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Montano C, Flores-Arenas C, Carpenter S. LncRNAs, nuclear architecture and the immune response. Nucleus 2024; 15:2350182. [PMID: 38738760 PMCID: PMC11093052 DOI: 10.1080/19491034.2024.2350182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/22/2024] [Indexed: 05/14/2024] Open
Abstract
Long noncoding RNAs (LncRNAs) are key regulators of gene expression and can mediate their effects in both the nucleus and cytoplasm. Some of the best-characterized lncRNAs are localized within the nucleus, where they modulate the nuclear architecture and influence gene expression. In this review, we discuss the role of lncRNAs in nuclear architecture in the context of their gene regulatory functions in innate immunity. Here, we discuss various approaches to functionally characterize nuclear-localized lncRNAs and the challenges faced in the field.
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Affiliation(s)
- Christy Montano
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Cristina Flores-Arenas
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Susan Carpenter
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
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2
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Refael T, Sudman M, Golan G, Pnueli L, Naik S, Preger-Ben Noon E, Henn A, Kaplan A, Melamed P. An i-motif-regulated enhancer, eRNA and adjacent lncRNA affect Lhb expression through distinct mechanisms in a sex-specific context. Cell Mol Life Sci 2024; 81:361. [PMID: 39158745 PMCID: PMC11335282 DOI: 10.1007/s00018-024-05398-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/21/2024] [Accepted: 08/05/2024] [Indexed: 08/20/2024]
Abstract
Genome-wide studies have demonstrated regulatory roles for diverse non-coding elements, but their precise and interrelated functions have often remained enigmatic. Addressing the need for mechanistic insight, we studied their roles in expression of Lhb which encodes the pituitary gonadotropic hormone that controls reproduction. We identified a bi-directional enhancer in gonadotrope-specific open chromatin, whose functional eRNA (eRNA2) supports permissive chromatin at the Lhb locus. The central untranscribed region of the enhancer contains an iMotif (iM), and is bound by Hmgb2 which stabilizes the iM and directs transcription specifically towards the functional eRNA2. A distinct downstream lncRNA, associated with an inducible G-quadruplex (G4) and iM, also facilitates Lhb expression, following its splicing in situ. GnRH activates Lhb transcription and increased levels of all three RNAs, eRNA2 showing the highest response, while estradiol, which inhibits Lhb, repressed levels of eRNA2 and the lncRNA. The levels of these regulatory RNAs and Lhb mRNA correlate highly in female mice, though strikingly not in males, suggesting a female-specific function. Our findings, which shed new light on the workings of non-coding elements and non-canonical DNA structures, reveal novel mechanisms regulating transcription which have implications not only in the central control of reproduction but also for other inducible genes.
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Affiliation(s)
- Tal Refael
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Maya Sudman
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Gil Golan
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Lilach Pnueli
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Sujay Naik
- Department of Genetics and Developmental Biology, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, 3109601, Israel
| | - Ella Preger-Ben Noon
- Department of Genetics and Developmental Biology, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, 3109601, Israel
| | - Arnon Henn
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Ariel Kaplan
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Philippa Melamed
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel.
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3
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Šenica P, Žele Vengušt D, Vengušt G, Kuhar U. Genomic revelations: investigating rotavirus a presence in wild ruminants and its zoonotic potential. Front Vet Sci 2024; 11:1429654. [PMID: 39211480 PMCID: PMC11358691 DOI: 10.3389/fvets.2024.1429654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 07/30/2024] [Indexed: 09/04/2024] Open
Abstract
Introduction Rotaviruses A (RVA) are a major cause of acute viral gastroenteritis in humans worldwide and are responsible for about two million hospitalizations per year. They can also infect other mammals such as pigs, calves, goats, lambs, and horses, in which they are also considered a major cause of viral diarrhea. While RVA is well studied in humans and domestic animals, its occurrence in wild ruminants is not well known. The RVA genome is a double-stranded RNA consisting of 11 segments, and genotyping is based on the VP7 (G) and VP4 (P) segments. Currently, there are 42G genotypes and 58P genotypes. RVA has a high mutation rate, and some combinations of G and P genotypes can infect different animal species, leading to speculation about the potential for zoonotic transmission. Materials and methods A total of 432 fecal samples were collected from roe deer, red deer, chamois, mouflon and Alpine ibex in Slovenia between 2017 and 2021. To investigate the presence of RVA in wild ruminants, real-time RT-PCR was used. Positive samples were subjected to next generation sequencing (NGS) using RIP-seq method. Results and discussion In total, 7 samples were RVA positive. Complete genomes were determined and phylogenetically analyzed for all 7 RVAs. Four different genotype constellations were present in 7 positive RVA animals: G8-P[14]-I2- R2-C2-M2-A3-N2-T6-E2-H3, G6-P [14]-I2-R2-C2-M2-A11-N2-T6-E2-H3, G10-P [15]-I2-R2-C2-M2-A3-N2-T6-E2-H3 and G10-P [15]-I2-R2-C2-M2-A11- N2-T6-E2-H3. Genotypes G6P[14] and G10P[15] were found in both roe deer and red deer, representing the first confirmed occurrence of RVA in red deer. In addition, genotype G8P[14] was found in chamois, representing the first known case of positive RVA in this species. Some of these genotypes have also been found in humans, indicating the potential for zoonotic transmission.
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Affiliation(s)
- Petra Šenica
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| | - Diana Žele Vengušt
- Veterinary Faculty, Institute of Pathology, Wild Animals, Fish and Bees, University of Ljubljana, Ljubljana, Slovenia
| | - Gorazd Vengušt
- Veterinary Faculty, Institute of Pathology, Wild Animals, Fish and Bees, University of Ljubljana, Ljubljana, Slovenia
| | - Urška Kuhar
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
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4
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Tamburri S, Rustichelli S, Amato S, Pasini D. Navigating the complexity of Polycomb repression: Enzymatic cores and regulatory modules. Mol Cell 2024:S1097-2765(24)00628-2. [PMID: 39178860 DOI: 10.1016/j.molcel.2024.07.030] [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: 05/18/2024] [Revised: 07/12/2024] [Accepted: 07/30/2024] [Indexed: 08/26/2024]
Abstract
Polycomb proteins are a fundamental repressive system that plays crucial developmental roles by orchestrating cell-type-specific transcription programs that govern cell identity. Direct alterations of Polycomb activity are indeed implicated in human pathologies, including developmental disorders and cancer. General Polycomb repression is coordinated by three distinct activities that regulate the deposition of two histone post-translational modifications: tri-methylation of histone H3 lysine 27 (H3K27me3) and histone H2A at lysine 119 (H2AK119ub1). These activities exist in large and heterogeneous multiprotein ensembles consisting of common enzymatic cores regulated by heterogeneous non-catalytic modules composed of a large number of accessory proteins with diverse biochemical properties. Here, we have analyzed the current molecular knowledge, focusing on the functional interaction between the core enzymatic activities and their regulation mediated by distinct accessory modules. This provides a comprehensive analysis of the molecular details that control the establishment and maintenance of Polycomb repression, examining their underlying coordination and highlighting missing information and emerging new features of Polycomb-mediated transcriptional control.
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Affiliation(s)
- Simone Tamburri
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; University of Milan, Department of Health Sciences, Via A. di Rudinì 8, 20142 Milan, Italy.
| | - Samantha Rustichelli
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Simona Amato
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Diego Pasini
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; University of Milan, Department of Health Sciences, Via A. di Rudinì 8, 20142 Milan, Italy.
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5
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Glossop MS, Chelysheva I, Ketley RF, Alagia A, Gullerova M. TIRR regulates mRNA export and association with P-bodies in response to DNA damage. Nucleic Acids Res 2024:gkae688. [PMID: 39119906 DOI: 10.1093/nar/gkae688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 07/15/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024] Open
Abstract
To ensure the integrity of our genetic code, a coordinated network of signalling and repair proteins, known as the DNA damage response (DDR), detects and repairs DNA insults, the most toxic being double-strand breaks (DSBs). Tudor interacting repair regulator (TIRR) is a key factor in DSB repair, acting through its interaction with p53 binding protein 1 (53BP1). TIRR is also an RNA binding protein, yet its role in RNA regulation during the DDR remains elusive. Here, we show that TIRR selectively binds to a subset of messenger RNAs (mRNAs) in response to DNA damage. Upon DNA damage, TIRR interacts with the nuclear export protein Exportin-1 through a nuclear export signal. Furthermore, TIRR plays a crucial role in the modulation of RNA processing bodies (PBs). TIRR itself and TIRR-bound RNA co-localize with PBs, and TIRR depletion results in nuclear RNA retention and impaired PB formation. We also suggest a potential link between TIRR-regulated RNA export and efficient DDR. This work reveals intricate involvement of TIRR in orchestrating mRNA nuclear export and storage within PBs, emphasizing its significance in the regulation of RNA-mediated DDR.
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Affiliation(s)
- Michelle S Glossop
- Sir William Dunn School of Pathology, Medical Sciences Division, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Irina Chelysheva
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford OX3 7LE, UK
| | - Ruth F Ketley
- Sir William Dunn School of Pathology, Medical Sciences Division, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Adele Alagia
- Sir William Dunn School of Pathology, Medical Sciences Division, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Monika Gullerova
- Sir William Dunn School of Pathology, Medical Sciences Division, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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Fan L, Sun W, Lyu Y, Ju F, Sun W, Chen J, Ma H, Yang S, Zhou X, Wu N, Yi W, Chen E, Villaseñor R, Baubec T, Yan J. Chrom-seq identifies RNAs at chromatin marks. SCIENCE ADVANCES 2024; 10:eadn1397. [PMID: 39083617 PMCID: PMC11290522 DOI: 10.1126/sciadv.adn1397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 06/25/2024] [Indexed: 08/02/2024]
Abstract
Chromatin marks are associated with transcriptional regulatory activities. However, very few lncRNAs have been characterized with the role in regulating epigenetic marks, largely due to the technical difficulty in identifying chromatin-associating RNA. Current methods are largely limited by the availability of ChIP-grade antibody and the crosslinking, which generates high noise. Here, we developed a method termed Chrom-seq to efficiently capture RNAs associated with various chromatin marks in living cells. Chrom-seq jointly applies highly specific chromatin mark reader with APEX2, which catalyzes the oxidation of biotin-aniline to label the adjacent RNAs for isolation by streptavidin-coated beads. Using the readers of mCBX7/dPC, mCBX1, and mTAF3, we detected RNA species significantly associated with H3K27me3, H3K9me3, and H3K4me3, respectively. We demonstrated that Chrom-seq outperformed other equivalent methods in terms of sensitivity, efficiency, and cost of practice. It provides an antibody-free approach to systematically map RNAs at chromatin marks with potential regulatory roles in epigenetic events.
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Affiliation(s)
- Ligang Fan
- Ministry of Education Key Laboratory of Resource Biology and Biotechnology in Western China; Shaanxi Provincial Key Laboratory of Biotechnology; School of Medicine, Northwest University, Xi’an, China
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences; The Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | | | - Yitong Lyu
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences; The Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Furong Ju
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences; The Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong SAR, China
| | - Wenju Sun
- Ministry of Education Key Laboratory of Resource Biology and Biotechnology in Western China; Shaanxi Provincial Key Laboratory of Biotechnology; School of Medicine, Northwest University, Xi’an, China
| | - Jie Chen
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences; The Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Haiqian Ma
- Ministry of Education Key Laboratory of Resource Biology and Biotechnology in Western China; Shaanxi Provincial Key Laboratory of Biotechnology; School of Medicine, Northwest University, Xi’an, China
| | - Shifei Yang
- Ministry of Education Key Laboratory of Resource Biology and Biotechnology in Western China; Shaanxi Provincial Key Laboratory of Biotechnology; School of Medicine, Northwest University, Xi’an, China
| | - Xiaomin Zhou
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences; The Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Nan Wu
- Ministry of Education Key Laboratory of Resource Biology and Biotechnology in Western China; Shaanxi Provincial Key Laboratory of Biotechnology; School of Medicine, Northwest University, Xi’an, China
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences; The Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Wenkai Yi
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences; The Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Erfei Chen
- Ministry of Education Key Laboratory of Resource Biology and Biotechnology in Western China; Shaanxi Provincial Key Laboratory of Biotechnology; School of Medicine, Northwest University, Xi’an, China
| | - Rodrigo Villaseñor
- Division of Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tuncay Baubec
- Institute of Biodynamics and Biocomplexity, Department of Biology, Science Faculty, Utrecht University, Utrecht, the Netherlands
| | - Jian Yan
- Ministry of Education Key Laboratory of Resource Biology and Biotechnology in Western China; Shaanxi Provincial Key Laboratory of Biotechnology; School of Medicine, Northwest University, Xi’an, China
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences; The Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
- Department of Precision Diagnostic and Therapeutic Technology, The City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, China
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7
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Yuan L, Zhao L, Lai J, Jiang Y, Zhang Q, Shen Z, Zheng CH, Huang DS. iCRBP-LKHA: Large convolutional kernel and hybrid channel-spatial attention for identifying circRNA-RBP interaction sites. PLoS Comput Biol 2024; 20:e1012399. [PMID: 39173070 PMCID: PMC11373821 DOI: 10.1371/journal.pcbi.1012399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 09/04/2024] [Accepted: 08/08/2024] [Indexed: 08/24/2024] Open
Abstract
Circular RNAs (circRNAs) play vital roles in transcription and translation. Identification of circRNA-RBP (RNA-binding protein) interaction sites has become a fundamental step in molecular and cell biology. Deep learning (DL)-based methods have been proposed to predict circRNA-RBP interaction sites and achieved impressive identification performance. However, those methods cannot effectively capture long-distance dependencies, and cannot effectively utilize the interaction information of multiple features. To overcome those limitations, we propose a DL-based model iCRBP-LKHA using deep hybrid networks for identifying circRNA-RBP interaction sites. iCRBP-LKHA adopts five encoding schemes. Meanwhile, the neural network architecture, which consists of large kernel convolutional neural network (LKCNN), convolutional block attention module with one-dimensional convolution (CBAM-1D) and bidirectional gating recurrent unit (BiGRU), can explore local information, global context information and multiple features interaction information automatically. To verify the effectiveness of iCRBP-LKHA, we compared its performance with shallow learning algorithms on 37 circRNAs datasets and 37 circRNAs stringent datasets. And we compared its performance with state-of-the-art DL-based methods on 37 circRNAs datasets, 37 circRNAs stringent datasets and 31 linear RNAs datasets. The experimental results not only show that iCRBP-LKHA outperforms other competing methods, but also demonstrate the potential of this model in identifying other RNA-RBP interaction sites.
