1
|
Weissman JD, Kotekar A, Barbash Z, Mu J, Singer DS. CCAAT Promoter element regulates transgenerational expression of the MHC class I gene. Chromosoma 2024:10.1007/s00412-024-00820-2. [PMID: 38922437 DOI: 10.1007/s00412-024-00820-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 06/27/2024]
Abstract
Transgenerational gene expression depends on both underlying DNA sequences and epigenetic modifications. The latter, which can result in transmission of variegated gene expression patterns across multiple generations without DNA alterations, has been termed epigenetic inheritance and has been documented in plants, worms, flies and mammals. Whereas transcription factors binding to cognate DNA sequence elements regulate gene expression, the molecular basis for epigenetic inheritance has been linked to histone and DNA modifications and non-coding RNA. Here we report that mutation of the CCAAT box promoter element abrogates NF-Y binding and disrupts the stable transgenerational expression of an MHC class I transgene. Transgenic mice with a mutated CCAAT box in the MHC class I transgene display variegated expression of the transgene among littermates and progeny in multiple independently derived transgenic lines. After 4 generations, CCAAT mutant transgenic lines derived from a single founder stably displayed distinct patterns of expression. Histone modifications and RNA polymerase II binding correlate with expression of CCAAT mutant transgenic lines, whereas DNA methylation and nucleosome occupancy do not. Mutation of the CCAAT box also results in changes to CTCF binding and DNA looping patterns across the transgene that correlate with expression status. These studies identify the CCAAT promoter element as a regulator of stable transgenerational gene expression such that mutation of the CCAAT box results in variegated transgenerational inheritance. Considering that the CCAAT box is present in 30% of eukaryotic promoters, this study provides insights into how fidelity of gene expression patterns is maintained through multiple generations.
Collapse
Affiliation(s)
- Jocelyn D Weissman
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bldg 10, Room 4B-36, Bethesda, MD, 20892, USA
| | - Aparna Kotekar
- NIH Center for Human Immunology, Inflammation, and Autoimmunity (CHI), National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, 20892, USA
| | | | - Jie Mu
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bldg 10, Room 4B-36, Bethesda, MD, 20892, USA
| | - Dinah S Singer
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bldg 10, Room 4B-36, Bethesda, MD, 20892, USA.
| |
Collapse
|
2
|
Weissman JD, Kotekar A, Barbash Z, Mu J, Singer DS. Transgenerational Epigenetic Inheritance of MHC Class I Gene Expression is Regulated by the CCAAT Promoter Element. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.13.536772. [PMID: 37333336 PMCID: PMC10274869 DOI: 10.1101/2023.04.13.536772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Transgenerational epigenetic inheritance is defined as the transmission of traits or gene expression patterns across multiple generations that do not derive from DNA alterations. The effect of multiple stress factors or metabolic changes resulting in such inheritance have been documented in plants, worms and flies and mammals. The molecular basis for epigenetic inheritance has been linked to histone and DNA modifications and non-coding RNA. In this study, we show that mutation of a promoter element, the CCAAT box, disrupts stable expression of an MHC Class I transgene, resulting in variegated expression among progeny for at least 4 generations in multiple independently derived transgenic lines. Histone modifications and RNA polII binding correlate with expression, whereas DNA methylation and nucleosome occupancy do not. Mutation of the CCAAT box abrogates NF-Y binding and results in changes to CTCF binding and DNA looping patterns across the gene that correlate with expression status from one generation to the next. These studies identify the CCAAT promoter element as a regulator of stable transgenerational epigenetic inheritance. Considering that the CCAAT box is present in 30% of eukaryotic promoters, this study could provide important insights into how fidelity of gene expression patterns is maintained through multiple generations.
