Nucleus

Existing databases of interphase chromosome conformations typically store three-dimensional coordinates of genomic segments. However, since interphase chromatin is highly dynamic, such databases are dominated by transient configurations and unstructured regions, whose positions vary continuously between cells and over time, unlike folded proteins such as globin, which adopt similar structures in every cell. These drawbacks motivated the inception of a database based on strion (a portmanteau of a string capturing structure and function). A strion concisely describes the structure and activity of all transcription units in one cell, by retaining only functionally relevant positional information. Sets of strions describing structures in different cells sampled at different times are compiled into a super-strion. Then, 46 super-strions summarise the range of structure and activity of a human cell type, including information on all transcription units, how often each co-fires and co-clusters with others in transcription factories/hubs, enhancer interactomes and small-world expression networks. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/724942v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@13a1263org.highwire.dtl.DTLVardef@18d2c78org.highwire.dtl.DTLVardef@162865corg.highwire.dtl.DTLVardef@1631d65_HPS_FORMAT_FIGEXP M_FIG C_FIG

Centromeric chromatin is defined by the presence of the histone H3 variant CENP-A, which forms a specialized nucleosome required for kinetochore assembly. Compared to canonical H3 nucleosomes, CENP-A nucleosomes exhibit an open DNA conformation that leaves an additional 13 base pairs of DNA accessible at the entry and exit sites. While the CENP-A N-helix has previously been implicated in promoting this enhanced DNA breathing, the contributions of the intrinsically disordered N-terminal tail and adjacent latch regions of CENP-A in nucleosome conformation remain unknown. The intrinsically disordered N-terminal regions of histone H3 are known to facilitate interactions with DNA to stabilize overall nucleosome conformation. Here, we systematically tested the contribution of each N-terminal histone region to maintaining H3 histones by utilizing a combination of MNase digestion assays and coarse-grained molecular dynamics simulations of H3/CENP-A chimera histone nucleosomes containing targeted swaps of the tail, latch, and N-helix regions. Removal or substitution of individual H3 with CENP-A N-terminal regions increased DNA accessibility and nucleosome unwrapping. While any single CENP-A N-terminal region was sufficient to open the canonical nucleosomal DNA conformation, replacement of any single CENP-A N-terminal region with its H3 counterpart was insufficient to restore the wrapped DNA conformation characteristic of canonical H3 nucleosomes. Instead, progressive incorporation of multiple H3-derived regions produced increasingly closed DNA conformations, demonstrating that the H3 tail, latch, and N-helices act cooperatively to stabilize wrapped nucleosomal DNA. Taken together, these findings demonstrate that the more restricted DNA breathing of canonical nucleosomes arises from coordinated contributions across multiple N-terminal regions and suggest that the multi-region redundancy in the conformational flexibility of the centromeric nucleosome could emphasize the importance of retaining flexibility in the centromeric nucleosome, even upon post-translational modification and binding to structural proteins. SIGNIFICANCEThe centromere is marked by nucleosomes containing CENP-A, which adopt a more open and accessible DNA conformation than canonical nucleosomes. However, the molecular determinants underlying this difference remain unclear. Previous structural investigations of the centromeric nucleosome have placed less emphasis on the intrinsically disordered N-terminal regions of CENP-A. Here, we systematically dissect the contributions of the N-terminal tail, latch, and N-helix via MNase digestion assays and molecular dynamics simulations on nucleosomes containing H3/CENP-A chimeras. We demonstrate that no individual H3-derived region is sufficient to impart a closed conformation to the nucleosomal DNA. Instead, multiple regions act together to stabilize DNA, revealing that nucleosome conformation is controlled by concerted histone-DNA interactions.

