1
|
Johnson CJ, Zhang Z, Zhang H, Shang R, Piekarz KM, Bi P, Stolfi A. A change in cis-regulatory logic underlying obligate versus facultative muscle multinucleation in chordates. Development 2024; 151:dev202968. [PMID: 39114943 DOI: 10.1242/dev.202968] [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: 04/16/2024] [Accepted: 07/25/2024] [Indexed: 08/16/2024]
Abstract
Vertebrates and tunicates are sister groups that share a common fusogenic factor, Myomaker (Mymk), that drives myoblast fusion and muscle multinucleation. Yet they are divergent in when and where they express Mymk. In vertebrates, all developing skeletal muscles express Mymk and are obligately multinucleated. In tunicates, Mymk is expressed only in post-metamorphic multinucleated muscles, but is absent from mononucleated larval muscles. In this study, we demonstrate that cis-regulatory sequence differences in the promoter region of Mymk underlie the different spatiotemporal patterns of its transcriptional activation in tunicates and vertebrates. Although in vertebrates myogenic regulatory factors (MRFs) such as MyoD1 alone are required and sufficient for Mymk transcription in all skeletal muscles, we show that transcription of Mymk in post-metamorphic muscles of the tunicate Ciona requires the combinatorial activity of MRF, MyoD and Early B-cell Factor (Ebf). This macroevolutionary difference appears to be encoded in cis, likely due to the presence of a putative Ebf-binding site adjacent to predicted MRF binding sites in the Ciona Mymk promoter. We further discuss how Mymk and myoblast fusion might have been regulated in the last common ancestor of tunicates and vertebrates, for which we propose two models.
Collapse
Affiliation(s)
- Christopher J Johnson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Zheng Zhang
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
- Center for Molecular Medicine, University of Georgia, Athens, GA 30602, USA
| | - Haifeng Zhang
- Center for Molecular Medicine, University of Georgia, Athens, GA 30602, USA
| | - Renjie Shang
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
- Center for Molecular Medicine, University of Georgia, Athens, GA 30602, USA
| | - Katarzyna M Piekarz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Pengpeng Bi
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
- Center for Molecular Medicine, University of Georgia, Athens, GA 30602, USA
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| |
Collapse
|
2
|
Jindal GA, Lim F, Tellez K, Song BP, Bantle AT, Farley EK. Protocol to electroporate DNA plasmids into Ciona robusta embryos at the 1-cell stage. STAR Protoc 2024; 5:103107. [PMID: 38963758 PMCID: PMC11269276 DOI: 10.1016/j.xpro.2024.103107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 03/20/2024] [Accepted: 05/13/2024] [Indexed: 07/06/2024] Open
Abstract
Electroporation is a technique to introduce DNA constructs into cells using electric current. Here, we present a protocol to electroporate DNA plasmids into Ciona robusta embryos at the 1-cell stage. We describe steps for setting up and conducting electroporation. We then detail procedures for collecting, fixing, and mounting embryos and counting expression. This protocol can be used to study the expression of enhancers via reporter assays, manipulating cells using genes or modified genes such as dominant negatives, and genome editing. For complete details on the use and execution of this protocol, please refer to Song, et al.1.
Collapse
Affiliation(s)
- Granton A Jindal
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Fabian Lim
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Krissie Tellez
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Benjamin P Song
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alexis T Bantle
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emma K Farley
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
3
|
Goluguri RR, Ghosh C, Quintong J, Sadqi M, Muñoz V. How to scan naked DNA using promiscuous recognition and no clamping: a model for pioneer transcription factors. Nucleic Acids Res 2024:gkae790. [PMID: 39287129 DOI: 10.1093/nar/gkae790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 08/22/2024] [Accepted: 09/03/2024] [Indexed: 09/19/2024] Open
Abstract
Most DNA scanning proteins uniquely recognize their cognate sequence motif and slide on DNA assisted by some sort of clamping interface. The pioneer transcription factors that control cell fate in eukaryotes must forgo both elements to gain access to DNA in naked and chromatin forms; thus, whether or how these factors scan naked DNA is unknown. Here, we use single-molecule techniques to investigate naked DNA scanning by the Engrailed homeodomain (enHD) as paradigm of highly promiscuous recognition and open DNA binding interface. We find that enHD scans naked DNA quite effectively, and about 200000-fold faster than expected for a continuous promiscuous slide. To do so, enHD scans about 675 bp of DNA in 100 ms and then redeploys stochastically to another location 530 bp afar in just 10 ms. During the scanning phase enHD alternates between slow- and medium-paced modes every 3 and 40 ms, respectively. We also find that enHD binds nucleosomes and does so with enhanced affinity relative to naked DNA. Our results demonstrate that pioneer-like transcription factors can in principle do both, target nucleosomes and scan active DNA efficiently. The hybrid scanning mechanism used by enHD appears particularly well suited for the highly complex genomic signals of eukaryotic cells.
Collapse
Affiliation(s)
- Rama Reddy Goluguri
- CREST Center for Cellular and Biomolecular Machines, University of California Merced, Merced, CA 95343, USA
- Department of Bioengineering, University of California Merced, Merced, CA 95343, USA
| | - Catherine Ghosh
- CREST Center for Cellular and Biomolecular Machines, University of California Merced, Merced, CA 95343, USA
- Department of Bioengineering, University of California Merced, Merced, CA 95343, USA
| | - Joshua Quintong
- CREST Center for Cellular and Biomolecular Machines, University of California Merced, Merced, CA 95343, USA
- Department of Bioengineering, University of California Merced, Merced, CA 95343, USA
| | - Mourad Sadqi
- CREST Center for Cellular and Biomolecular Machines, University of California Merced, Merced, CA 95343, USA
- Department of Bioengineering, University of California Merced, Merced, CA 95343, USA
| | - Victor Muñoz
- CREST Center for Cellular and Biomolecular Machines, University of California Merced, Merced, CA 95343, USA
- Department of Bioengineering, University of California Merced, Merced, CA 95343, USA
| |
Collapse
|
4
|
He AY, Danko CG. Dissection of core promoter syntax through single nucleotide resolution modeling of transcription initiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.583868. [PMID: 38559255 PMCID: PMC10979970 DOI: 10.1101/2024.03.13.583868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
How the DNA sequence of cis -regulatory elements encode transcription initiation patterns remains poorly understood. Here we introduce CLIPNET, a deep learning model trained on population-scale PRO-cap data that predicts the position and quantity of transcription initiation with single nucleotide resolution from DNA sequence more accurately than existing approaches. Interpretation of CLIPNET revealed a complex regulatory syntax consisting of DNA-protein interactions in five major positions between - 200 and + 50 bp relative to the transcription start site, as well as more subtle positional preferences among transcriptional activators. Transcriptional activator and core promoter motifs work non-additively to encode distinct aspects of initiation, with the former driving initiation quantity and the latter initiation position. We identified core promoter motifs that explain initiation patterns in the majority of promoters and enhancers, including DPR motifs and AT-rich TBP binding sequences in TATA-less promoters. Our results provide insights into the sequence architecture governing transcription initiation.
Collapse
Affiliation(s)
- Adam Y. He
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University
- Graduate Field of Computational Biology, Cornell University
| | - Charles G. Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University
| |
Collapse
|
5
|
Kosicki M, Zhang B, Pampari A, Akiyama JA, Plajzer-Frick I, Novak CS, Tran S, Zhu Y, Kato M, Hunter RD, von Maydell K, Barton S, Beckman E, Kundaje A, Dickel DE, Visel A, Pennacchio LA. Mutagenesis Sensitivity Mapping of Human Enhancers In Vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.06.611737. [PMID: 39282388 PMCID: PMC11398460 DOI: 10.1101/2024.09.06.611737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
Distant-acting enhancers are central to human development. However, our limited understanding of their functional sequence features prevents the interpretation of enhancer mutations in disease. Here, we determined the functional sensitivity to mutagenesis of human developmental enhancers in vivo. Focusing on seven enhancers active in the developing brain, heart, limb and face, we created over 1700 transgenic mice for over 260 mutagenized enhancer alleles. Systematic mutation of 12-basepair blocks collectively altered each sequence feature in each enhancer at least once. We show that 69% of all blocks are required for normal in vivo activity, with mutations more commonly resulting in loss (60%) than in gain (9%) of function. Using predictive modeling, we annotated critical nucleotides at base-pair resolution. The vast majority of motifs predicted by these machine learning models (88%) coincided with changes to in vivo function, and the models showed considerable sensitivity, identifying 59% of all functional blocks. Taken together, our results reveal that human enhancers contain a high density of sequence features required for their normal in vivo function and provide a rich resource for further exploration of human enhancer logic.
Collapse
Affiliation(s)
- Michael Kosicki
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Boyang Zhang
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Anusri Pampari
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Jennifer A Akiyama
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Catherine S Novak
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Stella Tran
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Yiwen Zhu
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Momoe Kato
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Riana D Hunter
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Kianna von Maydell
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Sarah Barton
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Erik Beckman
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Diane E Dickel
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Axel Visel
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
- School of Natural Sciences, University of California, Merced, CA 95343, USA
- U.S. Department of Energy Joint Genome Institute, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Len A Pennacchio
- Environmental Genomics & System Biology Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, One Cyclotron Road, Berkeley, CA 94720, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA 94720, USA
| |
Collapse
|
6
|
Kim S, Liu TT, Ou F, Murphy TL, Murphy KM. Anatomy of a superenhancer. Adv Immunol 2024; 163:51-96. [PMID: 39271259 DOI: 10.1016/bs.ai.2024.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2024]
Abstract
Interferon regulatory factor-8 (IRF8) is the lineage determining transcription factor for the type one classical dendritic cell (cDC1) subset, a terminal selector for plasmacytoid dendritic cells and important for the function of monocytes. Studies of Irf8 gene regulation have identified several enhancers controlling its activity during development of progenitors in the bone marrow that precisely regulate expression at distinct developmental stages. Each enhancer responds to distinct transcription factors that are expressed at each stage. IRF8 is first expressed in early progenitors that form the monocyte dendritic cell progenitor (MDP) in response to induction of the transcription factor CCAAT/enhancer-binding protein alpha (C/EBPα) acting at the Irf8 +56 kb enhancer. IRF8 levels increase further as the MDP transits into the common dendritic cell progenitor (CDP) in response to E protein activity at the Irf8 +41 kb enhancer. Upon Nfil3-induction in CDPs leading to specification of the cDC1 progenitor, abrupt induction of BATF3 forms the JUN/BATF3/IRF8 heterotrimer that activates the Irf8 +32 kb enhancer that sustains Irf8 autoactivation throughout the cDC1 lifetime. Deletions of each of these enhancers has revealed their stage dependent activation. Surprisingly, studies of compound heterozygotes for each combination of enhancer deletions revealed that activation of each subsequent enhancer requires the successful activation of the previous enhancer in strictly cis-dependent mechanism. Successful progression of enhancer activation is finely tuned to alter the functional accessibility of subsequent enhancers to factors active in the next stage of development. The molecular basis for these phenomenon is still obscure but could have implications for genomic regulation in a broader developmental context.
