1
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Hummel NFC, Markel K, Stefani J, Staller MV, Shih PM. Systematic identification of transcriptional activation domains from non-transcription factor proteins in plants and yeast. Cell Syst 2024:S2405-4712(24)00151-0. [PMID: 38866009 DOI: 10.1016/j.cels.2024.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 04/26/2024] [Accepted: 05/22/2024] [Indexed: 06/14/2024]
Abstract
Transcription factors can promote gene expression through activation domains. Whole-genome screens have systematically mapped activation domains in transcription factors but not in non-transcription factor proteins (e.g., chromatin regulators and coactivators). To fill this knowledge gap, we employed the activation domain predictor PADDLE to analyze the proteomes of Arabidopsis thaliana and Saccharomyces cerevisiae. We screened 18,000 predicted activation domains from >800 non-transcription factor genes in both species, confirming that 89% of candidate proteins contain active fragments. Our work enables the annotation of hundreds of nuclear proteins as putative coactivators, many of which have never been ascribed any function in plants. Analysis of peptide sequence compositions reveals how the distribution of key amino acids dictates activity. Finally, we validated short, "universal" activation domains with comparable performance to state-of-the-art activation domains used for genome engineering. Our approach enables the genome-wide discovery and annotation of activation domains that can function across diverse eukaryotes.
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Affiliation(s)
- Niklas F C Hummel
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA; Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Kasey Markel
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA; Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jordan Stefani
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Max V Staller
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub-San Francisco, San Francisco, CA 9415, USA.
| | - Patrick M Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA; Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
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2
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Villiger L, Joung J, Koblan L, Weissman J, Abudayyeh OO, Gootenberg JS. CRISPR technologies for genome, epigenome and transcriptome editing. Nat Rev Mol Cell Biol 2024; 25:464-487. [PMID: 38308006 DOI: 10.1038/s41580-023-00697-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2023] [Indexed: 02/04/2024]
Abstract
Our ability to edit genomes lags behind our capacity to sequence them, but the growing understanding of CRISPR biology and its application to genome, epigenome and transcriptome engineering is narrowing this gap. In this Review, we discuss recent developments of various CRISPR-based systems that can transiently or permanently modify the genome and the transcriptome. The discovery of further CRISPR enzymes and systems through functional metagenomics has meaningfully broadened the applicability of CRISPR-based editing. Engineered Cas variants offer diverse capabilities such as base editing, prime editing, gene insertion and gene regulation, thereby providing a panoply of tools for the scientific community. We highlight the strengths and weaknesses of current CRISPR tools, considering their efficiency, precision, specificity, reliance on cellular DNA repair mechanisms and their applications in both fundamental biology and therapeutics. Finally, we discuss ongoing clinical trials that illustrate the potential impact of CRISPR systems on human health.
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Affiliation(s)
- Lukas Villiger
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA
| | - Julia Joung
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Luke Koblan
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jonathan Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Omar O Abudayyeh
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA.
| | - Jonathan S Gootenberg
- McGovern Institute for Brain Research, Massachusetts Institute of Technology Cambridge, Cambridge, MA, USA.
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3
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Zhang X, Mille-Fragoso LS, Kaseniit KE, Call CC, Zhang M, Hu Y, Xie Y, Gao XJ. Post-Transcriptional Modular Synthetic Receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592453. [PMID: 38746461 PMCID: PMC11092781 DOI: 10.1101/2024.05.03.592453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Inspired by the power of transcriptional synthetic receptors and hoping to complement them to expand the toolbox for cell engineering, we establish LIDAR (Ligand-Induced Dimerization Activating RNA editing), a modular post-transcriptional synthetic receptor platform that harnesses RNA editing by ADAR. LIDAR is compatible with various receptor architectures in different cellular contexts, and enables the sensing of diverse ligands and the production of functional outputs. Furthermore, LIDAR can sense orthogonal signals in the same cell and produce synthetic spatial patterns, potentially enabling the programming of complex multicellular behaviors. Finally, LIDAR is compatible with compact encoding and can be delivered by synthetic mRNA. Thus, LIDAR expands the family of synthetic receptors, holding the promise to empower basic research and therapeutic applications.
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4
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Steinhauser S, Estoppey D, Buehler DP, Xiong Y, Pizzato N, Rietsch A, Wu F, Leroy N, Wunderlin T, Claerr I, Tropberger P, Müller M, Davison LM, Sheng Q, Bergling S, Wild S, Moulin P, Liang J, English WJ, Williams B, Knehr J, Altorfer M, Reyes A, Mickanin C, Hoepfner D, Nigsch F, Frederiksen M, Flynn CR, Fodor BD, Brown JD, Kolter C. The transcription factor ZNF469 regulates collagen production in liver fibrosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591188. [PMID: 38712281 PMCID: PMC11071482 DOI: 10.1101/2024.04.25.591188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Non-alcoholic fatty liver disease (NAFLD) - characterized by excess accumulation of fat in the liver - now affects one third of the world's population. As NAFLD progresses, extracellular matrix components including collagen accumulate in the liver causing tissue fibrosis, a major determinant of disease severity and mortality. To identify transcriptional regulators of fibrosis, we computationally inferred the activity of transcription factors (TFs) relevant to fibrosis by profiling the matched transcriptomes and epigenomes of 108 human liver biopsies from a deeply-characterized cohort of patients spanning the full histopathologic spectrum of NAFLD. CRISPR-based genetic knockout of the top 100 TFs identified ZNF469 as a regulator of collagen expression in primary human hepatic stellate cells (HSCs). Gain- and loss-of-function studies established that ZNF469 regulates collagen genes and genes involved in matrix homeostasis through direct binding to gene bodies and regulatory elements. By integrating multiomic large-scale profiling of human biopsies with extensive experimental validation we demonstrate that ZNF469 is a transcriptional regulator of collagen in HSCs. Overall, these data nominate ZNF469 as a previously unrecognized determinant of NAFLD-associated liver fibrosis.
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5
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Lambourne L, Mattioli K, Santoso C, Sheynkman G, Inukai S, Kaundal B, Berenson A, Spirohn-Fitzgerald K, Bhattacharjee A, Rothman E, Shrestha S, Laval F, Yang Z, Bisht D, Sewell JA, Li G, Prasad A, Phanor S, Lane R, Campbell DM, Hunt T, Balcha D, Gebbia M, Twizere JC, Hao T, Frankish A, Riback JA, Salomonis N, Calderwood MA, Hill DE, Sahni N, Vidal M, Bulyk ML, Fuxman Bass JI. Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584681. [PMID: 38617209 PMCID: PMC11014633 DOI: 10.1101/2024.03.12.584681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Most human Transcription factors (TFs) genes encode multiple protein isoforms differing in DNA binding domains, effector domains, or other protein regions. The global extent to which this results in functional differences between isoforms remains unknown. Here, we systematically compared 693 isoforms of 246 TF genes, assessing DNA binding, protein binding, transcriptional activation, subcellular localization, and condensate formation. Relative to reference isoforms, two-thirds of alternative TF isoforms exhibit differences in one or more molecular activities, which often could not be predicted from sequence. We observed two primary categories of alternative TF isoforms: "rewirers" and "negative regulators", both of which were associated with differentiation and cancer. Our results support a model wherein the relative expression levels of, and interactions involving, TF isoforms add an understudied layer of complexity to gene regulatory networks, demonstrating the importance of isoform-aware characterization of TF functions and providing a rich resource for further studies.
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Affiliation(s)
- Luke Lambourne
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kaia Mattioli
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Clarissa Santoso
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - Gloria Sheynkman
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sachi Inukai
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Babita Kaundal
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anna Berenson
- Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, MA, USA
| | - Kerstin Spirohn-Fitzgerald
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anukana Bhattacharjee
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Elisabeth Rothman
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Florent Laval
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- TERRA Teaching and Research Centre, University of Liège, Gembloux, Belgium
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège, Belgium
| | - Zhipeng Yang
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Deepa Bisht
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jared A Sewell
- Department of Biology, Boston University, Boston, MA, USA
| | - Guangyuan Li
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Anisa Prasad
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Harvard College, Cambridge MA, USA
| | - Sabrina Phanor
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ryan Lane
- Department of Biology, Boston University, Boston, MA, USA
| | | | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Dawit Balcha
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marinella Gebbia
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health System, Toronto, Ontario, Canada
| | - Jean-Claude Twizere
- TERRA Teaching and Research Centre, University of Liège, Gembloux, Belgium
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège, Belgium
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Adam Frankish
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège, Belgium
| | - Josh A Riback
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Nathan Salomonis
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Juan I Fuxman Bass
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
- Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, MA, USA
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6
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Yan J, Oyler-Castrillo P, Ravisankar P, Ward CC, Levesque S, Jing Y, Simpson D, Zhao A, Li H, Yan W, Goudy L, Schmidt R, Solley SC, Gilbert LA, Chan MM, Bauer DE, Marson A, Parsons LR, Adamson B. Improving prime editing with an endogenous small RNA-binding protein. Nature 2024; 628:639-647. [PMID: 38570691 PMCID: PMC11023932 DOI: 10.1038/s41586-024-07259-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 02/29/2024] [Indexed: 04/05/2024]
Abstract
Prime editing enables the precise modification of genomes through reverse transcription of template sequences appended to the 3' ends of CRISPR-Cas guide RNAs1. To identify cellular determinants of prime editing, we developed scalable prime editing reporters and performed genome-scale CRISPR-interference screens. From these screens, a single factor emerged as the strongest mediator of prime editing: the small RNA-binding exonuclease protection factor La. Further investigation revealed that La promotes prime editing across approaches (PE2, PE3, PE4 and PE5), edit types (substitutions, insertions and deletions), endogenous loci and cell types but has no consistent effect on genome-editing approaches that rely on standard, unextended guide RNAs. Previous work has shown that La binds polyuridine tracts at the 3' ends of RNA polymerase III transcripts2. We found that La functionally interacts with the 3' ends of polyuridylated prime editing guide RNAs (pegRNAs). Guided by these results, we developed a prime editor protein (PE7) fused to the RNA-binding, N-terminal domain of La. This editor improved prime editing with expressed pegRNAs and engineered pegRNAs (epegRNAs), as well as with synthetic pegRNAs optimized for La binding. Together, our results provide key insights into how prime editing components interact with the cellular environment and suggest general strategies for stabilizing exogenous small RNAs therein.
