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Hu K, Ni P, Xu M, Zou Y, Chang J, Gao X, Li Y, Ruan J, Hu B, Wang J. HiTE: a fast and accurate dynamic boundary adjustment approach for full-length transposable element detection and annotation. Nat Commun 2024; 15:5573. [PMID: 38956036 PMCID: PMC11219922 DOI: 10.1038/s41467-024-49912-8] [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: 07/09/2023] [Accepted: 06/25/2024] [Indexed: 07/04/2024] Open
Abstract
Recent advancements in genome assembly have greatly improved the prospects for comprehensive annotation of Transposable Elements (TEs). However, existing methods for TE annotation using genome assemblies suffer from limited accuracy and robustness, requiring extensive manual editing. In addition, the currently available gold-standard TE databases are not comprehensive, even for extensively studied species, highlighting the critical need for an automated TE detection method to supplement existing repositories. In this study, we introduce HiTE, a fast and accurate dynamic boundary adjustment approach designed to detect full-length TEs. The experimental results demonstrate that HiTE outperforms RepeatModeler2, the state-of-the-art tool, across various species. Furthermore, HiTE has identified numerous novel transposons with well-defined structures containing protein-coding domains, some of which are directly inserted within crucial genes, leading to direct alterations in gene expression. A Nextflow version of HiTE is also available, with enhanced parallelism, reproducibility, and portability.
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Affiliation(s)
- Kang Hu
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Xiangjiang Laboratory, Changsha, 410205, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China
| | - Peng Ni
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Xiangjiang Laboratory, Changsha, 410205, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China
| | - Minghua Xu
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China
| | - You Zou
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China
| | - Jianye Chang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Xin Gao
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Center of Excellence on Smart Health, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Yaohang Li
- Department of Computer Science, Old Dominion University, Norfolk, VA, 23529, USA
| | - Jue Ruan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Bin Hu
- Key Laboratory of Brain Health Intelligent Evaluation and Intervention, Ministry of Education (Beijing Institute of Technology), Beijing, P. R. China.
- School of Medical Technology, Beijing Institute of Technology, Beijing, P. R. China.
| | - Jianxin Wang
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China.
- Xiangjiang Laboratory, Changsha, 410205, China.
- Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, 410083, China.
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2
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Feng C, Tie R, Xin S, Chen Y, Li S, Chen Y, Hu X, Zhou Y, Liu Y, Hu Y, Hu Y, Pan H, Wu Z, Chao H, Zhang S, Ni Q, Huang J, Luo W, Huang H, Chen M. Systematic single-cell analysis reveals dynamic control of transposable element activity orchestrating the endothelial-to-hematopoietic transition. BMC Biol 2024; 22:143. [PMID: 38937802 PMCID: PMC11209969 DOI: 10.1186/s12915-024-01939-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 06/14/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND The endothelial-to-hematopoietic transition (EHT) process during definitive hematopoiesis is highly conserved in vertebrates. Stage-specific expression of transposable elements (TEs) has been detected during zebrafish EHT and may promote hematopoietic stem cell (HSC) formation by activating inflammatory signaling. However, little is known about how TEs contribute to the EHT process in human and mouse. RESULTS We reconstructed the single-cell EHT trajectories of human and mouse and resolved the dynamic expression patterns of TEs during EHT. Most TEs presented a transient co-upregulation pattern along the conserved EHT trajectories, coinciding with the temporal relaxation of epigenetic silencing systems. TE products can be sensed by multiple pattern recognition receptors, triggering inflammatory signaling to facilitate HSC emergence. Interestingly, we observed that hypoxia-related signals were enriched in cells with higher TE expression. Furthermore, we constructed the hematopoietic cis-regulatory network of accessible TEs and identified potential TE-derived enhancers that may boost the expression of specific EHT marker genes. CONCLUSIONS Our study provides a systematic vision of how TEs are dynamically controlled to promote the hematopoietic fate decisions through transcriptional and cis-regulatory networks, and pre-train the immunity of nascent HSCs.
