1
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van Breugel ME, Gerber A, van Leeuwen F. The choreography of chromatin in RNA polymerase III regulation. Biochem Soc Trans 2024; 52:1173-1189. [PMID: 38666598 DOI: 10.1042/bst20230770] [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: 03/07/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 06/27/2024]
Abstract
Regulation of eukaryotic gene expression involves a dynamic interplay between the core transcriptional machinery, transcription factors, and chromatin organization and modification. While this applies to transcription by all RNA polymerase complexes, RNA polymerase III (RNAPIII) seems to be atypical with respect to its mechanisms of regulation. One distinctive feature of most RNAPIII transcribed genes is that they are devoid of nucleosomes, which relates to the high levels of transcription. Moreover, most of the regulatory sequences are not outside but within the transcribed open chromatin regions. Yet, several lines of evidence suggest that chromatin factors affect RNAPIII dynamics and activity and that gene sequence alone does not explain the observed regulation of RNAPIII. Here we discuss the role of chromatin modification and organization of RNAPIII transcribed genes and how they interact with the core transcriptional RNAPIII machinery and regulatory DNA elements in and around the transcribed genes.
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Affiliation(s)
- Maria Elize van Breugel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands
| | - Alan Gerber
- Department of Neurosurgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands
- Cancer Center Amsterdam, Cancer Biology, Amsterdam 1081HV, The Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, The Netherlands
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2
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Schwank K, Schmid C, Fremter T, Engel C, Milkereit P, Griesenbeck J, Tschochner H. Features of yeast RNA polymerase I with special consideration of the lobe binding subunits. Biol Chem 2023; 404:979-1002. [PMID: 37823775 DOI: 10.1515/hsz-2023-0184] [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: 04/14/2023] [Accepted: 07/13/2023] [Indexed: 10/13/2023]
Abstract
Ribosomal RNAs (rRNAs) are structural components of ribosomes and represent the most abundant cellular RNA fraction. In the yeast Saccharomyces cerevisiae, they account for more than 60 % of the RNA content in a growing cell. The major amount of rRNA is synthesized by RNA polymerase I (Pol I). This enzyme transcribes exclusively the rRNA gene which is tandemly repeated in about 150 copies on chromosome XII. The high number of transcribed rRNA genes, the efficient recruitment of the transcription machinery and the dense packaging of elongating Pol I molecules on the gene ensure that enough rRNA is generated. Specific features of Pol I and of associated factors confer promoter selectivity and both elongation and termination competence. Many excellent reviews exist about the state of research about function and regulation of Pol I and how Pol I initiation complexes are assembled. In this report we focus on the Pol I specific lobe binding subunits which support efficient, error-free, and correctly terminated rRNA synthesis.
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Affiliation(s)
- Katrin Schwank
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Catharina Schmid
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Tobias Fremter
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Christoph Engel
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Philipp Milkereit
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Joachim Griesenbeck
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Herbert Tschochner
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
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3
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Farina FM, Weber C, Santovito D. The emerging landscape of non-conventional RNA functions in atherosclerosis. Atherosclerosis 2023; 374:74-86. [PMID: 36725418 DOI: 10.1016/j.atherosclerosis.2023.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/15/2022] [Accepted: 01/12/2023] [Indexed: 01/22/2023]
Abstract
Most of the human genome is transcribed into non-coding RNAs (ncRNAs), which encompass a heterogeneous family of transcripts including microRNAs (miRNAs), long ncRNAs (lncRNAs), circular RNAs (circRNAs), and others. Although the detailed modes of action of some classes are not fully elucidated, the common notion is that ncRNAs contribute to sculpting gene expression of eukaryotic cells at multiple levels. These range from the regulation of chromatin remodeling and transcriptional activity to post-transcriptional regulation of messenger RNA splicing, stability, and decay. Many of these functions ultimately govern the expression of coding and non-coding genes to affect diverse physiological and pathological mechanisms in vascular biology and beyond. As such, different classes of ncRNAs emerged as crucial regulators of vascular integrity as well as active players in the pathophysiology of atherosclerosis from the early stages of endothelial dysfunction to the clinically relevant complications. However, research in recent years revealed unexpected findings such as small ncRNAs being able to biophysically regulate protein function, the glycosylation of ncRNAs to be exposed on the cell surface, the release of ncRNAs in the extracellular space to act as ligands of receptors, and even the ability of non-coding portion of messenger RNAs to mediate structural functions. This evidence expanded the functional repertoire of ncRNAs far beyond gene regulation and highlighted an additional layer of biological control of cell function. In this Review, we will discuss these emerging aspects of ncRNA biology, highlight the implications for the mechanisms of vascular biology and atherosclerosis, and discuss possible translational implications.
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Affiliation(s)
- Floriana Maria Farina
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU), Munich, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Christian Weber
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU), Munich, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany; Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, the Netherlands; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
| | - Donato Santovito
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU), Munich, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany; Institute for Genetic and Biomedical Research (IRGB), Unit of Milan, National Research Council, Milan, Italy.
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4
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Lee YS, Lee YS. nc886, an RNA Polymerase III-Transcribed Noncoding RNA Whose Expression Is Dynamic and Regulated by Intriguing Mechanisms. Int J Mol Sci 2023; 24:ijms24108533. [PMID: 37239877 DOI: 10.3390/ijms24108533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/28/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
nc886 is a medium-sized non-coding RNA that is transcribed by RNA polymerase III (Pol III) and plays diverse roles in tumorigenesis, innate immunity, and other cellular processes. Although Pol III-transcribed ncRNAs were previously thought to be expressed constitutively, this concept is evolving, and nc886 is the most notable example. The transcription of nc886 in a cell, as well as in human individuals, is controlled by multiple mechanisms, including its promoter CpG DNA methylation and transcription factor activity. Additionally, the RNA instability of nc886 contributes to its highly variable steady-state expression levels in a given situation. This comprehensive review discusses nc886's variable expression in physiological and pathological conditions and critically examines the regulatory factors that determine its expression levels.
