads-on-a-string structure of chromatin. Although the nucleosomes are physical obstacles for the DNA-transcribing RNA polymerase II, it somehow passes through them while maintaining their structure. Ehara
et al
. obtained structural snapshots of the polymerase passaging through a nucleosome using cryo–electron microscopy. They found that the polymerase forms a huge elongation complex with multiple transcription elongation factors, which mediates the disassembly of the downstream nucleosome and its subsequent reassembly behind the polymerase with the aid of the histone chaperone FACT. —DJ
Cryo-EM captures how the RNA polymerase II transcription elongation complex passes through a nucleosome with the aid of a histone chaperone.
INTRODUCTION
In the eukaryotic cell nucleus, genomic DNA is stored as chromatin, comprising multiple nucleosomes carrying various genetic and epigenetic information. Gene transcription by RNA polymerase II (RNAPII) intrinsically affects nucleosome structures because it requires temporary unfolding of the nucleosomes to read the DNA sequence. However, RNAPII transcribes genes while maintaining the nucleosome structures, suggesting the existence of a transcription-coupled mechanism to restore the nucleosomes. However, this mechanism has remained elusive.
RATIONALE
We designed nucleosomal DNA templates so that the RNAPII elongation complex (EC) would stall at the 42-, 49-, 58-, and 115-bp positions from the nucleosome entry. When EC stalls at these positions, its leading edge is near super helical locations (SHLs) –1, 0, +1, and +6, respectively, of the nucleosome. Transcription was conducted in the presence of the transcription elongation factors Spn1, Spt6, Spt4/5, Elf1, Paf1C, and TFIIS and the histone chaperone FACT. The ECs formed at these positions were analyzed by cryo–electron microscopy single-particle analysis.
RESULTS
We obtained six nucleosome-transcribing EC structures: EC42, EC49, EC49B, EC58
hex
, EC58
oct
, and EC115, where the numbers denote the DNA positions where EC stalled. The ECs contain the RNAPII-associated Spn1, Spt6, Spt4/5, Elf1, and Paf1C proteins, which constitute the EC downstream and/or upstream edge. The structures represent serial snapshots of the EC passage through the nucleosome. In EC42, the EC leading edge resides near SHL(–1) within the downstream nucleosome, in which an ~60-bp DNA segment is removed from the histone octamer surface. One of the H2A-H2B dimers is exposed and bound with the C-terminal tail of the Spt16 subunit of FACT. In EC49, the EC leading edge is just before the nucleosomal dyad SHL(0), and an ~70-bp DNA segment is removed from the histone octamer. As one of the H3-H4 dimers is exposed, the main body of FACT engages with the histones primarily through Spt16. An ~30-bp DNA segment is also removed from the distal end of the nucleosome, and thus only a third of the histone octamer surface is covered by DNA. This FACT-histone complex probably represents the state before its detachment from the DNA and its subsequent transfer. In EC49B, the nucleosome is shifted downstream by ~17 bp, which might have originated by the downstream transfer of the FACT-histone intermediate. By contrast, EC58
hex
and EC58
oct
, in which the EC leading edge has overrun the dyad of the original nucleosome, reveal a FACT-histone complex transferred upstream of the EC. In EC58
hex
, a FACT-histone hexamer H2A-H2B-(H3-H4)
2
complex is deposited onto the emerging DNA at the EC DNA exit site, and the resultant hexasome is wrapped by an ~40 bp DNA segment. In EC58
oct
, the remaining H2A-H2B dimer is deposited onto the histone hexamer to form the histone octamer (octasome), which is wrapped by an ~75-bp DNA segment. Finally, EC115 reveals a near-complete nucleosome on the EC upstream side, with the histone octamer covered by an ~120-bp DNA segment. At the rim of the EC DNA exit, the domains of Spt4, Spt5, Spt6, Leo1, and Rtf1 form a “cradle” that flexibly adapts to the subnucleosome intermediates in EC58
hex
, EC58
oct
, and EC115, supporting the sequential nucleosome reassembly process upstream of the EC.
CONCLUSION
The obtained structures visualize key steps of nucleosome traversal by the EC accompanied by the downstream nucleosome disassembly, followed by its reassembly upstream of the EC with the aid of FACT. When the EC passes through the nucleosomal dyad, the downstream-to-upstream transfer of the nucleosomal histones occurs. These views explain the mechanism by which the nucleosome structures are maintained during transcription.
Transcription over a nucleosome mediated by the EC and FACT.
Cryo–electron microscopy structures of the nucleosome-transcribing ECs: EC42, EC49, EC58
hex
, EC58
oct
, and EC115. EC49B is omitted in this figure. The EC contains the transcription elongation factors Spn1, Spt6, Spt4/5, Elf1, and Paf1C. These structures show snapshots of the EC progression on DNA mediating downstream nucleosome disassembly, followed by reassembly upstream of the EC with the aid of FACT.
Histone H2A.J, a histone H2A variant conserved in mammals, may function in the expression of genes related to inflammation and cell proliferation. In the present study, we purified the human histone ...H2A.J variant and found that H2A.J is efficiently incorporated into the nucleosome in vitro. H2A.J formed the stable nucleosome, which accommodated the DNA ends. Mutations in the H2A.J-specific residues did not affect the nucleosome stability, although the mutation of the H2A.J Ala40 residue, which is conserved in some members of the canonical H2A class, reduced the nucleosome stability. Consistently, the crystal structure of the H2A.J nucleosome revealed that the H2A.J-specific residues, including the Ala40 residue, did not affect the nucleosome structure. These results provide basic information for understanding the function of the H2A.J nucleosome.
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