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Affiliation(s)
- Cong Feng
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Bioinformatics Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Ruxiu Tie
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 310058, China
- Institute of Hematology, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou, 310058, China
- Department of Hematology, The Second Clinical Medical College of Shanxi Medical University, Shanxi Medical University, Taiyuan, 030000, China
- Department of Hematology-Oncology, Taizhou Hospital of Zhejiang Province, Linhai, 317000, China
| | - Saige Xin
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yuhao Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Sida Li
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yifan Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiaotian Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yincong Zhou
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yongjing Liu
- Bioinformatics Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Yueming Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yanshi Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hang Pan
- Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, 310058, China
| | - Zexu Wu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Haoyu Chao
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shilong Zhang
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qingyang Ni
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jinyan Huang
- Bioinformatics Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Wenda Luo
- Department of Hematology-Oncology, Taizhou Hospital of Zhejiang Province, Linhai, 317000, China.
| | - He Huang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 310058, China.
- Institute of Hematology, Zhejiang University, Hangzhou, 310058, China.
- Zhejiang Province Engineering Laboratory for Stem Cell and Immunity Therapy, Hangzhou, 310058, China.
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
- Bioinformatics Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
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3
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Zhao C, Bian C, Mu X, Zhang X, Shi Q. Gonadal transcriptome sequencing reveals sexual dimorphism in expression profiling of sex-related genes in Asian arowana ( Scleropages formosus). Front Genet 2024; 15:1381832. [PMID: 38666292 PMCID: PMC11043485 DOI: 10.3389/fgene.2024.1381832] [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: 02/05/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
Asia arowana (Scleropages formosus) is an ornamental fish with high economic value, while its sex determination mechanism is still poorly understood. By far, no morphological evidence or molecular marker has been developed for effective distinguishment of genders, which poses a critical challenge to our captive breeding efforts. In this study, we sequenced gonadal transcriptomes of adult Asian arowanas and revealed differential expression profiling of sex-related genes. Based on the comparative transcriptomics analysis of testes (n = 3) and ovaries (n = 3), we identified a total of 8,872 differentially expressed genes (DEGs) and 18,490 differentially expressed transposable elements (TEs) between male and female individuals. Interestingly, the expression of TEs usually has been more significantly testis-biased than related coding genes. As expected, several genes related to females (such as foxl2 and cyp19a1a) are significantly transcribed in the ovary, and some genes related to male gonad development (such as dmrt1, gsdf and amh) are highly expressed in the testis. This sexual dimorphism is valuable for ascertaining the differential expression patterns of sex-related genes and enriching the genetic resources of this economically important species. These valuable genetic materials thereby provide instructive references for gender identification and one-to-one breeding practices so as to expand fish numbers for a rapid elevation of economic value.
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Affiliation(s)
- Chenxi Zhao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, China
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, China
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Xidong Mu
- Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Xinhui Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, China
| | - Qiong Shi
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, China
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
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Almeida MV, Blumer M, Yuan CU, Sierra P, Price JL, Quah FX, Friman A, Dallaire A, Vernaz G, Putman ALK, Smith AM, Joyce DA, Butter F, Haase AD, Durbin R, Santos ME, Miska EA. Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587621. [PMID: 38617250 PMCID: PMC11014572 DOI: 10.1101/2024.04.01.587621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. Here, we describe dynamic patterns of TE expression in African cichlid gonads and during early development. Orthology inference revealed an expansion of piwil1 genes in Lake Malawi cichlids, likely driven by PiggyBac TEs. The expanded piwil1 copies have signatures of positive selection and retain amino acid residues essential for catalytic activity. Furthermore, the gonads of African cichlids express a Piwi-interacting RNA (piRNA) pathway that target TEs. We define the genomic sites of piRNA production in African cichlids and find divergence in closely related species, in line with fast evolution of piRNA-producing loci. Our findings suggest dynamic co-evolution of TEs and host silencing pathways in the African cichlid radiations. We propose that this co-evolution has contributed to cichlid genomic diversity.
