SUMMARY R-loop, a three-stranded RNA/DNA structure, has been linked to induced genome instability and regulated gene expression. To enable precision analysis of R-loops in vivo, we develop an RNase-H-based approach; this reveals predominant R-loop formation near gene promoters with strong G/C skew and propensity to form G-quadruplex in non-template DNA, corroborating with all biochemically established properties of R-loops. Transcription perturbation experiments further indicate that R-loop induction correlates to transcriptional pausing. Interestingly, we note that most mapped R-loops are each linked to a nearby free RNA end; by using a ribozyme to co-transcriptionally cleave nascent RNA, we demonstrate that such a free RNA end coupled with a G/C-skewed sequence is necessary and sufficient to induce R-loop. These findings provide a topological solution for RNA invasion into duplex DNA and suggest an order for R-loop initiation and elongation in an opposite direction to that previously proposed.

The U2AF heterodimer has been well studied for its role in defining functional 3′ splice sites in pre-mRNA splicing, but many fundamental questions still remain unaddressed regarding the function of U2AF in mammalian genomes. Through genome-wide analysis of U2AF-RNA interactions, we report that U2AF has the capacity to directly define ~88% of functional 3′ splice sites in the human genome, but numerous U2AF binding events also occur in intronic locations. Mechanistic dissection reveals that upstream intronic binding events interfere with the immediate downstream 3′ splice site associated either with the alternative exon, to cause exon skipping, or with the competing constitutive exon, to induce exon inclusion. We further demonstrate partial functional impairment with leukemia-associated mutations in U2AF35, but not U2AF65, in regulated splicing. These findings reveal the genomic function and regulatory mechanism of U2AF in both normal and disease states.

Summary The nuclear matrix associated hnRNP U/SAF-A protein has been implicated in diverse pathways from transcriptional regulation to telomere length control to X inactivation, but the precise mechanism underlying each of these processes has remained elusive. Here, we report hnRNP U as a regulator of SMN2 splicing from a custom RNAi screen. Genome-wide analysis by CLIP-seq reveals that hnRNP U binds virtually to all classes of regulatory non-coding RNAs, including all snRNAs required for splicing of both major and minor classes of introns, leading to the discovery that hnRNP U regulates U2 snRNP maturation and Cajal body morphology in the nucleus. Global analysis of hnRNP U-dependent splicing by RNA-seq coupled with bioinformatic analysis of associated splicing signals suggests a general rule for splice site selection through modulating the core splicing machinery. These findings exemplify hnRNP U/SAF-A as a potent regulator of nuclear ribonucleoprotein particles in diverse gene expression pathways.

Memory is stored in neural networks via changes in synaptic strength mediated in part by NMDA receptor (NMDAR)-dependent long-term potentiation (LTP). Here we show that a cholecystokinin (CCK)-B receptor (CCKBR) antagonist blocks high-frequency stimulation-induced neocortical LTP, whereas local infusion of CCK induces LTP. CCK −/− mice lacked neocortical LTP and showed deficits in a cue-cue associative learning paradigm; and administration of CCK rescued associative learning deficits. Highfrequency stimulation-induced neocortical LTP was completely blocked by either the NMDAR antagonist or the CCKBR antagonist, while application of either NMDA or CCK induced LTP after lowfrequency stimulation. In the presence of CCK, LTP was still induced even after blockade of NMDARs. Local application of NMDA induced the release of CCK in the neocortex. These findings suggest that NMDARs control the release of CCK, which enables neocortical LTP and the formation of cue-cue associative memory. cholecystokinin | NMDA receptor | long-term potentiation | memory | entorhinal cortex M emory is stored in neural networks through changes in synaptic strength (1). Long-term potentiation (LTP) and long-term depression (LTD) are two forms of synaptic plasticity that are believed to represent a neural basis of memory in different brain regions (2-5). The major form of LTP in the hippocampus and neocortex is induced through theta burst stimulation or highfrequency stimulation (HFS) (2, 3). Previous studies have shown that NMDA receptors (NMDARs) play a crucial role in HFSinduced LTP in the hippocampus (6-9) and neocortex (2, 10), and in the formation and consolidation of associative memory (11,12).Serving as the gateway from the hippocampus to the neocortex, the entorhinal cortex forms strong reciprocal connections with the neocortex (13, 14) and shows extensive cholecystokinin (CCK) labeling (15-17) with projections to neocortical areas, including the auditory cortex (13,14,18). CCK is the most abundant cortical neuropeptide (19), and mice lacking the CCK gene exhibit poor performance in a passive avoidance task and display impaired spatial memory (20). Although many studies have focused on GABAergic CCK neurons (21-24), many glutamatergic neurons in the neocortex express CCK (25, 26). We previously found that local infusion of CCK into the auditory cortex of anesthetized rats induces plastic changes that enable auditory cortical neurons to start responding to a light stimulus after its pairing with an auditory stimulus (18). Activation of the entorhinal cortex potentiates neuronal responses in the auditory cortex, and this effect is suppressed by infusion of a CCK-B receptor (CCKBR) antagonist (18), suggesting that the entorhinal cortex enables neocortical plasticity via CCK-containing neurons projecting to the neocortex.If CCK enables cortical neuroplasticity and associative memory formation, then we would expect CCK-induced neuroplasticity to affect LTP. The release of neuropeptides occurs slowly in response to repetitive firing (27,28)....