Subnucleosomal structures and nucleosome asymmetry across a genome.

Genes are packaged into nucleosomal arrays, each nucleosome typically having two copies of histones H2A, H2B, H3, and H4. Histones have distinct posttranslational modifications, variant isoforms, and dynamics. Whether each histone copy within a nucleosome has distinct properties, particularly in relation to the direction of transcription, is unknown. Here we use chromatin immunoprecipitation-exonuclease (ChIP-exo) to resolve the organization of individual histones on a genomic scale. We detect widespread subnucleosomal structures in dynamic chromatin, including what appear to be half-nucleosomes consisting of one copy of each histone. We also detect interactions of H3 tails with linker DNA between nucleosomes, which may be negatively regulated by methylation of H3K36. Histone variant H2A.Z is enriched on the promoter-distal half of the +1 nucleosome, whereas H2BK123 ubiquitylation and H3K9 acetylation are enriched on the promoter-proximal half in a transcription-linked manner. Subnucleosome asymmetries might serve as molecular beacons that guide transcription.

Phylogenomics Reveals High Levels of Incomplete Lineage Sorting at the Ancestral Nodes of the Macaque Radiation.

The genus Macaca includes 23 species assigned into 4 to 7 groups. It exhibits the largest geographic range and represents the most successful example of adaptive radiation of nonhuman primates. However, intrageneric phylogenetic relationships among species remain controversial and have not been resolved so far. In this study, we conducted a phylogenomic analysis on 16 newly generated and 8 published macaque genomes. We found strong evidence supporting the division of this genus into 7 species groups. Incomplete lineage sorting (ILS) was the primary factor contributing to the discordance observed among gene trees; however, we also found evidence of hybridization events, specifically between the ancestral arctoides/sinica and silenus/nigra lineages that resulted in the hybrid formation of the fascicularis/mulatta group. Combined with fossil data, our phylogenomic data were used to establish a scenario for macaque radiation. These findings provide insights into ILS and potential ancient introgression events that were involved in the radiation of macaques, which will lead to a better understanding of the rapid speciation occurring in nonhuman primates.

Cancer-associated dynamics and potential regulators of intronic polyadenylation revealed by IPAFinder using standard RNA-seq data.

Intronic polyadenylation (IpA) usually leads to changes in the coding region of an mRNA, and its implication in diseases has been recognized, although at its very beginning status. Conveniently and accurately identifying IpA is of great importance for further evaluating its biological significance. Here, we developed IPAFinder, a bioinformatic method for the de novo identification of intronic poly(A) sites and their dynamic changes from standard RNA-seq data. Applying IPAFinder to 256 pan-cancer tumor/normal pairs across six tumor types, we discovered 490 recurrent dynamically changed IpA events, some of which are novel and derived from cancer-associated genes such as TSC1, SPERD2, and CCND2 Furthermore, IPAFinder revealed that IpA could be regulated by factors related to splicing and m6A modification. In summary, IPAFinder enables the global discovery and characterization of biologically regulated IpA with standard RNA-seq data and should reveal the biological significance of IpA in various processes.

Antisense Transcripts Delimit Exonucleolytic Activity of the Mitochondrial 3' Processome to Generate Guide RNAs.

Small, noncoding RNA biogenesis typically involves cleavage of structured precursor by RNase III-like endonucleases. However, guide RNAs (gRNAs) that direct U-insertion/deletion mRNA editing in mitochondria of trypanosomes maintain 5' triphosphate characteristic of the transcription initiation and possess a U-tail indicative of 3' processing and uridylation. Here, we identified a protein complex composed of RET1 TUTase, DSS1 3'-5' exonuclease, and three additional subunits. This complex, termed mitochondrial 3' processome (MPsome), is responsible for primary uridylation of ∼800 nt gRNA precursors, their processive degradation to a mature size of 40-60 nt, and secondary U-tail addition. Both strands of the gRNA gene are transcribed into sense and antisense precursors of similar lengths. Head-to-head hybridization of these transcripts blocks symmetrical 3'-5' degradation at a fixed distance from the double-stranded region. Together, our findings suggest a model in which gRNA is derived from the 5' extremity of a primary molecule by uridylation-induced, antisense transcription-controlled 3'-5' exonucleolytic degradation.

Occludin protects secretory cells from ER stress by facilitating SNARE-dependent apical protein exocytosis.

