Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells.

Transcription factors (TFs) are trans-acting proteins that bind cis-regulatory elements (CREs) in DNA to control gene expression. Here, we analyzed the genomic localization profiles of 529 sequence-specific TFs and 151 cofactors and chromatin regulators in the human cancer cell line HepG2, for a total of 680 broadly termed DNA-associated proteins (DAPs). We used this deep collection to model each TF's impact on gene expression, and identified a cohort of 26 candidate transcriptional repressors. We examine high occupancy target (HOT) sites in the context of three-dimensional genome organization and show biased motif placement in distal-promoter connections involving HOT sites. We also found a substantial number of closed chromatin regions with multiple DAPs bound, and explored their properties, finding that a MAFF/MAFK TF pair correlates with transcriptional repression. Altogether, these analyses provide novel insights into the regulatory logic of the human cell line HepG2 genome and show the usefulness of large genomic analyses for elucidation of individual TF functions.

The effects of domain knowledge and event structure on event processing.

Research suggests that domain knowledge facilitates memory for domain-specific information through two mechanisms: differentiation, which involves the ability to identify meaningful, fine-grained details within a sequence, and unitization, which involves binding individual components from a sequence into functional wholes. This study investigated the extent to which individuals engaged in differentiation and unitization when parsing continuous events into discrete, meaningful units (i.e., event segmentation) and recalling them. Participants watched and segmented basketball videos. They then rewatched the videos and provided descriptions afterward. Videos were coded for the presence of higher order goals (A2 actions) and the individual sub-actions that comprised them (A1 actions). Results suggested that event segmentation behavior for participants with less knowledge was more aligned with changes in basic actions (A1 actions) than for participants with greater knowledge. When describing events, participants with greater knowledge were more likely than participants with less knowledge to use statements that reflected unitization.

Semantic knowledge attenuates age-related differences in event segmentation and episodic memory.

While semantic and episodic memory may be distinct memory systems, their interdependence is substantial. For instance, decades of work have shown that semantic knowledge facilitates episodic memory. Here, we aim to clarify this interactive relationship by determining whether semantic knowledge facilitates the acquisition of new episodic memories, in part, by influencing an encoding mechanism, event segmentation. In the current study, we evaluated the extent to which semantic knowledge shapes how people segment ongoing activity and how such knowledge-related benefits in segmentation affect episodic memory performance. To investigate these effects, we combined data across three studies that had young and older adults segment and remember videos of everyday activities that were either familiar or unfamiliar to their age group. We found age-related differences in event-segmentation ability and memory performance, but only when older adults lacked semantic knowledge. Most importantly, when they had access to relevant semantic knowledge, older adults segmented and remembered information similar to young adults. Our findings indicate that older adults can use semantic knowledge to effectively encode and retrieve everyday information. These effects suggest that future interventions can leverage older adults' intact semantic knowledge to attenuate age-related deficits in event segmentation and episodic long-term memory.

Genome-wide strand asymmetry in massively parallel reporter activity favors genic strands.

Massively parallel reporter assays (MPRAs) are useful tools to characterize regulatory elements in human genomes. An aspect of MPRAs that is not typically the focus of analysis is their intrinsic ability to differentiate activity levels for a given sequence element when placed in both of its possible orientations relative to the reporter construct. Here, we describe pervasive strand asymmetry of MPRA signals in data sets from multiple reporter configurations in both published and newly reported data. These effects are reproducible across different cell types and in different treatments within a cell type and are observed both within and outside of annotated regulatory elements. From elements in gene bodies, MPRA strand asymmetry favors the sense strand, suggesting that function related to endogenous transcription is driving the phenomenon. Similarly, we find that within Alu mobile element insertions, strand asymmetry favors the transcribed strand of the ancestral retrotransposon. The effect is consistent across the multiplicity of Alu elements in human genomes and is more pronounced in less diverged Alu elements. We find sequence features driving MPRA strand asymmetry and show its prediction from sequence alone. We see some evidence for RNA stabilization and transcriptional activation mechanisms and hypothesize that the effect is driven by natural selection favoring efficient transcription. Our results indicate that strand asymmetry is a pervasive and reproducible feature in MPRA data. More importantly, the fact that MPRA asymmetry favors naturally transcribed strands suggests that it stems from preserved biological functions that have a substantial, global impact on gene and genome evolution.

Influences of domain knowledge on segmentation and memory.

