Central Dogma Research Articles

Defining multiple layers of intratumor heterogeneity based on variations of perturbations in multi-omics profiling

BackgroundIntratumor heterogeneity (ITH) plays a crucial role in tumor progression, relapse, immune evasion, and drug resistance. Existing ITH quantification methods based on a single molecular level are inadequate to capture ITH evolving from genotype to phenotype. MethodsWe designed a set of information entropy (IE)-based algorithms for quantifying ITH at the genome (somatic copy number alterations and mutations), mRNA, microRNA (miRNA), long non-coding RNA (lncRNA), protein, and epigenome level, respectively. We evaluated the performance of these algorithms by analyzing the correlations between their ITH scores and ITH-associated molecular and clinical features in 33 TCGA cancer types. Moreover, we evaluated the correlations between the ITH measures at different molecular levels by Spearman correlation and clustering analysis. ResultsThe IE-based ITH measures had significant correlations with unfavorable prognosis, tumor progression, genomic instability, antitumor immunosuppression, and drug resistance. The mRNA ITH showed stronger correlations with the miRNA, lncRNA, and epigenome ITH than with the genome ITH, supporting the regulatory relationships of miRNA, lncRNA, and DNA methylation towards mRNA. The protein-level ITH displayed stronger correlations with the transcriptome-level ITH than with the genome-level ITH, supporting the central dogma of molecular biology. Clustering analysis based on the ITH scores identified four subtypes of pan-cancer showing significantly different prognosis. Finally, the ITH integrating the seven ITH measures displayed more prominent properties of ITH than that at a single level. ConclusionsThis analysis provides landscapes of ITH at various molecular levels. Combining the ITH observation from different molecule levels will improve personalized management for cancer patients.

The Biological Responses of Staphylococcus aureus to Cold Plasma Treatment

Staphylococcus aureus is a bacterium that causes various diseases in humans. Cold plasma is found to be an alternative to eliminate S. aureus. Most studies of cold plasma on S. aureus mainly focus on the physiochemical changes of the cells. So far, biological responses of S. aureus to cold plasma treatment under different treatment durations have not yet been evaluated. In this study, the results showed that the cold plasma was effective in eliminating S. aureus. At the initial exposure (1 min), the treated cells showed gene upregulations of stress proteins, antioxidants, nitrosative stress, and transporter proteins, but no significant change in other biological processes, such as cell membrane synthesis, DNA repairing, transcription, and translation. This indicated that the cells actively countered the damage from cold plasma. In contrast, during the prolonged treatment (3 and 5 min), biological processes related to central dogma were affected, including the DNA repairing mechanism, transcription, and translation. In addition, the majority of the genes related to cell membrane synthesis were downregulated, indicating that the treated cells could no longer sustain their cell integrity. In conclusion, this study elucidated how cold plasma inactivated S. aureus in a series of cold plasma exposures and highlighted the sequential transcriptomic responses of S. aureus.

Principles, mechanisms, and biological implications of translation termination-reinitiation.

The gene expression pathway from DNA sequence to functional protein is not as straightforward as simple depictions of the central dogma might suggest. Each step is highly regulated, with complex and only partially understood molecular mechanisms at play. Translation is one step where the "one gene-one protein" paradigm breaks down, as often a single mature eukaryotic mRNA leads to more than one protein product. One way this occurs is through translation reinitiation, in which a ribosome starts making protein from one initiation site, translates until it terminates at a stop codon, but then escapes normal recycling steps and subsequently reinitiates at a different downstream site. This process is now recognized as both important and widespread, but we are only beginning to understand the interplay of factors involved in termination, recycling, and initiation that cause reinitiation events. There appear to be several ways to subvert recycling to achieve productive reinitiation, different types of stresses or signals that trigger this process, and the mechanism may depend in part on where the event occurs in the body of an mRNA. This perspective reviews the unique characteristics and mechanisms of reinitiation events, highlights the similarities and differences between three major scenarios of reinitiation, and raises outstanding questions that are promising avenues for future research.