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Affiliation(s)
- Yeon-Su Lee
- Rare Cancer Branch, Research Institute, National Cancer Center, Goyang 10408, Republic of Korea
| | - Yong Sun Lee
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408, Republic of Korea
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5
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Sizer RE, Chahid N, Butterfield SP, Donze D, Bryant NJ, White RJ. TFIIIC-based chromatin insulators through eukaryotic evolution. Gene X 2022; 835:146533. [PMID: 35623477 DOI: 10.1016/j.gene.2022.146533] [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: 08/12/2021] [Revised: 04/19/2022] [Accepted: 04/29/2022] [Indexed: 11/04/2022] Open
Abstract
Eukaryotic chromosomes are divided into domains with distinct structural and functional properties, such as differing levels of chromatin compaction and gene transcription. Domains of relatively compact chromatin and minimal transcription are termed heterochromatic, whereas euchromatin is more open and actively transcribed. Insulators separate these domains and maintain their distinct features. Disruption of insulators can cause diseases such as cancer. Many insulators contain tRNA genes (tDNAs), examples of which have been shown to block the spread of activating or silencing activities. This characteristic of specific tDNAs is conserved through evolution, such that human tDNAs can serve as barriers to the spread of silencing in fission yeast. Here we demonstrate that tDNAs from the methylotrophic fungus Pichia pastoris can function effectively as insulators in distantly-related budding yeast. Key to the function of tDNAs as insulators is TFIIIC, a transcription factor that is also required for their expression. TFIIIC binds additional loci besides tDNAs, some of which have insulator activity. Although the mechanistic basis of TFIIIC-based insulation has been studied extensively in yeast, it is largely uncharacterized in metazoa. Utilising publicly-available genome-wide ChIP-seq data, we consider the extent to which mechanisms conserved from yeast to man may suffice to allow efficient insulation by TFIIIC in the more challenging chromatin environments of metazoa and suggest features that may have been acquired during evolution to cope with new challenges. We demonstrate the widespread presence at human tDNAs of USF1, a transcription factor with well-established barrier activity in vertebrates. We predict that tDNA-based insulators in higher organisms have evolved through incorporation of modules, such as binding sites for factors like USF1 and CTCF that are absent from yeasts, thereby strengthening function and providing opportunities for regulation between cell types.
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Affiliation(s)
- Rebecca E Sizer
- Department of Biology, The University of York, York YO10 5DD, UK
| | - Nisreen Chahid
- Department of Biology, The University of York, York YO10 5DD, UK
| | | | - David Donze
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Nia J Bryant
- Department of Biology, The University of York, York YO10 5DD, UK
| | - Robert J White
- Department of Biology, The University of York, York YO10 5DD, UK.
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6
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Structural insights into nuclear transcription by eukaryotic DNA-dependent RNA polymerases. Nat Rev Mol Cell Biol 2022; 23:603-622. [PMID: 35505252 DOI: 10.1038/s41580-022-00476-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2022] [Indexed: 02/07/2023]
Abstract
The eukaryotic transcription apparatus synthesizes a staggering diversity of RNA molecules. The labour of nuclear gene transcription is, therefore, divided among multiple DNA-dependent RNA polymerases. RNA polymerase I (Pol I) transcribes ribosomal RNA, Pol II synthesizes messenger RNAs and various non-coding RNAs (including long non-coding RNAs, microRNAs and small nuclear RNAs) and Pol III produces transfer RNAs and other short RNA molecules. Pol I, Pol II and Pol III are large, multisubunit protein complexes that associate with a multitude of additional factors to synthesize transcripts that largely differ in size, structure and abundance. The three transcription machineries share common characteristics, but differ widely in various aspects, such as numbers of RNA polymerase subunits, regulatory elements and accessory factors, which allows them to specialize in transcribing their specific RNAs. Common to the three RNA polymerases is that the transcription process consists of three major steps: transcription initiation, transcript elongation and transcription termination. In this Review, we outline the common principles and differences between the Pol I, Pol II and Pol III transcription machineries and discuss key structural and functional insights obtained into the three stages of their transcription processes.
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7
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O’Geen H, Tomkova M, Combs JA, Tilley EK, Segal D. Determinants of heritable gene silencing for KRAB-dCas9 + DNMT3 and Ezh2-dCas9 + DNMT3 hit-and-run epigenome editing. Nucleic Acids Res 2022; 50:3239-3253. [PMID: 35234927 PMCID: PMC8989539 DOI: 10.1093/nar/gkac123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 02/01/2022] [Accepted: 02/08/2022] [Indexed: 11/12/2022] Open
Abstract
Precision epigenome editing has gained significant attention as a method to modulate gene expression without altering genetic information. However, a major limiting factor has been that the gene expression changes are often transient, unlike the life-long epigenetic changes that occur frequently in nature. Here, we systematically interrogate the ability of CRISPR/dCas9-based epigenome editors (Epi-dCas9) to engineer persistent epigenetic silencing. We elucidated cis regulatory features that contribute to the differential stability of epigenetic reprogramming, such as the active transcription histone marks H3K36me3 and H3K27ac strongly correlating with resistance to short-term repression and resistance to long-term silencing, respectively. H3K27ac inversely correlates with increased DNA methylation. Interestingly, the dependance on H3K27ac was only observed when a combination of KRAB-dCas9 and targetable DNA methyltransferases (DNMT3A-dCas9 + DNMT3L) was used, but not when KRAB was replaced with the targetable H3K27 histone methyltransferase Ezh2. In addition, programmable Ezh2/DNMT3A + L treatment demonstrated enhanced engineering of localized DNA methylation and was not sensitive to a divergent chromatin state. Our results highlight the importance of local chromatin features for heritability of programmable silencing and the differential response to KRAB- and Ezh2-based epigenetic editing platforms. The information gained in this study provides fundamental insights into understanding contextual cues to more predictably engineer persistent silencing.