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Affiliation(s)
- Lin Yuan
- Key Laboratory of Computing Power Network and Information Security, Ministry of Education, Shandong Computer Science Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
- Shandong Engineering Research Center of Big Data Applied Technology, Faculty of Computer Science and Technology, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
- Shandong Provincial Key Laboratory of Computer Networks, Shandong Fundamental Research Center for Computer Science, Jinan, China
| | - Ling Zhao
- Key Laboratory of Computing Power Network and Information Security, Ministry of Education, Shandong Computer Science Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
- Shandong Engineering Research Center of Big Data Applied Technology, Faculty of Computer Science and Technology, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
- Shandong Provincial Key Laboratory of Computer Networks, Shandong Fundamental Research Center for Computer Science, Jinan, China
| | - Jinling Lai
- Key Laboratory of Computing Power Network and Information Security, Ministry of Education, Shandong Computer Science Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
- Shandong Engineering Research Center of Big Data Applied Technology, Faculty of Computer Science and Technology, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
- Shandong Provincial Key Laboratory of Computer Networks, Shandong Fundamental Research Center for Computer Science, Jinan, China
| | - Yufeng Jiang
- Key Laboratory of Computing Power Network and Information Security, Ministry of Education, Shandong Computer Science Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
- Shandong Engineering Research Center of Big Data Applied Technology, Faculty of Computer Science and Technology, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
- Shandong Provincial Key Laboratory of Computer Networks, Shandong Fundamental Research Center for Computer Science, Jinan, China
| | - Qinhu Zhang
- Eastern Institute for Advanced Study, Eastern Institute of Technology, Ningbo, China
| | - Zhen Shen
- School of Computer and Software, Nanyang Institute of Technology, Nanyang, China
| | - Chun-Hou Zheng
- Key Lab of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, Hefei, China
| | - De-Shuang Huang
- Eastern Institute for Advanced Study, Eastern Institute of Technology, Ningbo, China
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8
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Jiang L, Huang L, Jiang W. H3K27me3-mediated epigenetic regulation in pluripotency maintenance and lineage differentiation. CELL INSIGHT 2024; 3:100180. [PMID: 39072246 PMCID: PMC11278802 DOI: 10.1016/j.cellin.2024.100180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/20/2024] [Accepted: 06/26/2024] [Indexed: 07/30/2024]
Abstract
Cell fate determination is an intricate process which is orchestrated by multiple regulatory layers including signal pathways, transcriptional factors, epigenetic modifications, and metabolic rewiring. Among the sophisticated epigenetic modulations, the repressive mark H3K27me3, deposited by PRC2 (polycomb repressive complex 2) and removed by demethylase KDM6, plays a pivotal role in mediating the cellular identity transition through its dynamic and precise alterations. Herein, we overview and discuss how H3K27me3 and its modifiers regulate pluripotency maintenance and early lineage differentiation. We primarily highlight the following four aspects: 1) the two subcomplexes PRC2.1 and PRC2.2 and the distribution of genomic H3K27 methylation; 2) PRC2 as a critical regulator in pluripotency maintenance and exit; 3) the emerging role of the eraser KDM6 in early differentiation; 4) newly identified additional factors influencing H3K27me3. We present a comprehensive insight into the molecular principles of the dynamic regulation of H3K27me3, as well as how this epigenetic mark participates in pluripotent stem cell-centered cell fate determination.
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Affiliation(s)
- Liwen Jiang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Linfeng Huang
- Wang-Cai Biochemistry Lab, Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, Jiangsu, China
| | - Wei Jiang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China
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Moindrot B, Imaizumi Y, Feil R. Differential 3D genome architecture and imprinted gene expression: cause or consequence? Biochem Soc Trans 2024; 52:973-986. [PMID: 38775198 PMCID: PMC11346452 DOI: 10.1042/bst20230143] [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: 02/12/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 06/27/2024]
Abstract
Imprinted genes provide an attractive paradigm to unravel links between transcription and genome architecture. The parental allele-specific expression of these essential genes - which are clustered in chromosomal domains - is mediated by parental methylation imprints at key regulatory DNA sequences. Recent chromatin conformation capture (3C)-based studies show differential organization of topologically associating domains between the parental chromosomes at imprinted domains, in embryonic stem and differentiated cells. At several imprinted domains, differentially methylated regions show allelic binding of the insulator protein CTCF, and linked focal retention of cohesin, at the non-methylated allele only. This generates differential patterns of chromatin looping between the parental chromosomes, already in the early embryo, and thereby facilitates the allelic gene expression. Recent research evokes also the opposite scenario, in which allelic transcription contributes to the differential genome organization, similarly as reported for imprinted X chromosome inactivation. This may occur through epigenetic effects on CTCF binding, through structural effects of RNA Polymerase II, or through imprinted long non-coding RNAs that have chromatin repressive functions. The emerging picture is that epigenetically-controlled differential genome architecture precedes and facilitates imprinted gene expression during development, and that at some domains, conversely, the mono-allelic gene expression also influences genome architecture.
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Affiliation(s)
- Benoit Moindrot
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Yui Imaizumi
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
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10
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Farhadova S, Ghousein A, Charon F, Surcis C, Gomez-Velazques M, Roidor C, Di Michele F, Borensztein M, De Sario A, Esnault C, Noordermeer D, Moindrot B, Feil R. The long non-coding RNA Meg3 mediates imprinted gene expression during stem cell differentiation. Nucleic Acids Res 2024; 52:6183-6200. [PMID: 38613389 PMCID: PMC11194098 DOI: 10.1093/nar/gkae247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/02/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
The imprinted Dlk1-Dio3 domain comprises the developmental genes Dlk1 and Rtl1, which are silenced on the maternal chromosome in different cell types. On this parental chromosome, the domain's imprinting control region activates a polycistron that produces the lncRNA Meg3 and many miRNAs (Mirg) and C/D-box snoRNAs (Rian). Although Meg3 lncRNA is nuclear and associates with the maternal chromosome, it is unknown whether it controls gene repression in cis. We created mouse embryonic stem cells (mESCs) that carry an ectopic poly(A) signal, reducing RNA levels along the polycistron, and generated Rian-/- mESCs as well. Upon ESC differentiation, we found that Meg3 lncRNA (but not Rian) is required for Dlk1 repression on the maternal chromosome. Biallelic Meg3 expression acquired through CRISPR-mediated demethylation of the paternal Meg3 promoter led to biallelic Dlk1 repression, and to loss of Rtl1 expression. lncRNA expression also correlated with DNA hypomethylation and CTCF binding at the 5'-side of Meg3. Using Capture Hi-C, we found that this creates a Topologically Associating Domain (TAD) organization that brings Meg3 close to Dlk1 on the maternal chromosome. The requirement of Meg3 for gene repression and TAD structure may explain how aberrant MEG3 expression at the human DLK1-DIO3 locus associates with imprinting disorders.
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Affiliation(s)
- Sabina Farhadova
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 34090 Montpellier, France
- University of Montpellier, 34090 Montpellier, France
- Genetic Resources Research Institute, Azerbaijan National Academy of Sciences (ANAS), AZ1106 Baku, Azerbaijan
| | - Amani Ghousein
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 34090 Montpellier, France
- University of Montpellier, 34090 Montpellier, France
| | - François Charon
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91190 Gif-sur-Yvette, France
| | - Caroline Surcis
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 34090 Montpellier, France
| | - Melisa Gomez-Velazques
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 34090 Montpellier, France
- University of Montpellier, 34090 Montpellier, France
| | - Clara Roidor
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 34090 Montpellier, France
- University of Montpellier, 34090 Montpellier, France
| | - Flavio Di Michele
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 34090 Montpellier, France
- University of Montpellier, 34090 Montpellier, France
| | - Maud Borensztein
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 34090 Montpellier, France
- University of Montpellier, 34090 Montpellier, France
| | - Albertina De Sario
- University of Montpellier, 34090 Montpellier, France
- PhyMedExp, Institut National de la Santé et de la Recherche Médicale (INSERM), CNRS, 34295 Montpellier, France
| | - Cyril Esnault
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 34090 Montpellier, France
- University of Montpellier, 34090 Montpellier, France
| | - Daan Noordermeer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91190 Gif-sur-Yvette, France
| | - Benoit Moindrot
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91190 Gif-sur-Yvette, France
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), Centre National de Recherche Scientifique (CNRS), 34090 Montpellier, France
- University of Montpellier, 34090 Montpellier, France
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11
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Gail EH, Healy E, Flanigan SF, Jones N, Ng XH, Uckelmann M, Levina V, Zhang Q, Davidovich C. Inseparable RNA binding and chromatin modification activities of a nucleosome-interacting surface in EZH2. Nat Genet 2024; 56:1193-1202. [PMID: 38744974 PMCID: PMC11176075 DOI: 10.1038/s41588-024-01740-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 04/02/2024] [Indexed: 05/16/2024]
Abstract
Polycomb repressive complex 2 (PRC2) interacts with RNA in cells, but there is no consensus on how RNA regulates PRC2 canonical functions, including chromatin modification and the maintenance of transcription programs in lineage-committed cells. We assayed two separation-of-function mutants of the PRC2 catalytic subunit EZH2, defective in RNA binding but functional in methyltransferase activity. We find that part of the RNA-binding surface of EZH2 is required for chromatin modification, yet this activity is independent of RNA. Mechanistically, the RNA-binding surface within EZH2 is required for chromatin modification in vitro and in cells, through interactions with nucleosomal DNA. Contrarily, an RNA-binding-defective mutant exhibited normal chromatin modification activity in vitro and in lineage-committed cells, accompanied by normal gene repression activity. Collectively, we show that part of the RNA-binding surface of EZH2, rather than the RNA-binding activity per se, is required for the histone methylation in vitro and in cells, through interactions with the substrate nucleosome.
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Affiliation(s)
- Emma H Gail
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Evan Healy
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Sarena F Flanigan
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Natasha Jones
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Xiao Han Ng
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Michael Uckelmann
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Vitalina Levina
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Qi Zhang
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia.
- South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia.
- EMBL-Australia at SAiGENCI, Adelaide, South Australia, Australia.
| | - Chen Davidovich
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia.
- EMBL-Australia, Clayton, Victoria, Australia.
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12
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Qin Y, Ren J, Yu H, He X, Cheng S, Chen W, Yang Z, Sun F, Wang C, Yuan S, Chen P, Wu D, Ren F, Huang A, Chen J. HOXA-AS2 Epigenetically Inhibits HBV Transcription by Recruiting the MTA1-HDAC1/2 Deacetylase Complex to cccDNA Minichromosome. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306810. [PMID: 38647380 PMCID: PMC11200093 DOI: 10.1002/advs.202306810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 03/27/2024] [Indexed: 04/25/2024]
Abstract
Persistent transcription of HBV covalently closed circular DNA (cccDNA) is critical for chronic HBV infection. Silencing cccDNA transcription through epigenetic mechanisms offers an effective strategy to control HBV. Long non-coding RNAs (lncRNAs), as important epigenetic regulators, have an unclear role in cccDNA transcription regulation. In this study, lncRNA sequencing (lncRNA seq) is conducted on five pairs of HBV-positive and HBV-negative liver tissue. Through analysis, HOXA-AS2 (HOXA cluster antisense RNA 2) is identified as a significantly upregulated lncRNA in HBV-infected livers. Further experiments demonstrate that HBV DNA polymerase (DNA pol) induces HOXA-AS2 after establishing persistent high-level HBV replication. Functional studies reveal that HOXA-AS2 physically binds to cccDNA and significantly inhibits its transcription. Mechanistically, HOXA-AS2 recruits the MTA1-HDAC1/2 deacetylase complex to cccDNA minichromosome by physically interacting with metastasis associated 1 (MTA1) subunit, resulting in reduced acetylation of histone H3 at lysine 9 (H3K9ac) and lysine 27 (H3K27ac) associated with cccDNA and subsequently suppressing cccDNA transcription. Altogether, the study reveals a mechanism to self-limit HBV replication, wherein the upregulation of lncRNA HOXA-AS2, induced by HBV DNA pol, can epigenetically suppress cccDNA transcription.