Tight junctions (TJs) are fundamental features of both epithelium and endothelium and are indispensable for vertebrate organ formation and homeostasis. However, mice lacking Occludin (Ocln) develop relatively normally to term. Here we show that Ocln is essential for mammary gland physiology, as mutant mice fail to produce milk. Surprisingly, Ocln null mammary glands showed intact TJ function and normal epithelial morphogenesis, cell differentiation, and tissue polarity, suggesting that Ocln is not required for these processes. Using single-cell transcriptomics, we identified milk-producing cells (MPCs) and found they were progressively more prone to endoplasmic reticulum (ER) stress as protein production increased exponentially during late pregnancy and lactation. Importantly, Ocln loss in MPCs resulted in greatly heightened ER stress; this in turn led to increased apoptosis and acute shutdown of protein expression, ultimately leading to lactation failure in the mutant mice. We show that the increased ER stress was caused by a secretory failure of milk proteins in Ocln null cells. Consistent with an essential role in protein secretion, Occludin was seen to reside on secretory vesicles and to be bound to SNARE proteins. Taken together, our results demonstrate that Ocln protects MPCs from ER stress by facilitating SNARE-dependent protein secretion and raise the possibility that other TJ components may participate in functions similar to Ocln.

Extending Ag Nanoparticles as Colorimetric Sensor to Industrial Zinc Electrolyte for Cobalt Ion Detection.

The direct and rapid determination of trace cobalt ion (Co2+) in the electrolyte of zinc smelting plants is urgently needed but is impeded by the severe interference of extremely high-concentration zinc ions in the solution. Herein, colorimetric detection of Co2+ by the polyvinylpyrrolidone functionalized silver nanoparticles (PVP-AgNPs) is realized in solutions with the Zn/Co ratio being high, up to (0.8-5) × 104, which is located within the ratio range in industrial solution. The high concentration of Zn2+ induces a strong attenuation of Co2+-related signals in ultraviolet-visible (UV-vis) extinction spectra; nevertheless, a good linear range for detecting 1-6 mg/L Co2+ in 50 g/L Zn2+ solution is still acquired. The strong anti-interference toward other metal ions and the mechanism understanding for trace Co2+ detection in such a high-concentration Zn2+ solution are also revealed by systematic analysis techniques. The results extend the AgNPs as colorimetric sensors to industrial solutions, providing a new strategy for detecting trace-metal ions in industrial plants.

Joint analysis of scATAC-seq datasets using epiConv.

BACKGROUND: Technical improvement in ATAC-seq makes it possible for high throughput profiling the chromatin states of single cells. However, data from multiple sources frequently show strong technical variations, which is referred to as batch effects. In order to perform joint analysis across multiple datasets, specialized method is required to remove technical variations between datasets while keep biological information. RESULTS: Here we present an algorithm named epiConv to perform joint analyses on scATAC-seq datasets. We first show that epiConv better corrects batch effects and is less prone to over-fitting problem than existing methods on a collection of PBMC datasets. In a collection of mouse brain data, we show that epiConv is capable of aligning low-depth scATAC-Seq from co-assay data (simultaneous profiling of transcriptome and chromatin) onto high-quality ATAC-seq reference and increasing the resolution of chromatin profiles of co-assay data. Finally, we show that epiConv can be used to integrate cells from different biological conditions (T cells in normal vs. germ-free mouse; normal vs. malignant hematopoiesis), which reveals hidden cell populations that would otherwise be undetectable. CONCLUSIONS: In this study, we introduce epiConv to integrate multiple scATAC-seq datasets and perform joint analysis on them. Through several case studies, we show that epiConv removes the batch effects and retains the biological signal. Moreover, joint analysis across multiple datasets improves the performance of clustering and differentially accessible peak calling, especially when the biological signal is weak in single dataset.

Network regression analysis in transcriptome-wide association studies.

