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Attention-deficit/hyperactivity disorder (ADHD) is a neurodevelopmental disorder characterized by inattention, hyperactivity, increased impulsivity and emotion dysregulation. Linkage analysis followed by fine-mapping identified variation in the gene coding for Latrophilin 3 (LPHN3), a putative adhesion-G protein-coupled receptor, as a risk factor for ADHD. In order to validate the link between LPHN3 and ADHD, and to understand the function of LPHN3 in the etiology of the disease, we examined its ortholog lphn3.1 during zebrafish development. Loss of lphn3.1 function causes a reduction and misplacement of dopamine-positive neurons in the ventral diencephalon and a hyperactive/impulsive motor phenotype. The behavioral phenotype can be rescued by the ADHD treatment drugs methylphenidate and atomoxetine. Together, our results implicate decreased Lphn3 activity in eliciting ADHD-like behavior, and demonstrate its correlated contribution to the development of the brain dopaminergic circuitry.

Delivery of therapeutic siRNA to specific tissues is a major challenge. Alvarez-Erviti et al . show that exosomes—small vesicles that are naturally secreted by many animal cells—can be engineered to transport siRNA specifically to the brain in mice. To realize the therapeutic potential of RNA drugs, efficient, tissue-specific and nonimmunogenic delivery technologies must be developed. Here we show that exosomes—endogenous nano-vesicles that transport RNAs and proteins 1 , 2 —can deliver short interfering (si)RNA to the brain in mice. To reduce immunogenicity, we used self-derived dendritic cells for exosome production. Targeting was achieved by engineering the dendritic cells to express Lamp2b, an exosomal membrane protein, fused to the neuron-specific RVG peptide 3 . Purified exosomes were loaded with exogenous siRNA by electroporation. Intravenously injected RVG-targeted exosomes delivered GAPDH siRNA specifically to neurons, microglia, oligodendrocytes in the brain, resulting in a specific gene knockdown. Pre-exposure to RVG exosomes did not attenuate knockdown, and non-specific uptake in other tissues was not observed. The therapeutic potential of exosome-mediated siRNA delivery was demonstrated by the strong mRNA (60%) and protein (62%) knockdown of BACE1 , a therapeutic target in Alzheimer's disease, in wild-type mice.

Although thousands of large intergenic non-coding RNAs (lincRNAs) have been identified in mammals, few have been functionally characterized, leading to debate about their biological role. To address this, we performed loss-of-function studies on most lincRNAs expressed in mouse embryonic stem (ES) cells and characterized the effects on gene expression. Here we show that knockdown of lincRNAs has major consequences on gene expression patterns, comparable to knockdown of well-known ES cell regulators. Notably, lincRNAs primarily affect gene expression in trans . Knockdown of dozens of lincRNAs causes either exit from the pluripotent state or upregulation of lineage commitment programs. We integrate lincRNAs into the molecular circuitry of ES cells and show that lincRNA genes are regulated by key transcription factors and that lincRNA transcripts bind to multiple chromatin regulatory proteins to affect shared gene expression programs. Together, the results demonstrate that lincRNAs have key roles in the circuitry controlling ES cell state. What non-coding RNA does Mammalian genomes encode many classes of RNA that do not correspond to messenger (protein-coding) RNAs, transfer RNAs or ribosomal RNAs. Whether these non-coding RNAs have a function, and what that might be, remain outstanding questions. Lander and colleagues have performed a systematic loss-of-function analysis of the long intergenic non-coding RNAs (lincRNAs) in mouse embryonic stem cells. Some of these are found to affect known regulators of the pluripotent state, indicating that they are functional. This work sets the stage for experiments to determine the precise mechanistic roles of lincRNAs.

Renal-carcinoma-inducing oncogene Using large-scale exome sequencing, Andrew Futreal and colleagues have identified a second frequently mutated gene (after VHL ) in clear cell renal cell carcinomas, the most frequent type of kidney cancer. PBRM1 , a member of the SWI/SNF complex involved in transcriptional regulation, is mutated in about 40% of cases and is shown to function as a tumour suppressor gene. PBRM1 was independently found as a putative cancer gene involved in pancreatic cancer in a mouse transposon screen. These results — together with the fact that other components of the same complex are known cancer genes — unambiguously identify PBRM1 as a major cancer gene. Using large-scale exome sequencing, this study identifies a second (after VHL ) frequently mutated gene in clear cell renal cell carcinomas, the most frequent type of kidney cancer. PBRM1 , a member of the SWI/SNF complex involved in transcriptional regulation, is mutated in about 40% of cases and shown to function as tumour suppressor gene. PBRM1 was independently found as a putative cancer gene involved in pancreatic cancer in a mouse transposon screen. The genetics of renal cancer is dominated by inactivation of the VHL tumour suppressor gene in clear cell carcinoma (ccRCC), the commonest histological subtype. A recent large-scale screen of ∼3,500 genes by PCR-based exon re-sequencing identified several new cancer genes in ccRCC including UTX (also known as KDM6A ) 1 , JARID1C (also known as KDM5C ) and SETD2 (ref. 2 ). These genes encode enzymes that demethylate ( UTX , JARID1C ) or methylate ( SETD2 ) key lysine residues of histone H3. Modification of the methylation state of these lysine residues of histone H3 regulates chromatin structure and is implicated in transcriptional control 3 . However, together these mutations are present in fewer than 15% of ccRCC, suggesting the existence of additional, currently unidentified cancer genes. Here, we have sequenced the protein coding exome in a series of primary ccRCC and report the identification of the SWI/SNF chromatin remodelling complex gene PBRM1 (ref. 4 ) as a second major ccRCC cancer gene, with truncating mutations in 41% (92/227) of cases. These data further elucidate the somatic genetic architecture of ccRCC and emphasize the marked contribution of aberrant chromatin biology.

