Biology subjects

Shi, G.

Publications and source records attributed to Shi, G..

At least 55 records · Page 3Linked to original sources

bioRxiv2022

Linear motif specificity in signaling through p38α and ERK2 mitogen-activated protein kinases

Mitogen-activated protein kinase (MAPK) cascades are essential for eukaryotic cells to integrate and respond to a wide array of stimuli. Maintaining specificity in signaling through MAPK networks is key to coupling specific inputs to appropriate cellular responses. One way that MAPKs achieve specificity is through transient interactions with docking sites: short linear motifs found in MAPK substrates, regulators, and scaffolds. Docking sites bind to a conserved groove located in the catalytic domain of all MAPKs including the ERK and p38 subfamilies, but how specificity is achieved remains unresolved. To understand the basis of docking selectivity for these two subfamilies, we screened a library of thousands of human proteome-derived sequences for docking to ERK2 and p38. We discovered a large number of sequences that bound specifically to only one MAPK or promiscuously to both, and that selective and non-selective interactors conformed to distinct sequence motifs. In particular, selective binding to p38 correlated with higher net charge in the docking site, and this phenomenon was driven by enrichment for Lys residues. A pair of acidic residues unique to the docking groove of p38 mediated selectivity for Lys-rich basic motifs. Finally, we validated a set of full-length proteins harboring docking sites selected as hits in our screens to be authentic MAPK interactors and identified ChREBP and TACC1 as cellular MAPK substrates. This study identifies distinguishing features that help define MAPK signaling networks and explains how specific docking motifs promote signaling integrity.

cell biology↗

bioRxiv2022

Using polygenic risk score about complex traits to predict production performance in crossbreeding of yeast

The cultivation of hybrids with favorable complex traits is one of the important goals for animal, plant, and microbial breeding practices. A method that can well predict the production performance of hybrids will be of great significance to the whole research and practice. In our study, polygenic risk scores (PRS) were introduced to estimate the production performance of Saccharomyces Cerevisiae. The genetic variation of 971 published isolates and their growth ratios under 35 medium conditions were analyzed by genome-wide association analysis, and the precise p-value threshold for each phenotype was calculated. Risk markers for the above 35 phenotypes were obtained. By estimating genotype of F1 hybrids according to that of the parents, the PRS of 613 F1 hybrids was predicted. There was a significant linear correlation between YPD40 and PRS in F1 and their parents (R2=0.2582, R2=0.2414, respectively), which indicates that PRS can be used to estimate the production performance of individuals and their hybrids. Our method can provide a reference for strains selection and F1 prediction in yeasts cross-breeding, reduce the workload and improve the work efficiency.

genetics↗

bioRxiv2022

Structural changes in chromosomes driven by multiple condensin motors during mitosis

We created a computational framework that describes the loop extrusion (LE) by multiple condensin I and II motors in order to investigate the changes in chromosome organization during mitosis. The theory accurately reproduces the experimentally measured contact probability profiles for the mitotic chromosomes in HeLa and DT40 cells. The rate of loop extrusion is smaller at the start of mitosis and increases as the cells approach the metaphase. The mean loop size generated by condensin II is about six times larger than the ones created by condensin I. The loops, which overlap with each other, are stapled to a central dynamically changing helical scaffold formed by the motors during the LE process. The structures of the mitotic chromosomes, using a data-driven method that uses the Hi-C contact map as input, are best described as random helix perversion (RHP) in which the handedness changes randomly along the scaffold. The extent of propagation in the RHP structures is less in HeLa cells than in the DT40 chromosomes.

biophysics↗

bioRxiv2022

Transcription-induced active forces suppress chromatin motion by inducing a transient disorder-to-order transition