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Affiliation(s)
- YiPing Qin
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized TreatmentChongqing University Cancer HospitalChongqing400030China
| | - JiHua Ren
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - HaiBo Yu
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - Xin He
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - ShengTao Cheng
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - WeiXian Chen
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - Zhen Yang
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - FengMing Sun
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education)College of Laboratory MedicineChongqing Medical UniversityChongqing400016China
| | - ChunDuo Wang
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - SiYu Yuan
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - Peng Chen
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - DaiQing Wu
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - Fang Ren
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - AiLong Huang
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
| | - Juan Chen
- Institute for Viral HepatitisKey Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education)Department of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing400010China
- State Key Laboratory of Ultrasound in Medicine and EngineeringCollege of Biomedical EngineeringChongqing Medical UniversityChongqing400016China
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13
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Völkers M, Preiss T, Hentze MW. RNA-binding proteins in cardiovascular biology and disease: the beat goes on. Nat Rev Cardiol 2024; 21:361-378. [PMID: 38163813 DOI: 10.1038/s41569-023-00958-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/06/2023] [Indexed: 01/03/2024]
Abstract
Cardiac development and function are becoming increasingly well understood from different angles, including signalling, transcriptional and epigenetic mechanisms. By contrast, the importance of the post-transcriptional landscape of cardiac biology largely remains to be uncovered, building on the foundation of a few existing paradigms. The discovery during the past decade of hundreds of additional RNA-binding proteins in mammalian cells and organs, including the heart, is expected to accelerate progress and has raised intriguing possibilities for better understanding the intricacies of cardiac development, metabolism and adaptive alterations. In this Review, we discuss the progress and new concepts on RNA-binding proteins and RNA biology and appraise them in the context of common cardiovascular clinical conditions, from cell and organ-wide perspectives. We also discuss how a better understanding of cardiac RNA-binding proteins can fill crucial knowledge gaps in cardiology and might pave the way to developing better treatments to reduce cardiovascular morbidity and mortality.
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Affiliation(s)
- Mirko Völkers
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg and Mannheim, Germany
| | - Thomas Preiss
- Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
| | - Matthias W Hentze
- European Molecular Biology Laboratory, Heidelberg, Germany.
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany.
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14
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Lee YW, Weissbein U, Blum R, Lee JT. G-quadruplex folding in Xist RNA antagonizes PRC2 activity for stepwise regulation of X chromosome inactivation. Mol Cell 2024; 84:1870-1885.e9. [PMID: 38759625 DOI: 10.1016/j.molcel.2024.04.015] [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: 05/31/2023] [Revised: 11/25/2023] [Accepted: 04/19/2024] [Indexed: 05/19/2024]
Abstract
How Polycomb repressive complex 2 (PRC2) is regulated by RNA remains an unsolved problem. Although PRC2 binds G-tracts with the potential to form RNA G-quadruplexes (rG4s), whether rG4s fold extensively in vivo and whether PRC2 binds folded or unfolded rG4 are unknown. Using the X-inactivation model in mouse embryonic stem cells, here we identify multiple folded rG4s in Xist RNA and demonstrate that PRC2 preferentially binds folded rG4s. High-affinity rG4 binding inhibits PRC2's histone methyltransferase activity, and stabilizing rG4 in vivo antagonizes H3 at lysine 27 (H3K27me3) enrichment on the inactive X chromosome. Surprisingly, mutagenizing the rG4 does not affect PRC2 recruitment but promotes its release and catalytic activation on chromatin. H3K27me3 marks are misplaced, however, and gene silencing is compromised. Xist-PRC2 complexes become entrapped in the S1 chromosome compartment, precluding the required translocation into the S2 compartment. Thus, Xist rG4 folding controls PRC2 activity, H3K27me3 enrichment, and the stepwise regulation of chromosome-wide gene silencing.
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Affiliation(s)
- Yong Woo Lee
- Department of Molecular Biology, Massachusetts General Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Uri Weissbein
- Department of Molecular Biology, Massachusetts General Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Roy Blum
- Department of Molecular Biology, Massachusetts General Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA.
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15
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Guo JK, Blanco MR, Walkup WG, Bonesteele G, Urbinati CR, Banerjee AK, Chow A, Ettlin O, Strehle M, Peyda P, Amaya E, Trinh V, Guttman M. Denaturing purifications demonstrate that PRC2 and other widely reported chromatin proteins do not appear to bind directly to RNA in vivo. Mol Cell 2024; 84:1271-1289.e12. [PMID: 38387462 PMCID: PMC10997485 DOI: 10.1016/j.molcel.2024.01.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/01/2023] [Accepted: 01/30/2024] [Indexed: 02/24/2024]
Abstract
Polycomb repressive complex 2 (PRC2) is reported to bind to many RNAs and has become a central player in reports of how long non-coding RNAs (lncRNAs) regulate gene expression. Yet, there is a growing discrepancy between the biochemical evidence supporting specific lncRNA-PRC2 interactions and functional evidence demonstrating that PRC2 is often dispensable for lncRNA function. Here, we revisit the evidence supporting RNA binding by PRC2 and show that many reported interactions may not occur in vivo. Using denaturing purification of in vivo crosslinked RNA-protein complexes in human and mouse cell lines, we observe a loss of detectable RNA binding to PRC2 and chromatin-associated proteins previously reported to bind RNA (CTCF, YY1, and others), despite accurately mapping bona fide RNA-binding sites across others (SPEN, TET2, and others). Taken together, these results argue for a critical re-evaluation of the broad role of RNA binding to orchestrate various chromatin regulatory mechanisms.
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Affiliation(s)
- Jimmy K Guo
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Mario R Blanco
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Ward G Walkup
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Grant Bonesteele
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Carl R Urbinati
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Biology, Loyola Marymount University, Los Angeles, CA 90045, USA
| | - Abhik K Banerjee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Amy Chow
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Olivia Ettlin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mackenzie Strehle
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Parham Peyda
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Enrique Amaya
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Vickie Trinh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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16
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Zhang X, He H, Yu H, Teng X, Wang Z, Li C, Li J, Yang H, Shen J, Wu T, Zhang F, Zhang Y, Wu Q. Maternal RNA transcription in Dlk1-Dio3 domain is critical for proper development of the mouse placental vasculature. Commun Biol 2024; 7:363. [PMID: 38521877 PMCID: PMC10960817 DOI: 10.1038/s42003-024-06038-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 03/11/2024] [Indexed: 03/25/2024] Open
Abstract
The placenta is a unique organ for ensuring normal embryonic growth in the uterine. Here, we found that maternal RNA transcription in Dlk1-Dio3 imprinted domain is essential for placentation. PolyA signals were inserted into Gtl2 to establish a mouse model to prevent the expression of maternal RNAs in the domain. The maternal allele knock-in (MKI) and homozygous (HOMO) placentas showed an expanded junctional zone, reduced labyrinth and poor vasculature impacting both fetal and maternal blood spaces. The MKI and HOMO models displayed dysregulated gene expression in the Dlk1-Dio3 domain. In situ hybridization detected Dlk1, Gtl2, Rtl1, miR-127 and Rian dysregulated in the labyrinth vasculature. MKI and HOMO induced Dlk1 to lose imprinting, and DNA methylation changes of IG-DMR and Gtl2-DMR, leading to abnormal gene expression, while the above changes didn't occur in paternal allele knock-in placentas. These findings demonstrate that maternal RNAs in the Dlk1-Dio3 domain are involved in placental vasculature, regulating gene expression, imprinting status and DNA methylation.
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Affiliation(s)
- Ximeijia Zhang
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150006, Heilongjiang, China
| | - Hongjuan He
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150006, Heilongjiang, China
| | - Haoran Yu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150006, Heilongjiang, China
| | - Xiangqi Teng
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150006, Heilongjiang, China
| | - Ziwen Wang
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150006, Heilongjiang, China
| | - Chenghao Li
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150006, Heilongjiang, China
| | - Jiahang Li
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150006, Heilongjiang, China
| | - Haopeng Yang
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150006, Heilongjiang, China
| | - Jiwei Shen
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150006, Heilongjiang, China
| | - Tong Wu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150006, Heilongjiang, China
| | - Fengwei Zhang
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150006, Heilongjiang, China
| | - Yan Zhang
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150006, Heilongjiang, China
| | - Qiong Wu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150006, Heilongjiang, China.
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17
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Avila-Lopez P, Lauberth SM. Exploring new roles for RNA-binding proteins in epigenetic and gene regulation. Curr Opin Genet Dev 2024; 84:102136. [PMID: 38128453 PMCID: PMC11245729 DOI: 10.1016/j.gde.2023.102136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/12/2023] [Accepted: 11/15/2023] [Indexed: 12/23/2023]
Abstract
A significant portion of the human proteome comprises RNA-binding proteins (RBPs) that play fundamental roles in numerous biological processes. In the last decade, there has been a staggering increase in RBP identification and classification, which has fueled interest in the evolving roles of RBPs and RBP-driven molecular mechanisms. Here, we focus on recent insights into RBP-dependent regulation of the epigenetic and transcriptional landscape. We describe advances in methodologies that define the RNA-protein interactome and machine-learning algorithms that are streamlining RBP discovery and predicting new RNA-binding regions. Finally, we present how RBP dysregulation leads to alterations in tumor-promoting gene expression and discuss the potential for targeting these RBPs for the development of new cancer therapeutics.
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Affiliation(s)
- Pedro Avila-Lopez
- Simpson Querrey Institute for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Shannon M Lauberth
- Simpson Querrey Institute for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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18
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Weinberg-Shukron A, Youngson NA, Ferguson-Smith AC, Edwards CA. Epigenetic control and genomic imprinting dynamics of the Dlk1-Dio3 domain. Front Cell Dev Biol 2023; 11:1328806. [PMID: 38155837 PMCID: PMC10754522 DOI: 10.3389/fcell.2023.1328806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 11/27/2023] [Indexed: 12/30/2023] Open
Abstract
Genomic imprinting is an epigenetic process whereby genes are monoallelically expressed in a parent-of-origin-specific manner. Imprinted genes are frequently found clustered in the genome, likely illustrating their need for both shared regulatory control and functional inter-dependence. The Dlk1-Dio3 domain is one of the largest imprinted clusters. Genes in this region are involved in development, behavior, and postnatal metabolism: failure to correctly regulate the domain leads to Kagami-Ogata or Temple syndromes in humans. The region contains many of the hallmarks of other imprinted domains, such as long non-coding RNAs and parental origin-specific CTCF binding. Recent studies have shown that the Dlk1-Dio3 domain is exquisitely regulated via a bipartite imprinting control region (ICR) which functions differently on the two parental chromosomes to establish monoallelic expression. Furthermore, the Dlk1 gene displays a selective absence of imprinting in the neurogenic niche, illustrating the need for precise dosage modulation of this domain in different tissues. Here, we discuss the following: how differential epigenetic marks laid down in the gametes cause a cascade of events that leads to imprinting in the region, how this mechanism is selectively switched off in the neurogenic niche, and why studying this imprinted region has added a layer of sophistication to how we think about the hierarchical epigenetic control of genome function.
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Affiliation(s)
| | - Neil A. Youngson
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | | | - Carol A. Edwards
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
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19
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Ma M, Chen M, Wu X, Sooranna SR, Liu Q, Shi D, Wang J, Li H. A newly identified lncRNA lnc000100 regulates proliferation and differentiation of cattle skeletal muscle cells. Epigenetics 2023; 18:2270864. [PMID: 37910666 PMCID: PMC10768731 DOI: 10.1080/15592294.2023.2270864] [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: 12/05/2022] [Accepted: 09/01/2023] [Indexed: 11/03/2023] Open
Abstract
Cattle skeletal muscle development is a complex and highly coordinated biological process mediated by a series of myogenic regulators, which plays a critical role in beef yield and quality. Long non-coding RNAs (lncRNAs) have been shown to regulate skeletal muscle development. However, the molecular mechanism by which lncRNAs regulate skeletal muscle development is largely unknown. We performed transcriptome analysis of muscle tissues of adult and embryo Angus cattle to investigate the mechanism by which lncRNA regulates skeletal muscle development between adult and embryo cattle. A total of 37,115 candidate lncRNAs were detected, and a total of 1,998 lncRNAs were differentially expressed between the muscle tissue libraries of adult and embryo cattle, including 1,229 up-regulated lncRNAs and 769 down-regulated lncRNAs (adult cattle were the control group). We verified the expression of 7 differentially expressed lncRNAs by quantitative real-time PCR (RT-qPCR), and analysed the tissue expression profile of lnc000100, which is down-regulated in the longest dorsal muscle during foetal life and which is highly specifically expressed in muscle tissue. We found that the interference of lnc000100 significantly inhibited cell proliferation and promoted cell differentiation. Lnc000100 was located in the nucleus by RNA-FISH. Our research provides certain resources for the analysis of lncRNA regulating cattle skeletal muscle development, and may also provide new insights for improving beef production and breed selection.