The medial prefrontal cortex (mPFC) is implicated in processing sensory-discriminative and affective pain. Nonetheless, the underlying mechanisms are poorly understood. Here we demonstrate a role for excitatory neurons in the prelimbic cortex (PL), a sub-region of mPFC, in the regulation of pain sensation and anxiety-like behaviours. Using a chronic inflammatory pain model, we show that lesion of the PL contralateral but not ipsilateral to the inflamed paw attenuates hyperalgesia and anxiety-like behaviours in rats. Optogenetic activation of contralateral PL excitatory neurons exerts analgesic and anxiolytic effects in mice subjected to chronic pain, whereas inhibition is anxiogenic in naive mice. The intrinsic excitability of contralateral PL excitatory neurons is decreased in chronic pain rats; knocking down cyclin-dependent kinase 5 reverses this deactivation and alleviates behavioural impairments. Together, our findings provide novel insights into the role of PL excitatory neurons in the regulation of sensory and affective pain. The medial prefrontal cortex (mPFC) is implicated in pain regulation, yet the underlying mechanisms are poorly understood. Here the authors establish a critical role for mPFC in regulating pain sensation and pain-related anxiety, mediated by activation of the cyclin-dependent kinase 5 signalling pathway.

Long-range genetic regulation A major question in developmental biology is how functionally related groups of genes are switched on at the right time and in the right place. Long intergenic non-coding RNAs (lincRNAs) have been implicated in both gene silencing and activation, and could be a means of long-range control of gene expression. A lincRNA termed HOTTIP that coordinates the activation of multiple 5' HOXA regulatory genes has now been identified at the 5' tip of the HOXA locus. Chromosomal looping brings HOTTIP close its target genes, where it facilitates histone H3 lysine 4 trimethylation and gene transcription. Long intergenic non-coding RNAs (lincRNAs) have been implicated in both gene silencing and activation, and could be a means for long-range control of gene expression. Here a lincRNA termed HOTTIP is identified at the 5′ tip of the HOXA locus that coordinates the activation of multiple 5′ HOXA genes. Chromosomal looping brings HOTTIP into the proximity of its target genes, where it seems to be required to facilitate histone H3 lysine 4 trimethylation and gene transcription. The genome is extensively transcribed into long intergenic noncoding RNAs (lincRNAs), many of which are implicated in gene silencing 1 , 2 . Potential roles of lincRNAs in gene activation are much less understood 3 , 4 , 5 . Development and homeostasis require coordinate regulation of neighbouring genes through a process termed locus control 6 . Some locus control elements and enhancers transcribe lincRNAs 7 , 8 , 9 , 10 , hinting at possible roles in long-range control. In vertebrates, 39 Hox genes, encoding homeodomain transcription factors critical for positional identity, are clustered in four chromosomal loci; the Hox genes are expressed in nested anterior-posterior and proximal-distal patterns colinear with their genomic position from 3′ to 5′of the cluster 11 . Here we identify HOTTIP , a lincRNA transcribed from the 5′ tip of the HOXA locus that coordinates the activation of several 5′ HOXA genes in vivo . Chromosomal looping brings HOTTIP into close proximity to its target genes. HOTTIP RNA binds the adaptor protein WDR5 directly and targets WDR5/MLL complexes across HOXA , driving histone H3 lysine 4 trimethylation and gene transcription. Induced proximity is necessary and sufficient for HOTTIP RNA activation of its target genes. Thus, by serving as key intermediates that transmit information from higher order chromosomal looping into chromatin modifications, lincRNAs may organize chromatin domains to coordinate long-range gene activation.