Citrullination is a charge-modifying post-translational modification whereby proteinogenic arginine is converted to the non-coded amino acid citrulline by calcium-activated protein arginine deiminases (PADs; EC 3.5.3.15). The five known PAD enzymes in humans (PADs 1, 2, 3, 4, and 6) are differentially expressed and have distinct targets, including histones. While some PAD histone citrullination sites are known, a comprehensive investigation of all histone tail arginines targeted by catalytically active PADs 1-4 is lacking. Here, we sought to identify PAD citrullination sites in histone tails, both within histone peptides and in reconstituted nucleosomes. Toward this objective, we utilized a real-time 1H-15N NMR spectroscopy-based assay. By monitoring both arginine and citrulline backbone amide peak intensities over time, we identified sites of citrullination in 15N-labeled histone tails within peptides and reconstituted nucleosome core particles. We found that PADs 1, 2, and 4 citrullinate all directly observable histone tail arginines to varying degrees. This is distinct from PAD3, which only moderately citrullinates H2A and H4 arginine residues and does not modify H3 tail arginines. Together, these data suggest a level of histone arginine specificity by each PAD. Furthermore, histone tail citrullination is altered within nucleosomes compared to isolated peptides, which we interpret to reflect changes in conformation and accessibility. We speculate that citrullination increases nucleosomal histone tail dynamics, with implications for crosstalk between sites of histone citrullination and other important sites of regulation by PTMs (including lysines) within and between tails.

Abnormalities in nuclear morphology are an important diagnostic tool to determine malignancy in cancer cells and are characterised by nuclear blebbing and deformations. Nuclear shape is mostly maintained by a dense protein meshwork of lamins, consisting of 4 lamin subtypes, of which the individual contribution to nuclear shape maintenance remains elusive. In this study, we decouple the roles of lamin A, C, and B1 across cancer cell lines with varying malignant potential (HeLa, HT1080, and MDA-MB-231). Using single-cell correlation analysis, we directly link reduced lamin A/C, and not lamin B1, expression levels to nuclear deformability. We found that the nuclear shape of the more malignant MDA-MB-231 cells is approximately 4-fold more sensitive to lamin A/C than HeLa and HT1080 cells. Biochemical analyses reveal cell-type-specific variation in lamin A/C interactions and homodimer formation that correlates with nuclear shape deformations. In contrast to healthy mouse embryonic fibroblast cells, malignant cells exhibit reduced dimerisation, which correlates with nuclear deformability. As such, our study links, for the first time, the lamin A/C dimerisation state to nuclear abnormalities, thereby providing new avenues for investigating cancer progression.

Genomic organization within the nucleus is crucial for gene regulation and cell health, as disruptions in this organization are linked to genetic disorders and cancers. Recent studies suggest that molecular-scale organization of chromatin near the nuclear periphery (lamina-associated domains, LADs) affects gene regulation, providing transciptional supression, but the biophysical mechanisms of supression behind remain unclear. LADs are large heterochromatic regions near the nuclear lamina, where transcriptional factors and RNA polymerase are scarce, implying a nonspecific filtering property. Here, we investigate the steric filtering capabilities of LADs by performing coarse-grained polymer simulations. Our results show that LAD thickness can be affected by the interaction between chromatin and nuclear periphery as well as chromatin self-compaction. Regardless, the LAD layer acts as a size-selective steric partitioning environment for protein particles limiting their access to nuclear periphery. Notably, increasing bulk protein levels enhances protein access linearly. These results align with experimental observations and suggest that LADs could control the presence of transcription machinery on the periphery of the nucleus, providing a polymer-physical mechanism for gene regulation in nuclei.