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Affiliation(s)
- Mengke Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Mengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Xiaoyun Wu
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Suren R. Sooranna
- Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Jian Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Hui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
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20
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Lei WL, Du Z, Meng TG, Su R, Li YY, Liu W, Sun SM, Liu MY, Hou Y, Zhang CH, Gui Y, Schatten H, Han Z, Liu C, Sun F, Wang ZB, Qian WP, Sun QY. SRSF2 is required for mRNA splicing during spermatogenesis. BMC Biol 2023; 21:231. [PMID: 37867192 PMCID: PMC10591377 DOI: 10.1186/s12915-023-01736-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 10/13/2023] [Indexed: 10/24/2023] Open
Abstract
BACKGROUND RNA splicing plays significant roles in fundamental biological activities. However, our knowledge about the roles of alternative splicing and underlying mechanisms during spermatogenesis is limited. RESULTS Here, we report that Serine/arginine-rich splicing factor 2 (SRSF2), also known as SC35, plays critical roles in alternative splicing and male reproduction. Male germ cell-specific deletion of Srsf2 by Stra8-Cre caused complete infertility and defective spermatogenesis. Further analyses revealed that deletion of Srsf2 disrupted differentiation and meiosis initiation of spermatogonia. Mechanistically, by combining RNA-seq data with LACE-seq data, we showed that SRSF2 regulatory networks play critical roles in several major events including reproductive development, spermatogenesis, meiotic cell cycle, synapse organization, DNA recombination, chromosome segregation, and male sex differentiation. Furthermore, SRSF2 affected expression and alternative splicing of Stra8, Stag3 and Atr encoding critical factors for spermatogenesis in a direct manner. CONCLUSIONS Taken together, our results demonstrate that SRSF2 has important functions in spermatogenesis and male fertility by regulating alternative splicing.
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Affiliation(s)
- Wen-Long Lei
- Guangdong and Shenzhen Key Laboratory of Reproductive Medicine and Genetics, The Center of Reproductive Medicine, Peking University Shenzhen Hospital, 1120 Lianhua Rd, Futian District, Shenzhen, 518000, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- Department of Urology & Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, #3 Qingchun East Road, Shangcheng District, Hangzhou, 310016, China
| | - Zongchang Du
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tie-Gang Meng
- Fertility Preservation Lab, Guangdong-Hongkong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, #466 Xin-Gang-Zhong-Lu, Haizhu District, Guangzhou, 510317, China
| | - Ruibao Su
- Fertility Preservation Lab, Guangdong-Hongkong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, #466 Xin-Gang-Zhong-Lu, Haizhu District, Guangzhou, 510317, China
| | - Yuan-Yuan Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, #1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Wenbo Liu
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine/Department of Fetal Medicine and Prenatal Diagnosis/BioResource Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Si-Min Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, #1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Meng-Yu Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, #1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Yi Hou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, #1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Chun-Hui Zhang
- Guangdong and Shenzhen Key Laboratory of Reproductive Medicine and Genetics, The Center of Reproductive Medicine, Peking University Shenzhen Hospital, 1120 Lianhua Rd, Futian District, Shenzhen, 518000, China
| | - Yaoting Gui
- Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, 518036, China
| | - Heide Schatten
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, 65211, USA
| | - Zhiming Han
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, #1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Chenli Liu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Fei Sun
- Department of Urology & Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, #3 Qingchun East Road, Shangcheng District, Hangzhou, 310016, China.
| | - Zhen-Bo Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, #1 Beichen West Road, Chaoyang District, Beijing, 100101, China.
| | - Wei-Ping Qian
- Guangdong and Shenzhen Key Laboratory of Reproductive Medicine and Genetics, The Center of Reproductive Medicine, Peking University Shenzhen Hospital, 1120 Lianhua Rd, Futian District, Shenzhen, 518000, China.
| | - Qing-Yuan Sun
- Fertility Preservation Lab, Guangdong-Hongkong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, #466 Xin-Gang-Zhong-Lu, Haizhu District, Guangzhou, 510317, China.
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21
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Song J, Gooding AR, Hemphill WO, Love BD, Robertson A, Yao L, Zon LI, North TE, Kasinath V, Cech TR. Structural basis for inactivation of PRC2 by G-quadruplex RNA. Science 2023; 381:1331-1337. [PMID: 37733873 PMCID: PMC11191771 DOI: 10.1126/science.adh0059] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 08/22/2023] [Indexed: 09/23/2023]
Abstract
Polycomb repressive complex 2 (PRC2) silences genes through trimethylation of histone H3K27. PRC2 associates with numerous precursor messenger RNAs (pre-mRNAs) and long noncoding RNAs (lncRNAs) with a binding preference for G-quadruplex RNA. In this work, we present a 3.3-Å-resolution cryo-electron microscopy structure of PRC2 bound to a G-quadruplex RNA. Notably, RNA mediates the dimerization of PRC2 by binding both protomers and inducing a protein interface composed of two copies of the catalytic subunit EZH2, thereby blocking nucleosome DNA interaction and histone H3 tail accessibility. Furthermore, an RNA-binding loop of EZH2 facilitates the handoff between RNA and DNA, another activity implicated in PRC2 regulation by RNA. We identified a gain-of-function mutation in this loop that activates PRC2 in zebrafish. Our results reveal mechanisms for RNA-mediated regulation of a chromatin-modifying enzyme.
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Affiliation(s)
- Jiarui Song
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Anne R. Gooding
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Wayne O. Hemphill
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Brittney D. Love
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA
- Stem Cell Program, Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Anne Robertson
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA
- Stem Cell Program, Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Liqi Yao
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Leonard I. Zon
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA
- Stem Cell Program, Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Trista E. North
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA
- Stem Cell Program, Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Vignesh Kasinath
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Thomas R. Cech
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA
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22
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Di Michele F, Chillón I, Feil R. Imprinted Long Non-Coding RNAs in Mammalian Development and Disease. Int J Mol Sci 2023; 24:13647. [PMID: 37686455 PMCID: PMC10487962 DOI: 10.3390/ijms241713647] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023] Open
Abstract
Imprinted genes play diverse roles in mammalian development, homeostasis, and disease. Most imprinted chromosomal domains express one or more long non-coding RNAs (lncRNAs). Several of these lncRNAs are strictly nuclear and their mono-allelic expression controls in cis the expression of protein-coding genes, often developmentally regulated. Some imprinted lncRNAs act in trans as well, controlling target gene expression elsewhere in the genome. The regulation of imprinted gene expression-including that of imprinted lncRNAs-is susceptible to stochastic and environmentally triggered epigenetic changes in the early embryo. These aberrant changes persist during subsequent development and have long-term phenotypic consequences. This review focuses on the expression and the cis- and trans-regulatory roles of imprinted lncRNAs and describes human disease syndromes associated with their perturbed expression.
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Affiliation(s)
- Flavio Di Michele
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, 1919 Route de Mende, 34093 Montpellier, France
- University of Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
| | - Isabel Chillón
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, 1919 Route de Mende, 34093 Montpellier, France
- University of Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, 1919 Route de Mende, 34093 Montpellier, France
- University of Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
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23
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Hou W, Zong M, Zhao Q, Yang X, Zhang J, Liu S, Li X, Chen L, Tang C, Wang X, Dong Z, Gao M, Su J, Kong Q. Network characterization linc1393 in the maintenance of pluripotency provides the principles for lncRNA targets prediction. iScience 2023; 26:107469. [PMID: 37588167 PMCID: PMC10425947 DOI: 10.1016/j.isci.2023.107469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 06/07/2023] [Accepted: 07/21/2023] [Indexed: 08/18/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been implicated in diverse biological processes. However, the functional mechanisms have not yet been fully explored. Characterizing the interactions of lncRNAs with chromatin is central to determining their functions but, due to precise and efficient approaches lacking, our understanding of their functional mechanisms has progressed slowly. In this study, we demonstrate that a nuclear lncRNA linc1393 maintains mouse ESC pluripotency by recruiting SET1A near its binding sites, to establish H3K4me3 status and activate the expression of specific pluripotency-related genes. Moreover, we characterized the principles of lncRNA-chromatin interaction and transcriptional regulation. Accordingly, we developed a computational framework based on the XGBoost model, LncTargeter, to predict the targets of a given lncRNA, and validated its reliability in various cellular contexts. Together, these findings elucidate the roles and mechanisms of lncRNA on pluripotency maintenance, and provide a promising tool for predicting the regulatory networks of lncRNAs.
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Affiliation(s)
- Weibo Hou
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Ming Zong
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Qi Zhao
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xu Yang
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jiaming Zhang
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Shuanghui Liu
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xuanwen Li
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Lijun Chen
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Chun Tang
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xinyu Wang
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhixiong Dong
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Meiling Gao
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jianzhong Su
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou Medical University, Wenzhou, Zhejiang, China
- School of Optometry and Ophthalmology and Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qingran Kong
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
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24
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Dar MS, Mensah IK, He M, McGovern S, Sohal IS, Whitlock HC, Bippus NE, Ceminsky M, Emerson ML, Tan HJ, Hall MC, Gowher H. Dnmt3bas coordinates transcriptional induction and alternative exon inclusion to promote catalytically active Dnmt3b expression. Cell Rep 2023; 42:112587. [PMID: 37294637 PMCID: PMC10592478 DOI: 10.1016/j.celrep.2023.112587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 03/16/2023] [Accepted: 05/16/2023] [Indexed: 06/11/2023] Open
Abstract
Embryonic expression of DNMT3B is critical for establishing de novo DNA methylation. This study uncovers the mechanism through which the promoter-associated long non-coding RNA (lncRNA) Dnmt3bas controls the induction and alternative splicing of Dnmt3b during embryonic stem cell (ESC) differentiation. Dnmt3bas recruits the PRC2 (polycomb repressive complex 2) at cis-regulatory elements of the Dnmt3b gene expressed at a basal level. Correspondingly, Dnmt3bas knockdown enhances Dnmt3b transcriptional induction, whereas overexpression of Dnmt3bas dampens it. Dnmt3b induction coincides with exon inclusion, switching the predominant isoform from the inactive Dnmt3b6 to the active Dnmt3b1. Intriguingly, overexpressing Dnmt3bas further enhances the Dnmt3b1:Dnmt3b6 ratio, attributed to its interaction with hnRNPL (heterogeneous nuclear ribonucleoprotein L), a splicing factor that promotes exon inclusion. Our data suggest that Dnmt3bas coordinates alternative splicing and transcriptional induction of Dnmt3b by facilitating the hnRNPL and RNA polymerase II (RNA Pol II) interaction at the Dnmt3b promoter. This dual mechanism precisely regulates the expression of catalytically active DNMT3B, ensuring fidelity and specificity of de novo DNA methylation.
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Affiliation(s)
- Mohd Saleem Dar
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Isaiah K Mensah
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Ming He
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Sarah McGovern
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Ikjot Singh Sohal
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA; Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | | | - Nina Elise Bippus
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Madison Ceminsky
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Martin L Emerson
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Hern J Tan
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Mark C Hall
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
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25
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Gil N, Perry RBT, Mukamel Z, Tuck A, Bühler M, Ulitsky I. Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus. Cell Rep 2023; 42:112569. [PMID: 37256750 PMCID: PMC10320833 DOI: 10.1016/j.celrep.2023.112569] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/07/2023] [Accepted: 05/12/2023] [Indexed: 06/02/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are implicated in a plethora of cellular processes, but an in-depth understanding of their functional features or their mechanisms of action is currently lacking. Here we study Meteor, a lncRNA transcribed near the gene encoding EOMES, a pleiotropic transcription factor implicated in various processes throughout development and in adult tissues. Using a wide array of perturbation techniques, we show that transcription elongation through the Meteor locus is required for Eomes activation in mouse embryonic stem cells, with Meteor repression linked to a change in the subpopulation primed to differentiate to the mesoderm lineage. We further demonstrate that a distinct functional feature of the locus-namely, the underlying DNA element-is required for suppressing Eomes expression following neuronal differentiation. Our results demonstrate the complex regulation that can be conferred by a single locus and emphasize the importance of careful selection of perturbation techniques when studying lncRNA loci.
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Affiliation(s)
- Noa Gil
- Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rotem Ben-Tov Perry
- Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Zohar Mukamel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alex Tuck
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel.