Collapse
Affiliation(s)
- Sunkyung Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States.
| | - Tian-Tian Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Feiya Ou
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Theresa L Murphy
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Kenneth M Murphy
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States.
| |
Collapse
|
7
|
Xu C, Kleinschmidt H, Yang J, Leith EM, Johnson J, Tan S, Mahony S, Bai L. Systematic dissection of sequence features affecting binding specificity of a pioneer factor reveals binding synergy between FOXA1 and AP-1. Mol Cell 2024; 84:2838-2855.e10. [PMID: 39019045 PMCID: PMC11334613 DOI: 10.1016/j.molcel.2024.06.022] [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: 01/09/2024] [Revised: 04/23/2024] [Accepted: 06/21/2024] [Indexed: 07/19/2024]
Abstract
Despite the unique ability of pioneer factors (PFs) to target nucleosomal sites in closed chromatin, they only bind a small fraction of their genomic motifs. The underlying mechanism of this selectivity is not well understood. Here, we design a high-throughput assay called chromatin immunoprecipitation with integrated synthetic oligonucleotides (ChIP-ISO) to systematically dissect sequence features affecting the binding specificity of a classic PF, FOXA1, in human A549 cells. Combining ChIP-ISO with in vitro and neural network analyses, we find that (1) FOXA1 binding is strongly affected by co-binding transcription factors (TFs) AP-1 and CEBPB; (2) FOXA1 and AP-1 show binding cooperativity in vitro; (3) FOXA1's binding is determined more by local sequences than chromatin context, including eu-/heterochromatin; and (4) AP-1 is partially responsible for differential binding of FOXA1 in different cell types. Our study presents a framework for elucidating genetic rules underlying PF binding specificity and reveals a mechanism for context-specific regulation of its binding.
Collapse
Affiliation(s)
- Cheng Xu
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Holly Kleinschmidt
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jianyu Yang
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Erik M Leith
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jenna Johnson
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Song Tan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Shaun Mahony
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA; Department of Physics, The Pennsylvania State University, University Park, PA 16802, USA.
| |
Collapse
|
8
|
Naderi J, Magalhaes AP, Kibar G, Stik G, Zhang Y, Mackowiak SD, Wieler HM, Rossi F, Buschow R, Christou-Kent M, Alcoverro-Bertran M, Graf T, Vingron M, Hnisz D. An activity-specificity trade-off encoded in human transcription factors. Nat Cell Biol 2024; 26:1309-1321. [PMID: 38969762 PMCID: PMC11321997 DOI: 10.1038/s41556-024-01411-0] [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: 01/27/2023] [Accepted: 03/20/2024] [Indexed: 07/07/2024]
Abstract
Transcription factors (TFs) control specificity and activity of gene transcription, but whether a relationship between these two features exists is unclear. Here we provide evidence for an evolutionary trade-off between the activity and specificity in human TFs encoded as submaximal dispersion of aromatic residues in their intrinsically disordered protein regions. We identified approximately 500 human TFs that encode short periodic blocks of aromatic residues in their intrinsically disordered regions, resembling imperfect prion-like sequences. Mutation of periodic aromatic residues reduced transcriptional activity, whereas increasing the aromatic dispersion of multiple human TFs enhanced transcriptional activity and reprogramming efficiency, promoted liquid-liquid phase separation in vitro and more promiscuous DNA binding in cells. Together with recent work on enhancer elements, these results suggest an important evolutionary role of suboptimal features in transcriptional control. We propose that rational engineering of amino acid features that alter phase separation may be a strategy to optimize TF-dependent processes, including cellular reprogramming.
Collapse
Affiliation(s)
- Julian Naderi
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Alexandre P Magalhaes
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Gözde Kibar
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Gregoire Stik
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | - Yaotian Zhang
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Sebastian D Mackowiak
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Hannah M Wieler
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Francesca Rossi
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Rene Buschow
- Microscopy Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Marie Christou-Kent
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marc Alcoverro-Bertran
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Thomas Graf
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Denes Hnisz
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
| |
Collapse
|
9
|
Xu J, Ren B. Built to be imperfect. Nat Cell Biol 2024; 26:1229-1230. [PMID: 38969761 DOI: 10.1038/s41556-024-01408-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2024]
Affiliation(s)
- Jie Xu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.
- Center for Epigenomics, University of California, San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
| |
Collapse
|
10
|
Gigante ED, Piekarz KM, Gurgis A, Cohen L, Razy-Krajka F, Popsuj S, Johnson CJ, Ali HS, Mohana Sundaram S, Stolfi A. Specification and survival of post-metamorphic branchiomeric neurons in a non-vertebrate chordate. Development 2024; 151:dev202719. [PMID: 38895900 PMCID: PMC11273300 DOI: 10.1242/dev.202719] [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: 01/22/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024]
Abstract
Tunicates are the sister group to the vertebrates, yet most species have a life cycle split between swimming larva and sedentary adult phases. During metamorphosis, larval neurons are replaced by adult-specific ones. The regulatory mechanisms underlying this replacement remain largely unknown. Using tissue-specific CRISPR/Cas9-mediated mutagenesis in the tunicate Ciona, we show that orthologs of conserved hindbrain and branchiomeric neuron regulatory factors Pax2/5/8 and Phox2 are required to specify the 'neck', a cellular compartment set aside in the larva to give rise to cranial motor neuron-like neurons post-metamorphosis. Using bulk and single-cell RNA-sequencing analyses, we characterize the transcriptome of the neck downstream of Pax2/5/8. We present evidence that neck-derived adult ciliomotor neurons begin to differentiate in the larva and persist through metamorphosis, contrary to the assumption that the adult nervous system is formed after settlement and the death of larval neurons during metamorphosis. Finally, we show that FGF signaling during the larval phase alters the patterning of the neck and its derivatives. Suppression of FGF converts neck cells into larval neurons that fail to survive metamorphosis, whereas prolonged FGF signaling promotes an adult neural stem cell-like fate.
Collapse
Affiliation(s)
- Eduardo D. Gigante
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Katarzyna M. Piekarz
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Alexandra Gurgis
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Leslie Cohen
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Florian Razy-Krajka
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Sydney Popsuj
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Christopher J. Johnson
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Hussan S. Ali
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Shruthi Mohana Sundaram
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Alberto Stolfi
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| |
Collapse
|
11
|
Jores T, Tonnies J, Mueth NA, Romanowski A, Fields S, Cuperus JT, Queitsch C. Plant enhancers exhibit both cooperative and additive interactions among their functional elements. THE PLANT CELL 2024; 36:2570-2586. [PMID: 38513612 PMCID: PMC11218779 DOI: 10.1093/plcell/koae088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/16/2024] [Accepted: 03/04/2024] [Indexed: 03/23/2024]
Abstract
Enhancers are cis-regulatory elements that shape gene expression in response to numerous developmental and environmental cues. In animals, several models have been proposed to explain how enhancers integrate the activity of multiple transcription factors. However, it remains largely unclear how plant enhancers integrate transcription factor activity. Here, we use Plant STARR-seq to characterize 3 light-responsive plant enhancers-AB80, Cab-1, and rbcS-E9-derived from genes associated with photosynthesis. Saturation mutagenesis revealed mutations, many of which clustered in short regions, that strongly reduced enhancer activity in the light, in the dark, or in both conditions. When tested in the light, these mutation-sensitive regions did not function on their own; rather, cooperative interactions with other such regions were required for full activity. Epistatic interactions occurred between mutations in adjacent mutation-sensitive regions, and the spacing and order of mutation-sensitive regions in synthetic enhancers affected enhancer activity. In contrast, when tested in the dark, mutation-sensitive regions acted independently and additively in conferring enhancer activity. Taken together, this work demonstrates that plant enhancers show evidence for both cooperative and additive interactions among their functional elements. This knowledge can be harnessed to design strong, condition-specific synthetic enhancers.
Collapse
Affiliation(s)
- Tobias Jores
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Institute of Synthetic Biology, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
- Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Jackson Tonnies
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Graduate Program in Biology, University of Washington, Seattle, WA 98195, USA
| | - Nicholas A Mueth
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Andrés Romanowski
- Molecular Biology Group, Plant Sciences, Wageningen University & Research, 6708 PB Wageningen, the Netherlands
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
12
|
Falo-Sanjuan J, Diaz-Tirado Y, Turner MA, Davis J, Medrano C, Haines J, McKenna J, Eisen MB, Garcia HG. Targeted mutagenesis of specific genomic DNA sequences in animals for the in vivo generation of variant libraries. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598328. [PMID: 38915503 PMCID: PMC11195090 DOI: 10.1101/2024.06.10.598328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Understanding how the number, placement and affinity of transcription factor binding sites dictates gene regulatory programs remains a major unsolved challenge in biology, particularly in the context of multicellular organisms. To uncover these rules, it is first necessary to find the binding sites within a regulatory region with high precision, and then to systematically modulate this binding site arrangement while simultaneously measuring the effect of this modulation on output gene expression. Massively parallel reporter assays (MPRAs), where the gene expression stemming from 10,000s of in vitro-generated regulatory sequences is measured, have made this feat possible in high-throughput in single cells in culture. However, because of lack of technologies to incorporate DNA libraries, MPRAs are limited in whole organisms. To enable MPRAs in multicellular organisms, we generated tools to create a high degree of mutagenesis in specific genomic loci in vivo using base editing. Targeting GFP integrated in genome of Drosophila cell culture and whole animals as a case study, we show that the base editor AIDevoCDA1 stemming from sea lamprey fused to nCas9 is highly mutagenic. Surprisingly, longer gRNAs increase mutation efficiency and expand the mutating window, which can allow the introduction of mutations in previously untargetable sequences. Finally, we demonstrate arrays of >20 gRNAs that can efficiently introduce mutations along a 200bp sequence, making it a promising tool to test enhancer function in vivo in a high throughput manner.
Collapse
Affiliation(s)
- Julia Falo-Sanjuan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Yuliana Diaz-Tirado
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Meghan A. Turner
- Biophysics Graduate Group, University of California, Berkeley, CA, USA
| | - Julian Davis
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Claudia Medrano
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Jenna Haines
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Joey McKenna
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Michael B. Eisen
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Integrative Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Hernan G. Garcia
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Physics, University of California, Berkeley, CA, USA
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, CA, USA
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA, USA
- Biophysics Graduate Group, University of California, Berkeley, CA, USA
| |
Collapse
|
13
|
Ridnik M, Abberbock E, Alipov V, Lhermann SZ, Kaufman S, Lubman M, Poulat F, Gonen N. Two redundant transcription factor binding sites in a single enhancer are essential for mammalian sex determination. Nucleic Acids Res 2024; 52:5514-5528. [PMID: 38499491 PMCID: PMC11162780 DOI: 10.1093/nar/gkae178] [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: 11/07/2023] [Revised: 02/25/2024] [Accepted: 02/29/2024] [Indexed: 03/20/2024] Open
Abstract
Male development in mammals depends on the activity of the two SOX gene: Sry and Sox9, in the embryonic testis. As deletion of Enhancer 13 (Enh13) of the Sox9 gene results in XY male-to-female sex reversal, we explored the critical elements necessary for its function and hence, for testis and male development. Here, we demonstrate that while microdeletions of individual transcription factor binding sites (TFBS) in Enh13 lead to normal testicular development, combined microdeletions of just two SRY/SOX binding motifs can alone fully abolish Enh13 activity leading to XY male-to-female sex reversal. This suggests that for proper male development to occur, these few nucleotides of non-coding DNA must be intact. Interestingly, we show that depending on the nature of these TFBS mutations, dramatically different phenotypic outcomes can occur, providing a molecular explanation for the distinct clinical outcomes observed in patients harboring different variants in the same enhancer.