The organization of interphase chromosomes in a number of species is starting to emerge thanks to advances in a variety of experimental techniques. However, much less is known about the dynamics, especially in the functional states of chromatin. Some experiments have shown that the mobility of individual loci in human interphase chromosome decreases during transcription, and increases upon inhibiting transcription. This is a counter-intuitive finding because it is thought that the active mechanical force (F) on the order of ten pico-newtons, generated by RNA polymerase II (RNAPII) that is pre-sumably transmitted to the gene-rich region of the chromatin, would render it more open, thus enhancing the mobility. Inspired by these observations, we developed a minimal active copolymer model for interphase chromosomes to investigate how F affects the dynamical properties of chromatin. The movements of the loci in the gene-rich region are suppressed in an intermediate range of F, and are enhanced at small F values, which has also been observed in experiments. In the intermediate F, the bond length between consecutive loci increases, becoming commensurate with the distance at the minimum of the attractive interaction between non-bonded loci. This results in a transient disorder-to-order transition, leading to the decreased mobility during transcription. Strikingly, the F -dependent change in the locus dynamics preserves the organization of the chromosome at F = 0. Transient ordering of the loci, which is not found in the polymers with random epigenetic profiles, in the gene-rich region might be a plausible mechanism for nucleating a dynamic network involving transcription factors, RNAPII, and chromatin. Significance StatementIn order to explain a physically counter-intuitive experimental finding that chromatin mobility is reduced during transcription, we introduced a polymer model for interphase chromosome that accounts for RNA polymerase (RNAP) induced active force. The simulations show that, over a range of active forces, the mobility of the gene-rich loci is suppressed. Outside this range, chromosomes are compact and exhibit glass-like dynamics. Our study, which accounts for the experimental observations, leads to a novel and testable mechanism of how transcription could shape the coexistence of fluid- and solid-like properties within chromosomes.

biophysics↗

bioRxiv2022

Zfp503/Nlz2 is Required for RPE Differentiation and Optic Fissure Closure

PurposeUveal coloboma is a congenital eye malformation caused by failure of the optic fissure to close in early human development. Despite significant progress in identifying genes whose regulation is important for executing this closure, mutations are detected in a minority of cases using known gene panels, implying additional genetic complexity. We have previously shown knock down of znf503 (the ortholog of mouse Zfp503) in zebrafish causes coloboma. Here we characterize Zfp503 knock out (KO) mice and evaluate transcriptomic profiling of mutant vs. wild-type (WT) retinal pigment epithelium (RPE)/Choroid. MethodsZfp503 KO mice were generated by gene targeting using homologous recombination. Embryos were characterized grossly and histologically. Patterns and level of developmentally relevant proteins/genes were examined with immunostaining/in situ hybridization. The transcriptomic profile of E11.5 KO RPE/choroid was compared to that of WT. ResultsZfp503 is dynamically expressed in developing mouse eyes and that loss of its expression results in uveal coloboma. KO embryos exhibit altered mRNA levels and expression patterns of several key transcription factors involved in eye development, including Otx2, Mitf, Pax6, Pax2, Vax1 and Vax2, resulting in reduced melanin pigmentation in the presumptive RPE and its differentiation into neural-retina-like lineages. Comparison of RNA-Seq data from wild type and KO E11.5 embryos demonstrated reduced expression of melanin-related genes and significant overlap with genes known to be dynamically regulated at the optic fissure. ConclusionsThese results demonstrate a critical role of Zfp503 in RPE differentiation and in optic fissure closure.

developmental biology↗

bioRxiv2022

A method to predict 3D structural ensembles of chromatins from pairwise distances: Applications to Interphase Chromosomes and Structural Variants

The principles that govern the organization of genomes, which are needed for a deeper understanding of how chromosomes are packaged and function in eukaryotic cells, could be deciphered if the three dimensional (3D) structures are known. Recently, single-cell imaging experiments have determined the 3D coordinates of a number of loci in a chromosome. Here, we introduce a computational method (Distance Matrix to Ensemble of Structures, DIMES), based on the maximum entropy principle, with experimental pair-wise distances between loci as constraints, to generate a unique ensemble of 3D chromatin structures. Using the ensemble of structures, we quantitatively account for the distribution of pair-wise distances, three-body co-localization and higher-order interactions. We demonstrate that the DIMES method can be applied to both small length-scale and chromosome-scale imaging data to quantify the extent of heterogeneity and fluctuations in the shapes on various length scales. We develop a perturbation method that is used in conjunction with DIMES to predict the changes in 3D structures from structural variations. Our method also reveals quantitative differences between the 3D structures inferred from Hi-C and the ones measured in imaging experiments. Finally, the physical interpretation of the parameters extracted from DIMES provides insights into the origin of phase separation between euchromatin and heterochromatin domains.

