Small RNAs targeted to gene promoters in human cells have been shown to modulate both transcriptional gene suppression and activation. However, the mechanism involved in transcriptional activation has remained poorly defined, and an endogenous RNA trigger for transcriptional gene silencing has yet to be identified. Described here is an explanation for siRNA-directed transcriptional gene activation, as well as a role for non-coding antisense RNAs as effector molecules driving transcriptional gene silencing. Transcriptional activation of p21 gene expression was determined to be the result of Argonaute 2–dependent, post-transcriptional silencing of a p21-specific antisense transcript, which functions in Argonaute 1–mediated transcriptional control of p21 mRNA expression. The data presented here suggest that in human cells, bidirectional transcription is an endogenous gene regulatory mechanism whereby an antisense RNA directs epigenetic regulatory complexes to a sense promoter, resulting in RNA-directed epigenetic gene regulation. The observations presented here support the notion that epigenetic silencing of tumor suppressor genes, such as p21, may be the result of an imbalance in bidirectional transcription levels. This imbalance allows the unchecked antisense RNA to direct silent state epigenetic marks to the sense promoter, resulting in stable transcriptional gene silencing.

Small RNAs targeted to gene promoters in human cells can mediate transcriptional gene silencing (TGS) by directing silent state epigenetic modifications to targeted loci. Many mechanistic details of this process remain poorly defined, and the ability to stably modulate gene expression in this manner has not been explored. Here we describe the mechanisms of establishment and maintenance of long-term transcriptional silencing of the human ubiquitin C gene (UbC). Sustained targeting of the UbC promoter with a small RNA for a minimum of 3 days resulted in long-term silencing which correlated with an early increase in histone methylation and a later increase in DNA methylation at the targeted locus. Transcriptional silencing of UbC required the presence of a promoter-associated RNA. The establishment and maintenance of the TGS were shown to require distinct protein factors. Argonaute 1 (Ago1), DNA methyltransferase 3a (DNMT3a) and histone deacetylase 1 (HDAC1) were required for the initiation of silencing, and DNA methyltransferase 1 (DNMT1) was necessary for maintenance. Taken together the data presented here highlight the cellular pathway with which noncoding RNAs interact to epigenetically regulate gene expression in human cells.

Long non-coding RNAs (lncRNAs) have been shown to epigenetically regulate certain genes in human cells. Here we report evidence for the involvement of an antisense lncRNA in the transcriptional regulation of the pluripotency-associated factor Oct4. When an lncRNA antisense to Oct4-pseudogene 5 was suppressed, transcription of Oct4 and Oct4 pseudogenes 4 and 5 was observed to increase. This increase correlated with a loss of silent state epigenetic marks and the histone methyltransferase Ezh2 at the Oct4 promoter. We observed this lncRNA to interact with nucleolin and PURA, a 35 kD single-stranded DNA and RNA binding protein, and found that these proteins may act to negatively regulate this antisense transcript.

As conventional electronics is approaching its ultimate limits1, nanoscience has urgently sought for novel fast control concepts of electrons at the fundamental quantum level2. Lightwave electronics3 – the foundation of attosecond science4 – utilizes the oscillating carrier wave of intense light pulses to control the translational motion of the electron’s charge faster than a single cycle of light5–15. Despite being particularly promising information carriers, the internal quantum attributes of spin16 and valley pseudospin17–19 have not been switchable on the subcycle scale20–21. Here we demonstrate lightwave-driven changes of the valley pseudospin and introduce distinct signatures in the optical read out. Photogenerated electron–hole pairs in a monolayer of tungsten diselenide are accelerated and collided by a strong lightwave. The emergence of high odd-order sidebands and anomalous changes in their polarization direction directly attest to the ultrafast pseudospin dynamics. Quantitative computations combining density-functional theory with a non-perturbative quantum many-body approach assign the polarization of the sidebands to a lightwave-induced change of the valley pseudospin and confirm that the process is coherent and adiabatic. Our work opens the door to systematic valleytronic logic at optical clock rates.