Understanding cis-regulatory elements (CREs) at the single cell level is fundamental to deciphering transcriptional changes during development, cell differentiation, and homeostasis. Recent studies have shown that arbitrary peak-calling thresholds complicate data interpretation and cross-study comparisons. Furthermore, due to the inherent sparsity of single-nuclei ATAC-seq (snATAC-seq) data, distinguishing between truly inaccessible regions and technical dropouts remains challenging. Our analysis of snATAC-seq experiments performed in a well-established cell line suggests that the dichotomy between accessible (open) or inaccessible (close) CREs is misleading. Thousands of accessible regions are present in a very small fraction of cells of the population but they are repeatedly identified, suggesting that they have a low accessibility or are only transiently accessible. However, depending on the detection threshold selected they could be considered as either genuine CREs or noise. To resolve this inconsistency, we propose a model where chromatin accessibility is treated as a continuum, defined by a probability of accessibility (Pa) for each accessible region across cell types and conditions. Through computational simulations, we demonstrate that snATAC-seq results can be explained by a simple "balls into bins" probability model, offering a theoretical framework for calculating Pa distributions from any snATAC-seq dataset. Furthermore, we examine how Pa distributions shift following activation of the TGF{beta} signaling pathway. This probabilistic approach removes the reliance on arbitrary thresholds and supports a more quantitative, and dynamic understanding of accessible regions function.

Pancreatic ductal adenocarcinoma (PDA) arises from distinct precursor lesions with different clinical outcomes, yet the mechanisms linking epigenetic regulation to invasive cell behavior remain poorly understood. Here, we investigate how the chromatin remodeler Brg1 influences the dynamic properties of cancer cell migration. Using a biomimetic supported membrane system combined with label-free interferometric imaging, we quantitatively analyze the spatiotemporal dynamics of PDA cells derived from pancreatic intraepithelial neoplasia (PanIN) and intraductal papillary mucinous neoplasms (IPMN). Despite their similar morphology under conventional conditions, PanIN- and IPMN-derived PDA cells exhibit markedly different migration behaviors. PanIN-derived cells migrate faster and display enhanced dynamic remodeling, whereas IPMN-derived cells show persistent elongation with limited displacement. These differences are captured by quantitative analyses of cell trajectories and deformation dynamics. Mechanistically, PanIN-derived PDA cells exhibit elevated Rac1 activity, supporting a model in which a Brg1-Rac1 axis regulates cytoskeletal dynamics and migration behavior. Together, our findings demonstrate that epigenetic regulation is linked to distinct dynamic phenotypes of cancer cells and highlight the importance of quantitative analysis of cell behavior for understanding invasive potential.

Genomic DNA is subject to forces and torsion. Some arise mechanically, while others can be entropic, such as those due to crowding within the nuclear environment. Indeed, about 30-40% of the cell is occupied by molecules other than water, and of these, the vast majority are macromolecules. Here, we explore both experimentally and theoretically the interplay between tension, torsion, and macromolecular crowding. Using pharmaceutically relevant crowders of different molecular weights, Dextran 70, and polyethylene glycol (PEG), we observed that macromolecular crowding of unwound, stretched DNA effectively opposed the tension and promoted the formation of plectonemes. A theoretical model representing the equilibrium between B- and L-form DNA fit to the experimental measurements indicates the contractile tension produced by macromolecular crowding of DNA. SIGNIFICANCE STATEMENTDistinct DNA conformers are involved in different cellular processes. Genomic DNA is both stretched and unwound by enzymes in a crowded intracellular medium. This can induce conformational changes between extended, twisted and more compact, plectonemic forms. This study explores the effect of macro-molecular crowding on the conformations of DNA subject to tension and torque. Fitting experimental data to a model for the right-to-left-handed DNA transition, we show that macromolecular crowding induces a contractile force that favors DNA writhe and that such force depends both on the concentration and molecular weight of the crowder.