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Affiliation(s)
- Jun Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Paul Oyler-Castrillo
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Purnima Ravisankar
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Carl C Ward
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Sébastien Levesque
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute, Cambridge, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Yangwode Jing
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Danny Simpson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Anqi Zhao
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Hui Li
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Weihao Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Laine Goudy
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Arc Institute, Palo Alto, CA, USA
| | - Ralf Schmidt
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Sabrina C Solley
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Luke A Gilbert
- Arc Institute, Palo Alto, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Michelle M Chan
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute, Cambridge, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Lance R Parsons
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Britt Adamson
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
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7
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Lobel JH, Ingolia NT. Defining the mechanisms and properties of post-transcriptional regulatory disordered regions by high-throughput functional profiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578453. [PMID: 38370681 PMCID: PMC10871298 DOI: 10.1101/2024.02.01.578453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Disordered regions within RNA binding proteins are required to control mRNA decay and protein synthesis. To understand how these disordered regions modulate gene expression, we surveyed regulatory activity across the entire disordered proteome using a high-throughput functional assay. We identified hundreds of regulatory sequences within intrinsically disordered regions and demonstrate how these elements cooperate with core mRNA decay machinery to promote transcript turnover. Coupling high-throughput functional profiling with mutational scanning revealed diverse molecular features, ranging from defined motifs to overall sequence composition, underlying the regulatory effects of disordered peptides. Machine learning analysis implicated aromatic residues in particular contexts as critical determinants of repressor activity, consistent with their roles in forming protein-protein interactions with downstream effectors. Our results define the molecular principles and biochemical mechanisms that govern post-transcriptional gene regulation by disordered regions and exemplify the encoding of diverse yet specific functions in the absence of well-defined structure.
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Affiliation(s)
- Joseph H Lobel
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Lead contact
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8
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Doughty BR, Hinks MM, Schaepe JM, Marinov GK, Thurm AR, Rios-Martinez C, Parks BE, Tan Y, Marklund E, Dubocanin D, Bintu L, Greenleaf WJ. Single-molecule chromatin configurations link transcription factor binding to expression in human cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.02.578660. [PMID: 38352517 PMCID: PMC10862896 DOI: 10.1101/2024.02.02.578660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
The binding of multiple transcription factors (TFs) to genomic enhancers activates gene expression in mammalian cells. However, the molecular details that link enhancer sequence to TF binding, promoter state, and gene expression levels remain opaque. We applied single-molecule footprinting (SMF) to measure the simultaneous occupancy of TFs, nucleosomes, and components of the transcription machinery on engineered enhancer/promoter constructs with variable numbers of TF binding sites for both a synthetic and an endogenous TF. We find that activation domains enhance a TF's capacity to compete with nucleosomes for binding to DNA in a BAF-dependent manner, TF binding on nucleosome-free DNA is consistent with independent binding between TFs, and average TF occupancy linearly contributes to promoter activation rates. We also decompose TF strength into separable binding and activation terms, which can be tuned and perturbed independently. Finally, we develop thermodynamic and kinetic models that quantitatively predict both the binding microstates observed at the enhancer and subsequent time-dependent gene expression. This work provides a template for quantitative dissection of distinct contributors to gene activation, including the activity of chromatin remodelers, TF activation domains, chromatin acetylation, TF concentration, TF binding affinity, and TF binding site configuration.
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Affiliation(s)
| | - Michaela M Hinks
- Bioengineering Department, Stanford University, Stanford, CA 94305, USA
| | - Julia M Schaepe
- Bioengineering Department, Stanford University, Stanford, CA 94305, USA
| | - Georgi K Marinov
- Genetics Department, Stanford University, Stanford, CA 94305, USA
| | - Abby R Thurm
- Biophysics Graduate Program, Stanford University, Stanford, CA 94305, USA
| | | | - Benjamin E Parks
- Computer Science Department, Stanford University, Stanford, CA 94305, USA
| | - Yingxuan Tan
- Computer Science Department, Stanford University, Stanford, CA 94305, USA
| | - Emil Marklund
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Danilo Dubocanin
- Genetics Department, Stanford University, Stanford, CA 94305, USA
| | - Lacramioara Bintu
- Bioengineering Department, Stanford University, Stanford, CA 94305, USA
| | - William J Greenleaf
- Genetics Department, Stanford University, Stanford, CA 94305, USA
- Department of Applied Physics, Stanford University, Stanford, CA 94205, USA
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9
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Swain T, Pflueger C, Freytag S, Poppe D, Pflueger J, Nguyen T, Li J, Lister R. A modular dCas9-based recruitment platform for combinatorial epigenome editing. Nucleic Acids Res 2024; 52:474-491. [PMID: 38000387 PMCID: PMC10783489 DOI: 10.1093/nar/gkad1108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/28/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Targeted epigenome editing tools allow precise manipulation and investigation of genome modifications, however they often display high context dependency and variable efficacy between target genes and cell types. While systems that simultaneously recruit multiple distinct 'effector' chromatin regulators can improve efficacy, they generally lack control over effector composition and spatial organisation. To overcome this we have created a modular combinatorial epigenome editing platform, called SSSavi. This system is an interchangeable and reconfigurable docking platform fused to dCas9 that enables simultaneous recruitment of up to four different effectors, allowing precise control of effector composition and spatial ordering. We demonstrate the activity and specificity of the SSSavi system and, by testing it against existing multi-effector targeting systems, demonstrate its comparable efficacy. Furthermore, we demonstrate the importance of the spatial ordering of the recruited effectors for effective transcriptional regulation. Together, the SSSavi system enables exploration of combinatorial effector co-recruitment to enhance manipulation of chromatin contexts previously resistant to targeted editing.
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Affiliation(s)
- Tessa Swain
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
| | - Christian Pflueger
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Saskia Freytag
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
| | - Daniel Poppe
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Jahnvi Pflueger
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
| | - Trung Viet Nguyen
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
| | - Ji Kevin Li
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
| | - Ryan Lister
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
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10
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Schmok JC, Jain M, Street LA, Tankka AT, Schafer D, Her HL, Elmsaouri S, Gosztyla ML, Boyle EA, Jagannatha P, Luo EC, Kwon EJ, Jovanovic M, Yeo GW. Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion. Nat Biotechnol 2024:10.1038/s41587-023-02014-0. [PMID: 38168984 DOI: 10.1038/s41587-023-02014-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 09/29/2023] [Indexed: 01/05/2024]
Abstract
RNA-binding proteins (RBPs) modulate alternative splicing outcomes to determine isoform expression and cellular survival. To identify RBPs that directly drive alternative exon inclusion, we developed tethered function luciferase-based splicing reporters that provide rapid, scalable and robust readouts of exon inclusion changes and used these to evaluate 718 human RBPs. We performed enhanced cross-linking immunoprecipitation, RNA sequencing and affinity purification-mass spectrometry to investigate a subset of candidates with no prior association with splicing. Integrative analysis of these assays indicates surprising roles for TRNAU1AP, SCAF8 and RTCA in the modulation of hundreds of endogenous splicing events. We also leveraged our tethering assays and top candidates to identify potent and compact exon inclusion activation domains for splicing modulation applications. Using these identified domains, we engineered programmable fusion proteins that outperform current artificial splicing factors at manipulating inclusion of reporter and endogenous exons. This tethering approach characterizes the ability of RBPs to induce exon inclusion and yields new molecular parts for programmable splicing control.
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Affiliation(s)
- Jonathan C Schmok
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Manya Jain
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lena A Street
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Alex T Tankka
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Danielle Schafer
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Hsuan-Lin Her
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sara Elmsaouri
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Maya L Gosztyla
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Evan A Boyle
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Pratibha Jagannatha
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - En-Ching Luo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ester J Kwon
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
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11
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de Boer CG, Taipale J. Hold out the genome: a roadmap to solving the cis-regulatory code. Nature 2024; 625:41-50. [PMID: 38093018 DOI: 10.1038/s41586-023-06661-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/20/2023] [Indexed: 01/05/2024]
Abstract
Gene expression is regulated by transcription factors that work together to read cis-regulatory DNA sequences. The 'cis-regulatory code' - how cells interpret DNA sequences to determine when, where and how much genes should be expressed - has proven to be exceedingly complex. Recently, advances in the scale and resolution of functional genomics assays and machine learning have enabled substantial progress towards deciphering this code. However, the cis-regulatory code will probably never be solved if models are trained only on genomic sequences; regions of homology can easily lead to overestimation of predictive performance, and our genome is too short and has insufficient sequence diversity to learn all relevant parameters. Fortunately, randomly synthesized DNA sequences enable testing a far larger sequence space than exists in our genomes, and designed DNA sequences enable targeted queries to maximally improve the models. As the same biochemical principles are used to interpret DNA regardless of its source, models trained on these synthetic data can predict genomic activity, often better than genome-trained models. Here we provide an outlook on the field, and propose a roadmap towards solving the cis-regulatory code by a combination of machine learning and massively parallel assays using synthetic DNA.
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Affiliation(s)
- Carl G de Boer
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Jussi Taipale
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
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12
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Maes S, Deploey N, Peelman F, Eyckerman S. Deep mutational scanning of proteins in mammalian cells. CELL REPORTS METHODS 2023; 3:100641. [PMID: 37963462 PMCID: PMC10694495 DOI: 10.1016/j.crmeth.2023.100641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/06/2023] [Accepted: 10/20/2023] [Indexed: 11/16/2023]
Abstract
Protein mutagenesis is essential for unveiling the molecular mechanisms underlying protein function in health, disease, and evolution. In the past decade, deep mutational scanning methods have evolved to support the functional analysis of nearly all possible single-amino acid changes in a protein of interest. While historically these methods were developed in lower organisms such as E. coli and yeast, recent technological advancements have resulted in the increased use of mammalian cells, particularly for studying proteins involved in human disease. These advancements will aid significantly in the classification and interpretation of variants of unknown significance, which are being discovered at large scale due to the current surge in the use of whole-genome sequencing in clinical contexts. Here, we explore the experimental aspects of deep mutational scanning studies in mammalian cells and report the different methods used in each step of the workflow, ultimately providing a useful guide toward the design of such studies.
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Affiliation(s)
- Stefanie Maes
- VIB Center for Medical Biotechnology (CMB), Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium; Department of Biochemistry and Microbiology, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Nick Deploey
- VIB Center for Medical Biotechnology (CMB), Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Frank Peelman
- VIB Center for Medical Biotechnology (CMB), Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology (CMB), Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium.
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13
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Rosspopoff O, Trono D. Take a walk on the KRAB side. Trends Genet 2023; 39:844-857. [PMID: 37716846 DOI: 10.1016/j.tig.2023.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/18/2023] [Accepted: 08/18/2023] [Indexed: 09/18/2023]
Abstract
Canonical Krüppel-associated box (KRAB)-containing zinc finger proteins (KZFPs) act as major repressors of transposable elements (TEs) via the KRAB-mediated recruitment of the heterochromatin scaffold KRAB-associated protein (KAP)1. KZFP genes emerged some 420 million years ago in the last common ancestor of coelacanth, lungfish, and tetrapods, and dramatically expanded to give rise to lineage-specific repertoires in contemporary species paralleling their TE load and turnover. However, the KRAB domain displays sequence and function variations that reveal repeated diversions from a linear TE-KZFP trajectory. This Review summarizes current knowledge on the evolution of KZFPs and discusses how ancestral noncanonical KZFPs endowed with variant KRAB, SCAN or DUF3669 domains have been utilized to achieve KAP1-independent functions.