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Affiliation(s)
| | - Marketa Tomkova
- Genome Center, University of California, Davis, CA 95616, USA
| | | | - Emma K Tilley
- Genome Center, University of California, Davis, CA 95616, USA
| | - David J Segal
- Genome Center, University of California, Davis, CA 95616, USA
- Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
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8
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Superstructure Detection in Nucleosome Distribution Shows Common Pattern within a Chromosome and within the Genome. Life (Basel) 2022; 12:life12040541. [PMID: 35455033 PMCID: PMC9026121 DOI: 10.3390/life12040541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/16/2022] [Accepted: 03/23/2022] [Indexed: 11/17/2022] Open
Abstract
Nucleosome positioning plays an important role in crucial biological processes such as replication, transcription, and gene regulation. It has been widely used to predict the genome’s function and chromatin organisation. So far, the studies of patterns in nucleosome positioning have been limited to transcription start sites, CTCFs binding sites, and some promoter and loci regions. The genome-wide organisational pattern remains unknown. We have developed a theoretical model to coarse-grain nucleosome positioning data in order to obtain patterns in their distribution. Using hierarchical clustering on the auto-correlation function of this coarse-grained nucleosome positioning data, a genome-wide clustering is obtained for Candida albicans. The clustering shows the existence beyond hetero- and eu-chromatin inside the chromosomes. These non-trivial clusterings correspond to different nucleosome distributions and gene densities governing differential gene expression patterns. Moreover, these distribution patterns inside the chromosome appeared to be conserved throughout the genome and within species. The pipeline of the coarse grain nucleosome positioning sequence to identify underlying genomic organisation used in our study is novel, and the classifications obtained are unique and consistent.
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9
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Epigenetic regulation of human non-coding RNA gene transcription. Biochem Soc Trans 2022; 50:723-736. [PMID: 35285478 DOI: 10.1042/bst20210860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 12/12/2022]
Abstract
Recent investigations on the non-protein-coding transcriptome of human cells have revealed previously hidden layers of gene regulation relying on regulatory non-protein-coding (nc) RNAs, including the widespread ncRNA-dependent regulation of epigenetic chromatin states and of mRNA translation and stability. However, despite its centrality, the epigenetic regulation of ncRNA genes has received relatively little attention. In this mini-review, we attempt to provide a synthetic account of recent literature suggesting an unexpected complexity in chromatin-dependent regulation of ncRNA gene transcription by the three human nuclear RNA polymerases. Emerging common features, like the heterogeneity of chromatin states within ncRNA multigene families and their influence on 3D genome organization, point to unexplored issues whose investigation could lead to a better understanding of the whole human epigenomic network.
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10
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Singha DL, Das D, Sarki YN, Chowdhury N, Sharma M, Maharana J, Chikkaputtaiah C. Harnessing tissue-specific genome editing in plants through CRISPR/Cas system: current state and future prospects. PLANTA 2021; 255:28. [PMID: 34962611 DOI: 10.1007/s00425-021-03811-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
In a nutshell, tissue-specific CRISPR/Cas genome editing is the most promising approach for crop improvement which can bypass the hurdle associated with constitutive GE such as off target and pleotropic effects for targeted crop improvement. CRISPR/Cas is a powerful genome-editing tool with a wide range of applications for the genetic improvement of crops. However, the constitutive genome editing of vital genes is often associated with pleiotropic effects on other genes, needless metabolic burden, or interference in the cellular machinery. Tissue-specific genome editing (TSGE), on the other hand, enables researchers to study those genes in specific cells, tissues, or organs without disturbing neighboring groups of cells. Until recently, there was only limited proof of the TSGE concept, where the CRISPR-TSKO tool was successfully used in Arabidopsis, tomato, and cotton, laying a solid foundation for crop improvement. In this review, we have laid out valuable insights into the concept and application of TSGE on relatively unexplored areas such as grain trait improvement under favorable or unfavorable conditions. We also enlisted some of the prominent tissue-specific promoters and described the procedure of their isolation with several TSGE promoter expression systems in detail. Moreover, we highlighted potential negative regulatory genes that could be targeted through TSGE using tissue-specific promoters. In a nutshell, tissue-specific CRISPR/Cas genome editing is the most promising approach for crop improvement which can bypass the hurdle associated with constitutive GE such as off target and pleotropic effects for targeted crop improvement.
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Affiliation(s)
- Dhanawantari L Singha
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India.
| | - Debajit Das
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Yogita N Sarki
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Naimisha Chowdhury
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Monica Sharma
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Jitendra Maharana
- Distributed Information Centre (DIC), Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, India
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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11
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Yan B, Tzertzinis G, Schildkraut I, Ettwiller L. Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq. Genome Res 2021; 32:162-174. [PMID: 34815308 PMCID: PMC8744680 DOI: 10.1101/gr.275784.121] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 11/19/2021] [Indexed: 11/24/2022]
Abstract
Determination of eukaryotic transcription start sites (TSSs) has been based on methods that require the cap structure at the 5' end of transcripts derived from Pol II RNA polymerase. Consequently, these methods do not reveal TSSs derived from the other RNA polymerases that also play critical roles in various cell functions. To address this limitation, we developed ReCappable-seq, which comprehensively identifies TSS for both Pol II and non-Pol II transcripts at single-nucleotide resolution. The method relies on specific enzymatic exchange of 5' m7G caps and 5' triphosphates with a selectable tag. When applied to human transcriptomes, ReCappable-seq identifies Pol II TSSs that are in agreement with orthogonal methods such as CAGE. Additionally, ReCappable-seq reveals a rich landscape of TSSs associated with Pol III transcripts that have not previously been amenable to study at genome-wide scale. Novel TSS from non-Pol II transcription can be located in the nuclear and mitochondrial genomes. ReCappable-seq interrogates the regulatory landscape of coding and noncoding RNA concurrently and enables the classification of epigenetic profiles associated with Pol II and non-Pol II TSS.