Sakari Kauppinen and colleagues report a method for silencing miRNA families in vivo . They find that seed-targeting 8-mer LNA oligonucleotides, termed tiny LNAs, can lead to long-term miRNA silencing in normal tissues and breast tumors in mice. The challenge of understanding the widespread biological roles of animal microRNAs (miRNAs) has prompted the development of genetic and functional genomics technologies for miRNA loss-of-function studies. However, tools for exploring the functions of entire miRNA families are still limited. We developed a method that enables antagonism of miRNA function using seed-targeting 8-mer locked nucleic acid (LNA) oligonucleotides, termed tiny LNAs. Transfection of tiny LNAs into cells resulted in simultaneous inhibition of miRNAs within families sharing the same seed with concomitant upregulation of direct targets. In addition, systemically delivered, unconjugated tiny LNAs showed uptake in many normal tissues and in breast tumors in mice, coinciding with long-term miRNA silencing. Transcriptional and proteomic profiling suggested that tiny LNAs have negligible off-target effects, not significantly altering the output from mRNAs with perfect tiny LNA complementary sites. Considered together, these data support the utility of tiny LNAs in elucidating the functions of miRNA families in vivo .

George Daley and John Rinn and colleagues identify large intergenic non-coding RNAs that are upregulated during reprogramming of induced pluripotent stem cells, and they show a functional role for large intergenic non-coding RNA-RoR in induced pluripotent stem cell derivation. The conversion of lineage-committed cells to induced pluripotent stem cells (iPSCs) by reprogramming is accompanied by a global remodeling of the epigenome 1 , 2 , 3 , 4 , 5 , resulting in altered patterns of gene expression 2 , 6 , 7 , 8 , 9 . Here we characterize the transcriptional reorganization of large intergenic non-coding RNAs (lincRNAs) 10 , 11 that occurs upon derivation of human iPSCs and identify numerous lincRNAs whose expression is linked to pluripotency. Among these, we defined ten lincRNAs whose expression was elevated in iPSCs compared with embryonic stem cells, suggesting that their activation may promote the emergence of iPSCs. Supporting this, our results indicate that these lincRNAs are direct targets of key pluripotency transcription factors. Using loss-of-function and gain-of-function approaches, we found that one such lincRNA (lincRNA-RoR) modulates reprogramming, thus providing a first demonstration for critical functions of lincRNAs in the derivation of pluripotent stem cells.

FoxA genomic surveillance mechanism Transcriptional enhancers orchestrate cell-type-specific gene expression programs, but how they convey signal-activated transcriptional responses remains poorly understood. Here, the cell-lineage-specific transcription factor FoxA1 is shown to both facilitate and restrict the androgen receptor to act on distinct classes of enhancers. Lowered levels of FoxA1, such as those found in prostate cancer, can reprogram the hormonal response by causing a switch in androgen receptor binding to a set of pre-established, functional enhancers that are marked by enhancer-derived non-coding RNAs (eRNAs). This work points to the existence of a large repository of active enhancers that can be tuned to allow alternative gene expression programs in normal cell development and in disease progression. Mammalian genomes are populated with thousands of transcriptional enhancers that orchestrate cell-type-specific gene expression programs 1 , 2 , 3 , 4 , but how those enhancers are exploited to institute alternative, signal-dependent transcriptional responses remains poorly understood. Here we present evidence that cell-lineage-specific factors, such as FoxA1, can simultaneously facilitate and restrict key regulated transcription factors, exemplified by the androgen receptor (AR), to act on structurally and functionally distinct classes of enhancer. Consequently, FoxA1 downregulation, an unfavourable prognostic sign in certain advanced prostate tumours, triggers dramatic reprogramming of the hormonal response by causing a massive switch in AR binding to a distinct cohort of pre-established enhancers. These enhancers are functional, as evidenced by the production of enhancer-templated non-coding RNA (eRNA 5 ) based on global nuclear run-on sequencing (GRO-seq) analysis 6 , with a unique class apparently requiring no nucleosome remodelling to induce specific enhancer–promoter looping and gene activation. GRO-seq data also suggest that liganded AR induces both transcription initiation and elongation. Together, these findings reveal a large repository of active enhancers that can be dynamically tuned to elicit alternative gene expression programs, which may underlie many sequential gene expression events in development, cell differentiation and disease progression.

Less is known about the role of amygdala circuits in anxiety than in acute fear responses. In this study, the authors demonstrate that aversive experience induces anxiety in mice by regulating the excitability of a defined subset of central amygdala neurons via extrasynaptic α 5 GABA A receptors. Aversive experiences can lead to complex behavioral adaptations including increased levels of anxiety and fear generalization. The neuronal mechanisms underlying such maladaptive behavioral changes, however, are poorly understood. Here, using a combination of behavioral, physiological and optogenetic approaches in mouse, we identify a specific subpopulation of central amygdala neurons expressing protein kinase C δ (PKCδ) as key elements of the neuronal circuitry controlling anxiety. Moreover, we show that aversive experiences induce anxiety and fear generalization by regulating the activity of PKCδ + neurons via extrasynaptic inhibition mediated by α 5 subunit-containing GABA A receptors. Our findings reveal that the neuronal circuits that mediate fear and anxiety overlap at the level of defined subpopulations of central amygdala neurons and demonstrate that persistent changes in the excitability of a single cell type can orchestrate complex behavioral changes.