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Affiliation(s)
- Miguel Vasconcelos Almeida
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Moritz Blumer
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- These authors contributed equally
| | - Chengwei Ulrika Yuan
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- These authors contributed equally
| | - Pío Sierra
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Jonathan L. Price
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Fu Xiang Quah
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Aleksandr Friman
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Biophysics Graduate Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA
| | - Alexandra Dallaire
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Comparative Fungal Biology, Royal Botanic Gardens Kew, Jodrell Laboratory, Richmond TW9 3DS, UK
| | - Grégoire Vernaz
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- Present address: Zoological Institute, Department of Environmental Sciences, University of Basel, Vesalgasse 1, Basel, 4051, Switzerland
| | - Audrey L. K. Putman
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Alan M. Smith
- School of Natural Sciences, University of Hull, Hull, HU6 7RX, UK
| | - Domino A. Joyce
- School of Natural Sciences, University of Hull, Hull, HU6 7RX, UK
| | - Falk Butter
- Institute of Molecular Biology (IMB), Quantitative Proteomics, Ackermannweg 4, Mainz, 55128, Germany
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institute, Südufer, Greifswald, 17493, Germany
| | - Astrid D. Haase
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - M. Emília Santos
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Eric A. Miska
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
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Jiang T, Zhou ZM, Ling ZQ, Zhang Q, Wu ZZ, Yang JW, Yang SY, Yang B, Huang LS. Pig H3K4me3, H3K27ac, and gene expression profiles reveal reproductive tissue-specific activity of transposable elements. Zool Res 2024; 45:138-151. [PMID: 38155423 PMCID: PMC10839656 DOI: 10.24272/j.issn.2095-8137.2023.060] [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: 08/08/2023] [Accepted: 09/04/2023] [Indexed: 12/30/2023] Open
Abstract
Regulatory sequences and transposable elements (TEs) account for a large proportion of the genomic sequences of species; however, their roles in gene transcription, especially tissue-specific expression, remain largely unknown. Pigs serve as an excellent animal model for studying genomic sequence biology due to the extensive diversity among their wild and domesticated populations. Here, we conducted an integrated analysis using H3K27ac ChIP-seq, H3K4me3 ChIP-seq, and RNA-seq data from 10 different tissues of seven fetuses and eight closely related adult pigs. We aimed to annotate the regulatory elements and TEs to elucidate their associations with histone modifications and mRNA expression across different tissues and developmental stages. Based on correlation analysis between mRNA expression and H3K27ac and H3K4me3 peak activity, results indicated that H3K27ac exhibited stronger associations with gene expression than H3K4me3. Furthermore, 1.45% of TEs overlapped with either the H3K27ac or H3K4me3 peaks, with the majority displaying tissue-specific activity. Notably, a TE subfamily (LTR4C_SS), containing binding motifs for SIX1 and SIX4, showed specific enrichment in the H3K27ac peaks of the adult and fetal ovaries. RNA-seq analysis also revealed widespread expression of TEs in the exons or promoters of genes, including 4 688 TE-containing transcripts with distinct development stage-specific and tissue-specific expression. Of note, 1 967 TE-containing transcripts were enriched in the testes. We identified a long terminal repeat (LTR), MLT1F1, acting as a testis-specific alternative promoter in SRPK2 (a cell cycle-related protein kinase) in our pig dataset. This element was also conserved in humans and mice, suggesting either an ancient integration of TEs in genes specifically expressed in the testes or parallel evolutionary patterns. Collectively, our findings demonstrate that TEs are deeply embedded in the genome and exhibit important tissue-specific biological functions, particularly in the reproductive organs.