biophysics↗

bioRxiv2022

A global pangenome for the wheat fungal pathogen Pyrenophora tritici-repentis and prediction of effector protein structural homology

The adaptive potential of plant fungal pathogens is largely governed by the gene content of a species, comprised of core and ancillary genes across the pathogen isolate repertoire. To approximate the complete gene repertoire of a globally significant crop fungal pathogen, a pan genomic analysis was undertaken for Pyrenophora tritici-repentis (Ptr), the causal agent of tan (or yellow) spot disease in wheat. In this study, fifteen new Ptr genomes were sequenced, assembled and annotated, including isolates from three races not previously sequenced. Together with eleven previously published Ptr genomes, a pangenome for twenty-six Ptr isolates from Australia, Europe, North Africa and America, representing nearly all known races, revealed a conserved core-gene content of 57% and presents a new Ptr resource for searching natural homologues using remote protein structural homology. Here, we identify for the first time a nonsynonymous mutation in the Ptr effector gene ToxB, multiple copies of toxb, a distant natural Pyrenophora homologue of a known Parastagonopora nodorum effector, and clear genomic break points for the ToxA effector horizontal transfer region. This comprehensive genomic analysis of Ptr races includes nine isolates sequenced via long read technologies. Accordingly, these resources provide a more complete representation of the species, and serve as a resource to monitor variations potentially involved in pathogenicity. Author NotesAll supporting data, code and protocols have been provided within the article or through supplementary data files. Five supplementary data files and fifteen supplementary figures are available with the online version of this article. Impact StatementOur Pyrenophora tritici-repentis (Ptr) pangenome study provides resources and analyses for the identification of pathogen virulence factors, of high importance to microbial research. Key findings include: 1) Analysis of eleven new sequenced (with three new races not previously available) and previously published isolates, 26 genomes in total, representing the near complete Ptr race set for known effector production collected from Australia, Europe, North Africa and the Americas. 2) We show that although Ptr has low core gene conservation, the whole genome divergence of other wheat pathogens was greater. 3) The new PacBio sequenced genomes provide unambiguous genomic break points for the large ToxA effector horizontal transfer region, which is only present in ToxA producing races. 4) A new web-based Ptr resource for searching in silico remote protein structural homology is presented, and a distant natural Pyrenophora protein homologue of a known effector from another wheat pathogen is identified for the first time. Data SummaryThe sources and genomic sequences used throughout this study have been deposited in the National Centre for Biotechnology Information (NCBI), under the assembly accession numbers provided in Tables 1 and 2 (available in the online version of this article). The new M4 resource for protein structural homology is freely available through the BackPhyre web-portal URL, http://www.sbg.bio.ic.ac.uk/phyre2/. O_TBL View this table: org.highwire.dtl.DTLVardef@c6b2deorg.highwire.dtl.DTLVardef@1091da1org.highwire.dtl.DTLVardef@17860a4org.highwire.dtl.DTLVardef@10d4aaorg.highwire.dtl.DTLVardef@fa258f_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1.C_FLOATNO O_TABLECAPTIONSummary statistics for our four PacBio sequenced Ptr genome assemblies, compared with those of two previously published Ptr assemblies. C_TABLECAPTION C_TBL O_TBL View this table: org.highwire.dtl.DTLVardef@b7d0cforg.highwire.dtl.DTLVardef@1ee01e6org.highwire.dtl.DTLVardef@becc09org.highwire.dtl.DTLVardef@456c7corg.highwire.dtl.DTLVardef@1d55799_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 2.C_FLOATNO O_TABLECAPTIONIllumina sequenced genome assemblies of 11 new Ptr isolates. Table shows isolate source, race and de novo assembly statistics. C_TABLECAPTION C_TBL

genomics↗

bioRxiv2021

Proteome-wide screening for mitogen-activated protein kinase docking motifs and interactors