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26
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Hemphill W, Fenske R, Gooding A, Cech T. PRC2 direct transfer from G-quadruplex RNA to dsDNA has implications for RNA-binding chromatin modifiers. Proc Natl Acad Sci U S A 2023; 120:e2220528120. [PMID: 37252986 PMCID: PMC10266057 DOI: 10.1073/pnas.2220528120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/01/2023] [Indexed: 06/01/2023] Open
Abstract
The chromatin-modifying enzyme, Polycomb Repressive Complex 2 (PRC2), deposits the H3K27me3 epigenetic mark to negatively regulate expression at numerous target genes, and this activity has been implicated in embryonic development, cell differentiation, and various cancers. A biological role for RNA binding in regulating PRC2 histone methyltransferase activity is generally accepted, but the nature and mechanism of this relationship remains an area of active investigation. Notably, many in vitro studies demonstrate that RNA inhibits PRC2 activity on nucleosomes through mutually antagonistic binding, while some in vivo studies indicate that PRC2's RNA-binding activity is critical for facilitating its biological function(s). Here we use biochemical, biophysical, and computational approaches to interrogate PRC2's RNA and DNA-binding kinetics. Our findings demonstrate that PRC2-polynucleotide dissociation rates are dependent on the concentration of free ligand, indicating the potential for direct transfer between nucleic acid ligands without a free-enzyme intermediate. Direct transfer explains the variation in previously reported dissociation kinetics, allows reconciliation of prior in vitro and in vivo studies, and expands the potential mechanisms of RNA-mediated PRC2 regulation. Moreover, simulations indicate that such a direct transfer mechanism could be obligatory for RNA to recruit proteins to chromatin.
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Affiliation(s)
- Wayne O. Hemphill
- Department of Biochemistry, BioFrontiers Institute, University of Colorado Boulder, Boulder, CO80309
- HHMI, University of Colorado Boulder, Boulder, CO80309
| | - Regan Fenske
- Department of Biochemistry, BioFrontiers Institute, University of Colorado Boulder, Boulder, CO80309
- HHMI, University of Colorado Boulder, Boulder, CO80309
| | - Anne R. Gooding
- Department of Biochemistry, BioFrontiers Institute, University of Colorado Boulder, Boulder, CO80309
- HHMI, University of Colorado Boulder, Boulder, CO80309
| | - Thomas R. Cech
- Department of Biochemistry, BioFrontiers Institute, University of Colorado Boulder, Boulder, CO80309
- HHMI, University of Colorado Boulder, Boulder, CO80309
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27
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Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, Kanduri C, Kapranov P, Lawrence JB, Lee JT, Mendell JT, Mercer TR, Moore KJ, Nakagawa S, Rinn JL, Spector DL, Ulitsky I, Wan Y, Wilusz JE, Wu M. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol 2023; 24:430-447. [PMID: 36596869 PMCID: PMC10213152 DOI: 10.1038/s41580-022-00566-8] [Citation(s) in RCA: 483] [Impact Index Per Article: 483.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 01/05/2023]
Abstract
Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult. Most lncRNAs evolve more rapidly than protein-coding sequences, are cell type specific and regulate many aspects of cell differentiation and development and other physiological processes. Many lncRNAs associate with chromatin-modifying complexes, are transcribed from enhancers and nucleate phase separation of nuclear condensates and domains, indicating an intimate link between lncRNA expression and the spatial control of gene expression during development. lncRNAs also have important roles in the cytoplasm and beyond, including in the regulation of translation, metabolism and signalling. lncRNAs often have a modular structure and are rich in repeats, which are increasingly being shown to be relevant to their function. In this Consensus Statement, we address the definition and nomenclature of lncRNAs and their conservation, expression, phenotypic visibility, structure and functions. We also discuss research challenges and provide recommendations to advance the understanding of the roles of lncRNAs in development, cell biology and disease.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia.
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia.
| | - Paulo P Amaral
- INSPER Institute of Education and Research, São Paulo, Brazil
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ling-Ling Chen
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Caroline Dean
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia
| | - Katherine A Fitzgerald
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Maite Huarte
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra, Pamplona, Spain
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, Xiamen, China
| | - Jeanne B Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joshua T Mendell
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Timothy R Mercer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Kathryn J Moore
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - David L Spector
- Cold Spring Harbour Laboratory, Cold Spring Harbour, NY, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Yue Wan
- Laboratory of RNA Genomics and Structure, Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Mian Wu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
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Li J, Liu W, Peng F, Cao X, Xie X, Peng C. The multifaceted biology of lncR-Meg3 in cardio-cerebrovascular diseases. Front Genet 2023; 14:1132884. [PMID: 36968595 PMCID: PMC10036404 DOI: 10.3389/fgene.2023.1132884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 02/28/2023] [Indexed: 03/12/2023] Open
Abstract
Cardio-cerebrovascular disease, related to high mortality and morbidity worldwide, is a type of cardiovascular or cerebrovascular dysfunction involved in various processes. Therefore, it is imperative to conduct additional research into the pathogenesis and new therapeutic targets of cardiovascular and cerebrovascular disorders. Long non-coding RNAs (lncRNAs) have multiple functions and are involved in nearly all cellular biological processes, including translation, transcription, signal transduction, and cell cycle control. LncR-Meg3 is one of them and is becoming increasingly popular. By binding proteins or directly or competitively binding miRNAs, LncR-Meg3 is involved in apoptosis, inflammation, oxidative stress, endoplasmic reticulum stress, epithelial-mesenchymal transition, and other processes. Recent research has shown that LncR-Meg3 is associated with acute myocardial infarction and can be used to diagnose this condition. This article examines the current state of knowledge regarding the expression and regulatory function of LncR-Meg3 in relation to cardiovascular and cerebrovascular diseases. The abnormal expression of LncR-Meg3 can influence neuronal cell death, inflammation, apoptosis, smooth muscle cell proliferation, etc., thereby aggravating or promoting the disease. In addition, we review the bioactive components that target lncR-Meg3 and propose some potential delivery vectors. A comprehensive and in-depth analysis of LncR-Meg3’s role in cardiovascular disease suggests that targeting LncR-Meg3 may be an alternative therapy in the near future, providing new options for slowing the progression of cardiovascular disease.
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Affiliation(s)
- Jing Li
- Key Laboratory of Southwestern Chinese Medicine Resources, Key Laboratory of standardization of Chinese herbal medicine of MOE, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Wenxiu Liu
- Key Laboratory of Southwestern Chinese Medicine Resources, Key Laboratory of standardization of Chinese herbal medicine of MOE, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Fu Peng
- Key Laboratory of Southwestern Chinese Medicine Resources, Key Laboratory of standardization of Chinese herbal medicine of MOE, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Department of Pharmacology, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, China
- *Correspondence: Fu Peng, ; Xiaofang Xie, ; Cheng Peng,
| | - Xiaoyu Cao
- Key Laboratory of Southwestern Chinese Medicine Resources, Key Laboratory of standardization of Chinese herbal medicine of MOE, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiaofang Xie
- Key Laboratory of Southwestern Chinese Medicine Resources, Key Laboratory of standardization of Chinese herbal medicine of MOE, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- *Correspondence: Fu Peng, ; Xiaofang Xie, ; Cheng Peng,
| | - Cheng Peng
- Key Laboratory of Southwestern Chinese Medicine Resources, Key Laboratory of standardization of Chinese herbal medicine of MOE, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- *Correspondence: Fu Peng, ; Xiaofang Xie, ; Cheng Peng,
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Wang X, Zhang M, Long C, Yao L, Zhu M. Self-Attention Based Neural Network for Predicting RNA-Protein Binding Sites. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:1469-1479. [PMID: 36067103 DOI: 10.1109/tcbb.2022.3204661] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Proteins binding to Ribonucleic Acid (RNA) inside cells are called RNA-binding proteins (RBP), which play a crucial role in gene regulation. The identification of RNA-protein binding sites helps to understand the function of RBP better. Although many computational methods have been developed to predict RNA-protein binding sites, their prediction accuracy on small sample datasets needs improvement. To overcome this limitation, we propose a novel model called SA-Net, which utilizes k-mer embedding to encode RNA sequences and a self-attention-based neural network to extract sequence features. K-mer embedding assists the model to discover significant subsequence fragments associated with binding sites. The self-attention mechanism captures contextual information from the entire input sequence globally, performing well in small sample sequence learning. Experimental results demonstrate that SA-Net attains state-of-the-art results on the RBP-24 dataset. We find that 4-mer embedding aids the model to achieve optimal performance. We also show that the self-attention network outperforms the commonly used CNN and CNN-BLSTM models in sequence feature extraction.
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30
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Song J, Gooding AR, Hemphill WO, Kasinath V, Cech TR. Structural basis for inactivation of PRC2 by G-quadruplex RNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.06.527314. [PMID: 36798278 PMCID: PMC9934548 DOI: 10.1101/2023.02.06.527314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The histone methyltransferase PRC2 (Polycomb Repressive Complex 2) silences genes via successively attaching three methyl groups to lysine 27 of histone H3. PRC2 associates with numerous pre-mRNA and lncRNA transcripts with a binding preference for G-quadruplex RNA. Here, we present a 3.3Ã…-resolution cryo-EM structure of PRC2 bound to a G-quadruplex RNA. Notably, RNA mediates the dimerization of PRC2 by binding both protomers and inducing a protein interface comprised of two copies of the catalytic subunit EZH2, which limits nucleosome DNA interaction and occludes H3 tail accessibility to the active site. Our results reveal an unexpected mechanism for RNA-mediated inactivation of a chromatin-modifying enzyme. Furthermore, the flexible loop of EZH2 that helps stabilize RNA binding also facilitates the handoff between RNA and DNA, an activity implicated in PRC2 regulation by RNA. One-Sentence Summary Cryo-EM structure of RNA-bound PRC2 dimer elucidates an unexpected mechanism of PRC2 inhibition by RNA.
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31
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Becker J, Sun B, Alammari F, Haerty W, Vance KW, Szele FG. What has single-cell transcriptomics taught us about long non-coding RNAs in the ventricular-subventricular zone? Stem Cell Reports 2022; 18:354-376. [PMID: 36525965 PMCID: PMC9860170 DOI: 10.1016/j.stemcr.2022.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 11/14/2022] [Accepted: 11/14/2022] [Indexed: 12/16/2022] Open
Abstract
Long non-coding RNA (lncRNA) function is mediated by the process of transcription or through transcript-dependent associations with proteins or nucleic acids to control gene regulatory networks. Many lncRNAs are transcribed in the ventricular-subventricular zone (V-SVZ), a postnatal neural stem cell niche. lncRNAs in the V-SVZ are implicated in neurodevelopmental disorders, cancer, and brain disease, but their functions are poorly understood. V-SVZ neurogenesis capacity declines with age due to stem cell depletion and resistance to neural stem cell activation. Here we analyzed V-SVZ transcriptomics by pooling current single-cell RNA-seq data. They showed consistent lncRNA expression during stem cell activation, lineage progression, and aging. In conjunction with epigenetic and genetic data, we predicted V-SVZ lncRNAs that regulate stem cell activation and differentiation. Some of the lncRNAs validate known epigenetic mechanisms, but most remain uninvestigated. Our analysis points to several lncRNAs that likely participate in key aspects of V-SVZ stem cell activation and neurogenesis in health and disease.
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Affiliation(s)
- Jemima Becker
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Bin Sun
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Farah Alammari
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia,Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | | | - Keith W. Vance
- Department of Life Sciences, University of Bath, Bath, UK
| | - Francis George Szele
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.
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32
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Wen Z, He K, Zhan M, Li Y, Liu F, He X, Wei Y, Zhao W, Zhang Y, Xue Y, Xia Y, Wang F, Xia Z, Xin Y, Wu Y, Duan X, Xiao J, Shen F, Feng Y, Xiang G, Lu L. Distinct binding pattern of EZH2 and JARID2 on RNAs and DNAs in hepatocellular carcinoma development. Front Oncol 2022; 12:904633. [PMID: 36578923 PMCID: PMC9792092 DOI: 10.3389/fonc.2022.904633] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 09/14/2022] [Indexed: 12/14/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most malignant cancers worldwide, with high mortality. However, the molecular regulatory mechanisms of liver cancer, especially transcriptional and post-transcriptional mechanisms, should be further studied. Here we used chromatin and cross-linking immunoprecipitation with high throughput sequencing methods (ChIP-seq and CLIP-seq) to capture the global binding profiles on RNAs and DNAs of Enhancer of zeste homolog 2 (EZH2) and its partner Jumonji And AT-Rich Interaction Domain Containing 2 (JARID2) in liver carcinoma cell lines (HepG2) and normal liver cell line (THLE-2), respectively. We also integrated HCC transcriptome data from the TCGA to analyze the expression pattern of bound genes. We found that EZH2 and JARID2 both showed distinct binding profiles between HepG2 and THLE-2 cells. By binding to the primary RNAs, bound transcripts of EZH2 and JARID2 in HepG2 showed significantly increased transcriptional levels in HCC patients. By performing gene set enrichment analysis (GSEA), the bound transcripts were also highly related to HCC development. We also found EZH2 and JARID2 could specifically bind to several long noncoding RNAs (lncRNAs), including H19. By exploring the DNA binding profile, we detected a dramatically repressed DNA binding ability of EZH2 in HepG2 cells. We also found that the EZH2-bound genes showed slightly increased transcriptional levels in HepG2 cells. Integrating analysis of the RNA and DNA binding profiles suggests EZH2 and JARID2 shift their binding ability from DNA to RNA in HepG2 cells to promote cancer development in HCC. Our study provided a comprehensive and distinct binding profile on RNAs and DNAs of EZH2 and JARID2 in liver cancer cell lines, suggesting their potential novel functional manners to promote HCC development.