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Affiliation(s)
- Olga Rosspopoff
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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14
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Mahata B, Cabrera A, Brenner DA, Guerra-Resendez RS, Li J, Goell J, Wang K, Guo Y, Escobar M, Parthasarathy AK, Szadowski H, Bedford G, Reed DR, Kim S, Hilton IB. Compact engineered human mechanosensitive transactivation modules enable potent and versatile synthetic transcriptional control. Nat Methods 2023; 20:1716-1728. [PMID: 37813990 PMCID: PMC10630135 DOI: 10.1038/s41592-023-02036-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 09/05/2023] [Indexed: 10/11/2023]
Abstract
Engineered transactivation domains (TADs) combined with programmable DNA binding platforms have revolutionized synthetic transcriptional control. Despite recent progress in programmable CRISPR-Cas-based transactivation (CRISPRa) technologies, the TADs used in these systems often contain poorly tolerated elements and/or are prohibitively large for many applications. Here, we defined and optimized minimal TADs built from human mechanosensitive transcription factors. We used these components to construct potent and compact multipartite transactivation modules (MSN, NMS and eN3x9) and to build the CRISPR-dCas9 recruited enhanced activation module (CRISPR-DREAM) platform. We found that CRISPR-DREAM was specific and robust across mammalian cell types, and efficiently stimulated transcription from diverse regulatory loci. We also showed that MSN and NMS were portable across Type I, II and V CRISPR systems, transcription activator-like effectors and zinc finger proteins. Further, as proofs of concept, we used dCas9-NMS to efficiently reprogram human fibroblasts into induced pluripotent stem cells and demonstrated that mechanosensitive transcription factor TADs are efficacious and well tolerated in therapeutically important primary human cell types. Finally, we leveraged the compact and potent features of these engineered TADs to build dual and all-in-one CRISPRa AAV systems. Altogether, these compact human TADs, fusion modules and delivery architectures should be valuable for synthetic transcriptional control in biomedical applications.
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Affiliation(s)
- Barun Mahata
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Alan Cabrera
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | | | - Jing Li
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Jacob Goell
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Kaiyuan Wang
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Yannie Guo
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Mario Escobar
- Department of BioSciences, Rice University, Houston, TX, USA
| | | | - Hailey Szadowski
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, USA
| | - Guy Bedford
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Daniel R Reed
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Sunghwan Kim
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Isaac B Hilton
- Department of Bioengineering, Rice University, Houston, TX, USA.
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, USA.
- Department of BioSciences, Rice University, Houston, TX, USA.
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15
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Buell CR, Dardick C, Parrott W, Schmitz RJ, Shih PM, Tsai CJ, Urbanowicz B. Engineering custom morpho- and chemotypes of Populus for sustainable production of biofuels, bioproducts, and biomaterials. FRONTIERS IN PLANT SCIENCE 2023; 14:1288826. [PMID: 37965014 PMCID: PMC10642751 DOI: 10.3389/fpls.2023.1288826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023]
Abstract
Humans have been modifying plant traits for thousands of years, first through selection (i.e., domestication) then modern breeding, and in the last 30 years, through biotechnology. These modifications have resulted in increased yield, more efficient agronomic practices, and enhanced quality traits. Precision knowledge of gene regulation and function through high-resolution single-cell omics technologies, coupled with the ability to engineer plant genomes at the DNA sequence, chromatin accessibility, and gene expression levels, can enable engineering of complex and complementary traits at the biosystem level. Populus spp., the primary genetic model system for woody perennials, are among the fastest growing trees in temperate zones and are important for both carbon sequestration and global carbon cycling. Ample genomic and transcriptomic resources for poplar are available including emerging single-cell omics datasets. To expand use of poplar outside of valorization of woody biomass, chassis with novel morphotypes in which stem branching and tree height are modified can be fabricated thereby leading to trees with altered leaf to wood ratios. These morphotypes can then be engineered into customized chemotypes that produce high value biofuels, bioproducts, and biomaterials not only in specific organs but also in a cell-type-specific manner. For example, the recent discovery of triterpene production in poplar leaf trichomes can be exploited using cell-type specific regulatory sequences to synthesize high value terpenes such as the jet fuel precursor bisabolene specifically in the trichomes. By spatially and temporally controlling expression, not only can pools of abundant precursors be exploited but engineered molecules can be sequestered in discrete cell structures in the leaf. The structural diversity of the hemicellulose xylan is a barrier to fully utilizing lignocellulose in biomaterial production and by leveraging cell-type-specific omics data, cell wall composition can be modified in a tailored and targeted specific manner to generate poplar wood with novel chemical features that are amenable for processing or advanced manufacturing. Precision engineering poplar as a multi-purpose sustainable feedstock highlights how genome engineering can be used to re-imagine a crop species.
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Affiliation(s)
- C. Robin Buell
- Center for Applied Genetic Technologies, Institute of Plant Breeding, Genetics, and Genomics, Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - Christopher Dardick
- Agricultural Research Service, U.S. Department of Agriculture, Kearneysville, WV, United States
| | - Wayne Parrott
- Center for Applied Genetic Technologies, Institute of Plant Breeding, Genetics, and Genomics, Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - Robert J. Schmitz
- Department of Genetics, University of Georgia, Athens, GA, United States
| | - Patrick M. Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States
| | - Chung-Jui Tsai
- Department of Genetics, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, United States
| | - Breeanna Urbanowicz
- Center for Complex Carbohydrate Research, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
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16
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Sinha J, Nickels JF, Thurm AR, Ludwig CH, Archibald BN, Hinks MM, Wan J, Fang D, Bintu L. The H3.3 K36M oncohistone disrupts the establishment of epigenetic memory through loss of DNA methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562147. [PMID: 37873347 PMCID: PMC10592807 DOI: 10.1101/2023.10.13.562147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Histone H3.3 is frequently mutated in cancers, with the lysine 36 to methionine mutation (K36M) being a hallmark of chondroblastomas. While it is known that H3.3K36M changes the cellular epigenetic landscape, it remains unclear how it affects the dynamics of gene expression. Here, we use a synthetic reporter to measure the effect of H3.3K36M on silencing and epigenetic memory after recruitment of KRAB: a member of the largest class of human repressors, commonly used in synthetic biology, and associated with H3K9me3. We find that H3.3K36M, which decreases H3K36 methylation, leads to a decrease in epigenetic memory and promoter methylation weeks after KRAB release. We propose a new model for establishment and maintenance of epigenetic memory, where H3K36 methylation is necessary to convert H3K9me3 domains into DNA methylation for stable epigenetic memory. Our quantitative model can inform oncogenic mechanisms and guide development of epigenetic editing tools.
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Affiliation(s)
- Joydeb Sinha
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jan F. Nickels
- Niels Bohr Institute, University of Copenhagen, Copenhagen 2100, Denmark
| | - Abby R. Thurm
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Connor H. Ludwig
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Bella N. Archibald
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Michaela M. Hinks
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Jun Wan
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Dong Fang
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lacramioara Bintu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
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17
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Fujimori T, Rios-Martinez C, Thurm AR, Hinks MM, Doughty BR, Sinha J, Le D, Hafner A, Greenleaf WJ, Boettiger AN, Bintu L. Single-cell chromatin state transitions during epigenetic memory formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.03.560616. [PMID: 37873344 PMCID: PMC10592931 DOI: 10.1101/2023.10.03.560616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Repressive chromatin modifications are thought to compact chromatin to silence transcription. However, it is unclear how chromatin structure changes during silencing and epigenetic memory formation. We measured gene expression and chromatin structure in single cells after recruitment and release of repressors at a reporter gene. Chromatin structure is heterogeneous, with open and compact conformations present in both active and silent states. Recruitment of repressors associated with epigenetic memory produces chromatin compaction across 10-20 kilobases, while reversible silencing does not cause compaction at this scale. Chromatin compaction is inherited, but changes molecularly over time from histone methylation (H3K9me3) to DNA methylation. The level of compaction at the end of silencing quantitatively predicts epigenetic memory weeks later. Similarly, chromatin compaction at the Nanog locus predicts the degree of stem-cell fate commitment. These findings suggest that the chromatin state across tens of kilobases, beyond the gene itself, is important for epigenetic memory formation.
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Affiliation(s)
- Taihei Fujimori
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | - Abby R. Thurm
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Michaela M. Hinks
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | - Joydeb Sinha
- Department of Chemical & Systems Biology, Stanford University, Stanford, CA, USA
| | - Derek Le
- Department of Dermatology, Program in Epithelial Biology, Stanford University, Stanford, CA, USA
- Program in Cancer Biology, Stanford University, Stanford, CA, USA
| | - Antonina Hafner
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
- Current address: Department of Discovery Oncology, Genentech, CA, USA
| | - William J. Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Lacramioara Bintu
- Department of Bioengineering, Stanford University, Stanford, CA, USA
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18
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Kotha SR, Staller MV. Clusters of acidic and hydrophobic residues can predict acidic transcriptional activation domains from protein sequence. Genetics 2023; 225:iyad131. [PMID: 37462277 PMCID: PMC10550315 DOI: 10.1093/genetics/iyad131] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/03/2023] [Indexed: 10/06/2023] Open
Abstract
Transcription factors activate gene expression in development, homeostasis, and stress with DNA binding domains and activation domains. Although there exist excellent computational models for predicting DNA binding domains from protein sequence, models for predicting activation domains from protein sequence have lagged, particularly in metazoans. We recently developed a simple and accurate predictor of acidic activation domains on human transcription factors. Here, we show how the accuracy of this human predictor arises from the clustering of aromatic, leucine, and acidic residues, which together are necessary for acidic activation domain function. When we combine our predictor with the predictions of convolutional neural network (CNN) models trained in yeast, the intersection is more accurate than individual models, emphasizing that each approach carries orthogonal information. We synthesize these findings into a new set of activation domain predictions on human transcription factors.