Hierarchical multi-omics data integration and modeling predict cell-specific chemical proteomics and drug responses

Drug-induced phenotypes result from biomolecular interactions across various levels of a biological system.Characterization of pharmacological actions therefore requires integration of multi-omics data. Proteomics profiles, which may more directly reflect disease mechanisms and biomarkers than transcriptomics, have not been widely exploited due to data scarcity and frequent missing values. A computational method for inferring drug-induced proteome patterns would therefore enable progress in systems pharmacology. To predict the proteome profiles and corresponding phenotypes of an uncharacterized cell or tissue type that has been disturbed by an uncharacterized chemical, we developed an end-to-end deep learning framework: TransPro. TransPro hierarchically integrated multi-omics data, in line with the central dogma of molecular biology. Our in-depth assessments of TransPro's predictions of anti-cancer drug sensitivity and drug adverse reactions reveal that TransPro's accuracy is on par with that of experimental data. Hence,TransPro may facilitate the imputation of proteomics data and compound screening in systems pharmacology.

Special Issue: Spatial Omics

GEN BiotechnologyVol. 2, No. 2 Call for PapersFree AccessSpecial Issue: Spatial OmicsDeadline for Manuscript Submission: June 15, 2023Guest Editors: Rong Fan and Omer BayraktarGuest Editors: Rong FanYale UniversitySearch for more papers by this author and Omer BayraktarWellcome Sanger InstituteSearch for more papers by this authorPublished Online:18 Apr 2023https://doi.org/10.1089/genbio.2023.29076.cfp2AboutSectionsPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail Single-cell omics has revolutionized biological and biomedical research in the past decade despite the inability to measure single cells in the tissue context. Spatial omics, which allows for profiling a range of biomolecules with high spatial resolution across the central dogma of molecular biology directly in the tissue context, not only offers spatial information but unlocks unprecedented new opportunities to delve into clinical specimens for human biology research, therapeutic discovery, and translational medicine. Spatial omics is becoming one of the fastest-paced growth areas in the biotech industry and poised to drive the next wave of biology revolution with widespread and far-reaching impact in all major fields of life science and medicine.GEN Biotechnology is pleased to announce a call for papers for our inaugural special issue—Spatial Omics.This collection of research articles, reviews, and perspectives will be published in late 2023. We invite researchers to submit without delay manuscripts describing original research on any aspect of spatial and single-cell biological research. We will also consider relevant guest commentaries and review articles.Specific topics may include (but are not confined to): Sequencing based spatial omics (i.e., transcriptome, proteome, epigenome, genome).High-plex imaging of proteins, transcripts, or epigenomic/genomic featuresSpatial proteomics and metabolomicsSpatial multi-omics and multi-modality tissue profilingComputational methods and tools for spatial biology (machine learning, data deconvolution, mathematical modeling, data visualization)Spatial omics to profile tumor heterogeneity and microenvironmentsSpatial omics in neuroscience, neurological or neurodegenerative disease researchSpatial omics in aging, senescence, metabolic and chronic diseases.Manuscripts will receive prompt peer review and accepted articles will be published online (epub) ahead of print. Please refer to our Instructions for Authors at www.liebertpub.com/genbio before submitting your manuscript.Presubmission inquiries may be sent to GEN Biotechnology (editor@genbiotechjournal.com). This special issue will be published in late 2023.Advantages of publishing in GEN Biotechnology include:Rapid, high-quality peer review, and editorial oversightFast electronic submissionMaximum exposure: accessible in 170 countries worldwideHigh visibility: International press and social media outreachOpen Access options availableVisit the Instructions for Authors:www.liebertpub.com/genbioSubmit your paper for peer review online:https://mc.manuscriptcentral.com/genbioFiguresReferencesRelatedDetails Volume 2Issue 2Apr 2023 InformationCopyright 2023, Mary Ann Liebert, Inc., publishersTo cite this article:Guest Editors: Rong Fan and Omer Bayraktar.Special Issue: Spatial Omics.GEN Biotechnology.Apr 2023.61-62.http://doi.org/10.1089/genbio.2023.29076.cfp2Published in Volume: 2 Issue 2: April 18, 2023PDF download

Biomolecular Liquid-Liquid Phase Separation for Biotechnology.

