bioRxiv : the preprint server for biology最新文献

{"title":"Predicting the effect of CRISPR-Cas9-based epigenome editing.","authors":"Sanjit Singh Batra, Alan Cabrera, Jeffrey P Spence, Jacob Goell, Selvalakshmi S Anand, Isaac B Hilton, Yun S Song","doi":"10.1101/2023.10.03.560674","DOIUrl":"10.1101/2023.10.03.560674","url":null,"abstract":"<p><p>Epigenetic regulation orchestrates mammalian transcription, but functional links between them remain elusive. To tackle this problem, we use epigenomic and transcriptomic data from 13 ENCODE cell types to train machine learning models to predict gene expression from histone post-translational modifications (PTMs), achieving transcriptome-wide correlations of ∼ 0.70 - 0.79 for most cell types. Our models recapitulate known associations between histone PTMs and expression patterns, including predicting that acetylation of histone subunit H3 lysine residue 27 (H3K27ac) near the transcription start site (TSS) significantly increases expression levels. To validate this prediction experimentally and investigate how natural vs. engineered deposition of H3K27ac might differentially affect expression, we apply the synthetic dCas9-p300 histone acetyltransferase system to 8 genes in the HEK293T cell line and to 5 genes in the K562 cell line. Further, to facilitate model building, we perform MNase-seq to map genome-wide nucleosome occupancy levels in HEK293T. We observe that our models perform well in accurately ranking relative fold-changes among genes in response to the dCas9-p300 system; however, their ability to rank fold-changes within individual genes is noticeably diminished compared to predicting expression across cell types from their native epigenetic signatures. Our findings highlight the need for more comprehensive genome-scale epigenome editing datasets, better understanding of the actual modifications made by epigenome editing tools, and improved causal models that transfer better from endogenous cellular measurements to perturbation experiments. Together these improvements would facilitate the ability to understand and predictably control the dynamic human epigenome with consequences for human health.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10592942/pdf/nihpp-2023.10.03.560674v1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49694644","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-plateau force-extension curves of long double-stranded DNA molecules.","authors":"Alexander Y Afanasyev, Alexey V Onufriev","doi":"10.1101/2023.03.12.532320","DOIUrl":"10.1101/2023.03.12.532320","url":null,"abstract":"<p><p>When highly stretched, double-stranded DNA exhibits a plateau region in its force-extension curve. Using a bead-spring coarse-grained dynamic model based on a non-convex potential, we predict that a long double-stranded DNA fragment made of several consecutive segments with substantially different plateau force values for each segment will exhibit multiple distinct plateau regions in the force-extension curve under physiologically relevant solvent conditions. For example, a long composite double-stranded (ds) DNA fragment consisting of two equal-length segments characterized by two different plateau force values, such as the poly(dA-dT)-poly(dG-dC) fragment, is predicted to exhibit two distinct plateau regions in its force-extension curve; a long composite dsDNA fragment consisting of three segments having three different plateau force values is predicted to have three distinct plateau regions. The formation of mixed states of slightly and highly stretched DNA, co-existing with macroscopically distinct phases of uniformly stretched DNA is also predicted. When one of the segments overstretches, the extensions of the segments can differ drastically. For example, for the poly(dA-dT)-poly(dG-dC) composite fragment, in the middle of the first plateau, 96.7 % of the total extension of the fragment (relative to <math> <mrow><msub><mi>L</mi> <mi>x</mi></msub> <mo>/</mo> <msub><mi>L</mi> <mn>0</mn></msub> <mo>≈</mo> <mn>1.0</mn></mrow> </math> ) comes from the poly(dA-dT) segment, while only 3.3 % of it comes from the poly(dG-dC) segment. The order of the segments has little effect on the force-extension curve or the distribution of conformational states. We speculate that the distinct structural states of stretched double-stranded DNA may have functional importance. For example, these states may modulate, in a sequence-dependent manner, the rate of double-stranded DNA processing by key cellular machines.