In mammals, DNA methylation occurs mainly at CpG dinucleotides. Methylation of the promoter suppresses gene expression, but the functional role of gene-body DNA methylation in highly expressed genes has yet to be clarified. Here we show that, in mouse embryonic stem cells, Dnmt3b-dependent intragenic DNA methylation protects the gene body from spurious RNA polymerase II entry and cryptic transcription initiation. Using different genome-wide approaches, we demonstrate that this Dnmt3b function is dependent on its enzymatic activity and recruitment to the gene body by H3K36me3. Furthermore, the spurious transcripts can either be degraded by the RNA exosome complex or capped, polyadenylated, and delivered to the ribosome to produce aberrant proteins. Elongating RNA polymerase II therefore triggers an epigenetic crosstalk mechanism that involves SetD2, H3K36me3, Dnmt3b and DNA methylation to ensure the fidelity of gene transcription initiation, with implications for intragenic hypomethylation in cancer.

Light-gated ion channels and pumps have made it possible to probe intact neural circuits by manipulating the activity of groups of genetically similar neurons. What is needed now is a method for precisely aiming the stimulating light at single neuronal processes, neurons or groups of neurons. We developed a method that combines generalized phase contrast with temporal focusing (TF-GPC) to shape two-photon excitation for this purpose. The illumination patterns are generated automatically from fluorescence images of neurons and shaped to cover the cell body or dendrites, or distributed groups of cells. The TF-GPC two-photon excitation patterns generated large photocurrents in Channelrhodopsin-2-expressing cultured cells and neurons and in mouse acute cortical slices. The amplitudes of the photocurrents can be precisely modulated by controlling the size and shape of the excitation volume and, thereby, be used to trigger single action potentials or trains of action potentials.

Summary Odors elicit distributed activation of glomeruli in the olfactory bulb (OB). Crosstalk between co-active glomeruli has been proposed to perform a variety of computations, facilitating efficient extraction of sensory information by the cortex. Dopaminergic/GABAergic cells in the OB, which can be identified by their expression of the dopamine transporter (DAT), provide the earliest opportunity for such crosstalk. Here we show in mice that DAT+ cells carry concentration dependent odor signals and broadcast focal glomerular inputs throughout the OB to cause suppression of mitral/tufted (M/T) cell firing, an effect that is mediated by the external tufted (ET) cells coupled to DAT+ cells via chemical and electrical synapses. We find that DAT+ cells implement gain control and decorrelate odor representations in the M/T cell population. Our results further indicate that ET cells are gatekeepers of glomerular output and prime determinants of M/T responsiveness.

Access to three-dimensional structures in the brain is fundamental to probe signal processing at multiple levels, from integration of synaptic inputs to network activity mapping. Here, we present an optical method for independent three-dimensional photoactivation and imaging by combination of digital holography with remote-focusing. We experimentally demonstrate compensation of spherical aberration for out-of-focus imaging in a range of at least 300 μm, as well as scanless imaging along oblique planes. We apply this method to perform functional imaging along tilted dendrites of hippocampal pyramidal neurons in brain slices, after photostimulation by multiple spots glutamate uncaging. By bringing extended portions of tilted dendrites simultaneously in-focus, we monitor the spatial extent of dendritic calcium signals, showing a shift from a widespread to a spatially confined response upon blockage of voltage-gated Na channels. B rain architecture, from the cellular up to the anatomical level, develops in three dimensions (3D): Dendritic and axonal trees often spread in extensive spatial patterns, organizing neuronal circuits into complex volumes. As an essential step in understanding how information is processed in the brain and studying the relationship between structure and function in cerebral circuits, techniques to stimulate and record neuronal signals in 3D are required. This need is particularly evident in research fields such as the study of dendritic integration and plasticity (1) or of neuronal network activity mapping (2, 3). Optical methods for stimulation and imaging enable targeting of a wide range of structures-from subcellular compartments up to multiple cells-within intact neuronal circuits, with millisecond and submicron resolution. Caged neurotransmitters and, more recently, optogenetic tools such as channelrhodopsin and halorhodopsin provide a diverse toolbox for neuronal excitation and inhibition (4, 5), whereas optical reporters such as calcium and voltagesensitive dyes allow recording neuronal activity (6, 7).Both imaging and photostimulation have been performed in 3D by using scanning or parallel excitation methods (8-12). However, to reach a full optical control of 3D structures, these approaches need to be combined into a unique optical system. One of the main challenges, in this respect, is to axially decouple the imaging and stimulation planes when both optical pathways are combined (as it is often the case) into the same microscope objective. Until now, simultaneous imaging and photostimulation have been limited to restricted areas, for example to the relatively short portion of a dendrite which extends in the focal plane of the microscope (13, 14), or, in the case of functional mapping, to neuronal bodies located on the same plane (15).To overcome these limitations, we propose here a unique scanless optical system for simultaneous imaging and stimulation in 3D. Wide-field imaging on arbitrary oriented planes is achieved by using a remote-focusing technique adapted from Botcherby et a...