The liquid-liquid phase separation (LLPS) of biomolecules induces condensed assemblies called liquid droplets or membrane-less organelles. In contrast to organelles with lipid membrane barriers, the liquid droplets induced by LLPS do not have distinct barriers (lipid bilayer). Biomolecular LLPS in cells has attracted considerable attention in broad research fields from cellular biology to soft matter physics. The physical and chemical properties of LLPS exert a variety of functions in living cells: activating and deactivating biomolecules involving enzymes; controlling the localization, condensation, and concentration of biomolecules; the filtration and purification of biomolecules; and sensing environmental factors for fast, adaptive, and reversible responses. The versatility of LLPS plays an essential role in various biological processes, such as controlling the central dogma and the onset mechanism of pathological diseases. Moreover, biomolecular LLPS could be critical for developing new biotechnologies such as the condensation, purification, and activation of a series of biomolecules. In this review article, we introduce some fundamental aspects and recent progress of biomolecular LLPS in living cells and test tubes. Then, we discuss applications of biomolecular LLPS toward biotechnologies.

The in vivo measurement of replication fork velocity and pausing by lag-time analysis

An important step towards understanding the mechanistic basis of the central dogma is the quantitative characterization of the dynamics of nucleic-acid-bound molecular motors in the context of the living cell. To capture these dynamics, we develop lag-time analysis, a method for measuring in vivo dynamics. Using this approach, we provide quantitative locus-specific measurements of fork velocity, in units of kilobases per second, as well as replisome pause durations, some with the precision of seconds. The measured fork velocity is observed to be both locus and time dependent, even in wild-type cells. In this work, we quantitatively characterize known phenomena, detect brief, locus-specific pauses at ribosomal DNA loci in wild-type cells, and observe temporal fork velocity oscillations in three highly-divergent bacterial species.

The Long Road to a Synthetic Self-Replicating Central Dogma.

The construction of a biochemical system capable of self-replication is a key objective in bottom-up synthetic biology. Throughout the past two decades, a rapid progression in the design of in vitro cell-free systems has provided valuable insight into the requirements for the development of a minimal system capable of self-replication. The main limitations of current systems can be attributed to their macromolecular composition and how the individual macromolecules use the small molecules necessary to drive RNA and protein synthesis. In this Perspective, we discuss the recent steps that have been taken to generate a minimal cell-free system capable of regenerating its own macromolecular components and maintaining the homeostatic balance between macromolecular biogenesis and consumption of primary building blocks. By following the flow of biological information through the central dogma, we compare the current versions of these systems to date and propose potential alterations aimed at designing a model system for self-replicative synthetic cells.

Spatial epigenome–transcriptome co-profiling of mammalian tissues

Emerging spatial technologies, including spatial transcriptomics and spatial epigenomics, are becoming powerful tools for profiling of cellular states in the tissue context1–5. However, current methods capture only one layer of omics information at a time, precluding the possibility of examining the mechanistic relationship across the central dogma of molecular biology. Here, we present two technologies for spatially resolved, genome-wide, joint profiling of the epigenome and transcriptome by cosequencing chromatin accessibility and gene expression, or histone modifications (H3K27me3, H3K27ac or H3K4me3) and gene expression on the same tissue section at near-single-cell resolution. These were applied to embryonic and juvenile mouse brain, as well as adult human brain, to map how epigenetic mechanisms control transcriptional phenotype and cell dynamics in tissue. Although highly concordant tissue features were identified by either spatial epigenome or spatial transcriptome we also observed distinct patterns, suggesting their differential roles in defining cell states. Linking epigenome to transcriptome pixel by pixel allows the uncovering of new insights in spatial epigenetic priming, differentiation and gene regulation within the tissue architecture. These technologies are of great interest in life science and biomedical research.

Epitranscriptional Regulation: From the Perspectives of Cardiovascular Bioengineering.

The central dogma of gene expression involves DNA transcription to RNA and RNA translation into protein. As key intermediaries and modifiers, RNAs undergo various forms of modifications such as methylation, pseudouridylation, deamination, and hydroxylation. These modifications, termed epitranscriptional regulations, lead to functional changes in RNAs. Recent studies have demonstrated crucial roles for RNA modifications in gene translation, DNA damage response, and cell fate regulation. Epitranscriptional modifications play an essential role in development, mechanosensing, atherogenesis, and regeneration in the cardiovascular (CV) system, and their elucidation is critically important to understanding the molecular mechanisms underlying CV physiology and pathophysiology. This review aims at providing biomedical engineers with an overview of the epitranscriptome landscape, related key concepts, recent findings in epitranscriptional regulations, and tools for epitranscriptome analysis. The potential applications of this important field in biomedical engineering research are discussed.