Essential functions of mitogen-activated protein kinases (MAPKs) depend on their capacity to selectively phosphorylate a limited repertoire of substrates. MAPKs harbor a conserved groove located outside of the catalytic cleft that binds to short linear sequence motifs found in substrates and regulators. However, the weak and transient nature of these "docking" interactions poses a challenge to defining MAPK interactomes and associated sequence motifs. Here, we describe a yeast-based genetic screening pipeline to evaluate large collections of MAPK docking sequences in parallel. Using this platform we analyzed a combinatorial library based on the docking sequences from the MAPK kinases MKK6 and MKK7, defining features critical for binding to the stress-activated MAPKs JNK1 and p38. We subsequently screened a library consisting of ~12,000 sequences from the human proteome, revealing a large number of MAPK-selective interactors, including many not conforming to previously defined docking motifs. Analysis of p38/JNK1 exchange mutants identified specific docking groove residues mediating selective binding. Finally, we verified that docking sequences identified in the screen could function in substrate recruitment in vitro and in cultured cells. Collectively, these studies establish an approach for characterization of MAPK docking sequences and provide a resource for future investigation of signaling downstream of p38 and JNK MAP kinases.

cell biology↗

bioRxiv2021

Evolution of Learning in Technology Adoption: The case of the U.S. Soybean Seed Industry.

This paper examines how the evolution of learning affects technology adoption. We use a sequential adoption model that accounts for differences between forward-looking adopters, who consider future impacts of their learning, and myopic adopters, who only consider past learning. We apply the analysis to three panels of U.S. soybean farmers representing different stages of the genetically modified (GM) seed technology diffusion path. We show that uncertainty is considerably reduced over time due to increased learning efficiency. Our results indicate that a forward-looking model fits the early adopters and early majority stages better, while both models perform equally well in the laggard stage. JEL classificationD83, Q31, Q33, Q16

scientific communication and education↗

bioRxiv2021

Modulating the selective utilization of carbon sources by engineering the 3rd and 4th helices of the DNA-binding domain of catabolite control protein A (CcpA) in Bacillus licheniformis

The gram-positive bacterium Bacillus licheniformis exhibits obvious selective utilization on carbon sources. This process is mainly governed by the global regulator catabolite control protein A (CcpA), which can recognize and bind to multiple target genes widely distributed in metabolic pathways. Although the DNA-binding domain of CcpA has been predicted, the influence of key amino acids on target gene recognition and binding remains elusive. In this study, the impact of Lys31, Ile42 and Leu56 on in vitro protein-DNA interactions and in vivo carbon source selective utilization was investigated. The results showed that alanine substitution of Lys31 and Ile42, located within the 3rd helices of the DNA-binding domain, significantly weakened the binding strength between CcpA and target genes. These mutations also lead to alleviated repression of xylose utilization in the presence of glucose. On the other hand, the Leu56Arg mutant in the 4th helices exhibited enhanced binding affinity compared with that of the wild-type one. When this mutant was used to replace the native one in B. licheniformis cells, the selective utilization of glucose over xylose increased. The above research results are helpful for a deep understanding of how microorganisms can flexibly sense and adapt to changes in the external environment. Additionally, they can provide important theoretical basis for the rational design of biomass utilization and environmental adaptability of B. licheniformis cell factories. ImportanceBacillus licheniformis is widely used in producing various valuable products, such as enzymes, industrial chemicals and biocides. The carbon catabolite regulation process in the utilization of raw materials is crucial to maximizing the efficiency of this microbial cell factory. CcpA plays an important role in this process. This study represents a new paradigm to investigate the structure-function relationship in CcpA by fluorescence polarization experiments in vitro. The results also uncover key amino acids in the DNA-binding domain that affect the selective utilization of carbon sources. These results provide a theoretical basis for the rational design of industrial microorganisms.