Collapse
Affiliation(s)
- Meshi Ridnik
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Elisheva Abberbock
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Veronica Alipov
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Shelly Ziv Lhermann
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Shoham Kaufman
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Maor Lubman
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Francis Poulat
- Group “Development and Pathology of the Gonad”. Department of Genetics, Cell Biology and Development, Institute of Human Genetics, CNRS-University of Montpellier UMR9002, Montpellier, France
| | - Nitzan Gonen
- The Mina and Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| |
Collapse
|
14
|
Li T, Shahabi S, Biswas T, Tsodikov OV, Pan W, Huang DB, Wang VYF, Wang Y, Ghosh G. Transient interactions modulate the affinity of NF-κB transcription factors for DNA. Proc Natl Acad Sci U S A 2024; 121:e2405555121. [PMID: 38805268 PMCID: PMC11161749 DOI: 10.1073/pnas.2405555121] [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: 03/21/2024] [Accepted: 04/09/2024] [Indexed: 05/30/2024] Open
Abstract
The dimeric nuclear factor kappa B (NF-κB) transcription factors (TFs) regulate gene expression by binding to a variety of κB DNA elements with conserved G:C-rich flanking sequences enclosing a degenerate central region. Toward defining mechanistic principles of affinity regulated by degeneracy, we observed an unusual dependence of the affinity of RelA on the identity of the central base pair, which appears to be noncontacted in the complex crystal structures. The affinity of κB sites with A or T at the central position is ~10-fold higher than with G or C. The crystal structures of neither the complexes nor the free κB DNAs could explain the differences in affinity. Interestingly, differential dynamics of several residues were revealed in molecular dynamics simulation studies, where simulation replicates totaling 148 μs were performed on NF-κB:DNA complexes and free κB DNAs. Notably, Arg187 and Arg124 exhibited selectivity in transient interactions that orchestrated a complex interplay among several DNA-interacting residues in the central region. Binding and simulation studies with mutants supported these observations of transient interactions dictating specificity. In combination with published reports, this work provides insights into the nuanced mechanisms governing the discriminatory binding of NF-κB family TFs to κB DNA elements and sheds light on cancer pathogenesis of cRel, a close homolog of RelA.
Collapse
Affiliation(s)
- Tianjie Li
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region999077, China
| | - Shandy Shahabi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA92093
| | - Tapan Biswas
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA92093
| | - Oleg V. Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY40536
| | - Wenfei Pan
- Faculty of Health Sciences, University of Macau, Taipa, Macau Special Administrative Region999078, China
| | - De-Bin Huang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA92093
| | - Vivien Ya-Fan Wang
- Faculty of Health Sciences, University of Macau, Taipa, Macau Special Administrative Region999078, China
| | - Yi Wang
- Department of Physics, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region999077, China
| | - Gourisankar Ghosh
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA92093
| |
Collapse
|
15
|
Lalanne JB, Regalado SG, Domcke S, Calderon D, Martin BK, Li X, Li T, Suiter CC, Lee C, Trapnell C, Shendure J. Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters. Nat Methods 2024; 21:983-993. [PMID: 38724692 PMCID: PMC11166576 DOI: 10.1038/s41592-024-02260-3] [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: 01/06/2023] [Accepted: 03/22/2024] [Indexed: 06/13/2024]
Abstract
The inability to scalably and precisely measure the activity of developmental cis-regulatory elements (CREs) in multicellular systems is a bottleneck in genomics. Here we develop a dual RNA cassette that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. The resulting measurement of reporter expression is accurate over multiple orders of magnitude, with a precision approaching the limit set by Poisson counting noise. Together with RNA barcode stabilization via circularization, these scalable single-cell quantitative expression reporters provide high-contrast readouts, analogous to classic in situ assays but entirely from sequencing. Screening >200 regions of accessible chromatin in a multicellular in vitro model of early mammalian development, we identify 13 (8 previously uncharacterized) autonomous and cell-type-specific developmental CREs. We further demonstrate that chimeric CRE pairs generate cognate two-cell-type activity profiles and assess gain- and loss-of-function multicellular expression phenotypes from CRE variants with perturbed transcription factor binding sites. Single-cell quantitative expression reporters can be applied in developmental and multicellular systems to quantitatively characterize native, perturbed and synthetic CREs at scale, with high sensitivity and at single-cell resolution.
Collapse
Affiliation(s)
| | - Samuel G Regalado
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Silvia Domcke
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Diego Calderon
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Beth K Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Xiaoyi Li
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Tony Li
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Chase C Suiter
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Choli Lee
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
| |
Collapse
|
16
|
Naqvi S, Kim S, Tabatabaee S, Pampari A, Kundaje A, Pritchard JK, Wysocka J. Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596078. [PMID: 38853998 PMCID: PMC11160683 DOI: 10.1101/2024.05.28.596078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Deep learning approaches have made significant advances in predicting cell type-specific chromatin patterns from the identity and arrangement of transcription factor (TF) binding motifs. However, most models have been applied in unperturbed contexts, precluding a predictive understanding of how chromatin state responds to TF perturbation. Here, we used transfer learning to train and interpret deep learning models that use DNA sequence to predict, with accuracy approaching experimental reproducibility, how the concentration of two dosage-sensitive TFs (TWIST1, SOX9) affects regulatory element (RE) chromatin accessibility in facial progenitor cells. High-affinity motifs that allow for heterotypic TF co-binding and are concentrated at the center of REs buffer against quantitative changes in TF dosage and strongly predict unperturbed accessibility. In contrast, motifs with low-affinity or homotypic binding distributed throughout REs lead to sensitive responses with minimal contributions to unperturbed accessibility. Both buffering and sensitizing features show signatures of purifying selection. We validated these predictive sequence features using reporter assays and showed that a biophysical model of TF-nucleosome competition can explain the sensitizing effect of low-affinity motifs. Our approach of combining transfer learning and quantitative measurements of the chromatin response to TF dosage therefore represents a powerful method to reveal additional layers of the cis-regulatory code.
Collapse
Affiliation(s)
- Sahin Naqvi
- Departments of Chemical and Systems Biology and Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, California, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Lead contact
| | - Seungsoo Kim
- Departments of Chemical and Systems Biology and Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- These authors contributed equally
| | - Saman Tabatabaee
- Departments of Chemical and Systems Biology and Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- These authors contributed equally
| | - Anusri Pampari
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Jonathan K Pritchard
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Joanna Wysocka
- Departments of Chemical and Systems Biology and Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| |
Collapse
|
17
|
Wagner T, Priyanka P, Micheletti R, Friedman MJ, Nair SJ, Gamliel A, Taylor H, Song X, Cho M, Oh S, Li W, Han J, Ohgi KA, Abrass M, D'Antonio-Chronowska A, D'Antonio M, Hazuda H, Duggirala R, Blangero J, Ding S, Guzmann C, Frazer KA, Aggarwal AK, Zemljic-Harpf AE, Rosenfeld MG, Suh Y. Recruitment of CTCF to the SIRT1 promoter after Oxidative Stress mediates Cardioprotective Transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.17.594600. [PMID: 38798402 PMCID: PMC11118446 DOI: 10.1101/2024.05.17.594600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Because most DNA-binding transcription factors (dbTFs), including the architectural regulator CTCF, bind RNA and exhibit di-/multimerization, a central conundrum is whether these distinct properties are regulated post-transcriptionally to modulate transcriptional programs. Here, investigating stress-dependent activation of SIRT1, encoding an evolutionarily-conserved protein deacetylase, we show that induced phosphorylation of CTCF acts as a rheostat to permit CTCF occupancy of low-affinity promoter DNA sites to precisely the levels necessary. This CTCF recruitment to the SIRT1 promoter is eliciting a cardioprotective cardiomyocyte transcriptional activation program and provides resilience against the stress of the beating heart in vivo . Mice harboring a mutation in the conserved low-affinity CTCF promoter binding site exhibit an altered, cardiomyocyte-specific transcriptional program and a systolic heart failure phenotype. This transcriptional role for CTCF reveals that a covalent dbTF modification regulating signal-dependent transcription serves as a previously unsuspected component of the oxidative stress response.
Collapse
|
18
|
McCann AA, Baniulyte G, Woodstock DL, Sammons MA. Context dependent activity of p63-bound gene regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593326. [PMID: 38766006 PMCID: PMC11100809 DOI: 10.1101/2024.05.09.593326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The p53 family of transcription factors regulate numerous organismal processes including the development of skin and limbs, ciliogenesis, and preservation of genetic integrity and tumor suppression. p53 family members control these processes and gene expression networks through engagement with DNA sequences within gene regulatory elements. Whereas p53 binding to its cognate recognition sequence is strongly associated with transcriptional activation, p63 can mediate both activation and repression. How the DNA sequence of p63-bound gene regulatory elements is linked to these varied activities is not yet understood. Here, we use massively parallel reporter assays (MPRA) in a range of cellular and genetic contexts to investigate the influence of DNA sequence on p63-mediated transcription. Most regulatory elements with a p63 response element motif (p63RE) activate transcription, with those sites bound by p63 more frequently or adhering closer to canonical p53 family response element sequences driving higher transcriptional output. The most active regulatory elements are those also capable of binding p53. Elements uniquely bound by p63 have varied activity, with p63RE-mediated repression associated with lower overall GC content in flanking sequences. Comparison of activity across cell lines suggests differential activity of elements may be regulated by a combination of p63 abundance or context-specific cofactors. Finally, changes in p63 isoform expression dramatically alters regulatory element activity, primarily shifting inactive elements towards a strong p63-dependent activity. Our analysis of p63-bound gene regulatory elements provides new insight into how sequence, cellular context, and other transcription factors influence p63-dependent transcription. These studies provide a framework for understanding how p63 genomic binding locally regulates transcription. Additionally, these results can be extended to investigate the influence of sequence content, genomic context, chromatin structure on the interplay between p63 isoforms and p53 family paralogs.
Collapse
Affiliation(s)
- Abby A. McCann
- Department of Biological Sciences and The RNA Institute, University at Albany, State University of New York. 1400 washington Ave, Albany, NY 12222
| | - Gabriele Baniulyte
- Department of Biological Sciences and The RNA Institute, University at Albany, State University of New York. 1400 washington Ave, Albany, NY 12222
| | - Dana L. Woodstock
- Department of Biological Sciences and The RNA Institute, University at Albany, State University of New York. 1400 washington Ave, Albany, NY 12222
| | - Morgan A. Sammons
- Department of Biological Sciences and The RNA Institute, University at Albany, State University of New York. 1400 washington Ave, Albany, NY 12222
| |
Collapse
|
19
|
Nordin A, Pagella P, Zambanini G, Cantù C. Exhaustive identification of genome-wide binding events of transcriptional regulators. Nucleic Acids Res 2024; 52:e40. [PMID: 38499482 PMCID: PMC11040144 DOI: 10.1093/nar/gkae180] [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: 09/21/2023] [Revised: 02/20/2024] [Accepted: 02/29/2024] [Indexed: 03/20/2024] Open
Abstract
Genome-wide binding assays aspire to map the complete binding pattern of gene regulators. Common practice relies on replication-duplicates or triplicates-and high stringency statistics to favor false negatives over false positives. Here we show that duplicates and triplicates of CUT&RUN are not sufficient to discover the entire activity of transcriptional regulators. We introduce ICEBERG (Increased Capture of Enrichment By Exhaustive Replicate aGgregation), a pipeline that harnesses large numbers of CUT&RUN replicates to discover the full set of binding events and chart the line between false positives and false negatives. We employed ICEBERG to map the full set of H3K4me3-marked regions, the targets of the co-factor β-catenin, and those of the transcription factor TBX3, in human colorectal cancer cells. The ICEBERG datasets allow benchmarking of individual replicates, comparing the performance of peak calling and replication approaches, and expose the arbitrary nature of strategies to identify reproducible peaks. Instead of a static view of genomic targets, ICEBERG establishes a spectrum of detection probabilities across the genome for a given factor, underlying the intrinsic dynamicity of its mechanism of action, and permitting to distinguish frequent from rare regulation events. Finally, ICEBERG discovered instances, undetectable with other approaches, that underlie novel mechanisms of colorectal cancer progression.