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Affiliation(s)
- Zhili Wen
- Department of Gastroenterology, Second Affiliated Hospital, Nanchang University, Nanchang, China
- Infectious Hospital, Nanchang University, Nanchang, China
| | - Ke He
- Department of General Surgery, Guangdong Second Provincial General Hospital, Guangzhou, China
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory of Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Meixiao Zhan
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Yong Li
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Fei Liu
- Department of General Surgery, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Xu He
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Yanli Wei
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory of Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Wei Zhao
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Yu Zhang
- Center for Genome Analysis, ABLife Inc., Wuhan, China
| | - Yaqiang Xue
- Center for Genome Analysis, ABLife Inc., Wuhan, China
- Laboratory of Human Health and Genome Regulation, ABLife Inc., Wuhan, China
| | - Yong Xia
- Department of Hepatic Surgery, The Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai, China
| | - Fenfen Wang
- Department of Gastroenterology, Second Affiliated Hospital, Nanchang University, Nanchang, China
| | - Zhenglin Xia
- Department of General Surgery, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Yongjie Xin
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Yeye Wu
- Department of Hepatic Surgery, The Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai, China
| | - Xiaopeng Duan
- Department of General Surgery, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Jing Xiao
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Feng Shen
- Department of Hepatic Surgery, The Eastern Hepatobiliary Surgery Hospital, Navy Medical University, Shanghai, China
| | - Yuliang Feng
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
| | - Guoan Xiang
- Department of General Surgery, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Ligong Lu
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, China
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Liang N, Cheng D, Zhao L, Lu H, Xu L, Bi Y. Identification of the Genes Encoding B3 Domain-Containing Proteins Related to Vernalization of Beta vulgaris. Genes (Basel) 2022; 13:genes13122217. [PMID: 36553484 PMCID: PMC9778101 DOI: 10.3390/genes13122217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
Vernalization is the process of exposure to low temperatures, which is crucial for the transition from vegetative to reproductive growth of plants. In this study, the global landscape vernalization-related mRNAs and long noncoding RNAs (lncRNAs) were identified in Beta vulgaris. A total of 22,159 differentially expressed mRNAs and 4418 differentially expressed lncRNAs were uncovered between the vernalized and nonvernalized samples. Various regulatory proteins, such as zinc finger CCCH domain-containing proteins, F-box proteins, flowering-time-related proteins FY and FPA, PHD finger protein EHD3 and B3 domain proteins were identified. Intriguingly, a novel vernalization-related lncRNA-mRNA target-gene co-expression regulatory network and the candidate vernalization genes, VRN1, VRN1-like, VAL1 and VAL2, encoding B3 domain-containing proteins were also unveiled. The results of this study pave the way for further illumination of the molecular mechanisms underlying the vernalization of B. vulgaris.
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Affiliation(s)
- Naiguo Liang
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian 223001, China
- Correspondence:
| | - Dayou Cheng
- School of Chemical Engineering and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Li Zhao
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian 223001, China
| | - Hedong Lu
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian 223001, China
| | - Lei Xu
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian 223001, China
| | - Yanhong Bi
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian 223001, China
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34
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Kim NS, Ringeling FR, Zhou Y, Nguyen HN, Temme SJ, Lin YT, Eacker S, Dawson VL, Dawson TM, Xiao B, Hsu KS, Canzar S, Li W, Worley P, Christian KM, Yoon KJ, Song H, Ming GL. CYFIP1 Dosages Exhibit Divergent Behavioral Impact via Diametric Regulation of NMDA Receptor Complex Translation in Mouse Models of Psychiatric Disorders. Biol Psychiatry 2022; 92:815-826. [PMID: 34247782 PMCID: PMC8568734 DOI: 10.1016/j.biopsych.2021.04.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 01/09/2023]
Abstract
BACKGROUND Gene dosage imbalance caused by copy number variations (CNVs) is a prominent contributor to brain disorders. In particular, 15q11.2 CNV duplications and deletions have been associated with autism spectrum disorder and schizophrenia, respectively. The mechanism underlying these diametric contributions remains unclear. METHODS We established both loss-of-function and gain-of-function mouse models of Cyfip1, one of four genes within 15q11.2 CNVs. To assess the functional consequences of altered CYFIP1 levels, we performed systematic investigations on behavioral, electrophysiological, and biochemical phenotypes in both mouse models. In addition, we utilized RNA immunoprecipitation sequencing (RIP-seq) analysis to reveal molecular targets of CYFIP1 in vivo. RESULTS Cyfip1 loss-of-function and gain-of function mouse models exhibited distinct and shared behavioral abnormalities related to autism spectrum disorder and schizophrenia. RIP-seq analysis identified messenger RNA targets of CYFIP1 in vivo, including postsynaptic NMDA receptor (NMDAR) complex components. In addition, these mouse models showed diametric changes in levels of postsynaptic NMDAR complex components at synapses because of dysregulated protein translation, resulting in bidirectional alteration of NMDAR-mediated signaling. Importantly, pharmacological balancing of NMDAR signaling in these mouse models with diametric Cyfip1 dosages rescues behavioral abnormalities. CONCLUSIONS CYFIP1 regulates protein translation of NMDAR and associated complex components at synapses to maintain normal synaptic functions and behaviors. Our integrated analyses provide insight into how gene dosage imbalance caused by CNVs may contribute to divergent neuropsychiatric disorders.
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Affiliation(s)
- Nam-Shik Kim
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Francisca Rojas Ringeling
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland; Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ying Zhou
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ha Nam Nguyen
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Stephanie J Temme
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yu-Ting Lin
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Stephen Eacker
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Valina L Dawson
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ted M Dawson
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Bo Xiao
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kuei-Sen Hsu
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Stefan Canzar
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Weidong Li
- Bio-X Institutes, Key Laboratory for the Genetics of Development and Neuropsychiatric Disorders, Shanghai Jiao Tong University, Shanghai, China
| | - Paul Worley
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kimberly M Christian
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ki-Jun Yoon
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Hongjun Song
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cell and Developmental Biology, Perelman School for Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Institute for Regenerative Medicine, Perelman School for Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Epigenetics Institute, Perelman School for Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Guo-Li Ming
- Department of Neuroscience, Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Cell and Developmental Biology, Perelman School for Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Institute for Regenerative Medicine, Perelman School for Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Psychiatry, Perelman School for Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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35
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Chao Y, Qin Y, Zou X, Wang X, Hu C, Xia F, Zou C. Promising therapeutic aspects in human genetic imprinting disorders. Clin Epigenetics 2022; 14:146. [PMID: 36371218 PMCID: PMC9655922 DOI: 10.1186/s13148-022-01369-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022] Open
Abstract
Genomic imprinting is an epigenetic phenomenon of monoallelic gene expression pattern depending on parental origin. In humans, congenital imprinting disruptions resulting from genetic or epigenetic mechanisms can cause a group of diseases known as genetic imprinting disorders (IDs). Genetic IDs involve several distinct syndromes sharing homologies in terms of genetic etiologies and phenotypic features. However, the molecular pathogenesis of genetic IDs is complex and remains largely uncharacterized, resulting in a lack of effective therapeutic approaches for patients. In this review, we begin with an overview of the genomic and epigenomic molecular basis of human genetic IDs. Notably, we address ethical aspects as a priority of employing emerging techniques for therapeutic applications in human IDs. With a particular focus, we delineate the current field of emerging therapeutics for genetic IDs. We briefly summarize novel symptomatic drugs and highlight the key milestones of new techniques and therapeutic programs as they stand today which can offer highly promising disease-modifying interventions for genetic IDs accompanied by various challenges.
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Affiliation(s)
- Yunqi Chao
- grid.13402.340000 0004 1759 700XDepartment of Endocrinology, The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052 Zhejiang China
| | - Yifang Qin
- grid.13402.340000 0004 1759 700XDepartment of Endocrinology, The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052 Zhejiang China
| | - Xinyi Zou
- grid.13402.340000 0004 1759 700XZhejiang University City College, Hangzhou, 310015 Zhejiang China
| | - Xiangzhi Wang
- grid.13402.340000 0004 1759 700XDepartment of Endocrinology, The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052 Zhejiang China
| | - Chenxi Hu
- grid.13402.340000 0004 1759 700XDepartment of Endocrinology, The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052 Zhejiang China
| | - Fangling Xia
- grid.13402.340000 0004 1759 700XDepartment of Endocrinology, The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052 Zhejiang China
| | - Chaochun Zou
- grid.13402.340000 0004 1759 700XDepartment of Endocrinology, The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052 Zhejiang China
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36
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Egan D, Moran B, Wilkinson M, Pinyol M, Guerra E, Gatius S, Matias-Guiu X, Kolch W, le Roux CW, Brennan DJ. CRABP2 - A novel biomarker for high-risk endometrial cancer. Gynecol Oncol 2022; 167:314-322. [PMID: 36163055 DOI: 10.1016/j.ygyno.2022.09.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/12/2022] [Accepted: 09/17/2022] [Indexed: 11/04/2022]
Abstract
OBJECTIVE Investigate the clinical and functional implications of elevated CRABP2 expression in endometrial cancer (EC) patients. METHODS Patients were stratified into high and low CRABP2 expression groups using a decision tree classifier. Univariate and multivariate statistical analyses determined the prognostic and clinicopathological consequences of increased CRABP2 expression. A CRABP2 gene signature was generated using differential expression analysis, and analyzed using network-based approaches. The findings were validated in The Clinical Proteomic Tumor Analysis Consortium (CPTAC), a newly generated cohort of 120 endometrial tissues, and The Cancer Dependency Map (DepMap). RESULTS 60 (11%) patients in TCGA had high CRABP2 expression, whilst 468 (89%) had low expression. High expression was associated with serous EC, reduced overall survival, advanced stage and grade. Downstream retinoic acid receptors (RARG and RARA) were correlated with CRABP2 expression and were associated with worse prognosis in serous EC. The CRABP2 gene signature was enriched for Polycomb target gene sets, and was regulated by ELP3 and BMP7. BMP7 expression was increased in the CRABP2-high group, was associated with worse prognosis, and CRISPR-Cas9 screens revealed correlations in its cell-fitness score with CRABP2 following gene knockout. The opposite was true for ELP3, suggesting opposing effects from both master regulators. CONCLUSIONS CRABP2 expression is associated with poor prognosis and advanced EC. The expression of RARA and RARG correlates with CRABP2 and are associated with worse prognosis in advanced histological subtypes. Polycomb target gene sets and two master regulators, ELP3 and BMP7, were identified as functionally relevant mechanisms driving aberrant CRABP2 expression.
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Affiliation(s)
- Donagh Egan
- Systems Biology Ireland, UCD School of Medicine, Belfield, Dublin 4, Ireland.
| | - Bruce Moran
- Department of Pathology, St. Vincent's University Hospital, Dublin, Ireland
| | - Michael Wilkinson
- Diabetes Complications Research Centre, Conway Institute, University College Dublin, Dublin, Ireland
| | - Miquel Pinyol
- Department of Pathology, Hospital Universitari Arnau de Vilanova, University of Lleida, IRBLLEIDA, CIBERONC, Spain
| | - Esther Guerra
- Department of Pathology, Hospital Universitari de Bellvitge, University of Barcelona, IDIBELL, Spain
| | - Sonia Gatius
- Department of Pathology, Hospital Universitari Arnau de Vilanova, University of Lleida, IRBLLEIDA, CIBERONC, Spain
| | - Xavier Matias-Guiu
- Department of Pathology, Hospital Universitari Arnau de Vilanova, University of Lleida, IRBLLEIDA, CIBERONC, Spain; Department of Pathology, Hospital Universitari de Bellvitge, University of Barcelona, IDIBELL, Spain
| | - Walter Kolch
- Systems Biology Ireland, UCD School of Medicine, Belfield, Dublin 4, Ireland; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Carel W le Roux
- Diabetes Complications Research Centre, Conway Institute, University College Dublin, Dublin, Ireland
| | - Donal J Brennan
- Systems Biology Ireland, UCD School of Medicine, Belfield, Dublin 4, Ireland
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Khyzha N, Henikoff S, Ahmad K. Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation. Nat Methods 2022; 19:1383-1392. [PMID: 36192462 PMCID: PMC9636022 DOI: 10.1038/s41592-022-01618-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022]
Abstract
Whereas techniques to map chromatin-bound proteins are well developed, mapping chromatin-associated RNAs remains a challenge. Here, we describe Reverse Transcribe and Tagment (RT&Tag), in which RNAs associated with a chromatin epitope are targeted by an antibody followed by a protein A-Tn5 transposome. Localized reverse transcription generates RNA/cDNA hybrids that are subsequently tagmented by Tn5 transposases for downstream sequencing. We demonstrate the utility of RT&Tag in Drosophila cells for capturing the noncoding RNA roX2 with the dosage compensation complex and maturing transcripts associated with silencing histone modifications. We also show that RT&Tag can detect N6-methyladenosine-modified mRNAs, and show that genes producing methylated transcripts are characterized by extensive promoter pausing of RNA polymerase II. The high efficiency of in situ antibody tethering and tagmentation makes RT&Tag especially suitable for rapid low-cost profiling of chromatin-associated RNAs.