Much research has shown that experts possess superior memory in their domain of expertise. This memory benefit has been proposed to be the result of various encoding mechanisms, such as chunking and differentiation. Another potential encoding mechanism that is associated with memory is event segmentation, which is the process by which people parse continuous information into meaningful, discrete units. Previous research has found evidence that segmentation, to some extent, is affected by top-down processing. To date, few studies have investigated the influence of expertise on segmentation, and questions about expertise, segmentation ability, and their impact on memory remain. The goal of the current study was to investigate the influence of expertise on segmentation and memory ability for two different domains: basketball and Overwatch. Participants with high and low knowledge for basketball and with low knowledge for Overwatch viewed and segmented videos at coarse and fine grains, then completed memory tests. Differences in segmentation ability and memory were present between experts and control novices, specifically for the basketball videos; however, experts' segmentation only predicted memory for activities for which knowledge was lacking. Overall, this research suggests that experts' superior memory is not due to their segmentation ability and contributes to a growing body of literature showing evidence supporting conceptual effects on segmentation.

Occupancy maps of 208 chromatin-associated proteins in one human cell type.

Transcription factors are DNA-binding proteins that have key roles in gene regulation1,2. Genome-wide occupancy maps of transcriptional regulators are important for understanding gene regulation and its effects on diverse biological processes3-6. However, only a minority of the more than 1,600 transcription factors encoded in the human genome has been assayed. Here we present, as part of the ENCODE (Encyclopedia of DNA Elements) project, data and analyses from chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) experiments using the human HepG2 cell line for 208 chromatin-associated proteins (CAPs). These comprise 171 transcription factors and 37 transcriptional cofactors and chromatin regulator proteins, and represent nearly one-quarter of CAPs expressed in HepG2 cells. The binding profiles of these CAPs form major groups associated predominantly with promoters or enhancers, or with both. We confirm and expand the current catalogue of DNA sequence motifs for transcription factors, and describe motifs that correspond to other transcription factors that are co-enriched with the primary ChIP target. For example, FOX family motifs are enriched in ChIP-seq peaks of 37 other CAPs. We show that motif content and occupancy patterns can distinguish between promoters and enhancers. This catalogue reveals high-occupancy target regions at which many CAPs associate, although each contains motifs for only a minority of the numerous associated transcription factors. These analyses provide a more complete overview of the gene regulatory networks that define this cell type, and demonstrate the usefulness of the large-scale production efforts of the ENCODE Consortium.

Epitope Tagging ChIP-Seq of DNA Binding Proteins Using CETCh-Seq.

Chromatin immunoprecipitation followed by next-generation DNA sequencing (ChIP-seq) has been used to identify transcription factor (TF) binding proteins throughout the genome. Unfortunately, this approach traditionally requires commercially available, ChIP-seq grade antibodies that frequently fail to generate acceptable datasets. To obtain data for the many TFs for which there is no appropriate antibody, we recently developed a new method for performing ChIP-seq by epitope tagging endogenous TFs using CRISPR/Cas9 genome editing technology (CETCh-seq). Here, we describe our general protocol of CETCh-seq for both adherent and nonadherent cell lines using a commercially available FLAG antibody.

Differential effects of knowledge and aging on the encoding and retrieval of everyday activities.

We deconstruct continuous streams of action into smaller, meaningful events. Research has shown that the ability to segment continuous activity into such events and remember their contents declines with age; however, knowledge improves with age. We investigated how young and older adults use knowledge to more efficiently encode and later remember information from everyday events by having participants view a series of self-paced slideshows depicting everyday activities. For some activities, older adults produce more normative scripts than do young adults (older adult activities) and for other activities, young adults produce more normative scripts than do older adults (young adult activities). Overall, participants viewed event boundaries longer than within events (i.e., the event boundary advantage) replicating prior research (e.g., Hard, Recchia, & Tversky, 2011). Importantly, older adults demonstrated the boundary advantage for the older adult activities but not the young adult activities, and they also had better recognition memory for the older adult activities than the young adult activities. We also found that the magnitude of a participant's boundary advantage was associated with better memory, but only for the less knowledgeable activities. Results indicate that older adults use their intact knowledge to better encode and remember everyday activities, but that knowledge and event segmentation may have independent influences on event memory.

Does semantic knowledge influence event segmentation and recall of text?