BACKGROUND: Transcriptome-wide association studies (TWASs) have shown great promise in interpreting the findings from genome-wide association studies (GWASs) and exploring the disease mechanisms, by integrating GWAS and eQTL mapping studies. Almost all TWAS methods only focus on one gene at a time, with exception of only two published multiple-gene methods nevertheless failing to account for the inter-dependence as well as the network structure among multiple genes, which may lead to power loss in TWAS analysis as complex disease often owe to multiple genes that interact with each other as a biological network. We therefore developed a Network Regression method in a two-stage TWAS framework (NeRiT) to detect whether a given network is associated with the traits of interest. NeRiT adopts the flexible Bayesian Dirichlet process regression to obtain the gene expression prediction weights in the first stage, uses pointwise mutual information to represent the general between-node correlation in the second stage and can effectively take the network structure among different gene nodes into account. RESULTS: Comprehensive and realistic simulations indicated NeRiT had calibrated type I error control for testing both the node effect and edge effect, and yields higher power than the existed methods, especially in testing the edge effect. The results were consistent regardless of the GWAS sample size, the gene expression prediction model in the first step of TWAS, the network structure as well as the correlation pattern among different gene nodes. Real data applications through analyzing systolic blood pressure and diastolic blood pressure from UK Biobank showed that NeRiT can simultaneously identify the trait-related nodes as well as the trait-related edges. CONCLUSIONS: NeRiT is a powerful and efficient network regression method in TWAS.

Characterization of the evolution trajectory and immune profiling of new histologic patterns in lung adenocarcinoma.

In lung adenocarcinoma (LUAD), the appearance of morphologically diverse tumor regions, termed histological patterns, is closely associated with disease progression and lymph node metastasis. However, the molecular characteristics of the histological patterns in LUAD and the underlying molecular evolutionary mechanisms between the histological patterns in primary tumors and lymph node metastases are poorly understood. Here, we re-analyzed the large TCGA-LUAD dataset and depicted a comprehensive profiling of the genome and transcriptome across the histological patterns in LUAD. Tumor phylogenetic trajectory analysis suggested that the complex glands is more apt to metastasize to the lymph node. Further deconvolution of the tumor microenvironment demonstrated that the complex glands had a higher infiltration of cancer-associated fibroblasts (CAFs). Single-cell transcriptome profiling of complex glands pattern identified a novel CAF subtype co-expressing fibroblast activation protein-alpha (FAP) and stimulator of interferon genes (STING). Moreover, our data demonstrated that FAP is an important downstream effector of STING in CAFs. In summary, our results provide the basis for the development of innovative therapeutic guidelines and intervention strategies for LUAD patients.

NeiyiKangfu tablets control the progression of endometriosis through inhibiting RAF/MEK/ERK signal pathway by targeting RKIP.

BACKGROUND: NeiyiKangfu tablets (NYKF) are widely used clinically for the treatment of endometriosis (EMS), whose mechanism of action has been extensively studied. Researchers have found that NYKF may control the development of ectopic lesions by inhibiting angiogenesis and inflammatory cytokine secretion. Nevertheless, NYKF's mechanism of action remains unclear. METHODS: In the present study, the function of NYKF in the progression of EMS and the associated underlying mechanism was investigated by in vivo and in vitro experiments. EMS model mice were treated with NYKF and the pro-inflammatory factors and apoptosis of ectopic endometrium as well as RAF/mitogen-activated protein kinase kinase (MEK)/extracellular signal-regulated kinase (ERK) signaling activation were assessed. In addition, human endometriosis-derived immortalized entopic stromal (hEM15A) cells transfected with or without RAF kinase inhibitor protein (RKIP)-small-interfering RNA (siRNA) were also treated with NYKF and the proliferation, migration, apoptosis, and RAF/MEK/ERK signaling activation were measured by Cell Counting Kit-8 (CCK-8), flow cytometry, Transwell, and western blot, respectively. RESULTS: Results showed that NYKF increased the expression of RKIP, inhibited RAF/MEK/ERK signaling activation, and induced apoptosis while inhibiting proliferation and migration both in EMS mice and hEM15A cells. RKIP knockdown could inhibit the effect of NYKF treatment, leading to the activation of RAF/MEK/ERK signaling and the proliferation and migration of hEM15A cells. CONCLUSIONS: In conclusion, these results suggest that NYKF treatment promotes apoptosis and inhibits proliferation and migration in EMS by inhibiting the RAF/MEK/ERK signaling pathway by targeting RKIP.

Poly(A) binding KPAF4/5 complex stabilizes kinetoplast mRNAs in Trypanosoma brucei.