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Affiliation(s)
- Bo Yan
- New England Biolabs Incorporated, Ipswich, Massachusetts 01938, USA
| | | | - Ira Schildkraut
- New England Biolabs Incorporated, Ipswich, Massachusetts 01938, USA
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12
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Oocyte age and preconceptual alcohol use are highly correlated with epigenetic imprinting of a noncoding RNA ( nc886). Proc Natl Acad Sci U S A 2021; 118:2026580118. [PMID: 33723081 PMCID: PMC8000112 DOI: 10.1073/pnas.2026580118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Genomic imprinting occurs before fertilization, impacts every cell of the developing child, and may be sensitive to environmental perturbations. The noncoding RNA, nc886 (also called VTRNA2-1) is the only known example of the ∼100 human genes imprinted by DNA methylation, that shows polymorphic imprinting in the population. The nc886 gene is part of an ∼1.6-kb differentially methylated region (DMR) that is methylated in the oocyte and silenced on the maternal allele in about 75% of humans worldwide. Here, we show that the presence or absence of imprinting at the nc886 DMR in an individual is consistent across different tissues, confirming that the imprint is established before cellular differentiation and is maintained into adulthood. We investigated the relationships between the frequency of imprinting in newborns and maternal age, alcohol consumption and cigarette smoking before conception in more than 1,100 mother/child pairs from South Africa. The probability of imprinting in newborns was increased in older mothers and decreased in mothers who drank alcohol before conception. On the other hand, cigarette smoking had no apparent relationship with the frequency of imprinting. These data show an epigenetic change during oocyte maturation which is potentially subject to environmental influence. Much focus has been placed on avoiding alcohol consumption during pregnancy, but our data suggest that drinking before conception may affect the epigenome of the newborn.
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13
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Fort RS, Duhagon MA. Pan-cancer chromatin analysis of the human vtRNA genes uncovers their association with cancer biology. F1000Res 2021; 10:182. [PMID: 34354812 PMCID: PMC8287541 DOI: 10.12688/f1000research.28510.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/27/2021] [Indexed: 12/17/2022] Open
Abstract
Background: The vault RNAs (vtRNAs) are a class of 84-141-nt eukaryotic non-coding RNAs transcribed by RNA polymerase III, associated to the ribonucleoprotein complex known as vault particle. Of the four human vtRNA genes, vtRNA1-1, vtRNA1-2 and vtRNA1-3, clustered at locus 1, are integral components of the vault particle, while vtRNA2-1 is a more divergent homologue located in a second locus. Gene expression studies of vtRNAs in large cohorts have been hindered by their unsuccessful sequencing using conventional transcriptomic approaches. Methods: VtRNA expression in The Cancer Genome Atlas (TCGA) Pan-Cancer cohort was estimated using the genome-wide DNA methylation and chromatin accessibility data (ATAC-seq) of their genes as surrogate variables. The association between vtRNA expression and patient clinical outcome, immune subtypes and transcriptionally co-regulated gene programs was analyzed in the dataset. Results: VtRNAs promoters are enriched in transcription factors related to viral infection. VtRNA2-1 is likely the most independently regulated homologue. VtRNA1-1 has the most accessible chromatin, followed by vtRNA1-2, vtRNA2-1 and vtRNA1-3. VtRNA1-1 and vtRNA1-3 chromatin status does not significantly change in cancer tissues. Meanwhile, vtRNA2-1 and vtRNA1-2 expression is widely deregulated in neoplastic tissues and its alteration is compatible with a broad oncogenic role for vtRNA1-2, and both tumor suppressor and oncogenic functions for vtRNA2-1. Yet, vtRNA1-1, vtRNA1-2 and vtRNA2-1 promoter DNA methylation predicts a shorter patient overall survival cancer-wide. In addition, gene ontology analyses of vtRNAs co-regulated genes identify a chromosome regulatory domain, epithelial differentiation, immune and thyroid cancer gene sets for specific vtRNAs. Furthermore, vtRNA expression patterns are associated with cancer immune subtypes and vtRNA1-2 expression is positively associated with cell proliferation and wound healing. Conclusions: Our study presents the landscape of vtRNA chromatin status cancer-wide, identifying co-regulated gene networks and ontological pathways associated with the different vtRNA genes that may account for their diverse roles in cancer.
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Affiliation(s)
- Rafael Sebastián Fort
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Montevideo, 11400, Uruguay.,Depto. de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Montevideo, 11600, Uruguay
| | - María Ana Duhagon
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Montevideo, 11400, Uruguay.,Depto. de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Montevideo, 11400, Uruguay
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14
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Hahne JC, Lampis A, Valeri N. Vault RNAs: hidden gems in RNA and protein regulation. Cell Mol Life Sci 2021; 78:1487-1499. [PMID: 33063126 PMCID: PMC7904556 DOI: 10.1007/s00018-020-03675-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/27/2020] [Accepted: 10/05/2020] [Indexed: 12/11/2022]
Abstract
Non-coding RNAs are important regulators of differentiation during embryogenesis as well as key players in the fine-tuning of transcription and furthermore, they control the post-transcriptional regulation of mRNAs under physiological conditions. Deregulated expression of non-coding RNAs is often identified as one major contribution in a number of pathological conditions. Non-coding RNAs are a heterogenous group of RNAs and they represent the majority of nuclear transcripts in eukaryotes. An evolutionary highly conserved sub-group of non-coding RNAs is represented by vault RNAs, named since firstly discovered as component of the largest known ribonucleoprotein complexes called "vault". Although they have been initially described 30 years ago, vault RNAs are largely unknown and their molecular role is still under investigation. In this review we will summarize the known functions of vault RNAs and their involvement in cellular mechanisms.