Knowledge benefits episodic memory, particularly when provided before encoding (Anderson & Pichert in Journal of Verbal Learning and Verbal Behavior, 17(1), 1-12, 1978; Bransford & Johnson in Journal of Verbal Learning and Verbal Behavior, 11(6), 717-726, 1972). These benefits can occur through several encoding mechanisms, one of which may be event segmentation. Event segmentation is one's ability to parse information into meaningful units as an activity unfolds. The current experiment evaluated whether two top-down manipulations-providing context or perspective taking-influence the segmentation and memory of text. For the ambiguous texts in Experiment 1, half the participants received context in the form of a title, whereas the other half received no context. For the text in Experiment 2, half the participants read from the perspective of a burglar and the other half read from the perspective of a home buyer. In both experiments, participants read the passages, recalled the information, and then segmented the passages into meaningful units. Consistent with previous findings, participants who received context recalled more information compared with those who received no context, and participants in one perspective were more likely to recall information relevant to their perspective. Most importantly, we found that context and perspective facilitated more normative segmentation; however, the differences were small and suggest that effects of top-down processing on the segmentation of text may be modest at best. Thus, event segmentation processes that operate during text comprehension are influenced by semantic knowledge but may be more heavily driven by other factors (e.g., perceptual cues).

Temporal Chunking Makes Life's Events More Memorable.

Declines in episodic memory accompany both healthy aging and age-related diseases, such as dementia. Given that memory complaints are common in the aging population, a wealth of research has evaluated the underlying mechanisms of these declines and explored strategy interventions that could offset them. In the current paper, we describe a newer approach to improving memory: event segmentation training. Event segmentation is an encoding strategy in which individuals parse continuous activity into meaningful chunks. The ability to segment activity is associated with later memory for the events, but unfortunately, this segmentation ability declines with age. Importantly, interventions designed to improve event segmentation have resulted in memory improvements for both young and older adults. We will review these past experiments as well as some new event segmentation training work that uses older adults' semantic knowledge to improve their segmentation and episodic memory. We believe that future research on event segmentation is a promising avenue for improving older adults' ability to remember everyday activities.

Discovery of Indole- and Indazole-acylsulfonamides as Potent and Selective NaV1.7 Inhibitors for the Treatment of Pain.

3-Aryl-indole and 3-aryl-indazole derivatives were identified as potent and selective Nav1.7 inhibitors. Compound 29 was shown to be efficacious in the mouse formalin assay and also reduced complete Freund's adjuvant (CFA)-induced thermal hyperalgesia and chronic constriction injury (CCI) induced cold allodynia and models of inflammatory and neuropathic pain, respectively, following intraperitoneal (IP) doses of 30 mg/kg. The observed efficacy could be correlated with the mouse dorsal root ganglion exposure and NaV1.7 potency associated with 29.

A genome-wide interactome of DNA-associated proteins in the human liver.

Large-scale efforts like the ENCODE Project have made tremendous progress in cataloging the genomic binding patterns of DNA-associated proteins (DAPs), such as transcription factors (TFs). However, most chromatin immunoprecipitation-sequencing (ChIP-seq) analyses have focused on a few immortalized cell lines whose activities and physiology differ in important ways from endogenous cells and tissues. Consequently, binding data from primary human tissue are essential to improving our understanding of in vivo gene regulation. Here, we identify and analyze more than 440,000 binding sites using ChIP-seq data for 20 DAPs in two human liver tissue samples. We integrated binding data with transcriptome and phased WGS data to investigate allelic DAP interactions and the impact of heterozygous sequence variation on the expression of neighboring genes. Our tissue-based data set exhibits binding patterns more consistent with liver biology than cell lines, and we describe uses of these data to better prioritize impactful noncoding variation. Collectively, our rich data set offers novel insights into genome function in human liver tissue and provides a valuable resource for assessing disease-related disruptions.

Preclinical Characterization of (R)-3-((3S,4S)-3-fluoro-4-(4-hydroxyphenyl)piperidin-1-yl)-1-(4-methylbenzyl)pyrrolidin-2-one (BMS-986169), a Novel, Intravenous, Glutamate N-Methyl-d-Aspartate 2B Receptor Negative Allosteric Modulator with Potential in Major Depressive Disorder.