Collapse
Affiliation(s)
- Anna Nordin
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Pierfrancesco Pagella
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Gianluca Zambanini
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Claudio Cantù
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| |
Collapse
|
20
|
Negrón-Piñeiro LJ, Wu Y, Popsuj S, José-Edwards DS, Stolfi A, Di Gregorio A. Cis-regulatory interfaces reveal the molecular mechanisms underlying the notochord gene regulatory network of Ciona. Nat Commun 2024; 15:3025. [PMID: 38589372 PMCID: PMC11001920 DOI: 10.1038/s41467-024-46850-3] [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: 11/03/2022] [Accepted: 03/12/2024] [Indexed: 04/10/2024] Open
Abstract
Tissue-specific gene expression is fundamental in development and evolution, and is mediated by transcription factors and by the cis-regulatory regions (enhancers) that they control. Transcription factors and their respective tissue-specific enhancers are essential components of gene regulatory networks responsible for the development of tissues and organs. Although numerous transcription factors have been characterized from different organisms, the knowledge of the enhancers responsible for their tissue-specific expression remains fragmentary. Here we use Ciona to study the enhancers associated with ten transcription factors expressed in the notochord, an evolutionary hallmark of the chordate phylum. Our results illustrate how two evolutionarily conserved transcription factors, Brachyury and Foxa2, coordinate the deployment of other notochord transcription factors. The results of these detailed cis-regulatory analyses delineate a high-resolution view of the essential notochord gene regulatory network of Ciona, and provide a reference for studies of transcription factors, enhancers, and their roles in development, disease, and evolution.
Collapse
Affiliation(s)
- Lenny J Negrón-Piñeiro
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | - Yushi Wu
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | - Sydney Popsuj
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Diana S José-Edwards
- Post-Baccalaureate Premedical Program, Washington University, St. Louis, MO, 63130, USA
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Anna Di Gregorio
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA.
| |
Collapse
|
21
|
Johnson CJ, Zhang Z, Zhang H, Shang R, Piekarz KM, Bi P, Stolfi A. A change in cis-regulatory logic underlying obligate versus facultative muscle multinucleation in chordates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583753. [PMID: 38559144 PMCID: PMC10979880 DOI: 10.1101/2024.03.06.583753] [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: 04/04/2024]
Abstract
Vertebrates and tunicates are sister groups that share a common fusogenic factor, Myomaker (Mymk), that drives myoblast fusion and muscle multinucleation. Yet they are divergent in when and where they express Mymk. In vertebrates, all developing skeletal muscles express Mymk and are obligately multinucleated. In tunicates, Mymk is only expressed in post-metamorphic multinucleated muscles, but is absent from mononucleated larval muscles. In this study, we demonstrate that cis-regulatory sequence differences in the promoter region of Mymk underlie the different spatiotemporal patterns of its transcriptional activation in tunicates and vertebrates. While in vertebrates Myogenic Regulatory Factors (MRFs) like MyoD1 alone are required and sufficient for Mymk transcription in all skeletal muscles, we show that transcription of Mymk in post-metamorphic muscles of the tunicate Ciona requires the combinatorial activity of MRF/MyoD and Early B-Cell Factor (Ebf). This macroevolutionary difference appears to be encoded in cis, likely due to the presence of a putative Ebf binding site adjacent to predicted MRF binding sites in the Ciona Mymk promoter. We further discuss how Mymk and myoblast fusion might have been regulated in the last common ancestor of tunicates and vertebrates, for which we propose two models.
Collapse
Affiliation(s)
| | - Zheng Zhang
- Department of Genetics, University of Georgia, Athens, GA, USA
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
| | - Haifeng Zhang
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
| | - Renjie Shang
- Department of Genetics, University of Georgia, Athens, GA, USA
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
| | - Katarzyna M Piekarz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Pengpeng Bi
- Department of Genetics, University of Georgia, Athens, GA, USA
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| |
Collapse
|
22
|
Khetan S, Bulyk ML. Overlapping binding sites underlie TF genomic occupancy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.05.583629. [PMID: 38496549 PMCID: PMC10942454 DOI: 10.1101/2024.03.05.583629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Sequence-specific DNA binding by transcription factors (TFs) is a crucial step in gene regulation. However, current high-throughput in vitro approaches cannot reliably detect lower affinity TF-DNA interactions, which play key roles in gene regulation. Here, we developed PADIT-seq ( p rotein a ffinity to D NA by in vitro transcription and RNA seq uencing) to assay TF binding preferences to all 10-bp DNA sequences at far greater sensitivity than prior approaches. The expanded catalogs of low affinity DNA binding sites for the human TFs HOXD13 and EGR1 revealed that nucleotides flanking high affinity DNA binding sites create overlapping lower affinity sites that together modulate TF genomic occupancy in vivo . Formation of such extended recognition sequences stems from an inherent property of TF binding sites to interweave each other and expands the genomic sequence space for identifying noncoding variants that directly alter TF binding. One-Sentence Summary Overlapping DNA binding sites underlie TF genomic occupancy through their inherent propensity to interweave each other.
Collapse
|
23
|
Seitz EE, McCandlish DM, Kinney JB, Koo PK. Interpreting cis-regulatory mechanisms from genomic deep neural networks using surrogate models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.14.567120. [PMID: 38013993 PMCID: PMC10680760 DOI: 10.1101/2023.11.14.567120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Deep neural networks (DNNs) have greatly advanced the ability to predict genome function from sequence. Interpreting genomic DNNs in terms of biological mechanisms, however, remains difficult. Here we introduce SQUID, a genomic DNN interpretability framework based on surrogate modeling. SQUID approximates genomic DNNs in user-specified regions of sequence space using surrogate models, i.e., simpler models that are mechanistically interpretable. Importantly, SQUID removes the confounding effects that nonlinearities and heteroscedastic noise in functional genomics data can have on model interpretation. Benchmarking analysis on multiple genomic DNNs shows that SQUID, when compared to established interpretability methods, identifies motifs that are more consistent across genomic loci and yields improved single-nucleotide variant-effect predictions. SQUID also supports surrogate models that quantify epistatic interactions within and between cis-regulatory elements. SQUID thus advances the ability to mechanistically interpret genomic DNNs.
Collapse
Affiliation(s)
- Evan E Seitz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - David M McCandlish
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Justin B Kinney
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Peter K Koo
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| |
Collapse
|
24
|
Kwak IY, Kim BC, Lee J, Kang T, Garry DJ, Zhang J, Gong W. Proformer: a hybrid macaron transformer model predicts expression values from promoter sequences. BMC Bioinformatics 2024; 25:81. [PMID: 38378442 PMCID: PMC10877777 DOI: 10.1186/s12859-024-05645-5] [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: 05/24/2023] [Accepted: 01/08/2024] [Indexed: 02/22/2024] Open
Abstract
The breakthrough high-throughput measurement of the cis-regulatory activity of millions of randomly generated promoters provides an unprecedented opportunity to systematically decode the cis-regulatory logic that determines the expression values. We developed an end-to-end transformer encoder architecture named Proformer to predict the expression values from DNA sequences. Proformer used a Macaron-like Transformer encoder architecture, where two half-step feed forward (FFN) layers were placed at the beginning and the end of each encoder block, and a separable 1D convolution layer was inserted after the first FFN layer and in front of the multi-head attention layer. The sliding k-mers from one-hot encoded sequences were mapped onto a continuous embedding, combined with the learned positional embedding and strand embedding (forward strand vs. reverse complemented strand) as the sequence input. Moreover, Proformer introduced multiple expression heads with mask filling to prevent the transformer models from collapsing when training on relatively small amount of data. We empirically determined that this design had significantly better performance than the conventional design such as using the global pooling layer as the output layer for the regression task. These analyses support the notion that Proformer provides a novel method of learning and enhances our understanding of how cis-regulatory sequences determine the expression values.
Collapse
Affiliation(s)
- Il-Youp Kwak
- Department of Applied Statistics, Chung‑Ang University, Seoul, Republic of Korea
| | - Byeong-Chan Kim
- Department of Applied Statistics, Chung‑Ang University, Seoul, Republic of Korea
| | - Juhyun Lee
- Department of Applied Statistics, Chung‑Ang University, Seoul, Republic of Korea
| | - Taein Kang
- Department of Applied Statistics, Chung‑Ang University, Seoul, Republic of Korea
| | - Daniel J Garry
- Cardiovascular Division, Department of Medicine, Lillehei Heart Institute, University of Minnesota, 2231 6th St SE, Minneapolis, MN, 55455, USA.
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, 55455, USA.
- Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - Jianyi Zhang
- Department of Biomedical Engineering, The University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Wuming Gong
- Cardiovascular Division, Department of Medicine, Lillehei Heart Institute, University of Minnesota, 2231 6th St SE, Minneapolis, MN, 55455, USA.
| |
Collapse
|
25
|
Long T, Bhattacharyya T, Repele A, Naylor M, Nooti S, Krueger S, Manu. The contributions of DNA accessibility and transcription factor occupancy to enhancer activity during cellular differentiation. G3 (BETHESDA, MD.) 2024; 14:jkad269. [PMID: 38124496 PMCID: PMC11090500 DOI: 10.1093/g3journal/jkad269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 11/01/2023] [Indexed: 12/23/2023]
Abstract
During gene regulation, DNA accessibility is thought to limit the availability of transcription factor (TF) binding sites, while TFs can increase DNA accessibility to recruit additional factors that upregulate gene expression. Given this interplay, the causative regulatory events in the modulation of gene expression remain unknown for the vast majority of genes. We utilized deeply sequenced ATAC-Seq data and site-specific knock-in reporter genes to investigate the relationship between the binding-site resolution dynamics of DNA accessibility and the expression dynamics of the enhancers of Cebpa during macrophage-neutrophil differentiation. While the enhancers upregulate reporter expression during the earliest stages of differentiation, there is little corresponding increase in their total accessibility. Conversely, total accessibility peaks during the last stages of differentiation without any increase in enhancer activity. The accessibility of positions neighboring C/EBP-family TF binding sites, which indicates TF occupancy, does increase significantly during early differentiation, showing that the early upregulation of enhancer activity is driven by TF binding. These results imply that a generalized increase in DNA accessibility is not sufficient, and binding by enhancer-specific TFs is necessary, for the upregulation of gene expression. Additionally, high-coverage ATAC-Seq combined with time-series expression data can infer the sequence of regulatory events at binding-site resolution.
Collapse
Affiliation(s)
- Trevor Long
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Tapas Bhattacharyya
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Andrea Repele
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Madison Naylor
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Sunil Nooti
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Shawn Krueger
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| | - Manu
- Department of Biology, University of North Dakota, Grand Forks, ND 58202-9019, USA
| |
Collapse
|
26
|
Kim S, Morgunova E, Naqvi S, Goovaerts S, Bader M, Koska M, Popov A, Luong C, Pogson A, Swigut T, Claes P, Taipale J, Wysocka J. DNA-guided transcription factor cooperativity shapes face and limb mesenchyme. Cell 2024; 187:692-711.e26. [PMID: 38262408 PMCID: PMC10872279 DOI: 10.1016/j.cell.2023.12.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/23/2023] [Accepted: 12/27/2023] [Indexed: 01/25/2024]
Abstract
Transcription factors (TFs) can define distinct cellular identities despite nearly identical DNA-binding specificities. One mechanism for achieving regulatory specificity is DNA-guided TF cooperativity. Although in vitro studies suggest that it may be common, examples of such cooperativity remain scarce in cellular contexts. Here, we demonstrate how "Coordinator," a long DNA motif composed of common motifs bound by many basic helix-loop-helix (bHLH) and homeodomain (HD) TFs, uniquely defines the regulatory regions of embryonic face and limb mesenchyme. Coordinator guides cooperative and selective binding between the bHLH family mesenchymal regulator TWIST1 and a collective of HD factors associated with regional identities in the face and limb. TWIST1 is required for HD binding and open chromatin at Coordinator sites, whereas HD factors stabilize TWIST1 occupancy at Coordinator and titrate it away from HD-independent sites. This cooperativity results in the shared regulation of genes involved in cell-type and positional identities and ultimately shapes facial morphology and evolution.