Structural Maintenance Complexes (SMC) are energy consuming motors that are important in folding the genome by loop extrusion (LE) in all stages of the cell cycle. Single molecule magnetic tweezer pulling experiments have revealed that condensin, a member of the SMC family involved in mitosis, takes occasional backward steps, thus coughing up the gains in the length of the extruded loop. To reveal the mechanism of the forward and backward steps simultaneously, we developed a theory using the stochastic kinetic model and the scrunching mechanism for LE. The calculations quantitatively account for the measured force-dependent step size and dwell time distributions in both the directions. By postulating the existence of an intermediate state in the ATP-driven cycle that is poised to take a forward or a backward step, we predict that its lifetime increases as the external mechanical force increases till a critical value and subsequently decreases at higher forces. The surprising finding of lifetime increase in an active motor, at sub-piconewton forces, is the characteristic of catch bonds, known in force-induced rupture of several passive protein complexes. The identification of catch bond-like states in condensin not only expands our understanding of LE but also highlights the significance of mechanical forces in regulating genome organization.

Polycomb Repressive Complex 2 (PRC2) maintains repression of genes specific for other cell differentiation states. PRC2 binds RNA in vitro with a preference for G-rich sequences. UV-based crosslinking coupled with immunoprecipitation (CLIP) experiments have shown that PRC2 also binds RNA in cells. Recently, Guo et al reported that a stringent denaturing variant of CLIP called CLAP did not detect PRC2 RNA binding in cells. We present a reanalysis of CLAP data that supports direct interaction of PRC2 with RNA in cells. CLAP for Halo-tagged PRC2 subunits from mixed populations of human and mouse cells specifically enriched for RNA from the species in which the proteins were tagged. The lack of apparent PRC2 RNA binding in Guo and colleagues analysis stems from a scaling step that deflates enrichment scores for low-complexity CLAP samples. Our findings pave the way for studies seeking to determine the physiological roles of PRC2 RNA binding activity.

1Correlations between cellular variables, such as gene-expression levels, provide insights into regulatory mechanisms. We focus here on correlations between mRNA and protein levels and re-examine previously derived analytical predictions. We test this prediction on single-cell E. coli data and see substantial disagreement. We hypothesize that this discrepancy arises from the assumption of constant cell volume and develop a theoretical framework for mRNA-protein correlations in growing and dividing cells. Within this framework, we derive an analytical expression for mRNA- protein correlations and show that explicit incorporation of growth and division substantially alters these correlations. The resulting relation is invariant to upstream transcriptional dynamics, and we validate it using stochastic simulations across multiple gene-regulatory architectures. Finally, we show that the derived predictions are consistent with the E. coli data.

In Caenorhabditis elegans embryos, the nuclear transport receptor IMB-2 (Importin Beta Family-2, a karyopherin {beta}2) preferentially localizes to the nuclear envelope along with its encoding mRNA. This suggests that imb-2 mRNA is locally translated at the nuclear envelope. To test whether imb-2s two putative human orthologs, Transportin 1 (TNPO1) and Transportin 2 (TNPO2), exhibited similar mRNA localization and local translation, we performed smiFISH and microscopy in U2OS, HeLa, and human pluripotent stem cells. Neither human TNPO1 nor TNPO2 mRNA localized to the nuclear envelope in any tested human cell type. However, the human TNPO1 protein and the C. elegans IMB-2 protein both localized to the nucleus and its periphery. This suggests that despite their shared functional roles and high amino acid sequence identities (52% and 51%, respectively), these karyopherins differed in their translational dynamics.

Although calmodulin is best known as an intracellular calcium sensor, it also possesses calcium-independent functions in unicellular organisms. This is exemplified by the budding yeast S. cerevisiae calmodulin, which binds its essential targets, the pericentrin-like protein Spc110 and type I and V myosins, without needing calcium. Whether such calcium-independent cellular functions are conserved in other yeasts and vertebrates nevertheless remains an open question. Here, we examined the calcium-independent functions of the fission yeast S. pombe calmodulin Cam1 by measuring its intracellular distribution. Using quantitative fluorescence microscopy, we assessed the intracellular localization of two cam1 mutants, where binding of Ca2+ had been compromised by mutations in their EF hands, compared to the wild type protein. Both Cam1-2V and -3V reduced their localization by 90% to the yeast microtubule-organizing center spindle pole bodies (SPB). In contrast, these two mutants did not affect the myosin-dependent localization to the equatorial division plane and to the cell tips. Replacing the endogenous cam1 with cam1-2V decreased the SPB localization of pericentrin Pcp1 by 69%, without changing the localization of either type V or I myosins. Over-expression of Pcp1 rescued the mitotic defects of cam1-2V cells at the restrictive temperature. Surprisingly, the cytokinesis of this cam1 mutant was largely normal. We concluded that fission yeast calmodulin Cam1 depends on Ca2+to be a component of SPBs, suggesting that calcium plays a critical role in the assembly of SPBs.