(R)-3-((3S,4S)-3-fluoro-4-(4-hydroxyphenyl)piperidin-1-yl)-1-(4-methylbenzyl)pyrrolidin-2-one (BMS-986169) and the phosphate prodrug 4-((3S,4S)-3-fluoro-1-((R)-1-(4-methylbenzyl)-2-oxopyrrolidin-3-yl)piperidin-4-yl)phenyl dihydrogen phosphate (BMS-986163) were identified from a drug discovery effort focused on the development of novel, intravenous glutamate N-methyl-d-aspartate 2B receptor (GluN2B) negative allosteric modulators (NAMs) for treatment-resistant depression (TRD). BMS-986169 showed high binding affinity for the GluN2B subunit allosteric modulatory site (Ki = 4.03-6.3 nM) and selectively inhibited GluN2B receptor function in Xenopus oocytes expressing human N-methyl-d-aspartate receptor subtypes (IC50 = 24.1 nM). BMS-986169 weakly inhibited human ether-a-go-go-related gene channel activity (IC50 = 28.4 µM) and had negligible activity in an assay panel containing 40 additional pharmacological targets. Intravenous administration of BMS-986169 or BMS-986163 dose-dependently increased GluN2B receptor occupancy and inhibited in vivo [3H](+)-5-methyl-10,11-dihydro-5H-dibenzo[a,d]cyclohepten-5,10-imine ([3H]MK-801) binding, confirming target engagement and effective cleavage of the prodrug. BMS-986169 reduced immobility in the mouse forced swim test, an effect similar to intravenous ketamine treatment. Decreased novelty suppressed feeding latency, and increased ex vivo hippocampal long-term potentiation was also seen 24 hours after acute BMS-986163 or BMS-986169 administration. BMS-986169 did not produce ketamine-like hyperlocomotion or abnormal behaviors in mice or cynomolgus monkeys but did produce a transient working memory impairment in monkeys that was closely related to plasma exposure. Finally, BMS-986163 produced robust changes in the quantitative electroencephalogram power band distribution, a translational measure that can be used to assess pharmacodynamic activity in healthy humans. Due to the poor aqueous solubility of BMS-986169, BMS-986163 was selected as the lead GluN2B NAM candidate for further evaluation as a novel intravenous agent for TRD.

Effects of BMS-902483, an α7 nicotinic acetylcholine receptor partial agonist, on cognition and sensory gating in relation to receptor occupancy in rodents.

The α7 nicotinic acetylcholine receptor is thought to play an important role in human cognition. Here we describe the in vivo effects of BMS-902483, a selective potent α7 nicotinic acetylcholine receptor partial agonist, in relationship to α7 nicotinic acetylcholine receptor occupancy. BMS-902483 has low nanomolar affinity for rat and human α7 nicotinic acetylcholine receptors and elicits currents in cells expressing human or rat α7 nicotinic acetylcholine receptors that are about 60% of the maximal acetylcholine response. BMS-902483 improved 24h novel object recognition memory in mice with a minimal effective dose (MED) of 0.1mg/kg and reversed MK-801-induced deficits in a rat attentional set-shifting model of executive function with an MED of 3mg/kg. Enhancement of novel object recognition was blocked by the silent α7 nicotinic acetylcholine receptor agonist, NS6740, demonstrating that activity of BMS-902483 was mediated by α7 nicotinic acetylcholine receptors. BMS-902483 also reversed ketamine-induced deficits in auditory gating in rats, and enhanced ex vivo hippocampal long-term potentiation examined 24h after dosing in mice. Results from an ex vivo brain homogenate binding assay showed that α7 receptor occupancy ranged from 64% (novel object recognition) to ~90% (set shift and gating) at the MED for behavioral and sensory processing effects of BMS-902483.

Development of New Benzenesulfonamides As Potent and Selective Nav1.7 Inhibitors for the Treatment of Pain.

By taking advantage of certain features in piperidine 4, we developed a novel series of cyclohexylamine- and piperidine-based benzenesulfonamides as potent and selective Nav1.7 inhibitors. However, compound 24, one of the early analogs, failed to reduce phase 2 flinching in the mouse formalin test even at a dose of 100 mpk PO due to insufficient dorsal root ganglion (DRG) exposure attributed to poor membrane permeability. Two analogs with improved membrane permeability showed much increased DRG concentrations at doses of 30 mpk PO, but, confoundingly, only one of these was effective in the formalin test. More data are needed to understand the disconnect between efficacy and exposure relationships.

Genomic regulation of invasion by STAT3 in triple negative breast cancer.