Collapse
Affiliation(s)
- Seungsoo Kim
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford, CA 94305, USA
| | - Ekaterina Morgunova
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Seppe Goovaerts
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium; Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Maram Bader
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mervenaz Koska
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Christy Luong
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Angela Pogson
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford, CA 94305, USA
| | - Peter Claes
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium; Department of Human Genetics, KU Leuven, Leuven, Belgium; Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | - Jussi Taipale
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden; Department of Biochemistry, University of Cambridge, Cambridge, UK; Applied Tumor Genomics Program, University of Helsinki, Helsinki, Finland
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford, CA 94305, USA.
| |
Collapse
|
27
|
Lim F, Solvason JJ, Ryan GE, Le SH, Jindal GA, Steffen P, Jandu SK, Farley EK. Affinity-optimizing enhancer variants disrupt development. Nature 2024; 626:151-159. [PMID: 38233525 PMCID: PMC10830414 DOI: 10.1038/s41586-023-06922-8] [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: 01/11/2023] [Accepted: 11/30/2023] [Indexed: 01/19/2024]
Abstract
Enhancers control the location and timing of gene expression and contain the majority of variants associated with disease1-3. The ZRS is arguably the most well-studied vertebrate enhancer and mediates the expression of Shh in the developing limb4. Thirty-one human single-nucleotide variants (SNVs) within the ZRS are associated with polydactyly4-6. However, how this enhancer encodes tissue-specific activity, and the mechanisms by which SNVs alter the number of digits, are poorly understood. Here we show that the ETS sites within the ZRS are low affinity, and identify a functional ETS site, ETS-A, with extremely low affinity. Two human SNVs and a synthetic variant optimize the binding affinity of ETS-A subtly from 15% to around 25% relative to the strongest ETS binding sequence, and cause polydactyly with the same penetrance and severity. A greater increase in affinity results in phenotypes that are more penetrant and more severe. Affinity-optimizing SNVs in other ETS sites in the ZRS, as well as in ETS, interferon regulatory factor (IRF), HOX and activator protein 1 (AP-1) sites within a wide variety of enhancers, cause gain-of-function gene expression. The prevalence of binding sites with suboptimal affinity in enhancers creates a vulnerability in genomes whereby SNVs that optimize affinity, even slightly, can be pathogenic. Searching for affinity-optimizing SNVs in genomes could provide a mechanistic approach to identify causal variants that underlie enhanceropathies.
Collapse
Affiliation(s)
- Fabian Lim
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Biological Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Joe J Solvason
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Genevieve E Ryan
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Sophia H Le
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Granton A Jindal
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Paige Steffen
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Simran K Jandu
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Emma K Farley
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
28
|
Liu S, Gomez-Alcala P, Leemans C, Glassford WJ, Mann RS, Bussemaker HJ. Predicting the DNA binding specificity of mutated transcription factors using family-level biophysically interpretable machine learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.577115. [PMID: 38352411 PMCID: PMC10862739 DOI: 10.1101/2024.01.24.577115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Sequence-specific interactions of transcription factors (TFs) with genomic DNA underlie many cellular processes. High-throughput in vitro binding assays coupled with computational analysis have made it possible to accurately define such sequence recognition in a biophysically interpretable yet mechanism-agonistic way for individual TFs. The fact that such sequence-to-affinity models are now available for hundreds of TFs provides new avenues for predicting how the DNA binding specificity of a TF changes when its protein sequence is mutated. To this end, we developed an analytical framework based on a tetrahedron embedding that can be applied at the level of a given structural TF family. Using bHLH as a test case, we demonstrate that we can systematically map dependencies between the protein sequence of a TF and base preference within the DNA binding site. We also develop a regression approach to predict the quantitative energetic impact of mutations in the DNA binding domain of a TF on its DNA binding specificity, and perform SELEX-seq assays on mutated TFs to experimentally validate our results. Our results point to the feasibility of predicting the functional impact of disease mutations and allelic variation in the cell-wide TF repertoire by leveraging high-quality functional information across sets of homologous wild-type proteins.
Collapse
Affiliation(s)
- Shaoxun Liu
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Pilar Gomez-Alcala
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Christ Leemans
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - William J Glassford
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Richard S Mann
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| |
Collapse
|
29
|
Pickett CJ, Gruner HN, Davidson B. Lhx3/4 initiates a cardiopharyngeal-specific transcriptional program in response to widespread FGF signaling. PLoS Biol 2024; 22:e3002169. [PMID: 38271304 PMCID: PMC10810493 DOI: 10.1371/journal.pbio.3002169] [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: 05/04/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024] Open
Abstract
Individual signaling pathways, such as fibroblast growth factors (FGFs), can regulate a plethora of inductive events. According to current paradigms, signal-dependent transcription factors (TFs), such as FGF/MapK-activated Ets family factors, partner with lineage-determining factors to achieve regulatory specificity. However, many aspects of this model have not been rigorously investigated. One key question relates to whether lineage-determining factors dictate lineage-specific responses to inductive signals or facilitate these responses in collaboration with other inputs. We utilize the chordate model Ciona robusta to investigate mechanisms generating lineage-specific induction. Previous studies in C. robusta have shown that cardiopharyngeal progenitor cells are specified through the combined activity of FGF-activated Ets1/2.b and an inferred ATTA-binding transcriptional cofactor. Here, we show that the homeobox TF Lhx3/4 serves as the lineage-determining TF that dictates cardiopharyngeal-specific transcription in response to pleiotropic FGF signaling. Targeted knockdown of Lhx3/4 leads to loss of cardiopharyngeal gene expression. Strikingly, ectopic expression of Lhx3/4 in a neuroectodermal lineage subject to FGF-dependent specification leads to ectopic cardiopharyngeal gene expression in this lineage. Furthermore, ectopic Lhx3/4 expression disrupts neural plate morphogenesis, generating aberrant cell behaviors associated with execution of incompatible morphogenetic programs. Based on these findings, we propose that combinatorial regulation by signal-dependent and lineage-determinant factors represents a generalizable, previously uncategorized regulatory subcircuit we term "cofactor-dependent induction." Integration of this subcircuit into theoretical models will facilitate accurate predictions regarding the impact of gene regulatory network rewiring on evolutionary diversification and disease ontogeny.
Collapse
Affiliation(s)
- C. J. Pickett
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania, United States of America
| | - Hannah N. Gruner
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania, United States of America
| | - Bradley Davidson
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania, United States of America
| |
Collapse
|
30
|
Martyn GE, Montgomery MT, Jones H, Guo K, Doughty BR, Linder J, Chen Z, Cochran K, Lawrence KA, Munson G, Pampari A, Fulco CP, Kelley DR, Lander ES, Kundaje A, Engreitz JM. Rewriting regulatory DNA to dissect and reprogram gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572268. [PMID: 38187584 PMCID: PMC10769263 DOI: 10.1101/2023.12.20.572268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Regulatory DNA sequences within enhancers and promoters bind transcription factors to encode cell type-specific patterns of gene expression. However, the regulatory effects and programmability of such DNA sequences remain difficult to map or predict because we have lacked scalable methods to precisely edit regulatory DNA and quantify the effects in an endogenous genomic context. Here we present an approach to measure the quantitative effects of hundreds of designed DNA sequence variants on gene expression, by combining pooled CRISPR prime editing with RNA fluorescence in situ hybridization and cell sorting (Variant-FlowFISH). We apply this method to mutagenize and rewrite regulatory DNA sequences in an enhancer and the promoter of PPIF in two immune cell lines. Of 672 variant-cell type pairs, we identify 497 that affect PPIF expression. These variants appear to act through a variety of mechanisms including disruption or optimization of existing transcription factor binding sites, as well as creation of de novo sites. Disrupting a single endogenous transcription factor binding site often led to large changes in expression (up to -40% in the enhancer, and -50% in the promoter). The same variant often had different effects across cell types and states, demonstrating a highly tunable regulatory landscape. We use these data to benchmark performance of sequence-based predictive models of gene regulation, and find that certain types of variants are not accurately predicted by existing models. Finally, we computationally design 185 small sequence variants (≤10 bp) and optimize them for specific effects on expression in silico. 84% of these rationally designed edits showed the intended direction of effect, and some had dramatic effects on expression (-100% to +202%). Variant-FlowFISH thus provides a powerful tool to map the effects of variants and transcription factor binding sites on gene expression, test and improve computational models of gene regulation, and reprogram regulatory DNA.
Collapse
Affiliation(s)
- Gabriella E Martyn
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Science and Engineering Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
| | - Michael T Montgomery
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Science and Engineering Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
| | - Hank Jones
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Science and Engineering Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
| | - Katherine Guo
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Science and Engineering Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
| | - Benjamin R Doughty
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Ziwei Chen
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Kelly Cochran
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Kathryn A Lawrence
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Glen Munson
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anusri Pampari
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Charles P Fulco
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Present Address: Sanofi, Cambridge, MA, USA
| | | | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, MIT, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Jesse M Engreitz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Basic Science and Engineering Initiative, Stanford Children's Health, Betty Irene Moore Children's Heart Center, Stanford, CA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
| |
Collapse
|
31
|
Aarts MT, Wagner M, van der Wal T, van Boxtel AL, van Amerongen R. A molecular toolbox to study progesterone receptor signaling. J Mammary Gland Biol Neoplasia 2023; 28:24. [PMID: 38019315 PMCID: PMC10687192 DOI: 10.1007/s10911-023-09550-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/29/2023] [Indexed: 11/30/2023] Open
Abstract
Progesterone receptor (PR) signaling is required for mammary gland development and homeostasis. A major bottleneck in studying PR signaling is the lack of sensitive assays to measure and visualize PR pathway activity both quantitatively and spatially. Here, we develop new tools to study PR signaling in human breast epithelial cells. First, we generate optimized Progesterone Responsive Element (PRE)-luciferase constructs and demonstrate that these new reporters are a powerful tool to quantify PR signaling activity across a wide range of progesterone concentrations in two luminal breast cancer cell lines, MCF7 and T47D. We also describe a fluorescent lentiviral PRE-GFP reporter as a novel tool to visualize PR signaling at the single-cell level. Our reporter constructs are sensitive to physiological levels of progesterone. Second, we show that low background signaling, and high levels of PR expression are a prerequisite for robustly measuring PR signaling. Increasing PR expression by transient transfection, stable overexpression in MCF7 or clonal selection in T47D, drastically improves both the dynamic range of luciferase reporter assays, and the induction of endogenous PR target genes as measured by qRT-PCR. We find that the PR signaling response differs per cell line, target gene and hormone concentration used. Taken together, our tools allow a more rationally designed approach for measuring PR signaling in breast epithelial cells.
Collapse
Affiliation(s)
- Marleen T Aarts
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
| | - Muriel Wagner
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
| | - Tanne van der Wal
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
| | - Antonius L van Boxtel
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
| | - Renée van Amerongen
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands.
| |
Collapse
|
32
|
Xu C, Kleinschmidt H, Yang J, Leith E, Johnson J, Tan S, Mahony S, Bai L. Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.08.566246. [PMID: 37986839 PMCID: PMC10659273 DOI: 10.1101/2023.11.08.566246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Despite the unique ability of pioneer transcription factors (PFs) to target nucleosomal sites in closed chromatin, they only bind a small fraction of their genomic motifs. The underlying mechanism of this selectivity is not well understood. Here, we design a high-throughput assay called ChIP-ISO to systematically dissect sequence features affecting the binding specificity of a classic PF, FOXA1. Combining ChIP-ISO with in vitro and neural network analyses, we find that 1) FOXA1 binding is strongly affected by co-binding TFs AP-1 and CEBPB, 2) FOXA1 and AP-1 show binding cooperativity in vitro, 3) FOXA1's binding is determined more by local sequences than chromatin context, including eu-/heterochromatin, and 4) AP-1 is partially responsible for differential binding of FOXA1 in different cell types. Our study presents a framework for elucidating genetic rules underlying PF binding specificity and reveals a mechanism for context-specific regulation of its binding.