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Affiliation(s)
- Tao Jiang
- National Key Laboratory of Pig Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Zhi-Min Zhou
- National Key Laboratory of Pig Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Zi-Qi Ling
- National Key Laboratory of Pig Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Qing Zhang
- National Key Laboratory of Pig Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Zhong-Zi Wu
- National Key Laboratory of Pig Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Jia-Wen Yang
- National Key Laboratory of Pig Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Si-Yu Yang
- National Key Laboratory of Pig Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Bin Yang
- National Key Laboratory of Pig Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China. E-mail:
| | - Lu-Sheng Huang
- National Key Laboratory of Pig Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China. E-mail:
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Gebrie A. Transposable elements as essential elements in the control of gene expression. Mob DNA 2023; 14:9. [PMID: 37596675 PMCID: PMC10439571 DOI: 10.1186/s13100-023-00297-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/08/2023] [Indexed: 08/20/2023] Open
Abstract
Interspersed repetitions called transposable elements (TEs), commonly referred to as mobile elements, make up a significant portion of the genomes of higher animals. TEs contribute in controlling the expression of genes locally and even far away at the transcriptional and post-transcriptional levels, which is one of their significant functional effects on gene function and genome evolution. There are different mechanisms through which TEs control the expression of genes. First, TEs offer cis-regulatory regions in the genome with their inherent regulatory features for their own expression, making them potential factors for controlling the expression of the host genes. Promoter and enhancer elements contain cis-regulatory sites generated from TE, which function as binding sites for a variety of trans-acting factors. Second, a significant portion of miRNAs and long non-coding RNAs (lncRNAs) have been shown to have TEs that encode for regulatory RNAs, revealing the TE origin of these RNAs. Furthermore, it was shown that TE sequences are essential for these RNAs' regulatory actions, which include binding to the target mRNA. By being a member of cis-regulatory and regulatory RNA sequences, TEs therefore play essential regulatory roles. Additionally, it has been suggested that TE-derived regulatory RNAs and cis-regulatory regions both contribute to the evolutionary novelty of gene regulation. Additionally, these regulatory systems arising from TE frequently have tissue-specific functions. The objective of this review is to discuss TE-mediated gene regulation, with a particular emphasis on the processes, contributions of various TE types, differential roles of various tissue types, based mostly on recent studies on humans.
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Affiliation(s)
- Alemu Gebrie
- Department of Biomedical Sciences, School of Medicine, Debre Markos University, Debre Markos, Ethiopia.
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7
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Gasparotto E, Burattin FV, Di Gioia V, Panepuccia M, Ranzani V, Marasca F, Bodega B. Transposable Elements Co-Option in Genome Evolution and Gene Regulation. Int J Mol Sci 2023; 24:ijms24032610. [PMID: 36768929 PMCID: PMC9917352 DOI: 10.3390/ijms24032610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 01/31/2023] Open
Abstract
The genome is no longer deemed as a fixed and inert item but rather as a moldable matter that is continuously evolving and adapting. Within this frame, Transposable Elements (TEs), ubiquitous, mobile, repetitive elements, are considered an alive portion of the genomes to date, whose functions, although long considered "dark", are now coming to light. Here we will review that, besides the detrimental effects that TE mobilization can induce, TEs have shaped genomes in their current form, promoting genome sizing, genomic rearrangements and shuffling of DNA sequences. Although TEs are mostly represented in the genomes by evolutionarily old, short, degenerated, and sedentary fossils, they have been thoroughly co-opted by the hosts as a prolific and original source of regulatory instruments for the control of gene transcription and genome organization in the nuclear space. For these reasons, the deregulation of TE expression and/or activity is implicated in the onset and progression of several diseases. It is likely that we have just revealed the outermost layers of TE functions. Further studies on this portion of the genome are required to unlock novel regulatory functions that could also be exploited for diagnostic and therapeutic approaches.
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Affiliation(s)
- Erica Gasparotto
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- SEMM, European School of Molecular Medicine, 20139 Milan, Italy
| | - Filippo Vittorio Burattin
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Valeria Di Gioia
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- SEMM, European School of Molecular Medicine, 20139 Milan, Italy
| | - Michele Panepuccia
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
| | - Valeria Ranzani
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
| | - Federica Marasca
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
| | - Beatrice Bodega
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- Department of Biosciences, University of Milan, 20133 Milan, Italy
- Correspondence:
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