In Trypanosoma brucei, mitochondrial pre-mRNAs undergo 3'-5' exonucleolytic processing, 3' adenylation and uridylation, 5' pyrophosphate removal, and, often, U-insertion/deletion editing. The 3' modifications are modulated by pentatricopeptide repeat (PPR) Kinetoplast Polyadenylation Factors (KPAFs). We have shown that KPAF3 binding to the 3' region stabilizes properly trimmed transcripts and stimulates their A-tailing by KPAP1 poly(A) polymerase. Conversely, poly(A) binding KPAF4 shields the nascent A-tail from uridylation and decay thereby protecting pre-mRNA upon KPAF3 displacement by editing. While editing concludes in the 5' region, KPAF1/2 dimer induces A/U-tailing to activate translation. Remarkably, 5' end recognition and pyrophosphate hydrolysis by the PPsome complex also contribute to mRNA stabilization. Here, we demonstrate that KPAF4 functions as a heterodimer with KPAF5, a protein lacking discernable motifs. We show that KPAF5 stabilizes KPAF4 to enable poly(A) tail recognition, which likely leads to mRNA stabilization during the editing process and impedes spontaneous translational activation of partially-edited transcripts. Thus, KPAF4/5 represents a poly(A) binding element of the mitochondrial polyadenylation complex. We present evidence that RNA editing substrate binding complex bridges the 5' end-bound PPsome and 3' end-bound polyadenylation complexes. This interaction may enable mRNA circularization, an apparently critical element of mitochondrial mRNA stability and quality control.

CDK7 inhibition suppresses aberrant hedgehog pathway and overcomes resistance to smoothened antagonists.

The aberrant hedgehog (Hh) pathway plays important roles in multiple cancer types, therefore serving as a promising drug target. Current clinically available hedgehog-targeted drugs act mostly by antagonizing the upstream component smoothened; however, both primary and acquired resistance to FDA-approved smoothened inhibitor (SMOi) drugs have been described. We have recently demonstrated that the BET inhibitor effectively suppresses SMOi-resistant Hh-driven cancers through antagonizing transcription of GLI1 and GLI2, the core transcriptional factors of Hh pathway, suggesting epigenetic or transcriptional targeted therapy represents an anti-Hh therapeutic strategy that can overcome SMOi resistance. Here we performed an unbiased screening of epigenetic or transcriptional targeted small molecules to test their inhibitory effects on GLI1 and GLI2 transcription or cell viability of Hh-driven tumor lines. THZ1, a covalent inhibitor of cyclin-dependent kinase 7 (CDK7), is identified as the top hit in our screening. We then confirmed that antagonizing CDK7 by either small-molecule inhibitors or the CRISPR-Cas9 approach causes substantial suppression of GLI1 and GLI2 transcription, resulting in effective inhibition of Hh-driven cancers in vitro and in vivo. More importantly, antagonizing CDK7 retains inhibitory activity against Hh-driven cancers with almost all so-far described primary or acquired SMOi resistance. Furthermore, we reveal a synergy between CDK7 inhibition and BET inhibition on antagonizing aberrant Hh pathway and Hh-driven cancers that are either responsive or resistant to SMOi. Our results illustrate transcriptional inhibition through targeting CDK7 as a promising therapeutic strategy for treating Hh-driven cancers, especially those with primary or acquired resistance to SMOi drugs.

PRAGAN: Progressive Recurrent Attention GAN with Pretrained ViT Discriminator for Single-Image Deraining.

Images captured in bad weather are not conducive to visual tasks. Rain streaks in rainy images will significantly affect the regular operation of imaging equipment; to solve this problem, using multiple neural networks is a trend. The ingenious integration of network structures allows for full use of the powerful representation and fitting abilities of deep learning to complete low-level visual tasks. In this study, we propose a generative adversarial network (GAN) with multiple attention mechanisms for image rain removal tasks. Firstly, to the best of our knowledge, we propose a pretrained vision transformer (ViT) as the discriminator in GAN for single-image rain removal for the first time. Secondly, we propose a neural network training method that can use a small amount of data for training while maintaining promising results and reliable visual quality. A large number of experiments prove the correctness and effectiveness of our method. Our proposed method achieves better results on synthetic and real image datasets than multiple state-of-the-art methods, even when using less training data.

Joint Estimation for Time Delay and Direction of Arrival in Reconfigurable Intelligent Surface with OFDM.