Collapse
Affiliation(s)
- Cheng Xu
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Holly Kleinschmidt
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jianyu Yang
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Erik Leith
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jenna Johnson
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Song Tan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Shaun Mahony
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Physics, The Pennsylvania State University, University Park, PA 16802, USA
| |
Collapse
|
33
|
Seifert AW, Duncan EM, Zayas RM. Enduring questions in regenerative biology and the search for answers. Commun Biol 2023; 6:1139. [PMID: 37945686 PMCID: PMC10636051 DOI: 10.1038/s42003-023-05505-7] [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: 06/09/2023] [Accepted: 10/25/2023] [Indexed: 11/12/2023] Open
Abstract
The potential for basic research to uncover the inner workings of regenerative processes and produce meaningful medical therapies has inspired scientists, clinicians, and patients for hundreds of years. Decades of studies using a handful of highly regenerative model organisms have significantly advanced our knowledge of key cell types and molecular pathways involved in regeneration. However, many questions remain about how regenerative processes unfold in regeneration-competent species, how they are curtailed in non-regenerative organisms, and how they might be induced (or restored) in humans. Recent technological advances in genomics, molecular biology, computer science, bioengineering, and stem cell research hold promise to collectively provide new experimental evidence for how different organisms accomplish the process of regeneration. In theory, this new evidence should inform the design of new clinical approaches for regenerative medicine. A deeper understanding of how tissues and organs regenerate will also undoubtedly impact many adjacent scientific fields. To best apply and adapt these new technologies in ways that break long-standing barriers and answer critical questions about regeneration, we must combine the deep knowledge of developmental and evolutionary biologists with the hard-earned expertise of scientists in mechanistic and technical fields. To this end, this perspective is based on conversations from a workshop we organized at the Banbury Center, during which a diverse cross-section of the regeneration research community and experts in various technologies discussed enduring questions in regenerative biology. Here, we share the questions this group identified as significant and unanswered, i.e., known unknowns. We also describe the obstacles limiting our progress in answering these questions and how expanding the number and diversity of organisms used in regeneration research is essential for deepening our understanding of regenerative capacity. Finally, we propose that investigating these problems collaboratively across a diverse network of researchers has the potential to advance our field and produce unexpected insights into important questions in related areas of biology and medicine.
Collapse
Affiliation(s)
- Ashley W Seifert
- Department of Biology, University of Kentucky, Lexington, KY, 40506, USA.
| | - Elizabeth M Duncan
- Department of Biology, University of Kentucky, Lexington, KY, 40506, USA.
| | - Ricardo M Zayas
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA.
| |
Collapse
|
34
|
Syed S, Duan Y, Lim B. Modulation of protein-DNA binding reveals mechanisms of spatiotemporal gene control in early Drosophila embryos. eLife 2023; 12:e85997. [PMID: 37934571 PMCID: PMC10629816 DOI: 10.7554/elife.85997] [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: 01/06/2023] [Accepted: 10/19/2023] [Indexed: 11/08/2023] Open
Abstract
It is well known that enhancers regulate the spatiotemporal expression of their target genes by recruiting transcription factors (TFs) to the cognate binding sites in the region. However, the role of multiple binding sites for the same TFs and their specific spatial arrangement in determining the overall competency of the enhancer has yet to be fully understood. In this study, we utilized the MS2-MCP live imaging technique to quantitatively analyze the regulatory logic of the snail distal enhancer in early Drosophila embryos. Through systematic modulation of Dorsal and Twist binding motifs in this enhancer, we found that a mutation in any one of these binding sites causes a drastic reduction in transcriptional amplitude, resulting in a reduction in mRNA production of the target gene. We provide evidence of synergy, such that multiple binding sites with moderate affinities cooperatively recruit more TFs to drive stronger transcriptional activity than a single site. Moreover, a Hidden Markov-based stochastic model of transcription reveals that embryos with mutated binding sites have a higher probability of returning to the inactive promoter state. We propose that TF-DNA binding regulates spatial and temporal gene expression and drives robust pattern formation by modulating transcriptional kinetics and tuning bursting rates.
Collapse
Affiliation(s)
- Sahla Syed
- Department of Chemical and Biomolecular Engineering, University of PennsylvaniaPhiladelphiaUnited States
| | - Yifei Duan
- Department of Chemical and Biomolecular Engineering, University of PennsylvaniaPhiladelphiaUnited States
- Master of Biotechnology Program, University of PennsylvaniaPhiladelphiaUnited States
| | - Bomyi Lim
- Department of Chemical and Biomolecular Engineering, University of PennsylvaniaPhiladelphiaUnited States
| |
Collapse
|
35
|
Jindal GA, Bantle AT, Solvason JJ, Grudzien JL, D'Antonio-Chronowska A, Lim F, Le SH, Song BP, Ragsac MF, Klie A, Larsen RO, Frazer KA, Farley EK. Single-nucleotide variants within heart enhancers increase binding affinity and disrupt heart development. Dev Cell 2023; 58:2206-2216.e5. [PMID: 37848026 PMCID: PMC10720985 DOI: 10.1016/j.devcel.2023.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/07/2023] [Accepted: 09/20/2023] [Indexed: 10/19/2023]
Abstract
Transcriptional enhancers direct precise gene expression patterns during development and harbor the majority of variants associated with phenotypic diversity, evolutionary adaptations, and disease. Pinpointing which enhancer variants contribute to changes in gene expression and phenotypes is a major challenge. Here, we find that suboptimal or low-affinity binding sites are necessary for precise gene expression during heart development. Single-nucleotide variants (SNVs) can optimize the affinity of ETS binding sites, causing gain-of-function (GOF) gene expression, cell migration defects, and phenotypes as severe as extra beating hearts in the marine chordate Ciona robusta. In human induced pluripotent stem cell (iPSC)-derived cardiomyocytes, a SNV within a human GATA4 enhancer increases ETS binding affinity and causes GOF enhancer activity. The prevalence of suboptimal-affinity sites within enhancers creates a vulnerability whereby affinity-optimizing SNVs can lead to GOF gene expression, changes in cellular identity, and organismal-level phenotypes that could contribute to the evolution of novel traits or diseases.
Collapse
Affiliation(s)
- Granton A Jindal
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alexis T Bantle
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joe J Solvason
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jessica L Grudzien
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Fabian Lim
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sophia H Le
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Benjamin P Song
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michelle F Ragsac
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Adam Klie
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Reid O Larsen
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kelly A Frazer
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emma K Farley
- Department of Medicine, Health Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
36
|
Uttley K, Papanastasiou AS, Lahne M, Brisbane JM, MacDonald RB, Bickmore WA, Bhatia S. Unique activities of two overlapping PAX6 retinal enhancers. Life Sci Alliance 2023; 6:e202302126. [PMID: 37643867 PMCID: PMC10465922 DOI: 10.26508/lsa.202302126] [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: 05/01/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/31/2023] Open
Abstract
Enhancers play a critical role in development by precisely modulating spatial, temporal, and cell type-specific gene expression. Sequence variants in enhancers have been implicated in diseases; however, establishing the functional consequences of these variants is challenging because of a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development, with a regulatory landscape containing multiple enhancers driving the expression in the eye. Whether these enhancers perform additive, redundant or distinct functions is unknown. Here, we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers, HS5 and NRE. Using a unique combination of live imaging and single-cell RNA sequencing in dual enhancer-reporter zebrafish embryos, we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping, these enhancers have distinct activities in different cell types and therefore likely nonredundant functions. This work demonstrates that unique cell type-specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo.
Collapse
Affiliation(s)
- Kirsty Uttley
- https://ror.org/011jsc803 MRC Human Genetics Unithttps://ror.org/01nrxwf90 , Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Andrew S Papanastasiou
- https://ror.org/011jsc803 MRC Human Genetics Unithttps://ror.org/01nrxwf90 , Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Manuela Lahne
- https://ror.org/02jx3x895 UCL Institute of Ophthalmology, University College London, Greater London, UK
| | - Jennifer M Brisbane
- https://ror.org/011jsc803 MRC Human Genetics Unithttps://ror.org/01nrxwf90 , Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Ryan B MacDonald
- https://ror.org/02jx3x895 UCL Institute of Ophthalmology, University College London, Greater London, UK
| | - Wendy A Bickmore
- https://ror.org/011jsc803 MRC Human Genetics Unithttps://ror.org/01nrxwf90 , Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Shipra Bhatia
- https://ror.org/011jsc803 MRC Human Genetics Unithttps://ror.org/01nrxwf90 , Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| |
Collapse
|
37
|
Farley EK. Ciona, an ideal research organism to study the role of enhancers. Genesis 2023; 61:e23577. [PMID: 38009359 DOI: 10.1002/dvg.23577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/28/2023]
Affiliation(s)
- Emma Kirsten Farley
- Department of Medicine, University of California San Diego, La Jolla, California, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, California, USA
| |
Collapse
|
38
|
Arnold M, Stengel KR. Emerging insights into enhancer biology and function. Transcription 2023; 14:68-87. [PMID: 37312570 PMCID: PMC10353330 DOI: 10.1080/21541264.2023.2222032] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/15/2023] Open
Abstract
Cell type-specific gene expression is coordinated by DNA-encoded enhancers and the transcription factors (TFs) that bind to them in a sequence-specific manner. As such, these enhancers and TFs are critical mediators of normal development and altered enhancer or TF function is associated with the development of diseases such as cancer. While initially defined by their ability to activate gene transcription in reporter assays, putative enhancer elements are now frequently defined by their unique chromatin features including DNase hypersensitivity and transposase accessibility, bidirectional enhancer RNA (eRNA) transcription, CpG hypomethylation, high H3K27ac and H3K4me1, sequence-specific transcription factor binding, and co-factor recruitment. Identification of these chromatin features through sequencing-based assays has revolutionized our ability to identify enhancer elements on a genome-wide scale, and genome-wide functional assays are now capitalizing on this information to greatly expand our understanding of how enhancers function to provide spatiotemporal coordination of gene expression programs. Here, we highlight recent technological advances that are providing new insights into the molecular mechanisms by which these critical cis-regulatory elements function in gene control. We pay particular attention to advances in our understanding of enhancer transcription, enhancer-promoter syntax, 3D organization and biomolecular condensates, transcription factor and co-factor dependencies, and the development of genome-wide functional enhancer screens.
Collapse
Affiliation(s)
- Mirjam Arnold
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kristy R. Stengel
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
- Montefiore Einstein Cancer Center, Albert Einstein College of Medicine-Montefiore Health System, Bronx, NY, USA
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, USA
| |
Collapse
|
39
|
Kemmler CL, Smolikova J, Moran HR, Mannion BJ, Knapp D, Lim F, Czarkwiani A, Hermosilla Aguayo V, Rapp V, Fitch OE, Bötschi S, Selleri L, Farley E, Braasch I, Yun M, Visel A, Osterwalder M, Mosimann C, Kozmik Z, Burger A. Conserved enhancers control notochord expression of vertebrate Brachyury. Nat Commun 2023; 14:6594. [PMID: 37852970 PMCID: PMC10584899 DOI: 10.1038/s41467-023-42151-3] [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: 05/15/2023] [Accepted: 09/29/2023] [Indexed: 10/20/2023] Open
Abstract
The cell type-specific expression of key transcription factors is central to development and disease. Brachyury/T/TBXT is a major transcription factor for gastrulation, tailbud patterning, and notochord formation; however, how its expression is controlled in the mammalian notochord has remained elusive. Here, we identify the complement of notochord-specific enhancers in the mammalian Brachyury/T/TBXT gene. Using transgenic assays in zebrafish, axolotl, and mouse, we discover three conserved Brachyury-controlling notochord enhancers, T3, C, and I, in human, mouse, and marsupial genomes. Acting as Brachyury-responsive, auto-regulatory shadow enhancers, in cis deletion of all three enhancers in mouse abolishes Brachyury/T/Tbxt expression selectively in the notochord, causing specific trunk and neural tube defects without gastrulation or tailbud defects. The three Brachyury-driving notochord enhancers are conserved beyond mammals in the brachyury/tbxtb loci of fishes, dating their origin to the last common ancestor of jawed vertebrates. Our data define the vertebrate enhancers for Brachyury/T/TBXTB notochord expression through an auto-regulatory mechanism that conveys robustness and adaptability as ancient basis for axis development.