bioengineering↗

bioRxiv2021

Rapalogs downmodulate intrinsic immunity and promote cell entry of SARS-CoV-2

SARS-CoV-2 infection in immunocompromised individuals is associated with prolonged virus shedding and evolution of viral variants. Rapamycin and its analogs (rapalogs, including everolimus, temsirolimus, and ridaforolimus) are FDA-approved as mTOR inhibitors for the treatment of human diseases, including cancer and autoimmunity. Rapalog use is commonly associated with increased susceptibility to infection, which has been traditionally explained by impaired adaptive immunity. Here, we show that exposure to rapalogs increases susceptibility to SARS-CoV-2 infection in tissue culture and in immunologically naive rodents by antagonizing the cell-intrinsic immune response. By identifying one rapalog (ridaforolimus) that is less potent in this regard, we demonstrate that rapalogs promote Spike-mediated entry into cells by triggering the degradation of antiviral proteins IFITM2 and IFITM3 via an endolysosomal remodeling program called microautophagy. Rapalogs that increase virus entry inhibit the mTOR-mediated phosphorylation of the transcription factor TFEB, which facilitates its nuclear translocation and triggers microautophagy. In rodent models of infection, injection of rapamycin prior to and after virus exposure resulted in elevated SARS-CoV-2 replication and exacerbated viral disease, while ridaforolimus had milder effects. Overall, our findings indicate that preexisting use of certain rapalogs may elevate host susceptibility to SARS-CoV-2 infection and disease by activating lysosome-mediated suppression of intrinsic immunity. SignificanceRapamycin is an immunosuppressant used in humans to treat cancer, autoimmunity, and other disease states. Here, we show that rapamycin and related compounds promote the first step of the SARS-CoV-2 infection cycle--entry into cells--by disarming cell-intrinsic immune defenses. We outline the molecular basis for this effect by identifying a rapamycin derivative that is inactive, laying the foundation for improved mTOR inhibitors that do not suppress intrinsic immunity. We find that rapamycin analogs that promote SARS-CoV-2 entry are those that activate TFEB, a transcription factor that triggers the degradation of antiviral membrane proteins inside of cells. Finally, rapamycin administration to rodents prior to SARS-CoV-2 challenge results in enhanced viral disease, revealing that its use in humans may increase susceptibility to infection.

microbiology↗

bioRxiv2021

Chromatin dynamics controls epigenetic domain formation

In multicellular organisms, nucleosomes carry epigenetic information that defines distinct patterns of gene expression, which are inherited over multiple generations. The enhanced capacity for information storage arises by nucleosome modifications, triggered by enzymes. Modified nucleosomes can transfer the mark to others that are in proximity by a positive feedback (modification begets modification) mechanism. We created a polymer model in which each bead, representing a nucleosome, stochastically switches between unmodified (U) and modified (M) states depending on the states of the neighbors. Spreading is initiated at a specific nucleation site (NS) that is permanently in the M state. Modifications spread among the non-nucleation loci probabilistically. If the spreading rate is higher than the chromatin relaxation rate, domains containing the modified nucleosomes form without bound. In the opposite biologically relevant limit, finite-sized domains form, driven by contacts between nucleosomes through a three-dimensional looping mechanism, with chromatin remaining in an expanded state, as is appropriate for fission yeast. Surprisingly, finite bounded domains arise without the need for any boundary elements as long as the spreading is slow. Maintenance of spatially and temporally stable domains require the presence of the NS whose removal eliminates finite-sized modified domains. By varying the solvent quality we show that finite heterochromatin domains form as long as initially chromatin is not fully condensed. The predictions compare well with experimental data for H3K9me3 spreading in Mouse Embryonic Stem cell.