Ecotechnology of Hilsa-Seed Productions Digitally Under Fresh-Water-Ecology Whereas Hilsa-Seeds Can Be Boon To Experiment In Marine-Cages For Growths World-Wide, Which-Ever Countries May Opt The Best

Since decades authors are bit panicked from the then theory of Central dogma unless the rescue actions taken by all the immense bio-molecules of fats and lipids of Hilsa species that savoir mankind. Hilsa as a diet can adequately support and can protect the esteem mankind from any disasters and dealt the theory ‘Beyond the central dogma’ by virtue of developing all necessary immunities for every peaceful human being of mankind. All we may know protein may be immense needful however most proteins are hazardous unless the same is well protected with Fats. Hilsa species is such a species can provide adequate quality Fats to mankind and help us to remain protected from any evil of proteins or Virus. May be our esteem need to popularize Hilsa species globally that goes to marine. Hilsa often a marine species grown most time in marine environments under all known water qualities. Natural migration of Hilsa owing to seed production may not possible in all marine environments since migration are extremely slow in marine environments and takes prolonged times before the species to the other part of the world since aging Hisla survives around 10 – 12 years prior to that species re-enter the well known fresh waters of certain qualities unlike marine routes. Hence Hilsa species remained confined in few marine pockets only and can be inducted elsewhere marine cages, Hilsa breed under fresh waters conditions when Hilsa seeds produced under controlled Ecotechnology and again can be recruited in marine cages worldwide. All fish migrates owing to physiological requirements. This migration is based on water qualities, food and light and temperature. Usually Juvenille Hilsa species prefer a high TDS marine environments. During the breeding seasons Hilsa migrates to the as low as low TDS (< 110ppm) of waters and whenever species get a suitable osmotic-pressure or optimum Total Dissolved Solids i.e. TDS then Hilsa to breed. According to all water qualities with ranges of different parameters, intensity of light and coolness temperature are the criteria in Ecotechnology of Hilsa Breeding. In earlier days attempts were made reversedly when adult Hilsa species were tried to grow in fresh-waters and all Hilsa could not survived and projects remained unsuccessful. Present communications with mere IT, Ecotechnology, and biotechnological concepts can popularize Hilsa. May Hilsa in marine cages of TDS in a range of 190 TO 550 ppm get successful since its’ immense scientific ease globally. Hilsa may be the best quality fish so far known today due its high quality bio-molecular substances and prolific values.

Adding structure to biology’s central dogma for potential new cancer treatments

Adding structure to biology’s central dogma for potential new cancer treatments

Machine-learning-assisted single-vessel analysis of nanoparticle permeability in tumour vasculatures.

The central dogma that nanoparticle delivery to tumours requires enhanced leakiness of vasculatures is a topic of debate. To address this, we propose a single-vessel quantitative analysis method by taking advantage of protein-based nanoprobes and image-segmentation-based machine learning (nano-ISML). Using nano-ISML, >67,000 individual blood vessels from 32 tumour models were quantified, revealing highly heterogenous vascular permeability of protein-based nanoparticles. There was a >13-fold difference in the percentage of high-permeability vessels in different tumours and >100-fold penetration ability in vessels with the highest permeability compared with vessels with the lowest permeability. Our data suggest passive extravasation and transendothelial transport were the dominant mechanisms for high- and low-permeability tumour vessels, respectively. To exemplify the nano-ISML-assisted rational design of nanomedicines, genetically tailored protein nanoparticles with improved transendothelial transport in low-permeability tumours were developed. Our study delineates the heterogeneity of tumour vascular permeability and defines a direction for the rational design of next-generation anticancer nanomedicines.

Translating the Genome into Drugs.

