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Feng S, Rastogi C, Loker R, Glassford WJ, Tomas Rube H, Bussemaker HJ, Mann RS. Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors. Nat Commun 2022; 13:3808. [PMID: 35778382 PMCID: PMC9249852 DOI: 10.1038/s41467-022-31501-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 06/20/2022] [Indexed: 12/23/2022] Open
Abstract
In eukaryotes, members of transcription factor families often exhibit similar DNA binding properties in vitro, yet orchestrate paralog-specific gene regulatory networks in vivo. The serially homologous first (T1) and third (T3) thoracic legs of Drosophila, which are specified by the Hox proteins Scr and Ubx, respectively, offer a unique opportunity to address this paradox in vivo. Genome-wide analyses using epitope-tagged alleles of both Hox loci in the T1 and T3 leg imaginal discs, the precursors to the adult legs and ventral body regions, show that ~8% of Hox binding is paralog-specific. Binding specificity is mediated by interactions with distinct cofactors in different domains: the Hox cofactor Exd acts in the proximal domain and is necessary for Scr to bind many of its paralog-specific targets, while in the distal leg domain, the homeodomain protein Distal-less (Dll) enhances Scr binding to a different subset of loci. These findings reveal how Hox paralogs, and perhaps paralogs of other transcription factor families, orchestrate alternative downstream gene regulatory networks with the help of multiple, context-specific cofactors.
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Affiliation(s)
- Siqian Feng
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Chaitanya Rastogi
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Ryan Loker
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Genetics and Development, Columbia University, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
| | - William J Glassford
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - H Tomas Rube
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Department of Bioengineering, University of California, Merced, CA, USA
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, 10027, USA
| | - Richard S Mann
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA.
- Department of Systems Biology, Columbia University, New York, NY, 10027, USA.
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Fang C, Li J, Qi S, Lei Y, Zeng Y, Yu P, Hu Z, Zhou Y, Wang Y, Dai R, Li J, Huang S, Xu P, Chen K, Ding C, Yu FX. An alternatively transcribed TAZ variant negatively regulates JAK-STAT signaling. EMBO Rep 2019; 20:embr.201847227. [PMID: 30979708 DOI: 10.15252/embr.201847227] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 03/25/2019] [Accepted: 03/25/2019] [Indexed: 12/11/2022] Open
Abstract
Type I interferon (IFN)-induced Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signaling drives the expression of IFN-stimulated genes (ISGs) to mediate antiviral response. The strength and duration of JAK-STAT signaling are tightly regulated to ensure effective antiviral defense while avoiding pathological inflammation and autoimmunity. Here, we report that cTAZ, an isoform of the Hippo pathway effector TAZ, is transcribed by an alternative promoter. Although majority of C-terminal sequences of TAZ is retained, cTAZ is not regulated by the Hippo signaling and does not mediate its growth-inhibitory functions. Instead, cTAZ negatively regulates JAK-STAT signaling by inhibiting STAT1/2 nuclear localization and ISG expression, and its expression is induced by type I IFN Thus, cTAZ functions as a modulator of JAK-STAT signaling and may play a role in fine-tuning cellular antiviral response.
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Affiliation(s)
- Chuantao Fang
- Children's Hospital and Institutes of Biomedical Sciences, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China
| | - Jian Li
- Children's Hospital and Institutes of Biomedical Sciences, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China
| | - Sixian Qi
- Children's Hospital and Institutes of Biomedical Sciences, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China
| | - Yubin Lei
- Children's Hospital and Institutes of Biomedical Sciences, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China
| | - Yan Zeng
- Children's Hospital and Institutes of Biomedical Sciences, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China
| | - Pengcheng Yu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhaolan Hu
- Department of Anesthesiology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yufeng Zhou
- Children's Hospital and Institutes of Biomedical Sciences, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China
| | - Yulong Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ruping Dai
- Department of Anesthesiology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jin Li
- Children's Hospital and Institutes of Biomedical Sciences, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China
| | - Shenglin Huang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Pinglong Xu
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | - Kang Chen
- Perinatology Research Branch, Eunice Kennedy Shriver NICHD, National Institutes of Health, Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA.,Jiangsu Province Hospital of TCM, The Affiliated Hospital of Nanjing University of TCM, Nanjing, China
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Institutes of Biomedical Sciences, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Fa-Xing Yu
- Children's Hospital and Institutes of Biomedical Sciences, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China
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Jakobsen JS, Bagger FO, Hasemann MS, Schuster MB, Frank AK, Waage J, Vitting-Seerup K, Porse BT. Amplification of pico-scale DNA mediated by bacterial carrier DNA for small-cell-number transcription factor ChIP-seq. BMC Genomics 2015; 16:46. [PMID: 25652644 PMCID: PMC4328043 DOI: 10.1186/s12864-014-1195-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 12/22/2014] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Chromatin-Immunoprecipitation coupled with deep sequencing (ChIP-seq) is used to map transcription factor occupancy and generate epigenetic profiles genome-wide. The requirement of nano-scale ChIP DNA for generation of sequencing libraries has impeded ChIP-seq on in vivo tissues of low cell numbers. RESULTS We describe a robust, simple and scalable methodology for ChIP-seq of low-abundant cell populations, verified down to 10,000 cells. By employing non-mammalian genome mapping bacterial carrier DNA during amplification, we reliably amplify down to 50 pg of ChIP DNA from transcription factor (CEBPA) and histone mark (H3K4me3) ChIP. We further demonstrate that genomic profiles are highly resilient to changes in carrier DNA to ChIP DNA ratios. CONCLUSIONS This represents a significant advance compared to existing technologies, which involve either complex steps of pre-selection for nucleosome-containing chromatin or pre-amplification of precipitated DNA, making them prone to introduce experimental biases.
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Affiliation(s)
- Janus S Jakobsen
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. .,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. .,Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark.
| | - Frederik O Bagger
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. .,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. .,Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark. .,The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark.
| | - Marie S Hasemann
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. .,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. .,Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark.
| | - Mikkel B Schuster
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. .,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. .,Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark.
| | - Anne-Katrine Frank
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. .,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. .,Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark.
| | - Johannes Waage
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. .,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. .,Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark. .,The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. .,Present address: Danish Pediatric Asthma Center, Copenhagen University Hospital Gentofte, Ledreborg Alle 34, 2820, Gentofte, Denmark.
| | - Kristoffer Vitting-Seerup
- The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark.
| | - Bo T Porse
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. .,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. .,Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark.
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