Recently, the joint estimation for time delay (TD) and direction of arrival (DOA) has suffered from the high complexity of processing multi-dimensional signal models and the ineffectiveness of correlated/coherent signals. In order to improve this situation, a joint estimation method using orthogonal frequency division multiplexing (OFDM) and a uniform planar array composed of reconfigurable intelligent surface (RIS) is proposed. First, the time-domain coding function of the RIS is combined with the multi-carrier characteristic of the OFDM signal to construct the coded channel frequency response in tensor form. Then, the coded channel frequency response covariance matrix is decomposed by CANDECOMP/PARAFAC (CPD) to separate the signal subspaces of TD and DOA. Finally, we perform a one-dimensional (1D) spectral search for TD values and a two-dimensional (2D) spectral search for DOA values. Compared to previous efforts, this algorithm not only enhances the adaptability of coherent signals, but also greatly decreases the complexity. Simulation results indicate the robustness and effectiveness for the proposed algorithm in independent, coherent, and mixed multipath environments and low signal-to-noise ratio (SNR) conditions.

Spatiotemporal evolving patterns of bike-share mobility networks and their associations with land-use conditions before and after the COVID-19 outbreak.

Recent months have seen ever-increasing levels of confirmed COVID-19 cases despite the accelerated adoption of vaccines. In the wake of the pandemic, travel patterns of individuals change as well. Understanding the changes in biking behaviors during evolving COVID-19 situations is a primary goal of this paper. It investigated usage patterns of the bike-share system in Singapore before, during, and after local authorities imposed lockdown measures. It also correlated the centrality attributes of biking mobility networks of different timestamps with land-use conditions. The results show that total ridership surprisingly climbed by 150% during the lockdown, compared with the pre-pandemic level. Biking mobility graphs became more locally clustered and polycentric as the epidemic develop. There existed a positive and sustained spatial autocorrelation between centrality measures and regions with high residential densities or levels of the land-use mixture. This study suggests that bike-share systems may serve as an alternative mode to fulfill mobility needs when public transit services are restricted due to lockdown policies. Shared-micromobility services have the potential to facilitate a disease-resilient transport system as societies may have to coexist with COVID in the future.

Genomic Mechanisms of Physiological and Morphological Adaptations of Limestone Langurs to Karst Habitats.

Knowledge of the physiological and morphological evolution and adaptation of nonhuman primates is critical to understand hominin origins, physiological ecology, morphological evolution, and applications in biomedicine. Particularly, limestone langurs represent a direct example of adaptations to the challenges of exploiting a high calcium and harsh environment. Here, we report a de novo genome assembly (Tfra_2.0) of a male François's langur (Trachypithecus francoisi) with contig N50 of 16.3 Mb and resequencing data of 23 individuals representing five limestone and four forest langur species. Comparative genomics reveals evidence for functional evolution in genes and gene families related to calcium signaling in the limestone langur genome, probably as an adaptation to naturally occurring high calcium levels present in water and plant resources in karst habitats. The genomic and functional analyses suggest that a single point mutation (Lys1905Arg) in the α1c subunit of the L-type voltage-gated calcium channel Cav1.2 (CACNA1C) attenuates the inward calcium current into the cells in vitro. Population genomic analyses and RNA-sequencing indicate that EDNRB is less expressed in white tail hair follicles of the white-headed langur (T. leucocephalus) compared with the black-colored François's langur and hence might be responsible for species-specific differences in body coloration. Our findings contribute to a new understanding of gene-environment interactions and physiomorphological adaptative mechanisms in ecologically specialized primate taxa.

PPR polyadenylation factor defines mitochondrial mRNA identity and stability in trypanosomes.

In Trypanosoma brucei, most mitochondrial mRNAs undergo internal changes by RNA editing and 3' end modifications. The temporally separated and functionally distinct modifications are manifested by adenylation prior to editing, and by post-editing extension of a short A-tail into a long A/U-heteropolymer. The A-tail stabilizes partially and fully edited mRNAs, while the A/U-tail enables mRNA binding to the ribosome. Here, we identify an essential pentatricopeptide repeat-containing RNA binding protein, kinetoplast polyadenylation factor 3 (KPAF3), and demonstrate its role in protecting pre-mRNA against degradation by the processome. We show that KPAF3 recruits KPAP1 poly(A) polymerase to the 3' terminus, thus leading to pre-mRNA stabilization, or decay depending on the occurrence and extent of editing. In vitro, KPAF3 stimulates KPAP1 activity and inhibits mRNA uridylation by RET1 TUTase. Our findings indicate that KPAF3 selectively directs pre-mRNA toward adenylation rather than uridylation, which is a default post-trimming modification characteristic of ribosomal and guide RNAs. As a quality control mechanism, KPAF3 binding ensures that mRNAs entering the editing pathway are adenylated and, therefore, competent for post-editing A/U-tailing and translational activation.