The Human Genome Project ultimately aimed to translate DNA sequence into drugs. With the draft in hand, the Molecular Libraries Program set out to prosecute all genome-encoded proteins for drug discovery with automated high-throughput screening (HTS). This ambitious vision remains unfulfilled, even while innovations in sequencing technology have fully democratized access to genome-scale sequencing. Why? While the central dogma of biology allows us to chart the entirety of cellular metabolism through sequencing, there is no direct coding for chemistry. The rules of base pairing that relate DNA gene to RNA transcript and amino acid sequence do not exist for relating small-molecule structure with macromolecular binding partners and subsequently cellular function. Obtaining such relationships genome-wide is unapproachable via state-of-the-art HTS, akin to attempting genome-wide association studies using turn-of-the-millennium Sanger DNA sequencing.Our laboratory has been engaged in a multipronged technology development campaign to revolutionize molecular screening through miniaturization in pursuit of genome-scale drug discovery capabilities. The compound library was ripe for miniaturization: it clearly needed to become a consumable. We employed DNA-encoded library (DEL) synthesis principles in the development of solid-phase DELs prepared on microscopic beads, each harboring 100 fmol of a single library member and a DNA tag whose sequence describes the structure of the library member. Loading these DEL beads into 100 pL microfluidic droplets followed by online photocleavage, incubation, fluorescence-activated droplet sorting, and DNA sequencing of the sorted DEL beads reveals the chemical structures of bioactive compounds. This scalable library synthesis and screening platform has proven useful in several proof-of-concept projects involving current clinical targets.Moving forward, we face the problem of druggability and proteome-scale assay development. Developing biochemical or cellular assays for all genome-encoded targets is not scalable and likely impossible as most proteins have ill-defined or unknown activity and may not function outside of their native contexts. These are the dark undruggable expanses, and charting them will require advanced synthesis and analytical technologies that can generalize probe discovery, irrespective of mature protein function, to fulfill the Genome Project's vision of proteome-wide control of cellular pharmacology.

What repeat expansion disorders can teach us about the Central Dogma

Pathogenic repeat sequences underlie several human disorders, including amyotrophic lateral sclerosis, Huntington's disease, and myotonic dystrophy. Here, we speak to several researchers about how repeat sequences have been implicated in affecting all aspects of the Central Dogma of molecular biology through their effects on DNA, RNA, and protein.

Special Issue: Spatial Omics

GEN BiotechnologyVol. 2, No. 1 Call for PapersFree AccessSpecial Issue: Spatial OmicsDeadline for Manuscript Submission: May 15, 2023Guest Editors: Rong Fan and Omer BayraktarGuest Editors: Rong FanYale UniversitySearch for more papers by this author and Omer BayraktarWellcome Sanger InstituteSearch for more papers by this authorPublished Online:15 Feb 2023https://doi.org/10.1089/genbio.2023.29076.cfpAboutSectionsPDF/EPUB Permissions & CitationsPermissionsDownload CitationsTrack CitationsAdd to favorites Back To Publication ShareShare onFacebookTwitterLinked InRedditEmail Single-cell omics has revolutionized biological and biomedical research in the past decade despite the inability to measure single cells in the tissue context. Spatial omics, which allows for profiling a range of biomolecules with high spatial resolution across the central dogma of molecular biology directly in the tissue context, not only offers spatial information but unlocks unprecedented new opportunities to delve into clinical specimens for human biology research, therapeutic discovery, and translational medicine. Spatial omics is becoming one of the fastest-paced growth areas in the biotech industry and poised to drive the next wave of biology revolution with widespread and far-reaching impact in all major fields of life science and medicine.GEN Biotechnology is pleased to announce a call for papers for our inaugural special issue—Spatial Omics.This collection of research articles, reviews, and perspectives will be published in late 2023. We invite researchers to submit without delay manuscripts describing original research on any aspect of spatial and single-cell biological research. We will also consider relevant guest commentaries and review articles.Specific topics may include (but are not confined to): Sequencing based spatial omics (i.e., transcriptome, proteome, epigenome, genome).High-plex imaging of proteins, transcripts, or epigenomic/genomic featuresSpatial proteomics and metabolomicsSpatial multi-omics and multi-modality tissue profilingComputational methods and tools for spatial biology (machine learning, data deconvolution, mathematical modeling, data visualization)Spatial omics to profile tumor heterogeneity and microenvironmentsSpatial omics in neuroscience, neurological or neurodegenerative disease researchSpatial omics in aging, senescence, metabolic and chronic diseases.Manuscripts will receive prompt peer review and accepted articles will be published online (epub) ahead of print. Please refer to our Instructions for Authors at www.liebertpub.com/genbio before submitting your manuscript.Presubmission inquiries may be sent to GEN Biotechnology (editor@genbiotechjournal.com). This special issue will be published in late 2023.Advantages of publishing in GEN Biotechnology include:Rapid, high-quality peer review, and editorial oversightFast electronic submissionMaximum exposure: accessible in 170 countries worldwideHigh visibility: International press and social media outreachOpen Access options availableVisit the Instructions for Authors:www.liebertpub.com/genbioSubmit your paper for peer review online:https://mc.manuscriptcentral.com/genbioFiguresReferencesRelatedDetails Volume 2Issue 1Feb 2023 InformationCopyright 2023, Mary Ann Liebert, Inc., publishersTo cite this article:Guest Editors: Rong Fan and Omer Bayraktar.Special Issue: Spatial Omics.GEN Biotechnology.Feb 2023.3-4.http://doi.org/10.1089/genbio.2023.29076.cfpPublished in Volume: 2 Issue 1: February 15, 2023PDF download

Centromere and telomere dynamics reveal heterogeneity of the human cell nucleus.