biophysics↗

bioRxiv2021

Genetic Diversity of Dianthus Plants Revealed by SRAP Markers

Dianthus is a valuable genetic resource for flower breeding. However, study on the genetic similarity of Dianthus plants is rare. In this work, 20 pairs of SRAP markers were used to analyze genetic diversity of 44 Dianthus plants, including 13 lines of wild Dianthus chinensis L., 7 lines of wild Dianthus superbus L. and 24 commercial varieties including Dianthus caryophyllus L., Dianthus plumarius L. and Dianthus barbatus L.. Results showed that precise interspecific and intraspecific genetic diversity was provided in Dianthus plants by using 20 pairs of SRAP molecular markers. The interspecific genetic diversity of Dianthus plants was much abundant and the intraspecific genetic difference of wild Dianthus species was related to their geographical distribution and habitats. In this work, theoretical basis and technical support were provided for crossbreeding and molecular mechanism research of Dianthus plants.

genetics↗

bioRxiv2020

In-vitro and in-vivo characterization of CRANAD-2 for multi-spectral optoacoustic tomography and fluorescence imaging of amyloid-beta deposits in Alzheimer mice

The abnormal deposition of fibrillar beta-amyloid (A{beta}) deposits in the brain is one of the major histopathological hallmarks of Alzheimers disease (AD). Here we characterize curcumin-derivative CRANAD-2 for multi-spectral optoacoustic tomography (MSOT) and fluorescence imaging of brain A{beta} deposits in the arcA{beta} mouse model of AD cerebral amyloidosis. CRANAD-2 shows a specific and quantitative detection of A fibrils in vitro, even in complex mixtures, and it is capable to distinguish between monomeric and fibrillar forms of A. In vivo epifluorescence and MSOT after intravenous CRANAD-2 administration demonstrated higher retention in arcA{beta} compared to non-transgenic littermate mice. Immunohistochemistry showed co-localization of CRANAD-2 and A{beta} deposits in arcA{beta} mouse brain sections, thus verifying the specificity of the probe. In conclusion, we demonstrate suitability of CRANAD-2 for fluorescence- and MSOT-based detection of A{beta} deposits in animal models of AD pathology, which facilitates mechanistic studies and the monitoring of putative treatments targeting A{beta} deposits.

neuroscience↗

bioRxiv2020

Opposing activities of IFITM proteins in SARS-CoV-2 infection

Interferon-induced transmembrane proteins (IFITMs) restrict infections by many viruses, but a subset of IFITMs enhance infections by specific coronaviruses through currently unknown mechanisms. Here we show that SARS-CoV-2 Spike-pseudotyped virus and genuine SARS-CoV-2 infections are generally restricted by expression of human IFITM1, IFITM2, and IFITM3, using both gain- and loss-of-function approaches. Mechanistically, restriction of SARS-CoV-2 occurred independently of IFITM3 S-palmitoylation sites, indicating a restrictive capacity that is distinct from reported inhibition of other viruses. In contrast, the IFITM3 amphipathic helix and its amphipathic properties were required for virus restriction. Mutation of residues within the human IFITM3 endocytosis-promoting Yxx{Phi} motif converted human IFITM3 into an enhancer of SARS-CoV-2 infection, and cell-to-cell fusion assays confirmed the ability of endocytic mutants to enhance Spike-mediated fusion with the plasma membrane. Overexpression of TMPRSS2, which reportedly increases plasma membrane fusion versus endosome fusion of SARS-CoV-2, attenuated IFITM3 restriction and converted amphipathic helix mutants into strong enhancers of infection. In sum, these data uncover new pro- and anti-viral mechanisms of IFITM3, with clear distinctions drawn between enhancement of viral infection at the plasma membrane and amphipathicity-based mechanisms used for endosomal virus restriction. Indeed, the net effect of IFITM3 on SARS-CoV-2 infections may be a result of these opposing activities, suggesting that shifts in the balance of these activities could be coopted by viruses to escape this important first line innate defense mechanism.

immunology↗

bioRxiv2020

Tubulin acetylation increases cytoskeletal stiffness to regulate mechanotransduction in striated muscle