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Affiliation(s)
- Nadiya Khyzha
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
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Navigating the Multiverse of Antisense RNAs: The Transcription- and RNA-Dependent Dimension. Noncoding RNA 2022; 8:ncrna8060074. [PMID: 36412909 PMCID: PMC9680235 DOI: 10.3390/ncrna8060074] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/21/2022] [Accepted: 10/23/2022] [Indexed: 12/14/2022] Open
Abstract
Evidence accumulated over the past decades shows that the number of identified antisense transcripts is continuously increasing, promoting them from transcriptional noise to real genes with specific functions. Indeed, recent studies have begun to unravel the complexity of the antisense RNA (asRNA) world, starting from the multidimensional mechanisms that they can exert in physiological and pathological conditions. In this review, we discuss the multiverse of the molecular functions of asRNAs, describing their action through transcription-dependent and RNA-dependent mechanisms. Then, we report the workflow and methodologies to study and functionally characterize single asRNA candidates.
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A comprehensive review of methods to study lncRNA-protein interactions in solution. Biochem Soc Trans 2022; 50:1415-1426. [PMID: 36250427 DOI: 10.1042/bst20220604] [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: 08/09/2022] [Revised: 09/10/2022] [Accepted: 09/27/2022] [Indexed: 11/17/2022]
Abstract
The long non-coding RNAs (lncRNAs) other than rRNA and tRNA were earlier assumed to be 'junk genomic material'. However, recent advancements in genomics methods have highlighted their roles not only in housekeeping but also in the progression of diseases like cancer as well as viral infections. lncRNAs owing to their length, have both short-range and long-range interactions resulting in complex folded structures that recruit various biomolecules enabling lncRNAs to undertake their various biological functions. Using cell lysate pull-down assays increasing number of lnRNAs-interacting proteins are being identified. These interactions can be further exploited to develop targeted novel therapeutic strategies to inhibit lncRNA-protein interactions. This review attempts to succinctly techniques that can identify and characterize the lnRNAs-protein interactions (i.e. affinity, stoichiometry, and thermodynamics). Furthermore, using other sophisticated biophysical techniques, one can also perform size estimations, and determine low-resolution structures. Since these methods study the biomolecules in solution, large-scale structural observations can be performed in real-time. This review attempts to briefly introduce the readers to biochemical and biophysical techniques, such that they can utilize these methods to obtain a holistic characterization of the biomolecules of interest. Additionally, it should be noted that the use of these methods is not limited to the characterization of the interacting molecules but can also be used to determine the efficacy of the therapeutic molecules to disrupt these interactions.
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Lv Y, Lu G, Cai Y, Su R, Liang L, Wang X, Mu W, He X, Huang T, Ma J, Zhao Y, Chen ZJ, Xue Y, Liu H, Chan WY. RBM46 is essential for gametogenesis and functions in post-transcriptional roles affecting meiotic cohesin subunits. Protein Cell 2022; 14:51-63. [PMID: 36726756 PMCID: PMC9871953 DOI: 10.1093/procel/pwac040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 08/21/2022] [Indexed: 02/04/2023] Open
Abstract
RBM46 is a germ cell-specific RNA-binding protein required for gametogenesis, but the targets and molecular functions of RBM46 remain unknown. Here, we demonstrate that RBM46 binds at specific motifs in the 3'UTRs of mRNAs encoding multiple meiotic cohesin subunits and show that RBM46 is required for normal synaptonemal complex formation during meiosis initiation. Using a recently reported, high-resolution technique known as LACE-seq and working with low-input cells, we profiled the targets of RBM46 at single-nucleotide resolution in leptotene and zygotene stage gametes. We found that RBM46 preferentially binds target mRNAs containing GCCUAU/GUUCGA motifs in their 3'UTRs regions. In Rbm46 knockout mice, the RBM46-target cohesin subunits displayed unaltered mRNA levels but had reduced translation, resulting in the failed assembly of axial elements, synapsis disruption, and meiotic arrest. Our study thus provides mechanistic insights into the molecular functions of RBM46 in gametogenesis and illustrates the power of LACE-seq for investigations of RNA-binding protein functions when working with low-abundance input materials.
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Affiliation(s)
| | | | | | | | - Liang Liang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xin Wang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Wenyu Mu
- Center for Reproductive Medicine, Shandong University, Jinan 250012, China,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan 250012, China
| | - Xiuqing He
- Center for Reproductive Medicine, Shandong University, Jinan 250012, China,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan 250012, China
| | - Tao Huang
- Center for Reproductive Medicine, Shandong University, Jinan 250012, China,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan 250012, China
| | - Jinlong Ma
- Center for Reproductive Medicine, Shandong University, Jinan 250012, China,CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan 250012, China
| | - Yueran Zhao
- Shandong Key Laboratory of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250012, China,Center for Reproductive Medicine, Shandong University, Jinan 250012, China,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan 250012, China
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Hernández-Romero IA, Valdes VJ. De Novo Polycomb Recruitment and Repressive Domain Formation. EPIGENOMES 2022; 6:25. [PMID: 35997371 PMCID: PMC9397058 DOI: 10.3390/epigenomes6030025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/15/2022] [Accepted: 08/18/2022] [Indexed: 11/29/2022] Open
Abstract
Every cell of an organism shares the same genome; even so, each cellular lineage owns a different transcriptome and proteome. The Polycomb group proteins (PcG) are essential regulators of gene repression patterning during development and homeostasis. However, it is unknown how the repressive complexes, PRC1 and PRC2, identify their targets and elicit new Polycomb domains during cell differentiation. Classical recruitment models consider the pre-existence of repressive histone marks; still, de novo target binding overcomes the absence of both H3K27me3 and H2AK119ub. The CpG islands (CGIs), non-core proteins, and RNA molecules are involved in Polycomb recruitment. Nonetheless, it is unclear how de novo targets are identified depending on the physiological context and developmental stage and which are the leading players stabilizing Polycomb complexes at domain nucleation sites. Here, we examine the features of de novo sites and the accessory elements bridging its recruitment and discuss the first steps of Polycomb domain formation and transcriptional regulation, comprehended by the experimental reconstruction of the repressive domains through time-resolved genomic analyses in mammals.
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Affiliation(s)
| | - Victor Julian Valdes
- Department of Cell Biology and Development, Institute of Cellular Physiology (IFC), National Autonomous University of Mexico (UNAM), Mexico City 04510, Mexico
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Li J, Yu D, Wang J, Li C, Wang Q, Wang J, Du W, Zhao S, Pang Y, Hao H, Zhao X, Zhu H, Li S, Zou H. Identification of the porcine IG-DMR and abnormal imprinting of DLK1-DIO3 in cloned pigs. Front Cell Dev Biol 2022; 10:964045. [PMID: 36036009 PMCID: PMC9400927 DOI: 10.3389/fcell.2022.964045] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/12/2022] [Indexed: 11/19/2022] Open
Abstract
Correct reprogramming of the DLK1-DIO3 imprinted region is critical for the development of cloned animals. However, in pigs, the imprinting and regulation of the DLK1-DIO3 region has not been systematically analyzed. The objective of this study was to investigate the imprinting status and methylation regulation of the DLK1-DIO3 region in wild-type and cloned neonatal pigs. We mapped the imprinting control region, IG-DMR, by homologous alignment and validated it in sperm, oocytes, fibroblasts, and parthenogenetic embryos. Subsequently, single nucleotide polymorphism-based sequencing and bisulfite sequencing polymerase chain reaction were conducted to analyze imprinting and methylation in different types of fibroblasts, as well as wild-type and cloned neonatal pigs. The results showed that Somatic cell nuclear transfer (SCNT) resulted in hypermethylation of the IG-DMR and aberrant gene expression in the DLK1-DIO3 region. Similar to wild-type pigs, imprinted expression and methylation were observed in the surviving cloned pigs, whereas in dead cloned pigs, the IG-DMR was hypermethylated and the expression of GTL2 was nearly undetectable. Our study reveals that abnormal imprinting of the DLK1-DIO3 region occurs in cloned pigs, which provides a theoretical basis for improving the cloning efficiency by gene editing to correct abnormal imprinting.
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Affiliation(s)
- Junliang Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Life Sciences, Hebei Agricultural University, Baoding, Hebei, China
| | - Dawei Yu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Germplasm Center of Domestic Animal Resources, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Dawei Yu, ; Huabin Zhu, ; Shijie Li, ; Huiying Zou,
| | - Jing Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Chongyang Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qingwei Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jing Wang
- Department of Human Genetics David Geffen School of Medicine University of California Los Angeles, Los Angeles, CA, United States
| | - Weihua Du
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shanjiang Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunwei Pang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haisheng Hao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xueming Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huabin Zhu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Dawei Yu, ; Huabin Zhu, ; Shijie Li, ; Huiying Zou,
| | - Shijie Li
- College of Life Sciences, Hebei Agricultural University, Baoding, Hebei, China
- *Correspondence: Dawei Yu, ; Huabin Zhu, ; Shijie Li, ; Huiying Zou,
| | - Huiying Zou
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Dawei Yu, ; Huabin Zhu, ; Shijie Li, ; Huiying Zou,
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Vicente-García C, Hernández-Camacho JD, Carvajal JJ. Regulation of myogenic gene expression. Exp Cell Res 2022; 419:113299. [DOI: 10.1016/j.yexcr.2022.113299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 12/22/2022]
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Severgnini M, D’Angiò M, Bungaro S, Cazzaniga G, Cifola I, Fazio G. Conjoined Genes as Common Events in Childhood Acute Lymphoblastic Leukemia. Cancers (Basel) 2022; 14:cancers14143523. [PMID: 35884588 PMCID: PMC9315513 DOI: 10.3390/cancers14143523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 07/15/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Acute lymphoblastic leukemia (ALL) is the most frequent childhood cancer. In recent years, broad application of NGS technologies enabled the discovery of novel genomically defined ALL. In this study, as a proof-of-principle, we applied RNA-seq technology to comprehensively profile the transcriptional landscape of a collection of 10 childhood BCP-ALL cases, and performed a deep bioinformatics analysis including several publicly available datasets, in order to characterize their full spectrum of transcriptional events. The paired-end RNA sequencing of our BCP-ALL pediatric cohort revealed a total of 9001 raw fusion events, which, after filtering, resulted in 245 candidate fusions. Overall, 235 out of 245 events were intra-chromosomal fusions, among which 229 involved two contiguous or overlapping genes, also known as conjoined genes (CGs). Among them, we identified a subset of 14 CGs (6.1%) exclusively expressed in leukemic cases but neither in solid cancers nor in normal samples. These events could be suggestive of a novel mechanism of transcriptional regulation in childhood leukemia and may represent novel potential leukemia-specific biomarkers. Abstract Acute lymphoblastic leukemia (ALL) is the most frequent childhood cancer. For the last three decades, conventional cytogenetic and molecular approaches allowed the identification of genetic abnormalities having prognostic and therapeutic relevance. Although the current cure rate in pediatric B cell acute leukemia is approximately 90%, it remains one of the leading causes of mortality in childhood. Furthermore, in the contemporary protocols, chemotherapy intensity was raised to the maximal levels of tolerability, and further improvements in the outcome will depend on the characterization and reclassification of the disease, as well as on the development of new targeted drugs. The recent technological advances in genome-wide profiling techniques have allowed the exploration of the molecular heterogeneity of this disease, even though some potentially interesting biomarkers such as conjoined genes have not been deeply investigated yet. In the present study, we performed the transcriptome sequencing (RNA-seq) of 10 pediatric B cell precursor (BCP)-ALL cases with different risk (four standard- and six high-risk patients) enrolled in the Italian AIEOP-BFM ALL2000 protocol, in order to characterize the full spectrum of transcriptional events and to identify novel potential genetic mechanisms sustaining their different early response to therapy. Total RNA was extracted from primary leukemic blasts and RNA-seq was performed by Illumina technology. Bioinformatics analysis focused on fusion transcripts, originated from either inter- or intra-chromosomal structural rearrangements. Starting from a raw list of 9001 candidate events, by employing a custom-made bioinformatics pipeline, we obtained a short list of 245 candidate fusions. Among them, 10 events were compatible with chromosomal translocations. Strikingly, 235/245 events were intra-chromosomal fusions, 229 of which involved two contiguous or overlapping genes, resulting in the so-called conjoined genes (CGs). To explore the specificity of these events in leukemia, we performed an extensive bioinformatics meta-analysis and evaluated the presence of the fusions identified in our 10 BCP-ALL cohort in several other publicly available RNA-seq datasets, including leukemic, solid tumor and normal sample collections. Overall, 14/229 (6.1%) CGs were found to be exclusively expressed in leukemic cases, suggesting an association between CGs and leukemia. Moreover, CGs were found to be common events both in standard- and high-risk BCP-ALL patients and it might be suggestive of a novel potential transcriptional regulation mechanism active in leukemic cells.