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Affiliation(s)
- Jens Claus Hahne
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
| | - Andrea Lampis
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Nicola Valeri
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Department of Medicine, The Royal Marsden NHS Foundation Trust, London, UK
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15
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Wakamori M, Okabe K, Ura K, Funatsu T, Takinoue M, Umehara T. Quantification of the effect of site-specific histone acetylation on chromatin transcription rate. Nucleic Acids Res 2021; 48:12648-12659. [PMID: 33238306 PMCID: PMC7736822 DOI: 10.1093/nar/gkaa1050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/15/2020] [Accepted: 10/20/2020] [Indexed: 12/13/2022] Open
Abstract
Eukaryotic transcription is epigenetically regulated by chromatin structure and post-translational modifications (PTMs). For example, lysine acetylation in histone H4 is correlated with activation of RNA polymerase I-, II- and III-driven transcription from chromatin templates, which requires prior chromatin remodeling. However, quantitative understanding of the contribution of particular PTM states to the sequential steps of eukaryotic transcription has been hampered partially because reconstitution of a chromatin template with designed PTMs is difficult. In this study, we reconstituted a di-nucleosome with site-specifically acetylated or unmodified histone H4, which contained two copies of the Xenopus somatic 5S rRNA gene with addition of a unique sequence detectable by hybridization-assisted fluorescence correlation spectroscopy. Using a Xenopus oocyte nuclear extract, we analyzed the time course of accumulation of nascent 5S rRNA-derived transcripts generated on chromatin templates in vitro. Our mathematically described kinetic model and fitting analysis revealed that tetra-acetylation of histone H4 at K5/K8/K12/K16 increases the rate of transcriptionally competent chromatin formation ∼3-fold in comparison with the absence of acetylation. We provide a kinetic model for quantitative evaluation of the contribution of epigenetic modifications to chromatin transcription.
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Affiliation(s)
- Masatoshi Wakamori
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan
| | - Kohki Okabe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.,PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Kiyoe Ura
- PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan.,Graduate School of Science, Chiba University, Chiba, Chiba 263-8522, Japan
| | - Takashi Funatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masahiro Takinoue
- PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan.,Department of Computer Science, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8502, Japan
| | - Takashi Umehara
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan.,PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
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16
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Gomes TM, Dias da Silva D, Carmo H, Carvalho F, Silva JP. Epigenetics and the endocannabinoid system signaling: An intricate interplay modulating neurodevelopment. Pharmacol Res 2020; 162:105237. [PMID: 33053442 DOI: 10.1016/j.phrs.2020.105237] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/16/2020] [Accepted: 10/02/2020] [Indexed: 01/08/2023]
Abstract
The endocannabinoid (eCB) system is a complex system comprising endogenous cannabinoids (eCBs), their synthesis and degradation enzymes, and cannabinoid receptors. These elements crucially regulate several biological processes during neurodevelopment, such as proliferation, differentiation, and migration. Recently, eCBs were also reported to have an epigenetic action on genes that play key functions in the neurotransmitter signaling, consequently regulating their expression. In turn, epigenetic modifications (e.g. DNA methylation, histone modifications) may also modulate the function of eCB system's elements. For example, the expression of the cnr gene in the central nervous system may be epigenetically regulated (e.g. DNA methylation, histone modifications), thus altering the function of the cannabinoid receptor type-1 (CB1R). Considering the importance of the eCB system during neurodevelopment, it is thus reasonable to expect that alterations in this interaction between the eCB system and epigenetic modifications may give rise to neurodevelopmental disorders. Here, we review key concepts related to the regulation of neuronal function by the eCB system and the different types of epigenetic modifications. In particular, we focus on the mechanisms involved in the intricate interplay between both signaling systems and how they control cell fate during neurodevelopment. Noteworthy, such mechanistic understanding assumes high relevance considering the implications of the dysregulation of key neurogenic processes towards the onset of neurodevelopment-related disorders. Moreover, considering the increasing popularity of cannabis and its synthetic derivatives among young adults, it becomes of utmost importance to understand how exogenous cannabinoids may epigenetically impact neurodevelopment.
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Affiliation(s)
- Telma Marisa Gomes
- UCIBIO, REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313, Porto, Portugal
| | - Diana Dias da Silva
- UCIBIO, REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313, Porto, Portugal
| | - Helena Carmo
- UCIBIO, REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313, Porto, Portugal
| | - Félix Carvalho
- UCIBIO, REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313, Porto, Portugal.
| | - João Pedro Silva
- UCIBIO, REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313, Porto, Portugal.