Microtubules tune cytoskeletal stiffness to regulate the mechanics and mechanotransduction of striated muscle. While recent evidence suggests that microtubules enriched in detyrosinated α-tubulin are responsible for these effects in healthy muscle, and for their excess in disease, the possible contribution from several other α-tubulin modifications has not been investigated. Here we used genetic or pharmacologic strategies in isolated cardiomyocytes or skeletal myofibers to increase the level of acetylated α-tubulin without altering the level of detyrosinated α-tubulin. We show that microtubules enriched in acetylated α-tubulin contribute to the cytoskeletal stiffness and viscoelastic resistance, showing slowed rates of contraction and relaxation during unloaded contraction, and increased activation of NADPH Oxidase 2 (Nox2) by mechanotransduction. Together these findings add to growing evidence that microtubules contribute to the mechanobiology of striated muscle in health and disease.Competing Interest StatementThe authors have declared no competing interest.View Full Text

physiology↗

bioRxiv2020

On the theory of condensin mediated loop extrusion in genomes

Condensation of hundreds of mega-base-pair-long human chromosomes in a small nuclear volume is a spectacular biological phenomenon. This process is driven by the formation of chromosome loops. The ATP consuming motor, condensin, interacts with chromatin segments to actively extrude loops. Motivated by real-time imaging of loop extrusion (LE), we created an analytically solvable model, predicting the LE velocity and step size distribution as a function of external load. The theory fits the available experimental data quantitatively, and suggests that condensin must undergo a large conformational change, induced by ATP binding, bringing distant parts of the motor to proximity. Simulations using a simple model confirm that the motor transitions between an open and a closed state in order to extrude loops by a scrunching mechanism, similar to that proposed in DNA bubble formation during bacterial transcription. Changes in the orientation of the motor domains are transmitted over ~ 50 nm, connecting the motor head and the hinge, thus providing an allosteric basis for LE.

biophysics↗

bioRxiv2020

From Hi-C Contact Map to Three-dimensional Organization of Interphase Human Chromosomes

The probability of two loci, separated by a certain genome length, being in contact can be inferred using the Chromosome Conformation Capture (3C) method and related Hi-C experiments. How to go from the contact map, a matrix listing the mean contact probabilities between a large number of pairs of loci, to an ensemble of three-dimensional structures is an open problem. A solution to this problem, without assuming an assumed energy function, would be the first step in understanding the way nature has solved the packaging of chromosomes in tight cellular spaces. We created a theory, based on polymer physics characteristics of chromosomes and the maximum entropy principles, referred to as HIPPS (Hi-C-Polymer-Physics-Structures) method, that allows us to calculate the 3D structures solely from Hi-C contact maps. The first step in the HIPPS method is to relate the mean contact probability [Formula] between loci i and j and the average spatial distance, [Formula]. This is a difficult problem to solve because the cell population is heterogeneous, which means that a given contact exists only in a small unknown fraction of cells. Despite the population heterogeneity, we first prove that there is a theoretical lower bound connecting [<]pij[>] and [Formula] via a power-law relation. We show, using simulations of a precisely solvable model, that the overall organization is accurately captured by constructing the distance map from the contact map even when if the cell population is highly heterogeneous, thus justifying the use of the lower bound. In the second step, the mean distance matrix, with elements [Formula], is used as a constraint in the maximum entropy principle to obtain the joint distribution of spatial positions of the loci. Using the two steps, we created an ensemble of 3D structures for the 23 chromosomes from lymphoblastoid cells using the measured contact maps as inputs. The HIPPS method shows that conformations of chromosomes are heterogeneous even in a single cell type. The differences in the conformational heterogeneity of the same chromosome in different cell types (normal as well as cancerous cells) can also be quantitatively discerned using our theory. We validate the method by showing that the calculated volumes of the 23 chromosomes from the predicted 3D structures are in good agreement with experimental estimates. Because the method is general, the 3D structures for any species may be calculated directly from the contact map without the need to assume a specific polymer model, as is customarily done.

biophysics↗