A proximity-tagging system to identify membrane protein-protein interactions.

The communication between cells and between cellular organelles is often controlled by the interaction of membrane proteins. Although many methods for the detection of protein-protein interactions (PPIs) exist, membrane PPIs remain difficult to detect. Here we developed a proximity-based tagging system, PUP-IT (pupylation-based interaction tagging), to identify membrane protein interactions. In this approach, a small protein tag, Pup, is applied to proteins that interact with a PafA-fused bait, enabling transient and weak interactions to be enriched and detected by mass spectrometry. Pup does not diffuse from the enzyme, which allows high-specificity labeling. We applied this approach to CD28, a critical costimulatory receptor for T lymphocyte activation, and identified known CD28 binding partners and multiple potential interacting proteins. In addition, we demonstrated that this method can identify the interaction between a cell surface receptor and its ligand.

Association between birth weight and risk of cardiovascular disease: Evidence from UK Biobank.

BACKGROUND AND AIMS: Birth weight has been linked to cardiovascular disease (CVD) risk in adulthood, but no consensus has emerged on the threshold of birth weight for the lowest CVD risk and few studies have examined potential interaction between birth weight and adult adiposity. METHODS AND RESULTS: A total of 256,787 participants, who had birth weight data and were free of CVD at baseline, were included from UK Biobank. Multivariate restricted cubic splines and Cox regression models were used to assess the association between birth weight and CVD. We observed nonlinear inverse associations of birth weight with the risk of coronary heart disease (CHD), stroke, and heart failure. Participants with the first quintile of birth weight (≤2.85 kg) had higher risks for CHD (hazard ratio [HR] = 1.23, 95% confidence interval [CI]: 1.15-1.32), stroke (HR = 1.19, 95% CI: 1.03-1.37), and heart failure (HR = 1.28, 95% CI: 1.11-1.48), as compared to the fourth quintile (3.41-3.79 kg). There was a significant interaction between birth weight and adult body mass index (BMI) on CHD and heart failure (both P for interaction <0.001), showing the highest risk for those who had birth weight ≤2.85 kg and BMI ≥30 kg/m2 (HR = 1.96, 95% CI: 1.70-2.25 and HR = 2.39, 95% CI: 1.77-3.22, respectively). CONCLUSIONS: Our findings indicate nonlinear inverse associations between birth weight and CVD risk, with a threshold of 3.41-3.79 kg for the lowest risk. Moreover, low birth weight may interact with adult obesity to increase the risk of CHD and heart failure.

Enhancer Reprogramming within Pre-existing Topologically Associated Domains Promotes TGF-ß-Induced EMT and Cancer Metastasis.

Transcription growth factor ß (TGF-ß) signaling-triggered epithelial-to-mesenchymal transition (EMT) process is associated with tumor stemness, metastasis, and chemotherapy resistance. However, the epigenomic basis for TGF-ß-induced EMT remains largely unknown. Here we reveal that HDAC1-mediated global histone deacetylation and the gain of specific histone H3 lysine 27 acetylation (H3K27ac)-marked enhancers are essential for the TGF-ß-induced EMT process. Enhancers gained upon TGF-ß treatment are linked to gene activation of EMT markers and cancer metastasis. Notably, dynamic enhancer gain or loss mainly occurs within pre-existing topologically associated domains (TADs) in epithelial cells, with minimal three-dimensional (3D) genome architecture reorganization. Through motif enrichment analysis of enhancers that are lost or gained upon TGF-ß stimulation, we identify FOXA2 as a key factor to activate epithelial-specific enhancer activity, and we also find that TEAD4 forms a complex with SMAD2/3 to mediate TGF-ß signaling-triggered mesenchymal enhancer reprogramming. Together, our results implicate that key transcription-factor (TF)-mediated enhancer reprogramming modulates the developmental transition in TGF-ß signaling-associated cancer metastasis.