The molecular behavior of viruses within respiratory aerosols plays a critical role in airborne disease transmission yet remains largely inaccessible to experimental characterization. Here, we use a billion-atom all-atom molecular dynamics simulation of a virus-laden respiratory aerosol to uncover how respiratory proteins, lipids, ions, and water collectively assemble around SARS-CoV-2, giving rise to structured microenvironments that influence viral stability and spike dynamics. We find that respiratory components rapidly evolve into heterogeneous networks characterized by protein-rich aggregates, patchy lipid assemblies, and spatially structured ion and water dynamics. These features create distinct microenvironments that constrain molecular transport and stabilize regions surrounding the virion. Within this crowded aerosol context, we observe sustained and selective interactions between aerosol components and the viral spike protein, including preferential recruitment of surfactant lipids and persistent coordination by divalent cations. These interactions modulate spike conformational dynamics, enhancing domain breathing motions and flexibility at key hinge regions while preserving a stable membrane anchor. Together, these observations reveal a condensate-like physical regime in which multivalent aerosol components coalesce into a soft, heterogeneous matrix that selectively modulates viral protein dynamics under extreme crowding. By framing virus-laden respiratory aerosols within this physical context, this work establishes an in situ molecular framework for understanding how aerosols influence viral persistence and offers a platform for exploring mechanisms relevant to airborne disease transmission and mitigation strategies. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/721971v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@4d0f60org.highwire.dtl.DTLVardef@12c9d1forg.highwire.dtl.DTLVardef@1ff6c29org.highwire.dtl.DTLVardef@15feec_HPS_FORMAT_FIGEXP M_FIG C_FIG SynopsisRespiratory aerosols exhibit condensate-like physical properties that govern the evolution of the particle and modulate the behavior of airborne SARS-CoV-2.

The long non-coding RNA NEAT1 is a fundamental architect of nuclear condensates, specifically paraspeckles. While the scaffold-essential isoform NEAT1-2 has been extensively characterized, the function and dynamics of its shorter isoform, NEAT1-1, remain poorly understood. Investigating NEAT1-1 in live cells has been historically hindered by its genomic overlap with NEAT1-2. Traditional visualization study designs require either the genetic ablation of NEAT1-2, which disrupts paraspeckle integrity, or the use of bulky tandem tagging arrays, which can sterically hinder RNA folding and partitioning. Here, we implemented a non-invasive imaging strategy and performed diffusivity analysis of NEAT1-1 using the fluorescence light-up aptamer biRhoBAST. This small, high-affinity RNA tag enables high-contrast visualization of NEAT1-1 while preserving the structural integrity of both isoforms and their associated nuclear bodies. By combining imaging and fluorescence fluctuation spectroscopy, we provide characterization of NEAT1-1 within intact micro-and para-speckles. Our results reveal that NEAT1-1 is not purely sequestered within visible condensates; rather, a fraction exists in a distinct diffusive state within the nucleoplasm, likely as nanoscale complexes. These findings suggest that NEAT1-1 possesses a previously unrecognized regulatory role independent of the primary paraspeckle scaffold, offering new insights into the functional diversity of the lncRNA isoforms.