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Affiliation(s)
- Sanjana R Kotha
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Center for Computational Biology, University of California, Berkeley, CA 94720, USA
| | - Max Valentín Staller
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Center for Computational Biology, University of California, Berkeley, CA 94720, USA
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
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19
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Vlahos AE, Call CC, Kadaba SE, Guo S, Gao XJ. Compact Programmable Control of Protein Secretion in Mammalian Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.04.560774. [PMID: 37873144 PMCID: PMC10592972 DOI: 10.1101/2023.10.04.560774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Synthetic biology currently holds immense potential to engineer the spatiotemporal control of intercellular signals for biomedicine. Programming behaviors using protein-based circuits has advantages over traditional gene circuits such as compact delivery and direct interactions with signaling proteins. Previously, we described a generalizable platform called RELEASE to enable the control of intercellular signaling through the proteolytic removal of ER-retention motifs compatible with pre-existing protease-based circuits. However, these tools lacked the ability to reliably program complex expression profiles and required numerous proteases, limiting delivery options. Here, we harness the recruitment and antagonistic behavior of endogenous 14-3-3 proteins to create RELEASE-NOT to turn off protein secretion in response to protease activity. By combining RELEASE and RELEASE-NOT, we establish a suite of protein-level processing and output modules called Compact RELEASE (compRELEASE). This innovation enables functions such as logic processing and analog signal filtering using a single input protease. Furthermore, we demonstrate the compactness of the post-translational design by using polycistronic single transcripts to engineer cells to control protein secretion via lentiviral integration and leverage mRNA delivery to selectively express cell surface proteins only in engineered cells harboring inducible proteases. CompRELEASE enables complex control of protein secretion and enhances the potential of synthetic protein circuits for therapeutic applications, while minimizing the overall genetic payload.
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Affiliation(s)
- Alexander E. Vlahos
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Connor C. Call
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Samarth E. Kadaba
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Siqi Guo
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
- The Chinese Undergraduate Visiting Research (UGVR) Program, Stanford, CA, 94305, USA
| | - Xiaojing J. Gao
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
- Neurosciences Interdepartmental Program, Stanford University, Stanford, CA, 94305, USA
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20
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Jores T, Hamm M, Cuperus JT, Queitsch C. Frontiers and techniques in plant gene regulation. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102403. [PMID: 37331209 DOI: 10.1016/j.pbi.2023.102403] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/12/2023] [Accepted: 05/19/2023] [Indexed: 06/20/2023]
Abstract
Understanding plant gene regulation has been a priority for generations of plant scientists. However, due to its complex nature, the regulatory code governing plant gene expression has yet to be deciphered comprehensively. Recently developed methods-often relying on next-generation sequencing technology and state-of-the-art computational approaches-have started to further our understanding of the gene regulatory logic used by plants. In this review, we discuss these methods and the insights into the regulatory code of plants that they can yield.
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Affiliation(s)
- Tobias Jores
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Morgan Hamm
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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21
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Mukund AX, Tycko J, Allen SJ, Robinson SA, Andrews C, Sinha J, Ludwig CH, Spees K, Bassik MC, Bintu L. High-throughput functional characterization of combinations of transcriptional activators and repressors. Cell Syst 2023; 14:746-763.e5. [PMID: 37543039 PMCID: PMC10642976 DOI: 10.1016/j.cels.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/26/2023] [Accepted: 07/06/2023] [Indexed: 08/07/2023]
Abstract
Despite growing knowledge of the functions of individual human transcriptional effector domains, much less is understood about how multiple effector domains within the same protein combine to regulate gene expression. Here, we measure transcriptional activity for 8,400 effector domain combinations by recruiting them to reporter genes in human cells. In our assay, weak and moderate activation domains synergize to drive strong gene expression, whereas combining strong activators often results in weaker activation. In contrast, repressors combine linearly and produce full gene silencing, and repressor domains often overpower activation domains. We use this information to build a synthetic transcription factor whose function can be tuned between repression and activation independent of recruitment to target genes by using a small-molecule drug. Altogether, we outline the basic principles of how effector domains combine to regulate gene expression and demonstrate their value in building precise and flexible synthetic biology tools. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Adi X Mukund
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Josh Tycko
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Sage J Allen
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Cecelia Andrews
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Joydeb Sinha
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Connor H Ludwig
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kaitlyn Spees
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Lacramioara Bintu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
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22
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Griffith AL, Zheng F, McGee AV, Miller NW, Szegletes ZM, Reint G, Gademann F, Nwolah I, Hegde M, Liu YV, Goodale A, Doench JG. Optimization of Cas12a for multiplexed genome-scale transcriptional activation. CELL GENOMICS 2023; 3:100387. [PMID: 37719144 PMCID: PMC10504673 DOI: 10.1016/j.xgen.2023.100387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/28/2023] [Accepted: 08/01/2023] [Indexed: 09/19/2023]
Abstract
Cas12a CRISPR technology, unlike Cas9, allows for facile multiplexing of guide RNAs from a single transcript, simplifying combinatorial perturbations. While Cas12a has been implemented for multiplexed knockout genetic screens, it has yet to be optimized for CRISPR activation (CRISPRa) screens in human cells. Here, we develop a new Cas12a-based transactivation domain (TAD) recruitment system using the ALFA nanobody and demonstrate simultaneous activation of up to four genes. We screen a genome-wide library to identify modulators of growth and MEK inhibition, and we compare these results with those obtained with open reading frame (ORF) overexpression and Cas9-based CRISPRa. We find that the activity of multiplexed arrays is largely predictable from the best-performing guide and provide criteria for selecting active guides. We anticipate that these results will greatly accelerate the exploration of gene function and combinatorial phenotypes at scale.
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Affiliation(s)
- Audrey L. Griffith
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Fengyi Zheng
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Abby V. McGee
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Nathan W. Miller
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Zsofia M. Szegletes
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Ganna Reint
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Fabian Gademann
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Ifunanya Nwolah
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Mudra Hegde
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Yanjing V. Liu
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - Amy Goodale
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
| | - John G. Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge, MA 02142, USA
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23
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Serebrenik YV, Mani D, Maujean T, Burslem GM, Shalem O. Pooled endogenous protein tagging and recruitment for scalable discovery of effectors for induced proximity therapeutics. RESEARCH SQUARE 2023:rs.3.rs-3161717. [PMID: 37790450 PMCID: PMC10543026 DOI: 10.21203/rs.3.rs-3161717/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The field of induced proximity therapeutics is in its ascendancy but is limited by a lack of scalable tools to systematically explore effector-target protein pairs in an unbiased manner. Here, we combined Scalable POoled Targeting with a LIgandable Tag at Endogenous Sites (SPOTLITES) for the high-throughput tagging of endogenous proteins, with generic small molecule-based protein recruitment to screen for novel proximity-based effectors. We apply this methodology in two orthogonal screens for targeted protein degradation: the first using fluorescence to monitor target protein levels directly, and the second using a cellular growth phenotype that depends on the degradation of an essential protein. Our screens revealed a multitude of potential new effector proteins for degradation and converged on members of the CTLH complex which we demonstrate potently induce degradation. Altogether, we introduce a platform for pooled induction of endogenous protein-protein interactions that can be used to expand our toolset of effector proteins for targeted protein degradation and other forms of induced proximity.
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Affiliation(s)
- Yevgeniy V. Serebrenik
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Deepak Mani
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Timothé Maujean
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - George M. Burslem
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ophir Shalem
- Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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24
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Hummel NFC, Markel K, Stefani J, Staller MV, Shih PM. Systematic identification of transcriptional activator domains from non-transcription factor proteins in plants and yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557247. [PMID: 37745555 PMCID: PMC10515812 DOI: 10.1101/2023.09.12.557247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Transcription factors promote gene expression via trans-regulatory activation domains. Although whole genome scale screens in model organisms (e.g. human, yeast, fly) have helped identify activation domains from transcription factors, such screens have been less extensively used to explore the occurrence of activation domains in non-transcription factor proteins, such as transcriptional coactivators, chromatin regulators and some cytosolic proteins, leaving a blind spot on what role activation domains in these proteins could play in regulating transcription. We utilized the activation domain predictor PADDLE to mine the entire proteomes of two model eukaryotes, Arabidopsis thaliana and Saccharomyces cerevisiae ( 1 ). We characterized 18,000 fragments covering predicted activation domains from >800 non-transcription factor genes in both species, and experimentally validated that 89% of proteins contained fragments capable of activating transcription in yeast. Peptides with similar sequence composition show a broad range of activities, which is explained by the arrangement of key amino acids. We also annotated hundreds of nuclear proteins with activation domains as putative coactivators; many of which have never been ascribed any function in plants. Furthermore, our library contains >250 non-nuclear proteins containing peptides with activation domain function across both eukaryotic lineages, suggesting that there are unknown biological roles of these peptides beyond transcription. Finally, we identify and validate short, 'universal' eukaryotic activation domains that activate transcription in both yeast and plants with comparable or stronger performance to state-of-the-art activation domains. Overall, our dual host screen provides a blueprint on how to systematically discover novel genetic parts for synthetic biology that function across a wide diversity of eukaryotes. Significance Statement Activation domains promote transcription and play a critical role in regulating gene expression. Although the mapping of activation domains from transcription factors has been carried out in previous genome-wide screens, their occurrence in non-transcription factors has been less explored. We utilize an activation domain predictor to mine the entire proteomes of Arabidopsis thaliana and Saccharomyces cerevisiae for new activation domains on non-transcription factor proteins. We validate peptides derived from >750 non-transcription factor proteins capable of activating transcription, discovering many potentially new coactivators in plants. Importantly, we identify novel genetic parts that can function across both species, representing unique synthetic biology tools.
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25
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Teixeira AP, Xue S, Huang J, Fussenegger M. Evolution of molecular switches for regulation of transgene expression by clinically licensed gluconate. Nucleic Acids Res 2023; 51:e85. [PMID: 37497781 PMCID: PMC10450161 DOI: 10.1093/nar/gkad600] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 06/22/2023] [Accepted: 07/16/2023] [Indexed: 07/28/2023] Open
Abstract
Synthetic biology holds great promise to improve the safety and efficacy of future gene and engineered cell therapies by providing new means of endogenous or exogenous control of the embedded therapeutic programs. Here, we focused on gluconate as a clinically licensed small-molecule inducer and engineered gluconate-sensitive molecular switches to regulate transgene expression in human cell cultures and in mice. Several switch designs were assembled based on the gluconate-responsive transcriptional repressor GntR from Escherichia coli. Initially we assembled OFF- and ON-type switches by rewiring the native gluconate-dependent binding of GntR to target DNA sequences in mammalian cells. Then, we utilized the ability of GntR to dimerize in the presence of gluconate to activate gene expression from a split transcriptional activator. By means of random mutagenesis of GntR combined with phenotypic screening, we identified variants that significantly enhanced the functionality of the genetic devices, enabling the construction of robust two-input logic gates. We also demonstrated the potential utility of the synthetic switch in two in vivo settings, one employing implantation of alginate-encapsulated engineered cells and the other involving modification of host cells by DNA delivery. Then, as proof-of-concept, the gluconate-actuated genetic switch was connected to insulin secretion, and the components encoding gluconate-induced insulin production were introduced into type-1 diabetic mice as naked DNA via hydrodynamic tail vein injection. Normoglycemia was restored, thereby showcasing the suitability of oral gluconate to regulate in situ production of a therapeutic protein.