The human genome contains genetic information essential for life, controlling all cellular processes via the central dogma of biology. It is a canonical example of a living polymer, yet the physical principles underlying its dynamical self-organization in the cell nucleus remain unknown. In this work, we study motions of centromeres and telomeres - the centers and free ends of chromosomes - at short time scales of seconds in live human cells. Our findings reveal a tenfold difference in their displacements, exceeding by far predictions of polymer theories. Remarkably, we find that this unexpectedly large difference arises due to centromere and telomere localization in unique nuclear environments, distinct in both their biological activity and physical properties. We locate the former in the genome's silenced parts, the latter in its transcriptionally active parts. Moreover, our data show that centromeres are embedded in a solid-like environment, while telomeres’ surroundings are liquid-like, directly affecting the timescales and length scales of their respective motions. Our results suggest a key role of nuclear heterogeneity in genome dynamics, which we corroborate by biochemical perturbations of nuclear structures such as heterochromatin and nuclear speckles. Finally, upon homogenizing the nuclear environment by a hypoosmotic shock, we observe equal centromeric and telomeric motions, confirming our hypothesis. Our observations show that the nuclear environment directly impacts timescales and length scales of local genomic motions, which may affect the spatiotemporal gene regulation across the cell nucleus [Clavijo AS, Ionov S & Zidovska A, Submitted].

The complexity of transferring genetic information

The Central Dogma has been a useful conceptualization of the transfer of genetic information, and our understanding of the detailed mechanisms involved in that transfer continues to evolve. Here, we speak to several scientists about their research, how it influences our understanding of information transfer, and questions for the future.

Basis of speed and fidelity in eukaryotic translation termination.

It was unclear how eukaryotic translation termination, which liberates newly synthesized polypeptides from the ribosome, is fast yet also specific for stop codons. Here we used an in vitro- reconstituted yeast translation system and single-molecule assays to directly observe the molecular choreography that underlies translation termination. We found that the highly conserved eukaryotic release factors bind rapidly to ribosomes and elicit termination via a multistep process that is similar to the selection of proper tRNAs in translation elongation. This work is not only the first direct observation of the order and timing of core events in the central dogma, but also explained how fidelity is maintained without sacrificing speed. We further found that a diverse set of stop-codon readthrough effectors also moonlight as termination inhibitors, suggesting a new potential route for the treatment of the 11% of heritable human diseases caused by premature stop codons.

Mechanical stress affects dynamics and rheology of the human genome.

Material properties of the genome are critical for proper cellular function - they directly affect timescales and length scales of DNA transactions such as transcription, replication and DNA repair, which in turn impact all cellular processes via the central dogma. Hence, elucidating the genome's rheology in vivo may help reveal physical principles underlying the genome's organization and function. Here, we present a novel noninvasive approach to study the genome's rheology and its response to mechanical stress inform of nuclear injection. Specifically, we use Displacement Correlation Spectroscopy [1] to map nucleus-wide genomic motions pre/post injection, during which we deposit rheological probes inside the nucleus [2]. While the former informs on the bulk rheology of the genome pre/post injection, the latter informs on the rheology of the probe's surroundings. Our results reveal that mechanical stress of injection leads to local as well as nucleus-wide changes in the genome's compaction, dynamics and rheology. We find that the genome pre-injection exhibits subdiffusive motions, which are coherent over several micrometers. In contrast, genomic motions post-injection become faster and uncorrelated, moreover, the genome becomes less compact and more viscous across the entire nucleus. In addition, we use the injected particles as rheological probes and find the genome to condense locally around them, mounting a local elastic response. Taken together, our results show that mechanical stress alters both dynamics and material properties of the genome. These changes are consistent with those observed upon DNA damage, suggesting that the genome experiences similar effects during the injection process [2].