Collapse
Affiliation(s)
- Jocelyn D Weissman
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Aparna Kotekar
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Zohar Barbash
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Jie Mu
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Dinah S Singer
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892
| |
Collapse
|
3
|
Kulski JK. Long Noncoding RNA HCP5, a Hybrid HLA Class I Endogenous Retroviral Gene: Structure, Expression, and Disease Associations. Cells 2019; 8:cells8050480. [PMID: 31137555 PMCID: PMC6562477 DOI: 10.3390/cells8050480] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 02/06/2023] Open
Abstract
The HCP5 RNA gene (NCBI ID: 10866) is located centromeric of the HLA-B gene and between the MICA and MICB genes within the major histocompatibility complex (MHC) class I region. It is a human species-specific gene that codes for a long noncoding RNA (lncRNA), composed mostly of an ancient ancestral endogenous antisense 3′ long terminal repeat (LTR, and part of the internal pol antisense sequence of endogenous retrovirus (ERV) type 16 linked to a human leukocyte antigen (HLA) class I promoter and leader sequence at the 5′-end. Since its discovery in 1993, many disease association and gene expression studies have shown that HCP5 is a regulatory lncRNA involved in adaptive and innate immune responses and associated with the promotion of some autoimmune diseases and cancers. The gene sequence acts as a genomic anchor point for binding transcription factors, enhancers, and chromatin remodeling enzymes in the regulation of transcription and chromatin folding. The HCP5 antisense retroviral transcript also interacts with regulatory microRNA and immune and cellular checkpoints in cancers suggesting its potential as a drug target for novel antitumor therapeutics.
Collapse
Affiliation(s)
- Jerzy K Kulski
- Faculty of Health and Medical Sciences, UWA Medical School, The University of Western Australia, Crawley, WA 6009, Australia.
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara 259-1193, Japan.
| |
Collapse
|
4
|
Hypoxia and hypoxia-inducible factor (HIF) downregulate antigen-presenting MHC class I molecules limiting tumor cell recognition by T cells. PLoS One 2017; 12:e0187314. [PMID: 29155844 PMCID: PMC5695785 DOI: 10.1371/journal.pone.0187314] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 10/17/2017] [Indexed: 11/19/2022] Open
Abstract
Human cancers are known to downregulate Major Histocompatibility Complex (MHC) class I expression thereby escaping recognition and rejection by anti-tumor T cells. Here we report that oxygen tension in the tumor microenvironment (TME) serves as an extrinsic cue that regulates antigen presentation by MHC class I molecules. In support of this view, hypoxia is shown to negatively regulate MHC expression in a HIF-dependent manner as evidenced by (i) lower MHC expression in the hypoxic TME in vivo and in hypoxic 3-dimensional (3D) but not 2-dimensional (2D) tumor cell cultures in vitro; (ii) decreased MHC in human renal cell carcinomas with constitutive expression of HIF due to genetic loss of von Hippel-Lindau (VHL) function as compared with isogenically paired cells with restored VHL function, and iii) increased MHC in tumor cells with siRNA-mediated knockdown of HIF. In addition, hypoxia downregulated antigen presenting proteins like TAP 1/2 and LMP7 that are known to have a dominant role in surface display of peptide-MHC complexes. Corroborating oxygen-dependent regulation of MHC antigen presentation, hyperoxia (60% oxygen) transcriptionally upregulated MHC expression and increased levels of TAP2, LMP2 and 7. In conclusion, this study reveals a novel mechanism by which intra-tumoral hypoxia and HIF can potentiate immune escape. It also suggests the use of hyperoxia to improve tumor cell-based cancer vaccines and for mining novel immune epitopes. Furthermore, this study highlights the advantage of 3D cell cultures in reproducing hypoxia-dependent changes observed in the TME.