The eukaryotic ribosomal genes are multi-copy genes, transcribed from the rDNA, and approximately one third of them is actively transcribed in differentiated cells. A number of lncRNAs have been identified from the intergenic spacer between the rRNA genes, among those the spacer RNA and PAPAS that are involved silencing of rRNA gene copies by altering the chromatin configuration. Here, we have identified lncRNAs that are transcribed from the human rDNA loci and modulate the loci; IGS38 positively regulates rRNA gene transcription by associating to the 47S rRNA gene promoter and modulating the rRNA promoter accessibility while IGS32as associates with heterochromatin. IGS38 binds to the 47S gene promoter through the RNA pol I factors TAF1C and RRN3 as well as the Williams Syndrome Transcription Factor (WSTF), a component of the B-WICH chromatin remodelling complex. The increased accessibility of the promoter stabilises the architectural protein Upstream Binding Factor (UBF) at the rRNA promoter, thereby facilitating RNA pol I promoter escape. Furthermore, IGS38 knock down displays and increased dsRNA abundance in the cytoplasm with a weak induction of the dsRNA sensor OAS2, typically induced by interferon and viral dsRNA. Overall, the both IGS38 and IGS32as are chromatin associated lncRNAs involved in rDNA chromatin changes, and IGS38 is stimulating, together with WSTF, rRNA gene transcription in human cells. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=199 HEIGHT=200 SRC="FIGDIR/small/722362v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@14d4159org.highwire.dtl.DTLVardef@fd773forg.highwire.dtl.DTLVardef@a0030dorg.highwire.dtl.DTLVardef@1285301_HPS_FORMAT_FIGEXP M_FIG C_FIG IGS stabilises 47S rRNA transcription, disruption of IGS38 expression leads to the release of dsRNA in the cytoplasm and a weak immune activation of OAS2. Created by biorender (https://biorender.com/shortURL)

Transcription factors (TFs) regulate gene expression by binding to specific DNA sequences. Widely used models of TF-DNA binding, such as position weight matrices (PWMs) and position-specific affinity matrices (PSAMs), assume binding free energy is the sum of independent base contributions. However, there is ample evidence that non-additive effects significantly influence TF binding. Here, we utilize data from a high-throughput in vitro assay (ivtFOODIE) to generate genome-scale TF-DNA dissociation constants (Kd) and systematically evaluate sequence-to-affinity models of increasing complexity. We demonstrate that pairwise additive models exhibit systematic deviations from the measured affinity landscapes. Models incorporating adjacent dinucleotide interactions and deep learning architectures achieve markedly improved agreement with experimental Kd values. The magnitude of this non-pairwise-additivity depends strongly on the TF family. In silico mutation screening reveals widespread, TF-specific long-range interposition dependencies, highlighting the role of energetic coupling across distant positions in target recognition. These results provide a quantitative framework for comparing non-pairwise-additive energetic effects across diverse TFs.

The zinc finger transcription factor Kaiso recognizes methylated CpG dinucleotides at silenced promoters and imprinted loci, but how it engages methylated DNA within the nucleosome remains unclear. To address this, we developed a DNMT1-based strategy for preparing site-specifically methylated nucleosomes with defined position and methylation state of the Kaiso recognition motif. Electrophoretic mobility shift assays show that Kaiso binds methylated nucleosomes with strong positional preference, with high-affinity engagement at the entry/exit site (SHL 6.5; Kd {approx} 100 nM), reduced affinity at SHL 5.5 (Kd {approx} 170 nM), and no methylation-dependent enhancement at dyad-proximal positions. Hemi- and fully methylated substrates bind Kaiso comparably at SHL 6.5, and the E535A mutation, which disrupts a key methyl-CpG contact, reduces binding in a methylation- and position-dependent manner. Solution NMR titrations of 15N-labeled H3 nucleosomes reveal that Kaiso binding perturbs a discrete set of H3 N-terminal tail residues, with chemical shifts trending toward free-peptide values, indicating release of the tail from its nucleosomal DNA contacts. This pattern closely resembles that produced by the pioneer factor Sox2 at the same nucleosomal region, suggesting H3 tail displacement is a general consequence of factor engagement at the nucleosome edge, independent of DNA-recognition mode. These results establish Kaiso as an active reader of methylated nucleosomal DNA that may prime local chromatin by exposing the H3 tail.