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":"29 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11888220/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73938937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dynamic representation of multidimensional object properties in the human brain.","authors":"Lina Teichmann, Martin N Hebart, Chris I Baker","doi":"10.1101/2023.09.08.556679","DOIUrl":"10.1101/2023.09.08.556679","url":null,"abstract":"<p><p>Our visual world consists of an immense number of unique objects and yet, we are easily able to identify, distinguish, interact, and reason about the things we see within a few hundred milliseconds. This requires that we integrate and focus on a wide array of object properties to support diverse behavioral goals. In the current study, we used a large-scale and comprehensively sampled stimulus set and developed an analysis approach to determine if we could capture how rich, multidimensional object representations unfold over time in the human brain. We modelled time-resolved MEG signals evoked by viewing single presentations of tens of thousands of object images based on millions of behavioral judgments. Extracting behavior-derived object dimensions from similarity judgments, we developed a data-driven approach to guide our understanding of the neural representation of the object space and found that every dimension is reflected in the neural signal. Studying the temporal profiles for different object dimensions we found that the time courses fell into two broad types, with either a distinct and early peak (∼125 ms) or a slow rise to a late peak (∼300 ms). Further, early effects were stable across participants, in contrast to later effects which showed more variability, suggesting that early peaks may carry stimulus-specific and later peaks more participant-specific information. Dimensions with early peaks appeared to be primarily visual dimensions and those with later peaks more conceptual, suggesting that conceptual representations are more variable across people. Together, these data provide a comprehensive account of how behavior-derived object properties unfold in the human brain and form the basis for the rich nature of object vision.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/7d/1e/nihpp-2023.09.08.556679v2.PMC10515754.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41170855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functional Identification of Language-Responsive Channels in Individual Participants in MEG Investigations.","authors":"Mathias Huybrechts, Rose Bruffaerts, Alvince Pongos, Cory Shain, Benjamin Lipkin, Matthew Siegelman, Vincent Wens, Martin Sjøgård, Idan Blank, Serge Goldman, Xavier De Tiège, Evelina Fedorenko","doi":"10.1101/2023.03.23.533424","DOIUrl":"10.1101/2023.03.23.533424","url":null,"abstract":"<p><p>Making meaningful inferences about the functional architecture of the language system requires the ability to refer to the same neural units across individuals and studies. Traditional brain imaging approaches align and average brains together in a common space. However, lateral frontal and temporal cortices, where the language system resides, is characterized by high structural and functional inter-individual variability, which reduces the sensitivity and functional resolution of group-averaging analyses. This issue is compounded by the fact that language areas lay in close proximity to regions of other large-scale networks with different functional profiles. A solution inspired by visual neuroscience is to identify language areas functionally in each individual brain using a 'localizer' task (e.g., a language comprehension task). This approach has proven productive in fMRI, yielding a number of robust and replicable findings about the language system. Here, we extend this approach to MEG. Across two experiments (one in Dutch speakers, n=19; one in English speakers, n=23), we examined neural responses to the processing of sentences and a control condition (nonword sequences). In both the time and frequency domains, we demonstrated that the topography of neural responses to language is spatially stable within individuals but varies across individuals. Consequently, analyses that take this inter-individual variability into account are characterized by greater sensitivity, compared to the group-level analyses. In summary, similar to fMRI, functional identification within individuals yields benefits in MEG, thus opening the door to future investigations of language processing including questions where whole-brain coverage and temporal resolution are both critical.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/98/e7/nihpp-2023.03.23.533424v1.PMC10055362.