Collapse
|
5
|
Hendy O, Campbell J, Weissman JD, Larson DR, Singer DS. Differential context-specific impact of individual core promoter elements on transcriptional dynamics. Mol Biol Cell 2017; 28:3360-3370. [PMID: 28931597 PMCID: PMC5687036 DOI: 10.1091/mbc.e17-06-0408] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 08/23/2017] [Accepted: 09/11/2017] [Indexed: 11/11/2022] Open
Abstract
The roles of individual core promoter elements in transcriptional dynamics of MHC class I gene expression were determined by smFISH in primary B-cells. The elements individually modulated transcriptional bursting, differentially contributing to burst size or burst frequency, to enable combinatorial fine-tuning of the level of transcription. Eukaryotic transcription occurs in bursts that vary in size and frequency, but the contribution of individual core promoter elements to transcriptional bursting is not known. Here we analyze the relative contributions to bursting of the individual core promoter elements—CCAAT, TATAA-like, Sp1BS, and Inr—of an MHC class I gene in primary B-cells during both basal and activated transcription. The TATAA-like, Sp1BS, and Inr elements all function as negative regulators of transcription, and each was found to contribute differentially to the overall bursting pattern of the promoter during basal transcription. Whereas the Sp1BS element regulates burst size, the Inr element regulates burst frequency. The TATAA-like element contributes to both. Surprisingly, each element has a distinct role in bursting during transcriptional activation by γ-interferon. The CCAAT element does not contribute significantly to the constitutive transcriptional dynamics of primary B-cells, but modulates both burst size and frequency in response to γ-interferon activation. The ability of core promoter elements to modulate transcriptional bursting individually allows combinatorial fine-tuning of the level of MHC class I gene expression in response to intrinsic and extrinsic signals.
Collapse
Affiliation(s)
- Oliver Hendy
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - John Campbell
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Jocelyn D Weissman
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Daniel R Larson
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Dinah S Singer
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| |
Collapse
|
6
|
Wang J, Zhao S, He W, Wei Y, Zhang Y, Pegg H, Shore P, Roberts SGE, Deng W. A transcription factor IIA-binding site differentially regulates RNA polymerase II-mediated transcription in a promoter context-dependent manner. J Biol Chem 2017; 292:11873-11885. [PMID: 28539359 DOI: 10.1074/jbc.m116.770412] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 05/23/2017] [Indexed: 12/11/2022] Open
Abstract
RNA polymerase II (pol II) is required for the transcription of all protein-coding genes and as such represents a major enzyme whose activity is tightly regulated. Transcriptional initiation therefore requires numerous general transcriptional factors and cofactors that associate with pol II at the core promoter to form a pre-initiation complex. Transcription factor IIA (TFIIA) is a general cofactor that binds TFIID and stabilizes the TFIID-DNA complex during transcription initiation. Previous studies showed that TFIIA can make contact with the DNA sequence upstream or downstream of the TATA box, and that the region bound by TFIIA could overlap with the elements recognized by another factor, TFIIB, at adenovirus major late core promoter. Whether core promoters contain a DNA motif recognized by TFIIA remains unknown. Here we have identified a core promoter element upstream of the TATA box that is recognized by TFIIA. A search of the human promoter database revealed that many natural promoters contain a TFIIA recognition element (IIARE). We show that the IIARE enhances TFIIA-promoter binding and enhances the activity of TATA-containing promoters, but represses or activates promoters that lack a TATA box. Chromatin immunoprecipitation assays revealed that the IIARE activates transcription by increasing the recruitment of pol II, TFIIA, TAF4, and P300 at TATA-dependent promoters. These findings extend our understanding of the role of TFIIA in transcription, and provide new insights into the regulatory mechanism of core promoter elements in gene transcription by pol II.