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17
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Asif‐Laidin A, Conesa C, Bonnet A, Grison C, Adhya I, Menouni R, Fayol H, Palmic N, Acker J, Lesage P. A small targeting domain in Ty1 integrase is sufficient to direct retrotransposon integration upstream of tRNA genes. EMBO J 2020; 39:e104337. [PMID: 32677087 PMCID: PMC7459421 DOI: 10.15252/embj.2019104337] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 06/09/2020] [Accepted: 06/18/2020] [Indexed: 12/25/2022] Open
Abstract
Integration of transposable elements into the genome is mutagenic. Mechanisms targeting integrations into relatively safe locations, hence minimizing deleterious consequences for cell fitness, have emerged during evolution. In budding yeast, integration of the Ty1 LTR retrotransposon upstream of RNA polymerase III (Pol III)-transcribed genes requires interaction between Ty1 integrase (IN1) and AC40, a subunit common to Pol I and Pol III. Here, we identify the Ty1 targeting domain of IN1 that ensures (i) IN1 binding to Pol I and Pol III through AC40, (ii) IN1 genome-wide recruitment to Pol I- and Pol III-transcribed genes, and (iii) Ty1 integration only at Pol III-transcribed genes, while IN1 recruitment by AC40 is insufficient to target Ty1 integration into Pol I-transcribed genes. Swapping the targeting domains between Ty5 and Ty1 integrases causes Ty5 integration at Pol III-transcribed genes, indicating that the targeting domain of IN1 alone confers Ty1 integration site specificity.
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Affiliation(s)
- Amna Asif‐Laidin
- INSERM U944, CNRS UMR 7212Genomes& Cell Biology of Disease UnitInstitut de Recherche Saint‐LouisHôpital Saint‐LouisUniversité de ParisParisFrance
| | - Christine Conesa
- CEACNRSInstitute for Integrative Biology of the Cell (I2BC)Université Paris‐SaclayGif‐sur‐YvetteFrance
| | - Amandine Bonnet
- INSERM U944, CNRS UMR 7212Genomes& Cell Biology of Disease UnitInstitut de Recherche Saint‐LouisHôpital Saint‐LouisUniversité de ParisParisFrance
| | - Camille Grison
- INSERM U944, CNRS UMR 7212Genomes& Cell Biology of Disease UnitInstitut de Recherche Saint‐LouisHôpital Saint‐LouisUniversité de ParisParisFrance
| | - Indranil Adhya
- CEACNRSInstitute for Integrative Biology of the Cell (I2BC)Université Paris‐SaclayGif‐sur‐YvetteFrance
| | - Rachid Menouni
- INSERM U944, CNRS UMR 7212Genomes& Cell Biology of Disease UnitInstitut de Recherche Saint‐LouisHôpital Saint‐LouisUniversité de ParisParisFrance
| | - Hélène Fayol
- INSERM U944, CNRS UMR 7212Genomes& Cell Biology of Disease UnitInstitut de Recherche Saint‐LouisHôpital Saint‐LouisUniversité de ParisParisFrance
| | - Noé Palmic
- INSERM U944, CNRS UMR 7212Genomes& Cell Biology of Disease UnitInstitut de Recherche Saint‐LouisHôpital Saint‐LouisUniversité de ParisParisFrance
| | - Joël Acker
- CEACNRSInstitute for Integrative Biology of the Cell (I2BC)Université Paris‐SaclayGif‐sur‐YvetteFrance
| | - Pascale Lesage
- INSERM U944, CNRS UMR 7212Genomes& Cell Biology of Disease UnitInstitut de Recherche Saint‐LouisHôpital Saint‐LouisUniversité de ParisParisFrance
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18
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Preece R, Georgiadis C, Gkazi SA, Etuk A, Christi A, Qasim W. 'Mini' U6 Pol III promoter exhibits nucleosome redundancy and supports multiplexed coupling of CRISPR/Cas9 effects. Gene Ther 2020; 27:451-458. [PMID: 32203198 DOI: 10.1038/s41434-020-0142-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 02/05/2020] [Accepted: 03/06/2020] [Indexed: 12/20/2022]
Abstract
RNA polymerase III (Pol III) promoters express short non-coding RNAs and have been adopted for expression of microRNA, interference RNA, and CRISPR single guide RNA (sgRNA). Vectors incorporating H1 and U6 Pol III promoters are being applied for therapeutic genome editing, including multiplexed CRISPR/Cas9 effects. We report a nucleosome-depleted, minimal U6 promoter, which when embedded within lentiviral long terminal repeat (LTR) regions, supports high level transcriptional activity. Furthermore, duplex minimal H1 & U6 promoters transcribed dual sgRNAs for simultaneous disruption of T cell receptor (TCR) and human leukocyte antigen (HLA) molecules, supporting efficient generation of 'universal' CAR T cells.
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Affiliation(s)
- Roland Preece
- Molecular and Cellular Immunology Unit, UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Christos Georgiadis
- Molecular and Cellular Immunology Unit, UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK.
| | - Soragia Athina Gkazi
- Molecular and Cellular Immunology Unit, UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Aniekan Etuk
- Molecular and Cellular Immunology Unit, UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Abraham Christi
- Molecular and Cellular Immunology Unit, UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Waseem Qasim
- Molecular and Cellular Immunology Unit, UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, 30 Guilford Street, London, WC1N 1EH, UK
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19
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Kramm K, Schröder T, Gouge J, Vera AM, Gupta K, Heiss FB, Liedl T, Engel C, Berger I, Vannini A, Tinnefeld P, Grohmann D. DNA origami-based single-molecule force spectroscopy elucidates RNA Polymerase III pre-initiation complex stability. Nat Commun 2020; 11:2828. [PMID: 32504003 PMCID: PMC7275037 DOI: 10.1038/s41467-020-16702-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 05/13/2020] [Indexed: 01/03/2023] Open
Abstract
The TATA-binding protein (TBP) and a transcription factor (TF) IIB-like factor are important constituents of all eukaryotic initiation complexes. The reason for the emergence and strict requirement of the additional initiation factor Bdp1 in the RNA polymerase (RNAP) III system, however, remained elusive. A poorly studied aspect in this context is the effect of DNA strain arising from DNA compaction and transcriptional activity on initiation complex formation. We made use of a DNA origami-based force clamp to follow the assembly of human initiation complexes in the RNAP II and RNAP III systems at the single-molecule level under piconewton forces. We demonstrate that TBP-DNA complexes are force-sensitive and TFIIB is sufficient to stabilise TBP on a strained promoter. In contrast, Bdp1 is the pivotal component that ensures stable anchoring of initiation factors, and thus the polymerase itself, in the RNAP III system. Thereby, we offer an explanation for the crucial role of Bdp1 for the high transcriptional output of RNAP III.