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Functional characterization of the transcriptome requires tools for the systematic investigation of RNA post-transcriptional modifications. 2΄-O-methylation (2΄-OMe) of the ribose moiety is one of the most abundant post-transcriptional modifications of RNA, although its systematic analysis is difficult due to the lack of reliable high-throughput mapping methods. We describe here a novel high-throughput approach, named 2OMe-seq, that enables fast and accurate mapping at single-base resolution, and relative quantitation, of 2΄-OMe modified residues. We compare our method to other state-of-art approaches, and show that it achieves higher sensitivity and specificity. By applying 2OMe-seq to HeLa cells, we show that it is able to recover the majority of the annotated 2΄-OMe sites on ribosomal RNA. By performing knockdown of the Fibrillarin methyltransferase in mouse embryonic stem cells (ESCs) we show the ability of 2OMe-seq to capture 2΄-O-Methylation level variations. Moreover, using 2OMe-seq data we here report the discovery of 12 previously unannotated 2΄-OMe sites across 18S and 28S rRNAs, 11 of which are conserved in both human and mouse cells, and assigned the respective snoRNAs for all sites. Our approach expands the repertoire of methods for transcriptome-wide mapping of RNA post-transcriptional modifications, and promises to provide novel insights into the role of this modification.

Ten eleven translocation (Tet) proteins oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC and 5caC can be further excised by thymine-DNA glycosylase (Tdg). Here, we present a genome-wide approach, named methylation-assisted bisulfite sequencing (MAB-seq), that enables single-base resolution mapping of 5fC and 5caC and measures their abundance. Application of this method to mouse embryonic stem cells (ESCs) shows the occurrence of 5fC and 5caC residues on the hypomethylated promoters of highly expressed genes, which is increased upon Tdg silencing, revealing active DNA demethylation on these promoters. Genome-wide mapping of Tdg reveals extensive colocalization with Tet1 on active promoters. These regions were found to be methylated by Dnmt1 and Dnmt3a and demethylated by a Tet-dependent mechanism. Our work demonstrates the DNA methylation dynamics that occurs on the promoters of the expressed genes and provides a genomic reference map of 5fC and 5caC in ESCs.

The use of optogenetics, the technology that combines genetic and optical methods to monitor and control the activity of specific cell populations, is now widely adopted in neuroscience. The development of optogenetic tools, such as natural photosensitive ion channels and pumps or calcium- and voltage-sensitive proteins, has been growing tremendously during the past 10 years, thanks to the improvement of their performances in terms of facilitating light stimulation. To this aim, efficient illumination methods are also needed. The most common way to photostimulate optogenetic tools has been, so far, widefield illumination with visible light. However, the necessity of addressing the complexity of brain architecture has recently imposed switching to the use of two-photon excitation, which provides a better spatial specificity and deeper penetration in scattering tissue. Two-photon excitation is still challenging, due to intrinsic characteristics of optogenetic tools (e.g., the low conductivity of light-sensitive channels), and efficient illumination methods are therefore essential for advancing in this domain. Here, we present a review on the existing two-photon optical approaches for photoactivation of optogenetic tools, and future perspectives for the widespread implementation of these techniques.