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9650999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Widespread epistasis shapes RNA Polymerase II active site function and evolution.","authors":"Bingbing Duan, Chenxi Qiu, Sing-Hoi Sze, Craig Kaplan","doi":"10.1101/2023.02.27.530048","DOIUrl":"10.1101/2023.02.27.530048","url":null,"abstract":"<p><p>Multi-subunit RNA Polymerases (msRNAPs) are responsible for transcription in all kingdoms of life. These enzymes rely on dynamic, highly conserved active site domains such as the so-called \"trigger loop\" (TL) to accomplish steps in the transcription cycle. Mutations in the RNA polymerase II (Pol II) TL confer a spectrum of biochemical and genetic phenotypes that suggest two main classes, which decrease or increase catalysis or other nucleotide addition cycle (NAC) events. The Pol II active site relies on networks of residue interactions to function and mutations likely perturb these networks in ways that may alter mechanisms. We have undertaken a structural genetics approach to reveal residue interactions within and surrounding the Pol II TL - determining its \"interaction landscape\" - by deep mutational scanning in <i>Saccharomyces cerevisiae</i> Pol II. This analysis reveals connections between TL residues and surrounding domains, demonstrating that TL function is tightly coupled to its specific enzyme context.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/5e/78/nihpp-2023.02.27.530048v2.PMC10002619.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9307975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"WITHDRAWN: <i>MHC-B</i> Diversity and Signs of Respiratory Illness in Wild, East African Chimpanzees ( <i>Pan troglodytes schweinfurthii</i> ).","authors":"S R Phillips","doi":"10.1101/2023.08.02.551731","DOIUrl":"10.1101/2023.08.02.551731","url":null,"abstract":"<p><p>bioRxiv has withdrawn this preprint following a formal investigation by the University of New Mexico Office of Research Integrity and Compliance.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10418158/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9991210","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"How a disordered linker in the Polycomb protein Polyhomeotic tunes phase separation and oligomerization.","authors":"Tim M Gemeinhardt, Roshan M Regy, Tien M Phan, Nanu Pal, Jyoti Sharma, Olga Senkovich, Andrea J Mendiola, Heather J Ledterman, Amy Henrickson, Daniel Lopes, Utkarsh Kapoor, Ashish Bihani, Djamouna Sihou, Young C Kim, David Jeruzalmi, Borries Demeler, Chongwoo A Kim, Jeetain Mittal, Nicole J Francis","doi":"10.1101/2023.10.26.564264","DOIUrl":"10.1101/2023.10.26.564264","url":null,"abstract":"<p><p>Biomolecular condensates are increasingly appreciated for their function in organizing and regulating biochemical processes in cells, including chromatin function. Condensate formation and properties are encoded in protein sequence but the mechanisms linking sequence to macroscale properties are incompletely understood. Cross species comparisons can reveal mechanisms either because they identify conserved functions or because they point to important differences. Here we use <i>in vitro</i> reconstitution and molecular dynamics simulations to compare <i>Drosophila</i> and human sequences that regulate condensate formation driven by the sterile alpha motif (SAM) oligomerization domain in the Polyhomeotic (Ph) subunit of the chromatin regulatory complex PRC1. We discover evolutionarily diverged contacts between the conserved SAM and the disordered linker that connects it to the rest of Ph. Linker-SAM interactions increase oligomerization and regulate formation and properties of reconstituted condensates. Oligomerization affects condensate dynamics but, in most cases, has little effect on their formation. Linker-SAM interactions also affect condensate formation in <i>Drosophila</i> and human cells, and growth in <i>Drosophila</i> imaginal discs. Our data show how evolutionary sequence changes in linkers connecting conserved structured domains can alter condensate properties.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10634872/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"92157768","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tree-based differential testing using inferential uncertainty for RNA-Seq.","authors":"Noor Pratap Singh, Euphy Y Wu, Jason Fan, Michael I Love, Rob Patro","doi":"10.1101/2023.12.25.573288","DOIUrl":"10.1101/2023.12.25.573288","url":null,"abstract":"<p><p>Identifying differentially expressed transcripts poses a crucial yet challenging problem in transcriptomics. Substantial uncertainty is associated with the abundance estimates of certain transcripts which, if ignored, can lead to the exaggeration of false positives and, if included, may lead to reduced power. Given a set of RNA-Seq samples, TreeTerminus arranges transcripts in a hierarchical tree structure that encodes different layers of resolution for interpretation of the abundance of transcriptional groups, with uncertainty generally decreasing as one ascends the tree from the leaves. We introduce mehenDi, which utilizes the tree structure from TreeTerminus for differential testing. The nodes output by mehenDi, called the selected nodes are determined in a data-driven manner to maximize the signal that can be extracted from the data while controlling for the uncertainty associated with estimating the transcript abundances. The identified selected nodes can include transcripts and inner nodes, with no two nodes having an ancestor/descendant relationship. We evaluated our method on both simulated and experimental datasets, comparing its performance with other tree-based differential methods as well as with uncertainty-aware differential transcript/gene expression methods. Our method detects inner nodes that show a strong signal for differential expression, which would have been overlooked when analyzing the transcripts alone.