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Affiliation(s)
- Ana Palma Teixeira
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058Basel, Switzerland
| | - Shuai Xue
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058Basel, Switzerland
| | - Jinbo Huang
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058Basel, Switzerland
- Faculty of Science, University of Basel, Mattenstrasse 26, CH-4058Basel, Switzerland
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26
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de Tribolet-Hardy J, Thorball CW, Forey R, Planet E, Duc J, Coudray A, Khubieh B, Offner S, Pulver C, Fellay J, Imbeault M, Turelli P, Trono D. Genetic features and genomic targets of human KRAB-zinc finger proteins. Genome Res 2023; 33:1409-1423. [PMID: 37730438 PMCID: PMC10547255 DOI: 10.1101/gr.277722.123] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 07/18/2023] [Indexed: 09/22/2023]
Abstract
Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) are one of the largest groups of transcription factors encoded by tetrapods, with 378 members in human alone. KZFP genes are often grouped in clusters reflecting amplification by gene and segment duplication since the gene family first emerged more than 400 million years ago. Previous work has revealed that many KZFPs recognize transposable element (TE)-embedded sequences as genomic targets, and that KZFPs facilitate the co-option of the regulatory potential of TEs for the benefit of the host. Here, we present a comprehensive survey of the genetic features and genomic targets of human KZFPs, notably completing past analyses by adding data on close to a hundred family members. General principles emerge from our study of the TE-KZFP regulatory system, which point to multipronged evolutionary mechanisms underlaid by highly complex and combinatorial modes of action with strong influences on human speciation.
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Affiliation(s)
- Jonas de Tribolet-Hardy
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Christian W Thorball
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Romain Forey
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Evarist Planet
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Julien Duc
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Alexandre Coudray
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Bara Khubieh
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Sandra Offner
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Cyril Pulver
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital (CHUV) and University of Lausanne, 1010 Lausanne, Switzerland
| | - Michael Imbeault
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Priscilla Turelli
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland;
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27
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Serebrenik YV, Mani D, Maujean T, Burslem GM, Shalem O. Pooled endogenous protein tagging and recruitment for scalable discovery of effectors for induced proximity therapeutics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.13.548759. [PMID: 37503056 PMCID: PMC10369964 DOI: 10.1101/2023.07.13.548759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The field of induced proximity therapeutics is in its ascendancy but is limited by a lack of scalable tools to systematically explore effector-target protein pairs in an unbiased manner. Here, we combined Scalable POoled Targeting with a LIgandable Tag at Endogenous Sites (SPOTLITES) for the high-throughput tagging of endogenous proteins, with generic small molecule-based protein recruitment to screen for novel proximity-based effectors. We apply this methodology in two orthogonal screens for targeted protein degradation: the first using fluorescence to monitor target protein levels directly, and the second using a cellular growth phenotype that depends on the degradation of an essential protein. Our screens revealed a multitude of potential new effector proteins for degradation and converged on members of the CTLH complex which we demonstrate potently induce degradation. Altogether, we introduce a platform for pooled induction of endogenous protein-protein interactions that can be used to expand our toolset of effector proteins for targeted protein degradation and other forms of induced proximity.
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28
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Ludwig CH, Thurm AR, Morgens DW, Yang KJ, Tycko J, Bassik MC, Glaunsinger BA, Bintu L. High-throughput discovery and characterization of viral transcriptional effectors in human cells. Cell Syst 2023; 14:482-500.e8. [PMID: 37348463 PMCID: PMC10350249 DOI: 10.1016/j.cels.2023.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 02/17/2023] [Accepted: 05/23/2023] [Indexed: 06/24/2023]
Abstract
Viruses encode transcriptional regulatory proteins critical for controlling viral and host gene expression. Given their multifunctional nature and high sequence divergence, it is unclear which viral proteins can affect transcription and which specific sequences contribute to this function. Using a high-throughput assay, we measured the transcriptional regulatory potential of over 60,000 protein tiles across ∼1,500 proteins from 11 coronaviruses and all nine human herpesviruses. We discovered hundreds of transcriptional effector domains, including a conserved repression domain in all coronavirus Spike homologs, dual activation-repression domains in viral interferon regulatory factors (VIRFs), and an activation domain in six herpesvirus homologs of the single-stranded DNA-binding protein that we show is important for viral replication and late gene expression in Kaposi's sarcoma-associated herpesvirus (KSHV). For the effector domains we identified, we investigated their mechanisms via high-throughput sequence and chemical perturbations, pinpointing sequence motifs essential for function. This work massively expands viral protein annotations, serving as a springboard for studying their biological and health implications and providing new candidates for compact gene regulation tools.
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Affiliation(s)
- Connor H Ludwig
- Bioengineering Department, Stanford University, Stanford, CA 94305, USA
| | - Abby R Thurm
- Biophysics Graduate Program, Stanford University, Stanford, CA 94305, USA
| | - David W Morgens
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA 94720, USA
| | - Kevin J Yang
- Department of Molecular and Cell Biology, UC Berkeley, Berkeley, CA 94720, USA
| | - Josh Tycko
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Britt A Glaunsinger
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, UC Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, UC Berkeley, Berkeley, CA 94720, USA
| | - Lacramioara Bintu
- Bioengineering Department, Stanford University, Stanford, CA 94305, USA.
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29
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Hummel NFC, Zhou A, Li B, Markel K, Ornelas IJ, Shih PM. The trans-regulatory landscape of gene networks in plants. Cell Syst 2023; 14:501-511.e4. [PMID: 37348464 DOI: 10.1016/j.cels.2023.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/21/2023] [Accepted: 05/11/2023] [Indexed: 06/24/2023]
Abstract
The transcriptional effector domains of transcription factors play a key role in controlling gene expression; however, their functional nature is poorly understood, hampering our ability to explore this fundamental dimension of gene regulatory networks. To map the trans-regulatory landscape in a complex eukaryote, we systematically characterized the putative transcriptional effector domains of over 400 Arabidopsis thaliana transcription factors for their capacity to modulate transcription. We demonstrate that transcriptional effector activity can be integrated into gene regulatory networks capable of elucidating the functional dynamics underlying gene expression patterns. We further show how our characterized domains can enhance genome engineering efforts and reveal how plant transcriptional activators share regulatory features conserved across distantly related eukaryotes. Our results provide a framework to systematically characterize the regulatory role of transcription factors at a genome-scale in order to understand the transcriptional wiring of biological systems.
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Affiliation(s)
- Niklas F C Hummel
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94705, USA; Department of Biology, Technische Universität Darmstadt, Darmstadt 64287, Germany
| | - Andy Zhou
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94705, USA
| | - Baohua Li
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94705, USA
| | - Kasey Markel
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94705, USA
| | - Izaiah J Ornelas
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94705, USA
| | - Patrick M Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94705, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
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30
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Mach P, Giorgetti L. Integrative approaches to study enhancer-promoter communication. Curr Opin Genet Dev 2023; 80:102052. [PMID: 37257410 PMCID: PMC10293802 DOI: 10.1016/j.gde.2023.102052] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/21/2023] [Accepted: 04/22/2023] [Indexed: 06/02/2023]
Abstract
The spatiotemporal control of gene expression in complex multicellular organisms relies on noncoding regulatory sequences such as enhancers, which activate transcription of target genes often over large genomic distances. Despite the advances in the identification and characterization of enhancers, the principles and mechanisms by which enhancers select and control their target genes remain largely unknown. Here, we review recent interdisciplinary and quantitative approaches based on emerging techniques that aim to address open questions in the field, notably how regulatory information is encoded in the DNA sequence, how this information is transferred from enhancers to promoters, and how these processes are regulated in time.
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Affiliation(s)
- Pia Mach
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; University of Basel, Basel, Switzerland. https://twitter.com/@MachPia
| | - Luca Giorgetti
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
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31
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Davey NE, Simonetti L, Ivarsson Y. The next wave of interactomics: Mapping the SLiM-based interactions of the intrinsically disordered proteome. Curr Opin Struct Biol 2023; 80:102593. [PMID: 37099901 DOI: 10.1016/j.sbi.2023.102593] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/09/2023] [Accepted: 03/17/2023] [Indexed: 04/28/2023]
Abstract
Short linear motifs (SLiMs) are a unique and ubiquitous class of protein interaction modules that perform key regulatory functions and drive dynamic complex formation. For decades, interactions mediated by SLiMs have accumulated through detailed low-throughput experiments. Recent methodological advances have opened this previously underexplored area of the human interactome to high-throughput protein-protein interaction discovery. In this article, we discuss that SLiM-based interactions represent a significant blind spot in the current interactomics data, introduce the key methods that are illuminating the elusive SLiM-mediated interactome of the human cell on a large scale, and discuss the implications for the field.
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Affiliation(s)
- Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK.
| | - Leandro Simonetti
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden.
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32
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Cermakova K, Hodges HC. Interaction modules that impart specificity to disordered protein. Trends Biochem Sci 2023; 48:477-490. [PMID: 36754681 PMCID: PMC10106370 DOI: 10.1016/j.tibs.2023.01.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 02/09/2023]
Abstract
Intrinsically disordered regions (IDRs) are especially enriched among proteins that regulate chromatin and transcription. As a result, mechanisms that influence specificity of IDR-driven interactions have emerged as exciting unresolved issues for understanding gene regulation. We review the molecular elements frequently found within IDRs that confer regulatory specificity. In particular, we summarize the differing roles of disordered low-complexity regions (LCRs) and short linear motifs (SLiMs) towards selective nuclear regulation. Examination of IDR-driven interactions highlights SLiMs as organizers of selectivity, with widespread roles in gene regulation and integration of cellular signals. Analysis of recurrent interactions between SLiMs and folded domains suggests diverse avenues for SLiMs to influence phase-separated condensates and highlights opportunities to manipulate these interactions for control of biological activity.