Background: The effects of providing ventilatory assistance to patients with severe chronic obstructive pulmonary disease (COPD) during a high intensity outpatient cycle exercise programme were examined. Methods: Nineteen patients (17 men) with severe COPD (mean (SD) forced expiratory volume in 1 second (FEV 1 ) 27 (7)% predicted) underwent a 6 week supervised outpatient cycle exercise programme. Ten patients were randomised to exercise with ventilatory assistance using proportional assist ventilation (PAV) and nine (two women) to exercise unaided. Before and after training patients performed a maximal symptom limited incremental cycle test to determine peak work rate (Wpeak) followed by a constant work rate (CWR) test at 70% of Wpeak achieved in the baseline incremental test. Minute ventilation (VE), heart rate, and arterialised venous plasma lactate concentration [La

T cell receptor (TCR) antigen–specific recognition is essential for the adaptive immune system. However, building a TCR-antigen interaction map has been challenging due to the staggering diversity of TCRs and antigens. Accordingly, highly multiplexed dextramer-TCR binding assays have been recently developed, but the utility of the ensuing large datasets is limited by the lack of robust computational methods for normalization and interpretation. Here, we present a computational framework comprising a novel method, ICON (Integrative COntext-specific Normalization), for identifying reliable TCR-pMHC (peptide–major histocompatibility complex) interactions and a neural network–based classifier TCRAI that outperforms other state-of-the-art methods for TCR-antigen specificity prediction. We further demonstrated that by combining ICON and TCRAI, we are able to discover novel subgroups of TCRs that bind to a given pMHC via different mechanisms. Our framework facilitates the identification and understanding of TCR-antigen–specific interactions for basic immunological research and clinical immune monitoring.

We find that, for sufficiently strong mid-IR fields, transitions between different conduction bands play an important role in the generation of high-order harmonics in a dielectric. The transitions make a significant contribution to the harmonic signal, and they can create a single effective band for the motion of an electron wave packet. We show how high harmonic spectra produced during the interaction of ultrashort laser pulses with periodic solids provide a spectroscopic tool for understanding the effective band structure that controls electron dynamics in these media.PACS numbers: 42.50. Hz, 42.65.Ky, High-order harmonic generation (HHG) from gas targets is now used as a spectroscopic tool for imaging nuclear (see e.g. [1][2][3]) and electronic (see e.g. [4][5][6][7]) dynamics on the atomic time-and length scales. It is sensitive to various aspects of electronic dynamics, from attosecond processes in neutral systems [8,9] to hole dynamics in ions [4][5][6][7], correlation-driven channel interaction [10][11][12], and time-and space-resolved information on electronic transitions from different molecular orbitals [13][14][15].We show that HHG spectra from periodic solids give insight into the effective band structure established by a strong driving mid-infrared laser field. Pioneering experiments on high harmonic generation from dielectrics [16,17] stimulated a simple model offering semi-classical insight into the underlying physics. In this model ([16, 18]; see also [19]) electrons first tunnel from a valence band (VB) to a conduction band (CB) at the maxima of the electric field. There, they are driven along the single conduction band by the field. The harmonic intensity at frequency ω is then given by |ωJ(ω)| 2 , where J(ω) is the Fourier transform of the current, j(t), in the conduction band, ε(k). Since in this model j(t) ∝ v(t) ∝ dε/dk, where v(t) is the electron group velocity, analysis of the harmonic spectrum can yield information about the band structure (dε/dk). This picture predicts that, when the driving mid-IR laser is sufficiently strong to rapidly accelerate electrons to the edge of the Brillouin zone (BZ), Bragg reflections (Bloch oscillations) within the single band would generate most of the high harmonics.However, if electrons quickly move past the gap between adjacent CBs, they may undergo an interband transition. In this case, the harmonic signal also comes from coherences between all participating bands, including the VB [17,20]. Additionally it is also important to account for the temporal structure of all interband transitions, including the VB to CB transition, see e.g. [21]. Recent theoretical analysis of HHG in bulk solids by Vampa et al. [22] and Higuchi et al. [23] accounted for the temporal structure of interband excitations, but as two-band models were used in both cases, transitions between conduction bands were not considered.We show that the inclusion of multiple conduction bands leads to additional contributions to the highharmonic signal and that, in spite of the increasin...

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