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Affiliation(s)
- Kevin Kramm
- Single-Molecule Biochemistry Lab, Institute of Microbiology and Archaea Centre, University of Regensburg, 93053, Regensburg, Germany
| | - Tim Schröder
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, 80539, München, Germany
| | - Jerome Gouge
- Division of Structural Biology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Andrés Manuel Vera
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, 80539, München, Germany
| | - Kapil Gupta
- Bristol Synthetic Biology Centre BrisSynBio, Biomedical Sciences, University of Bristol, 1 Tankard's Close, Clifton, BS8 1TD, UK
| | - Florian B Heiss
- Regensburg Center of Biochemistry (RCB), University of Regensburg, 93053, Regensburg, Germany
| | - Tim Liedl
- Faculty of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München, 80539, Munich, Germany
| | - Christoph Engel
- Regensburg Center of Biochemistry (RCB), University of Regensburg, 93053, Regensburg, Germany
| | - Imre Berger
- Bristol Synthetic Biology Centre BrisSynBio, Biomedical Sciences, University of Bristol, 1 Tankard's Close, Clifton, BS8 1TD, UK
| | - Alessandro Vannini
- Division of Structural Biology, The Institute of Cancer Research, London, SW7 3RP, UK
- Human Technopole Foundation, Centre of Structural Biology, 20157, Milan, Italy
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, 80539, München, Germany
| | - Dina Grohmann
- Single-Molecule Biochemistry Lab, Institute of Microbiology and Archaea Centre, University of Regensburg, 93053, Regensburg, Germany.
- Regensburg Center of Biochemistry (RCB), University of Regensburg, 93053, Regensburg, Germany.
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20
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Abstract
RNA-binding proteins typically change the fate of RNA, such as stability, translation or processing. Conversely, we recently uncovered that the small non-coding vault RNA 1-1 (vtRNA1-1) directly binds to the autophagic receptor p62/SQSTM1 and changes the protein's function. We refer to this process as 'riboregulation'. Here, we discuss this newly uncovered vault RNA function against the background of three decades of vault RNA research. We highlight the vtRNA1-1-p62 interaction as an example of riboregulation of a key cellular process.
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Affiliation(s)
- Magdalena Büscher
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Rastislav Horos
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Matthias W Hentze
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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21
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Mother-child transmission of epigenetic information by tunable polymorphic imprinting. Proc Natl Acad Sci U S A 2018; 115:E11970-E11977. [PMID: 30509985 PMCID: PMC6304996 DOI: 10.1073/pnas.1815005115] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
First, our work provides critical biological interpretation of intermediate DNA methylation readouts at the nc886 differentially methylated region (DMR). nc886 was identified in multiple large-scale epigenome-wide association studies (EWAS) that did not recognize that this region acts as a contiguous DMR imposed by genomic imprinting, highlighting the need to reexamine several 450k data sets. Second, strict control of genomic imprinting was thought to be required for organismal viability. Reports of polymorphic imprinting are limited to specific tissue types such as placenta and brain. In blood and somatic tissues, we show nc886 imprinting is mosaic in the population and influenced by maternal environment. Genomic imprinting mediated by DNA methylation restricts gene expression to a single allele determined by parental origin and is not generally considered to be under genetic or environmental influence. Here, we focused on a differentially methylated region (DMR) of approximately 1.9 kb that includes a 101-bp noncoding RNA gene (nc886/VTRNA2-1), which is maternally imprinted in ∼75% of humans. This is unlike other imprinted genes, which demonstrate monoallelic methylation in 100% of individuals. The DMR includes a CTCF binding site on the centromeric side defining the DMR boundary and is flanked by a CTCF binding site on the telomeric side. The centromeric CTCF binding site contains an A/C polymorphism (rs2346018); the C allele is associated with less imprinting. The frequency of imprinting of the nc886 DMR in infants was linked to at least two nongenetic factors, maternal age at delivery and season of conception. In a separate cohort, nc886 imprinting was associated with lower body mass index in children at 5 y of age. Thus, we propose that the imprinting status of the nc886 DMR is “tunable” in that it is associated with maternal haplotype and prenatal environment. This provides a potential mechanism for transmitting information, with phenotypic consequences, from mother to child.
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22
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Shukla A, Bhargava P. Regulation of tRNA gene transcription by the chromatin structure and nucleosome dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1861:295-309. [PMID: 29313808 DOI: 10.1016/j.bbagrm.2017.11.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 11/27/2017] [Accepted: 11/27/2017] [Indexed: 01/19/2023]
Abstract
The short, non-coding genes transcribed by the RNA polymerase (pol) III, necessary for survival of a cell, need to be repressed under the stress conditions in vivo. The pol III-transcribed genes have adopted several novel chromatin-based regulatory mechanisms to their advantage. In the budding yeast, the sub-nucleosomal size tRNA genes are found in the nucleosome-free regions, flanked by positioned nucleosomes at both the ends. With their chromosomes-wide distribution, all tRNA genes have a different chromatin context. A single nucleosome dynamics controls the accessibility of the genes for transcription. This dynamics operates under the influence of several chromatin modifiers in a gene-specific manner, giving the scope for differential regulation of even the isogenes within a tRNA gene family. The chromatin structure around the pol III-transcribed genes provides a context conducive for steady-state transcription as well as gene-specific transcriptional regulation upon signaling from the environmental cues. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.