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10793400/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139486614","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MET variants with activating N-lobe mutations identified in hereditary papillary renal cell carcinomas still require ligand stimulation.","authors":"Célia Guérin, Audrey Vinchent, Marie Fernandes, Isabelle Damour, Agathe Laratte, Rémi Tellier, Gabriella O Estevam, Jean-Pascal Meneboo, Céline Villenet, Clotilde Descarpentries, James S Fraser, Martin Figeac, Alexis B Cortot, Etienne Rouleau, David Tulasne","doi":"10.1101/2023.11.03.565283","DOIUrl":"10.1101/2023.11.03.565283","url":null,"abstract":"<p><p>In hereditary papillary renal cell carcinoma (HPRCC), the hepatocyte growth factor receptor (MET) receptor tyrosine kinase (RTK) mutations recorded to date are located in the kinase domain and lead to constitutive MET activation. This contrasts with MET mutations identified in non-small cell lung cancer (NSCLC), which lead to exon 14 skipping and deletion of a regulatory domain: in this latter case, the mutated receptor still requires ligand stimulation. Sequencing of MET in samples from 158 HPRCC and 2808 NSCLC patients revealed ten uncharacterized mutations. Four of these, all found in HPRCC and leading to amino acid substitutions in the N-lobe of the MET kinase, proved able to induce cell transformation, which was further enhanced by hepatocyte growth factor (HGF) stimulation: His1086Leu, Ile1102Thr, Leu1130Ser and Cis1125Gly. Similar to the variant resulting in MET exon 14 skipping, the two N-lobe MET variants His1086Leu and Ile1102Thr were found to require stimulation by HGF in order to strongly activate downstream signaling pathways and epithelial cell motility. The Ile1102Thr mutation also displayed transforming potential, promoting tumor growth in a xenograft model. In addition, the N-lobe-mutated MET variants were found to trigger a common HGF-stimulation-dependent transcriptional program, consistent with an observed increase in cell motility and invasion. Altogether, this functional characterization revealed that N-lobe variants still require ligand stimulation, in contrast to other RTK variants. This suggests that HGF expression in the tumor microenvironment is important for tumor growth. The sensitivity of these variants to MET inhibitors opens the way for use of targeted therapies for patients harboring the corresponding mutations.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10635098/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"107593017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Location- and feature-based selection histories make independent, qualitatively distinct contributions to urgent visuomotor performance.","authors":"Emily E Oor, Emilio Salinas, Terrence R Stanford","doi":"10.1101/2024.05.29.596532","DOIUrl":"10.1101/2024.05.29.596532","url":null,"abstract":"<p><p>Attention mechanisms guide visuomotor behavior by weighing physical salience and internal goals to prioritize stimuli as choices for action. Although less well studied, selection history, which reflects multiple facets of experience with recent events, is increasingly recognized as a distinct source of attentional bias. To examine how selection history impacts saccadic choices, we trained two macaque monkeys to perform an urgent version of an oddball search task in which a red target appeared among three green distracters, or vice versa. By imposing urgency, performance could be tracked continuously as it transitioned from uninformed guesses to informed choices as a function of processing time. This, in turn, permitted assessment of attentional control as manifest in motor biases, processing speed, and asymptotic accuracy. Here, we found that the probability of making a correct choice was strongly modulated by the histories of preceding target locations and target colors. Crucially, although both effects were gated by success (or reward), their dynamics were clearly distinct: whereas location history promoted a motor bias, color history modulated perceptual sensitivity, and these influences acted independently. Thus, combined selection histories can give rise to enormous swings in visuomotor performance even in simple tasks with highly discriminable stimuli.</p>","PeriodicalId":72407,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11160778/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141297437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}