Collapse
Affiliation(s)
- Juan Wang
- Institute of Biology and Medicine, Wuhan University of Science and Technology, Wuhan City, Hubei Province 430065, China
| | - Shasha Zhao
- Institute of Biology and Medicine, Wuhan University of Science and Technology, Wuhan City, Hubei Province 430065, China
| | - Wei He
- Institute of Biology and Medicine, Wuhan University of Science and Technology, Wuhan City, Hubei Province 430065, China
| | - Yun Wei
- Institute of Biology and Medicine, Wuhan University of Science and Technology, Wuhan City, Hubei Province 430065, China
| | - Yang Zhang
- Institute of Biology and Medicine, Wuhan University of Science and Technology, Wuhan City, Hubei Province 430065, China
| | - Henry Pegg
- School of Biological Sciences, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Paul Shore
- School of Biological Sciences, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Stefan G E Roberts
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, United Kingdom.
| | - Wensheng Deng
- Institute of Biology and Medicine, Wuhan University of Science and Technology, Wuhan City, Hubei Province 430065, China.
| |
Collapse
|
7
|
René C, Lozano C, Eliaou JF. Expression of classical HLA class I molecules: regulation and clinical impacts: Julia Bodmer Award Review 2015. HLA 2016; 87:338-49. [PMID: 27060357 DOI: 10.1111/tan.12787] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 03/04/2016] [Indexed: 12/19/2022]
Abstract
Human leukocyte antigen (HLA) class I genes are ubiquitously expressed, but in a tissue specific-manner. Their expression is primarily regulated at the transcriptional level and can be modulated both positively and negatively by different stimuli. Advances in sequencing technologies led to the identification of new regulatory variants located in the untranslated regions (UTRs), which could influence the expression. After a brief description of the mechanisms underlying the transcriptional regulation of HLA class I genes expression, we will review how the expression levels of HLA class I genes could affect biological and pathological processes. Then, we will discuss on the differential expression of HLA class I genes according to the locus, allele and UTR polymorphisms and its clinical impact. This interesting field of study led to a new dimension of HLA typing, going beyond a qualitative aspect.
Collapse
Affiliation(s)
- C René
- Department of Immunology, CHRU de Montpellier, University Hospital Saint-Eloi, Montpellier, France.,Faculté de Médecine, University of Montpellier, Montpellier, France.,INSERM U1183, Institute for Regenerative Medicine and Biotherapy (IRMB), CHU Montpellier, Montpellier, France
| | - C Lozano
- Department of Immunology, CHRU de Montpellier, University Hospital Saint-Eloi, Montpellier, France
| | - J-F Eliaou
- Department of Immunology, CHRU de Montpellier, University Hospital Saint-Eloi, Montpellier, France.,Faculté de Médecine, University of Montpellier, Montpellier, France.,INSERM U1194, IRCM, University of Montpellier, Montpellier, France
| |
Collapse
|
8
|
Taylor RL, Cruickshank MN, Karimi M, Ng HL, Quail E, Kaufman KM, Harley JB, Abraham LJ, Tsao BP, Boackle SA, Ulgiati D. Focused transcription from the human CR2/CD21 core promoter is regulated by synergistic activity of TATA and Initiator elements in mature B cells. Cell Mol Immunol 2016; 13:119-31. [PMID: 25640655 PMCID: PMC4711682 DOI: 10.1038/cmi.2014.138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 12/05/2014] [Accepted: 12/27/2014] [Indexed: 12/13/2022] Open
Abstract
Complement receptor 2 (CR2/CD21) is predominantly expressed on the surface of mature B cells where it forms part of a coreceptor complex that functions, in part, to modulate B-cell receptor signal strength. CR2/CD21 expression is tightly regulated throughout B-cell development such that CR2/CD21 cannot be detected on pre-B or terminally differentiated plasma cells. CR2/CD21 expression is upregulated at B-cell maturation and can be induced by IL-4 and CD40 signaling pathways. We have previously characterized elements in the proximal promoter and first intron of CR2/CD21 that are involved in regulating basal and tissue-specific expression. We now extend these analyses to the CR2/CD21 core promoter. We show that in mature B cells, CR2/CD21 transcription proceeds from a focused TSS regulated by a non-consensus TATA box, an initiator element and a downstream promoter element. Furthermore, occupancy of the general transcriptional machinery in pre-B versus mature B-cell lines correlate with CR2/CD21 expression level and indicate that promoter accessibility must switch from inactive to active during the transitional B-cell window.