Breast cancer is a heterogeneous disease comprised of four molecular subtypes defined by whether the tumor-originating cells are luminal or basal epithelial cells. Breast cancers arising from the luminal mammary duct often express estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth receptor 2 (HER2). Tumors expressing ER and/or PR are treated with anti-hormonal therapies, while tumors overexpressing HER2 are targeted with monoclonal antibodies. Immunohistochemical detection of ER, PR, and HER2 receptors/proteins is a critical step in breast cancer diagnosis and guided treatment. Breast tumors that do not express these proteins are known as "triple negative breast cancer" (TNBC) and are typically basal-like. TNBCs are the most aggressive subtype, with the highest mortality rates and no targeted therapy, so there is a pressing need to identify important TNBC tumor regulators. The signal transducer and activator of transcription 3 (STAT3) transcription factor has been previously implicated as a constitutively active oncogene in TNBC. However, its direct regulatory gene targets and tumorigenic properties have not been well characterized. By integrating RNA-seq and ChIP-seq data from 2 TNBC tumors and 5 cell lines, we discovered novel gene signatures directly regulated by STAT3 that were enriched for processes involving inflammation, immunity, and invasion in TNBC. Functional analysis revealed that STAT3 has a key role regulating invasion and metastasis, a characteristic often associated with TNBC. Our findings suggest therapies targeting STAT3 may be important for preventing TNBC metastasis.

CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins.

Chromatin immunoprecipitation followed by next-generation DNA sequencing (ChIP-seq) is a widely used technique for identifying transcription factor (TF) binding events throughout an entire genome. However, ChIP-seq is limited by the availability of suitable ChIP-seq grade antibodies, and the vast majority of commercially available antibodies fail to generate usable data sets. To ameliorate these technical obstacles, we present a robust methodological approach for performing ChIP-seq through epitope tagging of endogenous TFs. We used clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-based genome editing technology to develop CRISPR epitope tagging ChIP-seq (CETCh-seq) of DNA-binding proteins. We assessed the feasibility of CETCh-seq by tagging several DNA-binding proteins spanning a wide range of endogenous expression levels in the hepatocellular carcinoma cell line HepG2. Our data exhibit strong correlations between both replicate types as well as with standard ChIP-seq approaches that use TF antibodies. Notably, we also observed minimal changes to the cellular transcriptome and to the expression of the tagged TF. To examine the robustness of our technique, we further performed CETCh-seq in the breast adenocarcinoma cell line MCF7 as well as mouse embryonic stem cells and observed similarly high correlations. Collectively, these data highlight the applicability of CETCh-seq to accurately define the genome-wide binding profiles of DNA-binding proteins, allowing for a straightforward methodology to potentially assay the complete repertoire of TFs, including the large fraction for which ChIP-quality antibodies are not available.

Effect of acute NR2B antagonist treatment on long-term potentiation in the rat hippocampus.

The long lasting antidepressant response seen following acute, i.v. ketamine administration in patients with treatment-resistant depression (TRD) is thought to result from enhanced synaptic plasticity in cortical and hippocampal circuits. Using extracellular field recordings in rat hippocampal slices, we show that a single dose of the non-selective NMDA receptor antagonist ketamine or CP-101,606, a selective antagonist of the NR2B subunit of the NMDA receptor, enhances hippocampal synaptic plasticity induced with high frequency stimulation (HFS) 24h after dosing - a time at which plasma concentrations of the drug are no longer detectable in the animal. These results indicate that acute inhibition of NMDA receptors containing the NR2B subunit can lead to long-lasting changes in hippocampal plasticity.

Fully automated high-throughput chromatin immunoprecipitation for ChIP-seq: identifying ChIP-quality p300 monoclonal antibodies.

Chromatin immunoprecipitation coupled with DNA sequencing (ChIP-seq) is the major contemporary method for mapping in vivo protein-DNA interactions in the genome. It identifies sites of transcription factor, cofactor and RNA polymerase occupancy, as well as the distribution of histone marks. Consortia such as the ENCyclopedia Of DNA Elements (ENCODE) have produced large datasets using manual protocols. However, future measurements of hundreds of additional factors in many cell types and physiological states call for higher throughput and consistency afforded by automation. Such automation advances, when provided by multiuser facilities, could also improve the quality and efficiency of individual small-scale projects. The immunoprecipitation process has become rate-limiting, and is a source of substantial variability when performed manually. Here we report a fully automated robotic ChIP (R-ChIP) pipeline that allows up to 96 reactions. A second bottleneck is the dearth of renewable ChIP-validated immune reagents, which do not yet exist for most mammalian transcription factors. We used R-ChIP to screen new mouse monoclonal antibodies raised against p300, a histone acetylase, well-known as a marker of active enhancers, for which ChIP-competent monoclonal reagents have been lacking. We identified, validated for ChIP-seq, and made publicly available a monoclonal reagent called ENCITp300-1.