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Affiliation(s)
- Katerina Cermakova
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
| | - H Courtney Hodges
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA; Department of Bioengineering, Rice University, Houston, TX, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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33
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DelRosso N, Tycko J, Suzuki P, Andrews C, Aradhana, Mukund A, Liongson I, Ludwig C, Spees K, Fordyce P, Bassik MC, Bintu L. Large-scale mapping and mutagenesis of human transcriptional effector domains. Nature 2023; 616:365-372. [PMID: 37020022 PMCID: PMC10484233 DOI: 10.1038/s41586-023-05906-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 03/01/2023] [Indexed: 04/07/2023]
Abstract
Human gene expression is regulated by more than 2,000 transcription factors and chromatin regulators1,2. Effector domains within these proteins can activate or repress transcription. However, for many of these regulators we do not know what type of effector domains they contain, their location in the protein, their activation and repression strengths, and the sequences that are necessary for their functions. Here, we systematically measure the effector activity of more than 100,000 protein fragments tiling across most chromatin regulators and transcription factors in human cells (2,047 proteins). By testing the effect they have when recruited at reporter genes, we annotate 374 activation domains and 715 repression domains, roughly 80% of which are new and have not been previously annotated3-5. Rational mutagenesis and deletion scans across all the effector domains reveal aromatic and/or leucine residues interspersed with acidic, proline, serine and/or glutamine residues are necessary for activation domain activity. Furthermore, most repression domain sequences contain sites for small ubiquitin-like modifier (SUMO)ylation, short interaction motifs for recruiting corepressors or are structured binding domains for recruiting other repressive proteins. We discover bifunctional domains that can both activate and repress, some of which dynamically split a cell population into high- and low-expression subpopulations. Our systematic annotation and characterization of effector domains provide a rich resource for understanding the function of human transcription factors and chromatin regulators, engineering compact tools for controlling gene expression and refining predictive models of effector domain function.
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Affiliation(s)
| | - Josh Tycko
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Peter Suzuki
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Cecelia Andrews
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Aradhana
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Adi Mukund
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Ivan Liongson
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Connor Ludwig
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Kaitlyn Spees
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Polly Fordyce
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- ChEM-H Institute, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Lacramioara Bintu
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
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34
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Durrant MG, Fanton A, Tycko J, Hinks M, Chandrasekaran SS, Perry NT, Schaepe J, Du PP, Lotfy P, Bassik MC, Bintu L, Bhatt AS, Hsu PD. Systematic discovery of recombinases for efficient integration of large DNA sequences into the human genome. Nat Biotechnol 2023; 41:488-499. [PMID: 36217031 PMCID: PMC10083194 DOI: 10.1038/s41587-022-01494-w] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 09/01/2022] [Indexed: 11/09/2022]
Abstract
Large serine recombinases (LSRs) are DNA integrases that facilitate the site-specific integration of mobile genetic elements into bacterial genomes. Only a few LSRs, such as Bxb1 and PhiC31, have been characterized to date, with limited efficiency as tools for DNA integration in human cells. In this study, we developed a computational approach to identify thousands of LSRs and their DNA attachment sites, expanding known LSR diversity by >100-fold and enabling the prediction of their insertion site specificities. We tested their recombination activity in human cells, classifying them as landing pad, genome-targeting or multi-targeting LSRs. Overall, we achieved up to seven-fold higher recombination than Bxb1 and genome integration efficiencies of 40-75% with cargo sizes over 7 kb. We also demonstrate virus-free, direct integration of plasmid or amplicon libraries for improved functional genomics applications. This systematic discovery of recombinases directly from microbial sequencing data provides a resource of over 60 LSRs experimentally characterized in human cells for large-payload genome insertion without exposed DNA double-stranded breaks.
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Affiliation(s)
- Matthew G Durrant
- Arc Institute, Palo Alto, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Alison Fanton
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Josh Tycko
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Michaela Hinks
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Sita S Chandrasekaran
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Nicholas T Perry
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- University of California, Berkeley-University of California, San Francisco Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Julia Schaepe
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Peter P Du
- Department of Genetics, Stanford University, Stanford, CA, USA
- Cancer Biology Program, Stanford University, Stanford, CA, USA
| | - Peter Lotfy
- Laboratory of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - Lacramioara Bintu
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
| | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Medicine (Hematology), Stanford University, Stanford, CA, USA.
| | - Patrick D Hsu
- Arc Institute, Palo Alto, CA, USA.
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
- Laboratory of Molecular and Cell Biology, Salk Institute for Biological Studies, La Jolla, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
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35
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Kim S, Wysocka J. Deciphering the multi-scale, quantitative cis-regulatory code. Mol Cell 2023; 83:373-392. [PMID: 36693380 PMCID: PMC9898153 DOI: 10.1016/j.molcel.2022.12.032] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/24/2023]
Abstract
Uncovering the cis-regulatory code that governs when and how much each gene is transcribed in a given genome and cellular state remains a central goal of biology. Here, we discuss major layers of regulation that influence how transcriptional outputs are encoded by DNA sequence and cellular context. We first discuss how transcription factors bind specific DNA sequences in a dosage-dependent and cooperative manner and then proceed to the cofactors that facilitate transcription factor function and mediate the activity of modular cis-regulatory elements such as enhancers, silencers, and promoters. We then consider the complex and poorly understood interplay of these diverse elements within regulatory landscapes and its relationships with chromatin states and nuclear organization. We propose that a mechanistically informed, quantitative model of transcriptional regulation that integrates these multiple regulatory layers will be the key to ultimately cracking the cis-regulatory code.
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Affiliation(s)
- Seungsoo Kim
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joanna Wysocka
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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36
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Lue NZ, Garcia EM, Ngan KC, Lee C, Doench JG, Liau BB. Base editor scanning charts the DNMT3A activity landscape. Nat Chem Biol 2023; 19:176-186. [PMID: 36266353 PMCID: PMC10518564 DOI: 10.1038/s41589-022-01167-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 09/08/2022] [Indexed: 02/04/2023]
Abstract
DNA methylation is critical for regulating gene expression, necessitating its accurate placement by enzymes such as the DNA methyltransferase DNMT3A. Dysregulation of this process is known to cause aberrant development and oncogenesis, yet how DNMT3A is regulated holistically by its three domains remains challenging to study. Here, we integrate base editing with a DNA methylation reporter to perform in situ mutational scanning of DNMT3A in cells. We identify mutations throughout the protein that perturb function, including ones at an interdomain interface that block allosteric activation. Unexpectedly, we also find mutations in the PWWP domain, a histone reader, that modulate enzyme activity despite preserving histone recognition and protein stability. These effects arise from altered PWWP domain DNA affinity, which we show is a noncanonical function required for full activity in cells. Our findings highlight mechanisms of interdomain crosstalk and demonstrate a generalizable strategy to probe sequence-activity relationships of nonessential chromatin regulators.
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Affiliation(s)
- Nicholas Z Lue
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Emma M Garcia
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Kevin C Ngan
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ceejay Lee
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - John G Doench
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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37
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Klaus L, de Almeida BP, Vlasova A, Nemčko F, Schleiffer A, Bergauer K, Hofbauer L, Rath M, Stark A. Systematic identification and characterization of repressive domains in Drosophila transcription factors. EMBO J 2023; 42:e112100. [PMID: 36545802 PMCID: PMC9890238 DOI: 10.15252/embj.2022112100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/21/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022] Open
Abstract
All multicellular life relies on differential gene expression, determined by regulatory DNA elements and DNA-binding transcription factors that mediate activation and repression via cofactor recruitment. While activators have been extensively characterized, repressors are less well studied: the identities and properties of their repressive domains (RDs) are typically unknown and the specific co-repressors (CoRs) they recruit have not been determined. Here, we develop a high-throughput, next-generation sequencing-based screening method, repressive-domain (RD)-seq, to systematically identify RDs in complex DNA-fragment libraries. Screening more than 200,000 fragments covering the coding sequences of all transcription-related proteins in Drosophila melanogaster, we identify 195 RDs in known repressors and in proteins not previously associated with repression. Many RDs contain recurrent short peptide motifs, which are conserved between fly and human and are required for RD function, as demonstrated by motif mutagenesis. Moreover, we show that RDs that contain one of five distinct repressive motifs interact with and depend on different CoRs, such as Groucho, CtBP, Sin3A, or Smrter. These findings advance our understanding of repressors, their sequences, and the functional impact of sequence-altering mutations and should provide a valuable resource for further studies.
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Affiliation(s)
- Loni Klaus
- Research Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD ProgramDoctoral School of the University of Vienna and Medical University of ViennaViennaAustria
| | - Bernardo P de Almeida
- Research Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD ProgramDoctoral School of the University of Vienna and Medical University of ViennaViennaAustria
| | - Anna Vlasova
- Research Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)ViennaAustria
| | - Filip Nemčko
- Research Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD ProgramDoctoral School of the University of Vienna and Medical University of ViennaViennaAustria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)ViennaAustria
- Institute of Molecular Biotechnology (IMBA)Vienna BioCenter (VBC)ViennaAustria
| | - Katharina Bergauer
- Research Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)ViennaAustria
| | - Lorena Hofbauer
- Research Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD ProgramDoctoral School of the University of Vienna and Medical University of ViennaViennaAustria
| | - Martina Rath
- Research Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)ViennaAustria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)ViennaAustria
- Medical University of ViennaVienna BioCenter (VBC)ViennaAustria
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38
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Mills C, Riching A, Keller A, Stombaugh J, Haupt A, Maksimova E, Dickerson SM, Anderson E, Hemphill K, Ebmeier C, Schiel JA, Levenga J, Perkett M, Smith AVB, Strezoska Z. A Novel CRISPR Interference Effector Enabling Functional Gene Characterization with Synthetic Guide RNAs. CRISPR J 2022; 5:769-786. [PMID: 36257604 PMCID: PMC9805873 DOI: 10.1089/crispr.2022.0056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/15/2022] [Indexed: 01/31/2023] Open
Abstract
While CRISPR interference (CRISPRi) systems have been widely implemented in pooled lentiviral screening, there has been limited use with synthetic guide RNAs for the complex phenotypic readouts enabled by experiments in arrayed format. Here we describe a novel deactivated Cas9 fusion protein, dCas9-SALL1-SDS3, which produces greater target gene repression than first or second generation CRISPRi systems when used with chemically modified synthetic single guide RNAs (sgRNAs), while exhibiting high target specificity. We show that dCas9-SALL1-SDS3 interacts with key members of the histone deacetylase and Swi-independent three complexes, which are the endogenous functional effectors of SALL1 and SDS3. Synthetic sgRNAs can also be used with in vitro-transcribed dCas9-SALL1-SDS3 mRNA for short-term delivery into primary cells, including human induced pluripotent stem cells and primary T cells. Finally, we used dCas9-SALL1-SDS3 for functional gene characterization of DNA damage host factors, orthogonally to small interfering RNA, demonstrating the ability of the system to be used in arrayed-format screening.