Embryonically, the vertebrate brain begins as an approximately uniform, fluid-filled epithelial tube that undergoes rapid volumetric expansion and regionalization to form the morphologically distinct primary brain vesicles. Hydrostatic pressure from fluid secretion into the inner lumen generates tension in the neural tube that has been implicated as a potential driver of cell proliferation during these early stages of brain development. However, a quantitatively rigorous view of 3D morphology and cellular proliferation has remained elusive. Here, we provide a standardized mapping for the mechanical and biological landscape of the developing neuroepithelium along anatomical axes. Using this 3D morphometric framework in chicken embryos, we show that localized curvature characterizes compartmental boundaries. While rapid inflation would typically be expected to stretch and thin the epithelium, we find the opposite: global expansion is coupled with significant tissue thickening, identifying the early brain as an active shell. Moreover, spatial patterns of thickness remain invariant to local curvature. Our results demonstrate a decoupling of geometry and growth, showing that spatially stable distributions of tissue thickness and mitotic activity are maintained throughout massive volumetric expansion, independent of the dramatic geometric reorganization driven by luminal pressure. We conclude that, while tension in the neuroepithelium may contribute to proliferative growth at some level, biological pre-pattern likely plays a driving role in the regionalized expansion of the early embryonic brain. Why it mattersThe embryonic brain begins as a simple fluid-filled tube that undergoes rapid and heterogeneous expansion to set up the basic organizational plan of the adult brain. Errors in this process are linked to severe neurological and congenital disorders. This work investigates the biophysical basis of expansion and regionalization of the early brain, a complex three-dimensional process driven by inflation from internal fluid pressure together with active cell behaviors that ultimately produce regionally distinct growth and curvature profiles amid a complex mechanical landscape. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/726048v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@17c442forg.highwire.dtl.DTLVardef@1609374org.highwire.dtl.DTLVardef@170c00corg.highwire.dtl.DTLVardef@15080ad_HPS_FORMAT_FIGEXP M_FIG C_FIG

Selective deployment of multiple transcription start sites is a major regulatory feature of human transcriptomes. FANTOM CAGE data exhibit a near-universal TSS deployment parsimony which is disrupted in cancers. We have recently shown that TSS deployment is sensitive to gene function, futile upstream transcription, and cellular biosynthetic states. Patterns in FANTOM CAGE data can reveal mechanisms underlying TSS co-deployments. We propose and test the possibility that some TSSs act like epromoters and act as co-varying hubs of transcriptional activities for multiple other promoters. Using deep analysis of CAGE data implemented through neural networks we show that non-cancers implement transcription co-deployments through cores of epromoter-like TSSs which are generally proximal to their start codons. These TSSs show enhancer-like TFBSs profiles. A comparison with cancer CAGE data shows that the concentrated epromoter core is disrupted in cancers with multiple distal TSSs replacing the proximal TSS cores. We provide evidence that the core TSSs are rich in YY1 and CTCF binding sites and associated with genes coding for transcription factors. Our findings show that covariance of TSS deployment is sensitive to transcriptional resource cost and a parsimonic design of TSS co-deployments depends on proximal TSSs in non-cancers, a mechanism grossly disrupted in cancers. HighlightsO_LIHeterogeneous FANTOM CAGE data contains universal patterns of TSSs co-deployments. C_LIO_LITSS co-deployments exhibit a parsimonious "core-covariant" scheme which is disrupted in cancers. C_LIO_LICore TSSs are enriched in transcription factor binding sites and gene functions which justify biological features of the samples. C_LIO_LIThe DL pipeline we present identifies the core-covariant TSS sets in an unbiased manner. C_LI