Collapse
Affiliation(s)
- Cassie L Kemmler
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jana Smolikova
- Institute of Molecular Genetics of the ASCR, v. v. i., Prague, Czech Republic
| | - Hannah R Moran
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Brandon J Mannion
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA, 94720, USA
| | - Dunja Knapp
- Technische Universität Dresden, CRTD Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Fabian Lim
- Department of Medicine, Health Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Biological Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Anna Czarkwiani
- Technische Universität Dresden, CRTD Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Viviana Hermosilla Aguayo
- Program in Craniofacial Biology, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Vincent Rapp
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Olivia E Fitch
- Department of Integrative Biology and Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Seraina Bötschi
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Licia Selleri
- Program in Craniofacial Biology, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Emma Farley
- Department of Medicine, Health Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ingo Braasch
- Department of Integrative Biology and Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Maximina Yun
- Technische Universität Dresden, CRTD Center for Regenerative Therapies Dresden, Dresden, Germany
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden, Germany
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- School of Natural Sciences, University of California Merced, Merced, CA, USA
| | - Marco Osterwalder
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
- Department of Cardiology, Bern University Hospital, Bern, Switzerland
| | - Christian Mosimann
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Zbynek Kozmik
- Institute of Molecular Genetics of the ASCR, v. v. i., Prague, Czech Republic.
| | - Alexa Burger
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| |
Collapse
|
40
|
Trauernicht M, Rastogi C, Manzo S, Bussemaker H, van Steensel B. Optimisation of TP53 reporters by systematic dissection of synthetic TP53 response elements. Nucleic Acids Res 2023; 51:9690-9702. [PMID: 37650627 PMCID: PMC10570033 DOI: 10.1093/nar/gkad718] [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: 02/23/2023] [Revised: 07/24/2023] [Accepted: 08/22/2023] [Indexed: 09/01/2023] Open
Abstract
TP53 is a transcription factor that controls multiple cellular processes, including cell cycle arrest, DNA repair and apoptosis. The relation between TP53 binding site architecture and transcriptional output is still not fully understood. Here, we systematically examined in three different cell lines the effects of binding site affinity and copy number on TP53-dependent transcriptional output, and also probed the impact of spacer length and sequence between adjacent binding sites, and of core promoter identity. Paradoxically, we found that high-affinity TP53 binding sites are less potent than medium-affinity sites. TP53 achieves supra-additive transcriptional activation through optimally spaced adjacent binding sites, suggesting a cooperative mechanism. Optimally spaced adjacent binding sites have a ∼10-bp periodicity, suggesting a role for spatial orientation along the DNA double helix. We leveraged these insights to construct a log-linear model that explains activity from sequence features, and to identify new highly active and sensitive TP53 reporters.
Collapse
Affiliation(s)
- Max Trauernicht
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Chaitanya Rastogi
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Stefano G Manzo
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Department of Biosciences, University of Milan “La Statale”, 20133 Milan, Italy
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| |
Collapse
|
41
|
Shang R, Lai EC. Parameters of clustered suboptimal miRNA biogenesis. Proc Natl Acad Sci U S A 2023; 120:e2306727120. [PMID: 37788316 PMCID: PMC10576077 DOI: 10.1073/pnas.2306727120] [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: 04/24/2023] [Accepted: 08/23/2023] [Indexed: 10/05/2023] Open
Abstract
The nuclear cleavage of a suboptimal primary miRNA hairpin by the Drosha/DGCR8 complex ("Microprocessor") can be enhanced by an optimal miRNA neighbor, a phenomenon termed cluster assistance. Several features and biological impacts of this new layer of miRNA regulation are not fully known. Here, we elucidate the parameters of cluster assistance of a suboptimal miRNA and also reveal competitive interactions amongst optimal miRNAs within a cluster. We exploit cluster assistance as a functional assay for suboptimal processing and use this to invalidate putative suboptimal substrates, as well as identify a "solo" suboptimal miRNA. Finally, we report complexity in how specific mutations might affect the biogenesis of clustered miRNAs in disease contexts. This includes how an operon context can buffer the effect of a deleterious processing variant, but reciprocally how a point mutation can have a nonautonomous effect to impair the biogenesis of a clustered, suboptimal, neighbor. These data expand our knowledge regarding regulated miRNA biogenesis in humans and represent a functional assay for empirical definition of suboptimal Microprocessor substrates.
Collapse
Affiliation(s)
- Renfu Shang
- Department of Developmental Biology, Sloan Kettering Institute, New York, NY10065
| | - Eric C. Lai
- Department of Developmental Biology, Sloan Kettering Institute, New York, NY10065
| |
Collapse
|
42
|
Horton CA, Alexandari AM, Hayes MGB, Marklund E, Schaepe JM, Aditham AK, Shah N, Suzuki PH, Shrikumar A, Afek A, Greenleaf WJ, Gordân R, Zeitlinger J, Kundaje A, Fordyce PM. Short tandem repeats bind transcription factors to tune eukaryotic gene expression. Science 2023; 381:eadd1250. [PMID: 37733848 DOI: 10.1126/science.add1250] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/26/2023] [Indexed: 09/23/2023]
Abstract
Short tandem repeats (STRs) are enriched in eukaryotic cis-regulatory elements and alter gene expression, yet how they regulate transcription remains unknown. We found that STRs modulate transcription factor (TF)-DNA affinities and apparent on-rates by about 70-fold by directly binding TF DNA-binding domains, with energetic impacts exceeding many consensus motif mutations. STRs maximize the number of weakly preferred microstates near target sites, thereby increasing TF density, with impacts well predicted by statistical mechanics. Confirming that STRs also affect TF binding in cells, neural networks trained only on in vivo occupancies predicted effects identical to those observed in vitro. Approximately 90% of TFs preferentially bound STRs that need not resemble known motifs, providing a cis-regulatory mechanism to target TFs to genomic sites.
Collapse
Affiliation(s)
- Connor A Horton
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Amr M Alexandari
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Michael G B Hayes
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Emil Marklund
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Julia M Schaepe
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Arjun K Aditham
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Nilay Shah
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Peter H Suzuki
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Avanti Shrikumar
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Ariel Afek
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Raluca Gordân
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Computer Science, Duke University, Durham, NC 27708, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- The University of Kansas Medical Center, Kansas City, KS 66103, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Polly M Fordyce
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94110, USA
| |
Collapse
|
43
|
Bragdon MDJ, Patel N, Chuang J, Levien E, Bashor CJ, Khalil AS. Cooperative assembly confers regulatory specificity and long-term genetic circuit stability. Cell 2023; 186:3810-3825.e18. [PMID: 37552983 PMCID: PMC10528910 DOI: 10.1016/j.cell.2023.07.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 05/17/2023] [Accepted: 07/10/2023] [Indexed: 08/10/2023]
Abstract
A ubiquitous feature of eukaryotic transcriptional regulation is cooperative self-assembly between transcription factors (TFs) and DNA cis-regulatory motifs. It is thought that this strategy enables specific regulatory connections to be formed in gene networks between otherwise weakly interacting, low-specificity molecular components. Here, using synthetic gene circuits constructed in yeast, we find that high regulatory specificity can emerge from cooperative, multivalent interactions among artificial zinc-finger-based TFs. We show that circuits "wired" using the strategy of cooperative TF assembly are effectively insulated from aberrant misregulation of the host cell genome. As we demonstrate in experiments and mathematical models, this mechanism is sufficient to rescue circuit-driven fitness defects, resulting in genetic and functional stability of circuits in long-term continuous culture. Our naturally inspired approach offers a simple, generalizable means for building high-fidelity, evolutionarily robust gene circuits that can be scaled to a wide range of host organisms and applications.
Collapse
Affiliation(s)
- Meghan D J Bragdon
- Biological Design Center, Boston University, Boston, MA 02215, USA; Program in Molecular Biology, Cell Biology and Biochemistry, Boston University, Boston, MA 02215, USA
| | - Nikit Patel
- Biological Design Center, Boston University, Boston, MA 02215, USA; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - James Chuang
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ethan Levien
- Department of Mathematics, Dartmouth College, Hanover, NH 03755, USA
| | - Caleb J Bashor
- Department of Bioengineering, Rice University, Houston, TX 77030, USA; Department of Biosciences, Rice University, Houston, TX 77030, USA
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA 02215, USA; Program in Molecular Biology, Cell Biology and Biochemistry, Boston University, Boston, MA 02215, USA; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
| |
Collapse
|
44
|
Gigante ED, Piekarz KM, Gurgis A, Cohen L, Razy-Krajka F, Popsuj S, Ali HS, Sundaram SM, Stolfi A. Specification and survival of post-metamorphic branchiomeric neurons in the hindbrain of a non-vertebrate chordate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.16.545305. [PMID: 37645866 PMCID: PMC10461979 DOI: 10.1101/2023.06.16.545305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Tunicates are the sister group to the vertebrates, yet most species have a life cycle split between swimming larva and sedentary adult phases. During metamorphosis, larval neurons are largely replaced by adult-specific ones. Yet the regulatory mechanisms underlying this neural replacement remain largely unknown. Using tissue-specific CRISPR/Cas9-mediated mutagenesis in the tunicate Ciona, we show that orthologs of conserved hindbrain and branchiomeric neuron regulatory factors Pax2/5/8 and Phox2 are required to specify the "Neck", a compartment of cells set aside in the larva to give rise to cranial motor neuron-like neurons in the adult. Using bulk and single-cell RNAseq analyses, we also characterize the transcriptome of the Neck downstream of Pax2/5/8. Surprisingly, we find that Neck-derived adult ciliomotor neurons begin to differentiate in the larva, contrary to the long-held assumption that the adult nervous system is formed only after settlement and the death of larval neurons during metamorphosis. Finally, we show that manipulating FGF signaling during the larval phase alters the patterning of the Neck and its derivatives. Suppression of FGF converts Neck cells into larval neurons that fail to survive metamorphosis, while prolonged FGF signaling promotes an adult neural stem cell-like fate instead.
Collapse
Affiliation(s)
- Eduardo D Gigante
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332; USA
| | - Katarzyna M Piekarz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332; USA
| | - Alexandra Gurgis
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332; USA
- Department of Biology, Case Western Reserve University, Cleveland, OH, 44106; USA
| | - Leslie Cohen
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332; USA
| | - Florian Razy-Krajka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332; USA
| | - Sydney Popsuj
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332; USA
| | - Hussan S Ali
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332; USA
| | | | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332; USA
| |
Collapse
|
45
|
Gosai SJ, Castro RI, Fuentes N, Butts JC, Kales S, Noche RR, Mouri K, Sabeti PC, Reilly SK, Tewhey R. Machine-guided design of synthetic cell type-specific cis-regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552077. [PMID: 37609287 PMCID: PMC10441439 DOI: 10.1101/2023.08.08.552077] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Cis-regulatory elements (CREs) control gene expression, orchestrating tissue identity, developmental timing, and stimulus responses, which collectively define the thousands of unique cell types in the body. While there is great potential for strategically incorporating CREs in therapeutic or biotechnology applications that require tissue specificity, there is no guarantee that an optimal CRE for an intended purpose has arisen naturally through evolution. Here, we present a platform to engineer and validate synthetic CREs capable of driving gene expression with programmed cell type specificity. We leverage innovations in deep neural network modeling of CRE activity across three cell types, efficient in silico optimization, and massively parallel reporter assays (MPRAs) to design and empirically test thousands of CREs. Through in vitro and in vivo validation, we show that synthetic sequences outperform natural sequences from the human genome in driving cell type-specific expression. Synthetic sequences leverage unique sequence syntax to promote activity in the on-target cell type and simultaneously reduce activity in off-target cells. Together, we provide a generalizable framework to prospectively engineer CREs and demonstrate the required literacy to write regulatory code that is fit-for-purpose in vivo across vertebrates.