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Affiliation(s)
- Clarence Mills
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Andrew Riching
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Ashleigh Keller
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Jesse Stombaugh
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Amanda Haupt
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Elena Maksimova
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Sarah M. Dickerson
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Emily Anderson
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Kevin Hemphill
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Chris Ebmeier
- Mass Spectrometry Core Facility, University of Colorado-Boulder, Boulder, Colorado, USA
| | - John A. Schiel
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Josien Levenga
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Matthew Perkett
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Anja van Brabant Smith
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Zaklina Strezoska
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
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39
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Stoll GA, Pandiloski N, Douse CH, Modis Y. Structure and functional mapping of the KRAB-KAP1 repressor complex. EMBO J 2022; 41:e111179. [PMID: 36341546 PMCID: PMC9753469 DOI: 10.15252/embj.2022111179] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/09/2022] Open
Abstract
Transposable elements are a genetic reservoir from which new genes and regulatory elements can emerge. However, expression of transposable elements can be pathogenic and is therefore tightly controlled. KRAB domain-containing zinc finger proteins (KRAB-ZFPs) recruit the co-repressor KRAB-associated protein 1 (KAP1/TRIM28) to regulate many transposable elements, but how KRAB-ZFPs and KAP1 interact remains unclear. Here, we report the crystal structure of the KAP1 tripartite motif (TRIM) in complex with the KRAB domain from a human KRAB-ZFP, ZNF93. Structure-guided mutations in the KAP1-KRAB binding interface abolished repressive activity in an epigenetic transcriptional silencing assay. Deposition of H3K9me3 over thousands of loci is lost genome-wide in cells expressing a KAP1 variant with mutations that abolish KRAB binding. Our work identifies and functionally validates the KRAB-KAP1 molecular interface, which is critical for a central transcriptional control axis in vertebrates. In addition, the structure-based prediction of KAP1 recruitment efficiency will enable optimization of KRABs used in CRISPRi.
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Affiliation(s)
- Guido A Stoll
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular BiologyUniversity of CambridgeCambridgeUK,Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID)University of Cambridge School of Clinical MedicineCambridgeUK
| | - Ninoslav Pandiloski
- Department of Experimental Medical Science, Lund Stem Cell CenterLund UniversityLundSweden
| | - Christopher H Douse
- Department of Experimental Medical Science, Lund Stem Cell CenterLund UniversityLundSweden
| | - Yorgo Modis
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular BiologyUniversity of CambridgeCambridgeUK,Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID)University of Cambridge School of Clinical MedicineCambridgeUK
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40
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Escobar M, Li J, Patel A, Liu S, Xu Q, Hilton IB. Quantification of Genome Editing and Transcriptional Control Capabilities Reveals Hierarchies among Diverse CRISPR/Cas Systems in Human Cells. ACS Synth Biol 2022; 11:3239-3250. [PMID: 36162812 PMCID: PMC9594343 DOI: 10.1021/acssynbio.2c00156] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
CRISPR/Cas technologies have revolutionized the ability to redesign genomic information and tailor endogenous gene expression. Nevertheless, the discovery and development of new CRISPR/Cas systems has resulted in a lack of clarity surrounding the relative efficacies among these technologies in human cells. This deficit makes the optimal selection of CRISPR/Cas technologies in human cells unnecessarily challenging, which in turn hampers their adoption, and thus ultimately limits their utility. Here, we designed a series of endogenous testbed systems to methodically quantify and compare the genome editing, CRISPRi, and CRISPRa capabilities among 10 different natural and engineered Cas protein variants spanning Type II and Type V CRISPR/Cas families. We show that although all Cas protein variants are capable of genome editing and transcriptional control in human cells, hierarchies exist, particularly for genome editing and CRISPRa applications, wherein Cas9 ≥ Cas12a > Cas12e/Cas12j. Our findings also highlight the utility of our modular testbed platforms to rapidly and systematically quantify the functionality of practically any natural or engineered genomic-targeting Cas protein in human cells.
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Affiliation(s)
- Mario Escobar
- Department
of BioSciences, Rice University, Houston, Texas 77005, United States
| | - Jing Li
- Department
of Bioengineering, Rice University, Houston, Texas 77005, United States
| | - Aditi Patel
- Department
of BioSciences, Rice University, Houston, Texas 77005, United States
| | - Shizhe Liu
- Department
of BioSciences, Rice University, Houston, Texas 77005, United States
| | - Qi Xu
- Department
of Bioengineering, Rice University, Houston, Texas 77005, United States
| | - Isaac B. Hilton
- Department
of BioSciences, Rice University, Houston, Texas 77005, United States,Department
of Bioengineering, Rice University, Houston, Texas 77005, United States,
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41
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Staller MV. Transcription factors perform a 2-step search of the nucleus. Genetics 2022; 222:iyac111. [PMID: 35939561 PMCID: PMC9526044 DOI: 10.1093/genetics/iyac111] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/14/2022] [Indexed: 01/02/2023] Open
Abstract
Transcription factors regulate gene expression by binding to regulatory DNA and recruiting regulatory protein complexes. The DNA-binding and protein-binding functions of transcription factors are traditionally described as independent functions performed by modular protein domains. Here, I argue that genome binding can be a 2-part process with both DNA-binding and protein-binding steps, enabling transcription factors to perform a 2-step search of the nucleus to find their appropriate binding sites in a eukaryotic genome. I support this hypothesis with new and old results in the literature, discuss how this hypothesis parsimoniously resolves outstanding problems, and present testable predictions.
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Affiliation(s)
- Max Valentín Staller
- Corresponding author: Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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42
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Kartha VK, Duarte FM, Hu Y, Ma S, Chew JG, Lareau CA, Earl A, Burkett ZD, Kohlway AS, Lebofsky R, Buenrostro JD. Functional inference of gene regulation using single-cell multi-omics. CELL GENOMICS 2022; 2. [PMID: 36204155 PMCID: PMC9534481 DOI: 10.1016/j.xgen.2022.100166] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Cells require coordinated control over gene expression when responding to environmental stimuli. Here we apply scATAC-seq and single-cell RNA sequencing (scRNA-seq) in resting and stimulated human blood cells. Collectively, we generate ~91,000 single-cell profiles, allowing us to probe the cis-regulatory landscape of the immunological response across cell types, stimuli, and time. Advancing tools to integrate multi-omics data, we develop functional inference of gene regulation (FigR), a framework to computationally pair scA-TAC-seq with scRNA-seq cells, connect distal cis-regulatory elements to genes, and infer gene-regulatory networks (GRNs) to identify candidate transcription factor (TF) regulators. Utilizing these paired multi-omics data, we define domains of regulatory chromatin (DORCs) of immune stimulation and find that cells alter chromatin accessibility and gene expression at timescales of minutes. Construction of the stimulation GRN elucidates TF activity at disease-associated DORCs. Overall, FigR enables elucidation of regulatory interactions across single-cell data, providing new opportunities to understand the function of cells within tissues. Single-cell methods for measuring chromatin accessibility (ATAC-seq) and gene expression (RNA-seq) are rapidly evolving, but tools to integrate data and infer gene-regulatory relationships remain limited. Here we generate multi-omics data of resting and stimulated human blood cells and present a new computational framework for constructing gene-regulatory networks (GRNs). Specifically, we describe functional inference of gene regulation (FigR), a workflow to (1) pair scATAC-seq with scRNA-seq, (2) connect cis-regulatory elements to target genes, and (3) identify TF-gene relationships.
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Affiliation(s)
- Vinay K. Kartha
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Fabiana M. Duarte
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yan Hu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sai Ma
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Caleb A. Lareau
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew Earl
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | | | - Jason D. Buenrostro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Corresponding author
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43
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Raskó T, Pande A, Radscheit K, Zink A, Singh M, Sommer C, Wachtl G, Kolacsek O, Inak G, Szvetnik A, Petrakis S, Bunse M, Bansal V, Selbach M, Orbán TI, Prigione A, Hurst LD, Izsvák Z. A Novel Gene Controls a New Structure: PiggyBac Transposable Element-Derived 1, Unique to Mammals, Controls Mammal-Specific Neuronal Paraspeckles. Mol Biol Evol 2022; 39:6661922. [PMID: 36205081 PMCID: PMC9538788 DOI: 10.1093/molbev/msac175] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Although new genes can arrive from modes other than duplication, few examples are well characterized. Given high expression in some human brain subregions and a putative link to psychological disorders [e.g., schizophrenia (SCZ)], suggestive of brain functionality, here we characterize piggyBac transposable element-derived 1 (PGBD1). PGBD1 is nonmonotreme mammal-specific and under purifying selection, consistent with functionality. The gene body of human PGBD1 retains much of the original DNA transposon but has additionally captured SCAN and KRAB domains. Despite gene body retention, PGBD1 has lost transposition abilities, thus transposase functionality is absent. PGBD1 no longer recognizes piggyBac transposon-like inverted repeats, nonetheless PGBD1 has DNA binding activity. Genome scale analysis identifies enrichment of binding sites in and around genes involved in neuronal development, with association with both histone activating and repressing marks. We focus on one of the repressed genes, the long noncoding RNA NEAT1, also dysregulated in SCZ, the core structural RNA of paraspeckles. DNA binding assays confirm specific binding of PGBD1 both in the NEAT1 promoter and in the gene body. Depletion of PGBD1 in neuronal progenitor cells (NPCs) results in increased NEAT1/paraspeckles and differentiation. We conclude that PGBD1 has evolved core regulatory functionality for the maintenance of NPCs. As paraspeckles are a mammal-specific structure, the results presented here show a rare example of the evolution of a novel gene coupled to the evolution of a contemporaneous new structure.
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Affiliation(s)
- Tamás Raskó
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | | | | | - Annika Zink
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Manvendra Singh
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Christian Sommer
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Gerda Wachtl
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH, Budapest, Hungary,Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Orsolya Kolacsek
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH, Budapest, Hungary
| | - Gizem Inak
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
| | - Attila Szvetnik
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Spyros Petrakis
- Institute of Applied Biosciences/Centre for Research and Technology Hellas, 57001 Thessaloniki, Greece
| | - Mario Bunse
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Vikas Bansal
- Biomedical Data Science and Machine Learning Group, German Center for Neurodegenerative Diseases, Tübingen 72076, Germany
| | - Matthias Selbach
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Tamás I Orbán
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH, Budapest, Hungary
| | - Alessandro Prigione
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, Duesseldorf, Germany
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44
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Lensch S, Herschl MH, Ludwig CH, Sinha J, Hinks MM, Mukund A, Fujimori T, Bintu L. Dynamic spreading of chromatin-mediated gene silencing and reactivation between neighboring genes in single cells. eLife 2022; 11:e75115. [PMID: 35678392 PMCID: PMC9183234 DOI: 10.7554/elife.75115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 03/23/2022] [Indexed: 12/02/2022] Open
Abstract
In mammalian cells genes that are in close proximity can be transcriptionally coupled: silencing or activating one gene can affect its neighbors. Understanding these dynamics is important for natural processes, such as heterochromatin spreading during development and aging, and when designing synthetic gene regulation circuits. Here, we systematically dissect this process in single cells by recruiting and releasing repressive chromatin regulators at dual-gene synthetic reporters, and measuring how fast gene silencing and reactivation spread as a function of intergenic distance and configuration of insulator elements. We find that silencing by KRAB, associated with histone methylation, spreads between two genes within hours, with a time delay that increases with distance. This fast KRAB-mediated spreading is not blocked by the classical cHS4 insulators. Silencing by histone deacetylase HDAC4 of the upstream gene can also facilitate background silencing of the downstream gene by PRC2, but with a days-long delay that does not change with distance. This slower silencing can sometimes be stopped by insulators. Gene reactivation of neighboring genes is also coupled, with strong promoters and insulators determining the order of reactivation. Our data can be described by a model of multi-gene regulation that builds upon previous knowledge of heterochromatin spreading, where both gene silencing and gene reactivation can act at a distance, allowing for coordinated dynamics via chromatin regulator recruitment.