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Affiliation(s)
- Marco Severgnini
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, 20054 Milano, Italy; (M.S.); (I.C.)
| | - Mariella D’Angiò
- School of Medicine and Surgery, Università degli Studi di Milano Bicocca, 20126 Milano, Italy;
- Tettamanti Research Center, University of Milan Bicocca, 20900 Monza, Italy;
| | - Silvia Bungaro
- Ospedale San Gerardo, Fondazione Monza e Brianza per il Bambino e la sua Mamma (MBBM), 20900 Monza, Italy;
| | - Giovanni Cazzaniga
- School of Medicine and Surgery, Università degli Studi di Milano Bicocca, 20126 Milano, Italy;
- Tettamanti Research Center, University of Milan Bicocca, 20900 Monza, Italy;
- Correspondence: ; Tel.: +39-039-233-3661
| | - Ingrid Cifola
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, 20054 Milano, Italy; (M.S.); (I.C.)
| | - Grazia Fazio
- Tettamanti Research Center, University of Milan Bicocca, 20900 Monza, Italy;
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Liu R, Han M, Liu X, Yu K, Bai X, Dong Y. Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Longissimus dorsi Skeletal Muscle of Shandong Black Cattle and Luxi Cattle. Front Genet 2022; 13:849399. [PMID: 35651943 PMCID: PMC9149217 DOI: 10.3389/fgene.2022.849399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/08/2022] [Indexed: 12/27/2022] Open
Abstract
There is an increasing understanding of the possible regulatory role of long non-coding RNAs (LncRNA). Studies on livestock have mainly focused on the regulation of cell differentiation, fat synthesis, and embryonic development. However, there has been little study of skeletal muscle of domestic animals and the potential role of lncRNA. In this study, the transcriptome numbers of longissimus muscle of different beef cattle (Shandong black catle and Luxi catlle) were used to construct muscle related lncRNAs-miRNA-mRNA interaction network through bioinformatics analysis. This is helpful to clarify the molecular mechanism of bovine muscle development, and can be used to promote animal husbandry and improve animal husbandry production. According to the screening criteria of |FC|≧2 and q < 0.05, a total of 1,415 transcripts (of which 480 were LncRNAs) were differentially expressed (q < 0.05) in the different breeds. Further, we found that the most differentially expressed LncRNAs were found on chromosome 9, in which the differentially expressed LncRNAs targeted 1,164 protein coding genes (MYORG, Wnt4, PAK1, ADCY7,etc) (upstream and downstream<50 Kb). In addition, Pearson’s correlation coefficients of co-expression levels indicated a potential trans regulatory relationship between the differentially expressed LncRNAs and 43844 mRNAs (r > 0.9). The identified co-expressed mRNAs (MYORG, Dll1, EFNB2, SOX6, MYOCD, and MYLK3) are related to the formation of muscle structure, and enriched in muscle system process, strained muscle cell differentiation, muscle cell development, striated muscle tissue development, calcium signaling, and AMPK signaling. Additionally, we also found that some LncRNAs (LOC112444238, LOC101903367, LOC104975788, LOC112441863, LOC112449549, and LOC101907194) may interact with miRNAs related to cattle muscle growth and development. Based on this, we constructed a LncRNAs-miRNA-mRNA interaction network as the putative basis for biological regulation in cattle skeletal muscle. Interestingly, a candidate differential LncRNA (LOC104975788) and a protein-coding gene (Pax7) contain miR-133a binding sites and binding was confirmed by luciferase reporter assay. LOC104975788 may combined miR-133a competitively with Pax7, thus relieving the inhibitory effect of miR-133a on Pax7 to regulate skeletal muscle development. These results will provide the theoretical basis for further study of LncRNA regulation and activity in different cattle breeds.
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Affiliation(s)
- Ruili Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Mingxuan Han
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Xianxun Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Kun Yu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Xuejin Bai
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China.,Laboratory of Animal Molecular Shandong Black Cattle Breeding Engineering Technology Center, College of Animal Science, Qingdao Agricultural University, Qingdao, China
| | - Yajuan Dong
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China.,Laboratory of Animal Molecular Shandong Black Cattle Breeding Engineering Technology Center, College of Animal Science, Qingdao Agricultural University, Qingdao, China
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Cao L, Luo Y, Guo X, Liu S, Li S, Li J, Zhang Z, Zhao Y, Zhang Q, Gao F, Ji X, Gao X, Li Y, You F. SAFA facilitates chromatin opening of immune genes through interacting with anti-viral host RNAs. PLoS Pathog 2022; 18:e1010599. [PMID: 35658050 PMCID: PMC9200321 DOI: 10.1371/journal.ppat.1010599] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 06/15/2022] [Accepted: 05/17/2022] [Indexed: 12/19/2022] Open
Abstract
Regulation of chromatin structure and accessibility determines the transcription activities of genes, which endows the host with function-specific patterns of gene expression. Upon viral infection, the innate immune responses provide the first line of defense, allowing rapid production of variegated antiviral cytokines. Knowledge on how chromatin accessibility is regulated during host defense against viral infection remains limited. Our previous work found that the nuclear matrix protein SAFA surveilled viral RNA and regulated antiviral immune genes expression. However, how SAFA regulates the specific induction of antiviral immune genes remains unknown. Here, through integration of RNA-seq, ATAC-seq and ChIP-seq assays, we found that the depletion of SAFA specifically decreased the chromatin accessibility, activation and expression of virus induced genes. And mutation assays suggested that the RNA-binding ability of SAFA was essential for its function in regulating antiviral chromatin accessibility. RIP-seq results showed that SAFA exclusively bound with antiviral related RNAs following viral infection. Further, we combined the CRISPR-Cas13d mediated RNA knockdown system with ATAC-qPCR, and demonstrated that the binding between SAFA and according antiviral RNAs specifically mediated the openness of the corresponding chromatin and following robust transcription of antiviral genes. Moreover, knockdown of these associated RNAs dampened the accessibility of related genes in an extranuclear signaling pathway dependent manner. Interestingly, VSV infection cleaved SAFA protein at the C-terminus which deprived its RNA binding ability for immune evasion. Thus, our results demonstrated that SAFA and the interacting RNA products collaborated and remodeled chromatin accessibility to facilitate antiviral innate immune responses. Regulation of chromatin opening and gene expression underlies a key point during host defense against viral infection, which endows the host with timely and effective antiviral gene expression patterns. We previously reported that the nuclear matrix protein SAFA surveils viral RNA and regulates antiviral immune genes expression. However, how SAFA regulates the expression and what determines the specific induction of antiviral immune genes remains unclear. Here, we used a combination of high-throughput sequencing technologies and found that SAFA and the interacting RNA products collaborated and specifically remodeled chromatin accessibility to facilitate antiviral immune genes expression. We also found that VSV infection cleaved SAFA protein at the C-terminus and deprived its RNA binding ability for immune evasion. Our study provides new insights into the mechanism by which chromatin remodeling facilitates the induction of antiviral immune genes.
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Affiliation(s)
- Lili Cao
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Yujie Luo
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
| | - Xuefei Guo
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
| | - Shengde Liu
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing, China
| | - Siji Li
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
| | - Junhong Li
- CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Zeming Zhang
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
| | - Yingchi Zhao
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
| | - Qiao Zhang
- School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Feng Gao
- School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xiang Gao
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, School of life science, Shandong University, Qingdao, China
| | - Yunfei Li
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
- * E-mail: (YL); (FY)
| | - Fuping You
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
- * E-mail: (YL); (FY)
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Dong X, Chen K, Chen W, Wang J, Chang L, Deng J, Wei L, Han L, Huang C, He C. circRIP: an accurate tool for identifying circRNA-RBP interactions. Brief Bioinform 2022; 23:6596315. [PMID: 35641157 DOI: 10.1093/bib/bbac186] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/07/2022] [Accepted: 04/23/2022] [Indexed: 12/25/2022] Open
Abstract
Circular ribonucleic acids (RNAs) (circRNAs) are formed by covalently linking the downstream splice donor and the upstream splice acceptor. One of the most important functions of circRNAs is mainly exerted through binding RNA-binding proteins (RBPs). However, there is no efficient algorithm for identifying genome-wide circRNA-RBP interactions. Here, we developed a unique algorithm, circRIP, for identifying circRNA-RBP interactions from RNA immunoprecipitation sequencing (RIP-Seq) data. A simulation test demonstrated the sensitivity and specificity of circRIP. By applying circRIP, we identified 95 IGF2BP3-binding circRNAs based on the IGF2BP3 RIP-Seq dataset. We further identified 2823 and 1333 circRNAs binding to >100 RBPs in K562 and HepG2 cell lines, respectively, based on enhanced cross-linking immunoprecipitation (eCLIP) data, demonstrating the significance to survey the potential interactions between circRNAs and RBPs. In this study, we provide an accurate and sensitive tool, circRIP (https://github.com/bioinfolabwhu/circRIP), to systematically identify RBP and circRNA interactions from RIP-Seq and eCLIP data, which can significantly benefit the research community for the functional exploration of circRNAs.
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Affiliation(s)
- Xin Dong
- School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Ke Chen
- Department of Urology,Tongji Hospital, Tongji Medical College,Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Wenbo Chen
- School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Jun Wang
- School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Liuping Chang
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
| | - Jin Deng
- School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Lei Wei
- School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Leng Han
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - Chunhua Huang
- College of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Key Laboratory of Traditional Chinese Medicine Toxicology in Forensic Medicine, Guizhou Education Department, Guiyang 550025, China
| | - Chunjiang He
- School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China.,College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China
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The Disordered EZH2 Loop: Atomic Level Characterization by 1H N- and 1H α-Detected NMR Approaches, Interaction with the Long Noncoding HOTAIR RNA. Int J Mol Sci 2022; 23:ijms23116150. [PMID: 35682829 PMCID: PMC9181245 DOI: 10.3390/ijms23116150] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 02/06/2023] Open
Abstract
The 96-residue-long loop of EZH2 is proposed to play a role in the interaction with long non-coding RNAs (lncRNAs) and to contribute to EZH2 recruitment to the chromatin. However, molecular details of RNA recognition have not been described so far. Cellular studies have suggested that phosphorylation of the Thr345 residue localized in this loop influences RNA binding; however, no mechanistic explanation has been offered. To address these issues, a systematic NMR study was performed. As the 1HN-detected NMR approach presents many challenges under physiological conditions, our earlier developed, as well as improved, 1Hα-detected experiments were used. As a result of the successful resonance assignment, the obtained chemical shift values indicate the highly disordered nature of the EZH2 loop, with some nascent helical tendency in the Ser407–Ser412 region. Further investigations conducted on the phosphomimetic mutant EZH2T345D showed that the mutation has only a local effect, and that the loop remains disordered. On the other hand, the mutation influences the cis/trans Pro346 equilibrium. Interactions of both the wild-type and the phosphomimetic mutant with the lncRNA HOTAIR140 (1–140 nt) highlight that the Thr367–Ser375 region is affected. This segment does not resemble any of the previously reported RNA-binding motifs, therefore the identified binding region is unique. As no structural changes occur in the EZH2 loop upon RNA binding, we can consider the protein–RNA interaction as a “fuzzy” complex.
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50
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Kojima S, Shiochi N, Sato K, Yamaura M, Ito T, Yamamura N, Goto N, Odamoto M, Kobayashi S, Kimura T, Sekita Y. Epigenome editing reveals core DNA methylation for imprinting control in the Dlk1-Dio3 imprinted domain. Nucleic Acids Res 2022; 50:5080-5094. [PMID: 35544282 PMCID: PMC9122602 DOI: 10.1093/nar/gkac344] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/03/2022] [Accepted: 04/24/2022] [Indexed: 11/12/2022] Open
Abstract
The Dlk1-Dio3 imprinted domain is controlled by an imprinting control region (ICR) called IG-DMR that is hypomethylated on the maternal allele and hypermethylated on the paternal allele. Although several genetic mutation experiments have shown that IG-DMR is essential for imprinting control of the domain, how DNA methylation itself functions has not been elucidated. Here, we performed both gain and loss of DNA methylation experiments targeting IG-DMR by transiently introducing CRISPR/Cas9 based-targeted DNA methylation editing tools along with one guide RNA into mouse ES cells. Altered DNA methylation, particularly at IG-DMR-Rep, which is a tandem repeat containing ZFP57 methylated DNA-binding protein binding motifs, affected the imprinting state of the whole domain, including DNA methylation, imprinted gene expression, and histone modifications. Moreover, the altered imprinting states were persistent through neuronal differentiation. Our results suggest that the DNA methylation state at IG-DMR-Rep, but not other sites in IG-DMR, is a master element to determine whether the allele behaves as the intrinsic maternal or paternal allele. Meanwhile, this study provides a robust strategy and methodology to study core DNA methylation in cis-regulatory elements, such as ICRs and enhancers.
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Affiliation(s)
- Shin Kojima
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Naoya Shiochi
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Kazuki Sato
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Mamiko Yamaura
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Toshiaki Ito
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Nodoka Yamamura
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Naoki Goto
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Mika Odamoto
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Shin Kobayashi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koutou-ku, Tokyo 135-0064, Japan
| | - Tohru Kimura
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Yoichi Sekita
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
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