Collapse
Affiliation(s)
- SJ Gosai
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Graduate Program in Biological and Biomedical Science, Boston MA
- Department Of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - RI Castro
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - N Fuentes
- The Jackson Laboratory, Bar Harbor, ME, USA
- Harvard College, Harvard University, Cambridge, MA, USA
| | - JC Butts
- The Jackson Laboratory, Bar Harbor, ME, USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA
| | - S Kales
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - RR Noche
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, USA
- Yale Zebrafish Research Core, Yale School of Medicine, New Haven, CT, USA
| | - K Mouri
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - PC Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department Of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - SK Reilly
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Wu Tsai Institute, Yale University, New Haven, CT, USA
| | - R Tewhey
- The Jackson Laboratory, Bar Harbor, ME, USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA
- Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
| |
Collapse
|
46
|
Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK. DNA selection by the master transcription factor PU.1. Cell Rep 2023; 42:112671. [PMID: 37352101 PMCID: PMC10479921 DOI: 10.1016/j.celrep.2023.112671] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/07/2023] [Accepted: 06/02/2023] [Indexed: 06/25/2023] Open
Abstract
The master transcriptional regulator PU.1/Spi-1 engages DNA sites with affinities spanning multiple orders of magnitude. To elucidate this remarkable plasticity, we have characterized 22 high-resolution co-crystallographic PU.1/DNA complexes across the addressable affinity range in myeloid gene transactivation. Over a purine-rich core (such as 5'-GGAA-3') flanked by variable sequences, affinity is negotiated by direct readout on the 5' flank via a critical glutamine (Q226) sidechain and by indirect readout on the 3' flank by sequence-dependent helical flexibility. Direct readout by Q226 dynamically specifies PU.1's characteristic preference for purines and explains the pathogenic mutation Q226E in Waldenström macroglobulinemia. The structures also reveal how disruption of Q226 mediates strand-specific inhibition by DNA methylation and the recognition of non-canonical sites, including the authentic binding sequence at the CD11b promoter. A re-synthesis of phylogenetic and structural data on the ETS family, considering the centrality of Q226 in PU.1, unifies the model of DNA selection by ETS proteins.
Collapse
Affiliation(s)
- J Ross Terrell
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Samuel J Taylor
- Departments of Cell Biology, Oncology, and Medicine, Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Blood Cancer Institute, and the Montefiore Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Amelia L Schneider
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Yue Lu
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Tyler N Vernon
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Suela Xhani
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Ryan H Gumpper
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Ming Luo
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Ulrich Steidl
- Departments of Cell Biology, Oncology, and Medicine, Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Blood Cancer Institute, and the Montefiore Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
| |
Collapse
|
47
|
Kim S, Morgunova E, Naqvi S, Bader M, Koska M, Popov A, Luong C, Pogson A, Claes P, Taipale J, Wysocka J. DNA-guided transcription factor cooperativity shapes face and limb mesenchyme. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.29.541540. [PMID: 37398193 PMCID: PMC10312427 DOI: 10.1101/2023.05.29.541540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Transcription factors (TFs) can define distinct cellular identities despite nearly identical DNA-binding specificities. One mechanism for achieving regulatory specificity is DNA-guided TF cooperativity. Although in vitro studies suggest it may be common, examples of such cooperativity remain scarce in cellular contexts. Here, we demonstrate how 'Coordinator', a long DNA motif comprised of common motifs bound by many basic helix-loop-helix (bHLH) and homeodomain (HD) TFs, uniquely defines regulatory regions of embryonic face and limb mesenchyme. Coordinator guides cooperative and selective binding between the bHLH family mesenchymal regulator TWIST1 and a collective of HD factors associated with regional identities in the face and limb. TWIST1 is required for HD binding and open chromatin at Coordinator sites, while HD factors stabilize TWIST1 occupancy at Coordinator and titrate it away from HD-independent sites. This cooperativity results in shared regulation of genes involved in cell-type and positional identities, and ultimately shapes facial morphology and evolution.
Collapse
Affiliation(s)
- Seungsoo Kim
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305
- Howard Hughes Medical Institute, Stanford, CA 94305
| | - Ekaterina Morgunova
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305
- Department of Genetics, Stanford University, Stanford, CA 94305
| | - Maram Bader
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305
| | - Mervenaz Koska
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
| | | | - Christy Luong
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305
| | - Angela Pogson
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
| | - Peter Claes
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Jussi Taipale
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Applied Tumor Genomics Program, University of Helsinki, Helsinki, Finland
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305
- Howard Hughes Medical Institute, Stanford, CA 94305
| |
Collapse
|
48
|
Smith GD, Ching WH, Cornejo-Páramo P, Wong ES. Decoding enhancer complexity with machine learning and high-throughput discovery. Genome Biol 2023; 24:116. [PMID: 37173718 PMCID: PMC10176946 DOI: 10.1186/s13059-023-02955-4] [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: 07/18/2022] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Enhancers are genomic DNA elements controlling spatiotemporal gene expression. Their flexible organization and functional redundancies make deciphering their sequence-function relationships challenging. This article provides an overview of the current understanding of enhancer organization and evolution, with an emphasis on factors that influence these relationships. Technological advancements, particularly in machine learning and synthetic biology, are discussed in light of how they provide new ways to understand this complexity. Exciting opportunities lie ahead as we continue to unravel the intricacies of enhancer function.
Collapse
Affiliation(s)
- Gabrielle D Smith
- Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, Australia
| | - Wan Hern Ching
- Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, Australia
| | - Paola Cornejo-Páramo
- Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, Australia
| | - Emily S Wong
- Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, Australia.
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, Australia.
| |
Collapse
|
49
|
Kemmler CL, Smolikova J, Moran HR, Mannion BJ, Knapp D, Lim F, Czarkwiani A, Hermosilla Aguayo V, Rapp V, Fitch OE, Bötschi S, Selleri L, Farley E, Braasch I, Yun M, Visel A, Osterwalder M, Mosimann C, Kozmik Z, Burger A. Conserved enhancer logic controls the notochord expression of vertebrate Brachyury. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.20.536761. [PMID: 37131681 PMCID: PMC10153258 DOI: 10.1101/2023.04.20.536761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The cell type-specific expression of key transcription factors is central to development. Brachyury/T/TBXT is a major transcription factor for gastrulation, tailbud patterning, and notochord formation; however, how its expression is controlled in the mammalian notochord has remained elusive. Here, we identify the complement of notochord-specific enhancers in the mammalian Brachyury/T/TBXT gene. Using transgenic assays in zebrafish, axolotl, and mouse, we discover three Brachyury-controlling notochord enhancers T3, C, and I in human, mouse, and marsupial genomes. Acting as Brachyury-responsive, auto-regulatory shadow enhancers, deletion of all three enhancers in mouse abolishes Brachyury/T expression selectively in the notochord, causing specific trunk and neural tube defects without gastrulation or tailbud defects. Sequence and functional conservation of Brachyury-driving notochord enhancers with the brachyury/tbxtb loci from diverse lineages of fishes dates their origin to the last common ancestor of jawed vertebrates. Our data define the enhancers for Brachyury/T/TBXTB notochord expression as ancient mechanism in axis development.
Collapse
Affiliation(s)
- Cassie L. Kemmler
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jana Smolikova
- Institute of Molecular Genetics of the ASCR, v. v. i., Prague, Czech Republic
| | - Hannah R. Moran
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Brandon J. Mannion
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA 94720, USA
| | - Dunja Knapp
- Technische Universität Dresden, CRTD/Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Fabian Lim
- Department of Medicine, Health Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA USA
- Biological Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Anna Czarkwiani
- Technische Universität Dresden, CRTD/Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Viviana Hermosilla Aguayo
- Program in Craniofacial Biology, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Vincent Rapp
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Olivia E. Fitch
- Department of Integrative Biology and Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Seraina Bötschi
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Licia Selleri
- Program in Craniofacial Biology, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Emma Farley
- Department of Medicine, Health Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA USA
| | - Ingo Braasch
- Department of Integrative Biology and Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Maximina Yun
- Technische Universität Dresden, CRTD/Center for Regenerative Therapies Dresden, Dresden, Germany
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden, Germany
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- School of Natural Sciences, University of California Merced, Merced, CA, USA
| | - Marco Osterwalder
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
- Department of Cardiology, Berne University Hospital, Berne, Switzerland
| | - Christian Mosimann
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Zbynek Kozmik
- Institute of Molecular Genetics of the ASCR, v. v. i., Prague, Czech Republic
| | - Alexa Burger
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| |
Collapse
|
50
|
Long T, Bhattacharyya T, Repele A, Naylor M, Nooti S, Krueger S, Manu. The contributions of DNA accessibility and transcription factor occupancy to enhancer activity during cellular differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.22.529579. [PMID: 37090616 PMCID: PMC10120690 DOI: 10.1101/2023.02.22.529579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
The upregulation of gene expression by enhancers depends upon the interplay between the binding of sequence-specific transcription factors (TFs) and DNA accessibility. DNA accessibility is thought to limit the ability of TFs to bind to their sites, while TFs can increase accessibility to recruit additional factors that upregulate gene expression. Given this interplay, the causative regulatory events underlying the modulation of gene expression during cellular differentiation remain unknown for the vast majority of genes. We investigated the binding-site resolution dynamics of DNA accessibility and the expression dynamics of the enhancers of an important neutrophil gene, Cebpa, during macrophage-neutrophil differentiation. Reporter genes were integrated in a site-specific manner in PUER cells, which are progenitors that can be differentiated into neutrophils or macrophages in vitro by activating the pan-leukocyte TF PU.1. Time series data show that two enhancers upregulate reporter expression during the first 48 hours of neutrophil differentiation. Surprisingly, there is little or no increase in the total accessibility, measured by ATAC-Seq, of the enhancers during the same time period. Conversely, total accessibility peaks 96 hrs after PU.1 activation-consistent with its role as a pioneer-but the enhancers do not upregulate gene expression. Combining deeply sequenced ATAC-Seq data with a new bias-correction method allowed the profiling of accessibility at single-nucleotide resolution and revealed protected regions in the enhancers that match all previously characterized TF binding sites and ChIP-Seq data. Although the accessibility of most positions does not change during early differentiation, that of positions neighboring TF binding sites, an indicator of TF occupancy, did increase significantly. The localized accessibility changes are limited to nucleotides neighboring C/EBP-family TF binding sites, showing that the upregulation of enhancer activity during early differentiation is driven by C/EBP-family TF binding. These results show that increasing the total accessibility of enhancers is not sufficient for upregulating their activity and other events such as TF binding are necessary for upregulation. Also, TF binding can cause upregulation without a perceptible increase in total accessibility. Finally, this study demonstrates the feasibility of comprehensively mapping individual TF binding sites as footprints using high coverage ATAC-Seq and inferring the sequence of events in gene regulation by combining with time-series gene expression data.
Collapse
Affiliation(s)
- Trevor Long
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Tapas Bhattacharyya
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Andrea Repele
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Madison Naylor
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Sunil Nooti
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Shawn Krueger
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| | - Manu
- Department of Biology, University of North Dakota, Grand Forks, 58202-9019 ND, USA
| |
Collapse
|