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Affiliation(s)
- Sarah Lensch
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Michael H Herschl
- University of California, Berkeley—University of California, San Francisco Graduate Program in BioengineeringBerkeleyUnited States
| | - Connor H Ludwig
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Joydeb Sinha
- Department of Chemical and Systems Biology, Stanford UniversityStanfordUnited States
| | - Michaela M Hinks
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Adi Mukund
- Biophysics Program, Stanford UniversityStanfordUnited States
| | - Taihei Fujimori
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Lacramioara Bintu
- Department of Bioengineering, Stanford UniversityStanfordUnited States
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45
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Franklin KA, Shields CE, Haynes KA. Beyond the marks: reader-effectors as drivers of epigenetics and chromatin engineering. Trends Biochem Sci 2022; 47:417-432. [PMID: 35427480 PMCID: PMC9074927 DOI: 10.1016/j.tibs.2022.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 02/27/2022] [Accepted: 03/01/2022] [Indexed: 10/18/2022]
Abstract
Chromatin is a system of proteins and DNA that regulates chromosome organization and gene expression in eukaryotes. Essential features that support these processes include biochemical marks on histones and DNA, 'writer' enzymes that generate or remove these marks and proteins that translate the marks into transcriptional regulation: reader-effectors. Here, we review recent studies that reveal how reader-effectors drive chromatin-mediated processes. Advances in proteomics and epigenomics have accelerated the discovery of chromatin marks and their correlation with gene states, outpacing our understanding of the corresponding reader-effectors. Therefore, we summarize the current state of knowledge and open questions about how reader-effectors impact cellular function and human disease and discuss how synthetic biology can deepen our knowledge of reader-effector activity.
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Affiliation(s)
- Kierra A Franklin
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA 30322, USA
| | - Cara E Shields
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA 30322, USA
| | - Karmella A Haynes
- Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA 30322, USA.
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46
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Ichikawa D, Noyes M. Oncogenic inspiration for programmable activators. CELL GENOMICS 2022; 2:100122. [PMID: 36776529 PMCID: PMC9903755 DOI: 10.1016/j.xgen.2022.100122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The discovery of regulatory domains has been limited to the investigation of transcription factors and homologous protein sequences. In this issue of Cell Genomics, motivated by an oncogenic protein fusion, Tak et al.1 direct the regulatory potential of a nontraditional effector domain to novel genomic loci with fusions to programmable DNA-binding domains.
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Affiliation(s)
- David Ichikawa
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, 435 East 30th Street, New York, NY 10016, USA
- Institute for Systems Genetics, NYU Grossman School of Medicine, 435 East 30th Street, New York, NY 10016, USA
| | - Marcus Noyes
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, 435 East 30th Street, New York, NY 10016, USA
- Institute for Systems Genetics, NYU Grossman School of Medicine, 435 East 30th Street, New York, NY 10016, USA
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47
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Soto L, Li Z, Santoso CS, Berenson A, Ho I, Shen VX, Yuan S, Bass JIF. Compendium of human transcription factor effector domains. Mol Cell 2022; 82:514-526. [PMID: 34863368 PMCID: PMC8818021 DOI: 10.1016/j.molcel.2021.11.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/16/2021] [Accepted: 11/03/2021] [Indexed: 02/08/2023]
Abstract
Transcription factors (TFs) regulate gene expression by binding to DNA sequences and modulating transcriptional activity through their effector domains. Despite the central role of effector domains in TF function, there is a current lack of a comprehensive resource and characterization of effector domains. Here, we provide a catalog of 924 effector domains across 594 human TFs. Using this catalog, we characterized the amino acid composition of effector domains, their conservation across species and across the human population, and their roles in human diseases. Furthermore, we provide a classification system for effector domains that constitutes a valuable resource and a blueprint for future experimental studies of TF effector domain function.
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Affiliation(s)
- Luis Soto
- Escuela Profesional de Genética y Biotecnología, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima 15081, Perú
| | - Zhaorong Li
- Bioinformatics Program, Boston University, Boston MA 02215
| | - Clarissa S Santoso
- Biology Department, Boston University, Boston MA 02215,Molecular Biology, Cellular Biology and Biochemistry Program, Boston University, Boston MA 02215
| | - Anna Berenson
- Biology Department, Boston University, Boston MA 02215,Molecular Biology, Cellular Biology and Biochemistry Program, Boston University, Boston MA 02215
| | - Isabella Ho
- Biology Department, Boston University, Boston MA 02215
| | - Vivian X Shen
- Biology Department, Boston University, Boston MA 02215
| | - Samson Yuan
- Biology Department, Boston University, Boston MA 02215
| | - Juan I Fuxman Bass
- Bioinformatics Program, Boston University, Boston MA 02215,Biology Department, Boston University, Boston MA 02215,Molecular Biology, Cellular Biology and Biochemistry Program, Boston University, Boston MA 02215,correspondence:
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48
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Abstract
In this issue of Molecular Cell, Alerasool et al. (2022) present a proteome-scale functional screen to systematically uncover human proteins that can activate transcription.
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Affiliation(s)
- Filip Nemčko
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria; Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria.
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49
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Staller MV, Ramirez E, Kotha SR, Holehouse AS, Pappu RV, Cohen BA. Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains. Cell Syst 2022; 13:334-345.e5. [PMID: 35120642 PMCID: PMC9241528 DOI: 10.1016/j.cels.2022.01.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 10/20/2021] [Accepted: 01/05/2022] [Indexed: 01/01/2023]
Abstract
Acidic activation domains are intrinsically disordered regions of the transcription factors that bind coactivators. The intrinsic disorder and low evolutionary conservation of activation domains have made it difficult to identify the sequence features that control activity. To address this problem, we designed thousands of variants in seven acidic activation domains and measured their activities with a high-throughput assay in human cell culture. We found that strong activation domain activity requires a balance between the number of acidic residues and aromatic and leucine residues. These findings motivated a predictor of acidic activation domains that scans the human proteome for clusters of aromatic and leucine residues embedded in regions of high acidity. This predictor identifies known activation domains and accurately predicts previously unidentified ones. Our results support a flexible acidic exposure model of activation domains in which the acidic residues solubilize hydrophobic motifs so that they can interact with coactivators. A record of this paper’s transparent peer review process is included in the supplemental information. Transcriptional activation domains are poorly conserved, intrinsically disordered regions of the transcription factors that remain difficult to predict from protein sequences. A high-throughput method reveals how strong activation domains require a balance between acidic and hydrophobic residues. This balance powers an accurate predictor of activation domains on human transcription factors.
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Affiliation(s)
- Max V Staller
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, Saint Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, Saint Louis, MO 63110, USA; Center for Computational Biology, University of California Berkeley, Berkeley, CA 94720, USA.
| | - Eddie Ramirez
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, Saint Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, Saint Louis, MO 63110, USA
| | - Sanjana R Kotha
- Center for Computational Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, Saint Louis, MO 63110, USA; Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Rohit V Pappu
- Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Barak A Cohen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, Saint Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, Saint Louis, MO 63110, USA.
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50
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Lorenz P, Steinbeck F, Krause L, Thiesen HJ. The KRAB Domain of ZNF10 Guides the Identification of Specific Amino Acids That Transform the Ancestral KRAB-A-Related Domain Present in Human PRDM9 into a Canonical Modern KRAB-A Domain. Int J Mol Sci 2022; 23:ijms23031072. [PMID: 35162997 PMCID: PMC8835667 DOI: 10.3390/ijms23031072] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 12/14/2022] Open
Abstract
Krüppel-associated box (KRAB) zinc finger proteins are a large class of tetrapod transcription factors that usually exert transcriptional repression through recruitment of TRIM28/KAP1. The evolutionary root of modern KRAB domains (mKRAB) can be traced back to an ancestral motif (aKRAB) that occurs even in invertebrates. Here, we first stratified three subgroups of aKRAB sequences from the animal kingdom (PRDM9, SSX and coelacanth KZNF families) and defined ancestral subdomains for KRAB-A and KRAB-B. Using human ZNF10 mKRAB-AB as blueprints for function, we then identified the necessary amino acid changes that transform the inactive aKRAB-A of human PRDM9 into an mKRAB domain capable of mediating silencing and complexing TRIM28/KAP1 in human cells when employed as a hybrid with ZNF10-B. Full gain of function required replacement of residues KR by the conserved motif MLE (positionsA32-A34), which inserted an additional residue, and exchange of A9/S for F, A20/M for L, and A27/R for V. AlphaFold2 modelling documented an evolutionary conserved L-shaped body of two α-helices in all KRAB domains. It is transformed into a characteristic spatial arrangement typical for mKRAB-AB upon the amino acid replacements and in conjunction with a third helix supplied by mKRAB-B. Side-chains pointing outward from the core KRAB 3D structure may reveal a protein-protein interaction code enabling graded binding of TRIM28 to different KRAB domains. Our data provide basic insights into structure-function relationships and emulate transitions of KRAB during evolution.
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Affiliation(s)
- Peter Lorenz
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; (F.S.); (L.K.); (H.-J.T.)
- Correspondence: ; Tel.: +49-(0)381-494-5879; Fax: +49-(0)381-494-5882
| | - Felix Steinbeck
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; (F.S.); (L.K.); (H.-J.T.)
| | - Ludwig Krause
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; (F.S.); (L.K.); (H.-J.T.)
| | - Hans-Jürgen Thiesen
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; (F.S.); (L.K.); (H.-J.T.)
- Gesellschaft für Individualisierte Medizin (IndyMed) mbH, 17, 18055 Rostock, Germany
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