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Affiliation(s)
- Ashutosh Shukla
- Centre for Cellular and Molecular Biology (Council of Scientific and Industrial Research), Uppal Road, Hyderabad 500007, India
| | - Purnima Bhargava
- Centre for Cellular and Molecular Biology (Council of Scientific and Industrial Research), Uppal Road, Hyderabad 500007, India.
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23
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Van Bortle K, Phanstiel DH, Snyder MP. Topological organization and dynamic regulation of human tRNA genes during macrophage differentiation. Genome Biol 2017; 18:180. [PMID: 28931413 PMCID: PMC5607496 DOI: 10.1186/s13059-017-1310-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 08/25/2017] [Indexed: 12/11/2022] Open
Abstract
Background The human genome is hierarchically organized into local and long-range structures that help shape cell-type-specific transcription patterns. Transfer RNA (tRNA) genes (tDNAs), which are transcribed by RNA polymerase III (RNAPIII) and encode RNA molecules responsible for translation, are dispersed throughout the genome and, in many cases, linearly organized into genomic clusters with other tDNAs. Whether the location and three-dimensional organization of tDNAs contribute to the activity of these genes has remained difficult to address, due in part to unique challenges related to tRNA sequencing. We therefore devised integrated tDNA expression profiling, a method that combines RNAPIII mapping with biotin-capture of nascent tRNAs. We apply this method to the study of dynamic tRNA gene regulation during macrophage development and further integrate these data with high-resolution maps of 3D chromatin structure. Results Integrated tDNA expression profiling reveals domain-level and loop-based organization of tRNA gene transcription during cellular differentiation. tRNA genes connected by DNA loops, which are proximal to CTCF binding sites and expressed at elevated levels compared to non-loop tDNAs, change coordinately with tDNAs and protein-coding genes at distal ends of interactions mapped by in situ Hi-C. We find that downregulated tRNA genes are specifically marked by enhanced promoter-proximal binding of MAF1, a transcriptional repressor of RNAPIII activity, altogether revealing multiple levels of tDNA regulation during cellular differentiation. Conclusions We present evidence of both local and coordinated long-range regulation of human tDNA expression, suggesting the location and organization of tRNA genes contribute to dynamic tDNA activity during macrophage development. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1310-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kevin Van Bortle
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Douglas H Phanstiel
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, 27599, USA.,Thurston Arthritis Research Center and Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
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24
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Weaver ICG, Korgan AC, Lee K, Wheeler RV, Hundert AS, Goguen D. Stress and the Emerging Roles of Chromatin Remodeling in Signal Integration and Stable Transmission of Reversible Phenotypes. Front Behav Neurosci 2017; 11:41. [PMID: 28360846 PMCID: PMC5350110 DOI: 10.3389/fnbeh.2017.00041] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 02/24/2017] [Indexed: 01/02/2023] Open
Abstract
The influence of early life experience and degree of parental-infant attachment on emotional development in children and adolescents has been comprehensively studied. Structural and mechanistic insight into the biological foundation and maintenance of mammalian defensive systems (metabolic, immune, nervous and behavioral) is slowly advancing through the emerging field of developmental molecular (epi)genetics. Initial evidence revealed that differential nurture early in life generates stable differences in offspring hypothalamic-pituitary-adrenal (HPA) regulation, in part, through chromatin remodeling and changes in DNA methylation of specific genes expressed in the brain, revealing physical, biochemical and molecular paths for the epidemiological concept of gene-environment interactions. Herein, a primary molecular mechanism underpinning the early developmental programming and lifelong maintenance of defensive (emotional) responses in the offspring is the alteration of chromatin domains of specific genomic regions from a condensed state (heterochromatin) to a transcriptionally accessible state (euchromatin). Conversely, DNA methylation promotes the formation of heterochromatin, which is essential for gene silencing, genomic integrity and chromosome segregation. Therefore, inter-individual differences in chromatin modifications and DNA methylation marks hold great potential for assessing the impact of both early life experience and effectiveness of intervention programs—from guided psychosocial strategies focused on changing behavior to pharmacological treatments that target chromatin remodeling and DNA methylation enzymes to dietary approaches that alter cellular pools of metabolic intermediates and methyl donors to affect nutrient bioavailability and metabolism. In this review article, we discuss the potential molecular mechanism(s) of gene regulation associated with chromatin modeling and programming of endocrine (e.g., HPA and metabolic or cardiovascular) and behavioral (e.g., fearfulness, vigilance) responses to stress, including alterations in DNA methylation and the role of DNA repair machinery. From parental history (e.g., drugs, housing, illness, nutrition, socialization) to maternal-offspring exchanges of nutrition, microbiota, antibodies and stimulation, the nature of nurture provides not only mechanistic insight into how experiences propagate from external to internal variables, but also identifies a composite therapeutic target, chromatin modeling, for gestational/prenatal stress, adolescent anxiety/depression and adult-onset neuropsychiatric disease.
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Affiliation(s)
- Ian C G Weaver
- Department of Psychology and Neuroscience, and Department of Psychiatry, Dalhousie University Halifax, NS, Canada
| | - Austin C Korgan
- Department of Psychology and Neuroscience, and Department of Psychiatry, Dalhousie University Halifax, NS, Canada
| | - Kristen Lee
- Department of Psychology and Neuroscience, and Department of Psychiatry, Dalhousie University Halifax, NS, Canada
| | - Ryan V Wheeler
- Department of Psychology and Neuroscience, and Department of Psychiatry, Dalhousie University Halifax, NS, Canada
| | - Amos S Hundert
- Department of Psychology and Neuroscience, and Department of Psychiatry, Dalhousie University Halifax, NS, Canada
| | - Donna Goguen
- Department of Psychology and Neuroscience, and Department of Psychiatry, Dalhousie University Halifax, NS, Canada
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