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.

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.

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.

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.

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.

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).

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.

Evidence for multiple roles for grainyhead-like 2 in the establishment and maintenance of human mucociliary airway epithelium.[corrected].

Most of the airways of the human lung are lined by an epithelium made up of ciliated and secretory luminal cells and undifferentiated basal progenitor cells. The integrity of this epithelium and its ability to act as a selective barrier are critical for normal lung function. In other epithelia, there is evidence that transcription factors of the evolutionarily conserved grainyheadlike (GRHL) family play key roles in coordinating multiple cellular processes required for epithelial morphogenesis, differentiation, remodeling, and repair. However, only a few target genes have been identified, and little is known about GRHL function in the adult lung. Here we focus on the role of GRHL2 in primary human bronchial epithelial cells, both as undifferentiated progenitors and as they differentiate in air-liquid interface culture into an organized mucociliary epithelium with transepithelial resistance. Using a dominant-negative protein or shRNA to inhibit GRHL2, we follow changes in epithelial phenotype and gene transcription using RNA sequencing or microarray analysis. We identify several hundreds of genes that are directly or indirectly regulated by GRHL2 in both undifferentiated cells and air-liquid interface cultures. Using ChIP sequencing to map sites of GRHL2 binding in the basal cells, we identify 7,687 potential primary targets and confirm that GRHL2 binding is strongly enriched near GRHL2-regulated genes. Taken together, the results support the hypothesis that GRHL2 plays a key role in regulating many physiological functions of human airway epithelium, including those involving cell morphogenesis, adhesion, and motility.

Intricate interplay between astrocytes and motor neurons in ALS.

ALS results from the selective and progressive degeneration of motor neurons. Although the underlying disease mechanisms remain unknown, glial cells have been implicated in ALS disease progression. Here, we examine the effects of glial cell/motor neuron interactions on gene expression using the hSOD1(G93A) (the G93A allele of the human superoxide dismutase gene) mouse model of ALS. We detect striking cell autonomous and nonautonomous changes in gene expression in cocultured motor neurons and glia, revealing that the two cell types profoundly affect each other. In addition, we found a remarkable concordance between the cell culture data and expression profiles of whole spinal cords and acutely isolated spinal cord cells during disease progression in the G93A mouse model, providing validation of the cell culture approach. Bioinformatics analyses identified changes in the expression of specific genes and signaling pathways that may contribute to motor neuron degeneration in ALS, among which are TGF-ß signaling pathways.

Effects of sequence variation on differential allelic transcription factor occupancy and gene expression.

A complex interplay between transcription factors (TFs) and the genome regulates transcription. However, connecting variation in genome sequence with variation in TF binding and gene expression is challenging due to environmental differences between individuals and cell types. To address this problem, we measured genome-wide differential allelic occupancy of 24 TFs and EP300 in a human lymphoblastoid cell line GM12878. Overall, 5% of human TF binding sites have an allelic imbalance in occupancy. At many sites, TFs clustered in TF-binding hubs on the same homolog in especially open chromatin. While genetic variation in core TF binding motifs generally resulted in large allelic differences in TF occupancy, most allelic differences in occupancy were subtle and associated with disruption of weak or noncanonical motifs. We also measured genome-wide differential allelic expression of genes with and without heterozygous exonic variants in the same cells. We found that genes with differential allelic expression were overall less expressed both in GM12878 cells and in unrelated human cell lines. Comparing TF occupancy with expression, we found strong association between allelic occupancy and expression within 100 bp of transcription start sites (TSSs), and weak association up to 100 kb from TSSs. Sites of differential allelic occupancy were significantly enriched for variants associated with disease, particularly autoimmune disease, suggesting that allelic differences in TF occupancy give functional insights into intergenic variants associated with disease. Our results have the potential to increase the power and interpretability of association studies by targeting functional intergenic variants in addition to protein coding sequences.

Role of CCCTC binding factor (CTCF) and cohesin in the generation of single-cell diversity of protocadherin-α gene expression.

Extraordinary single-cell diversity is generated in the vertebrate nervous system by the combinatorial expression of the clustered protocadherin genes (Pcdhα, -ß, and -γ). This diversity is generated by a combination of stochastic promoter choice and alternative pre-mRNA splicing. Here we show that both the insulator-binding protein CTCF and the cohesin complex subunit Rad21 bind to two highly conserved DNA sequences, the first within and the second downstream of transcriptionally active Pcdhα promoters. Both CTCF and Rad21 bind to these sites in vitro and in vivo, this binding directly correlates with alternative isoform expression, and knocking down CTCF expression reduces alternative isoform expression. Remarkably, a similarly spaced pair of CTCF/Rad21 binding sites was identified within a distant enhancer element (HS5-1), which is required for normal levels of alternative isoform expression. We also identify an additional, unique regulatory role for cohesin, as Rad21 binds to another enhancer (HS7) independently of CTCF, and knockdown of Rad21 reduces expression of the constitutive, biallelically expressed Pcdhα isoforms αc1 and αc2. We propose that CTCF and the cohesin complex initiate and maintain Pcdhα promoter choice by mediating interactions between Pcdhα promoters and enhancers.

Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation.

The glucocorticoid steroid hormone cortisol is released by the adrenal glands in response to stress and serves as a messenger in circadian rhythms. Transcriptional responses to this hormonal signal are mediated by the glucocorticoid receptor (GR). We determined GR binding throughout the human genome by using chromatin immunoprecipitation followed by next-generation DNA sequencing, and measured related changes in gene expression with mRNA sequencing in response to the glucocorticoid dexamethasone (DEX). We identified 4392 genomic positions occupied by the GR and 234 genes with significant changes in expression in response to DEX. This genomic census revealed striking differences between gene activation and repression by the GR. While genes activated with DEX treatment have GR bound within a median distance of 11 kb from the transcriptional start site (TSS), the nearest GR binding for genes repressed with DEX treatment is a median of 146 kb from the TSS, suggesting that DEX-mediated repression occurs independently of promoter-proximal GR binding. In addition to the dramatic differences in proximity of GR binding, we found differences in the kinetics of gene expression response for induced and repressed genes, with repression occurring substantially after induction. We also found that the GR can respond to different levels of corticosteroids in a gene-specific manner. For example, low doses of DEX selectively induced PER1, a transcription factor involved in regulating circadian rhythms. Overall, the genome-wide determination and analysis of GR:DNA binding and transcriptional response to hormone reveals new insights into the complexities of gene regulatory activities managed by GR.

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.

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.

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.

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.