Collapse
Affiliation(s)
- Rhonda L Taylor
- School of Pathology and Laboratory Medicine, Centre for Genetic Origins of Health and Disease, The University of Western Australia, Crawley, WA, Australia
- Biochemistry and Molecular Biology, School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA, Australia
| | - Mark N Cruickshank
- Telethon Kids Institute, The University of Western Australia, Crawley, WA, Australia
| | - Mahdad Karimi
- Biochemistry and Molecular Biology, School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA, Australia
| | - Han Leng Ng
- School of Pathology and Laboratory Medicine, Centre for Genetic Origins of Health and Disease, The University of Western Australia, Crawley, WA, Australia
| | - Elizabeth Quail
- Biochemistry and Molecular Biology, School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA, Australia
| | - Kenneth M Kaufman
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - John B Harley
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Lawrence J Abraham
- School of Pathology and Laboratory Medicine, Centre for Genetic Origins of Health and Disease, The University of Western Australia, Crawley, WA, Australia
| | - Betty P Tsao
- Division of Rheumatology, Department of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Susan A Boackle
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Daniela Ulgiati
- School of Pathology and Laboratory Medicine, Centre for Genetic Origins of Health and Disease, The University of Western Australia, Crawley, WA, Australia
| |
Collapse
|
9
|
Roy AL, Singer DS. Core promoters in transcription: old problem, new insights. Trends Biochem Sci 2015; 40:165-71. [PMID: 25680757 DOI: 10.1016/j.tibs.2015.01.007] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 01/09/2015] [Accepted: 01/15/2015] [Indexed: 12/11/2022]
Abstract
Early studies established that transcription initiates within an approximately 50 bp DNA segment capable of nucleating the assembly of RNA polymerase II (Pol II) and associated general transcription factors (GTFs) necessary for transcriptional initiation; this region is called a core promoter. Subsequent analyses identified a series of conserved DNA sequence elements, present in various combinations or not at all, in core promoters. Recent genome-wide analyses have provided further insights into the complexity of core promoter architecture and function. Here we review recent studies that delineate the active role of core promoters in the transcriptional regulation of diverse physiological systems.
Collapse
Affiliation(s)
- Ananda L Roy
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA.
| | - Dinah S Singer
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
10
|
Mu J, Tai X, Iyer SS, Weissman JD, Singer A, Singer DS. Regulation of MHC class I expression by Foxp3 and its effect on regulatory T cell function. THE JOURNAL OF IMMUNOLOGY 2014; 192:2892-903. [PMID: 24523508 DOI: 10.4049/jimmunol.1302847] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Expression of MHC class I molecules, which provide immune surveillance against intracellular pathogens, is higher on lymphoid cells than on any other cell types. In T cells, this is a result of activation of class I transcription by the T cell enhanceosome consisting of Runx1, CBFβ, and LEF1. We now report that MHC class I transcription in T cells also is enhanced by Foxp3, resulting in higher levels of class I in CD4(+)CD25(+) T regulatory cells than in conventional CD4(+)CD25(-) T cells. Interestingly, the effect of Foxp3 regulation of MHC class I transcription is cell type specific: Foxp3 increases MHC class I expression in T cells but represses it in epithelial tumor cells. In both cell types, Foxp3 targets the upstream IFN response element and downstream core promoter of the class I gene. Importantly, expression of MHC class I contributes to the function of CD4(+)CD25(+) T regulatory cells by enhancing immune suppression, both in in vitro and in vivo. These findings identify MHC class I genes as direct targets of Foxp3 whose expression augments regulatory T cell function.
Collapse
Affiliation(s)
- Jie Mu
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | | | | | | | | | | |
Collapse
|