1
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Oh JW, Beer MA. Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals. Nat Commun 2024; 15:6464. [PMID: 39085231 PMCID: PMC11291912 DOI: 10.1038/s41467-024-50708-z] [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: 10/27/2023] [Accepted: 07/17/2024] [Indexed: 08/02/2024] Open
Abstract
Gene regulatory elements drive complex biological phenomena and their mutations are associated with common human diseases. The impacts of human regulatory variants are often tested using model organisms such as mice. However, mapping human enhancers to conserved elements in mice remains a challenge, due to both rapid enhancer evolution and limitations of current computational methods. We analyze distal enhancers across 45 matched human/mouse cell/tissue pairs from a comprehensive dataset of DNase-seq experiments, and show that while cell-specific regulatory vocabulary is conserved, enhancers evolve more rapidly than promoters and CTCF binding sites. Enhancer conservation rates vary across cell types, in part explainable by tissue specific transposable element activity. We present an improved genome alignment algorithm using gapped-kmer features, called gkm-align, and make genome wide predictions for 1,401,803 orthologous regulatory elements. We show that gkm-align discovers 23,660 novel human/mouse conserved enhancers missed by previous algorithms, with strong evidence of conserved functional activity.
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Affiliation(s)
- Jin Woo Oh
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Michael A Beer
- Department of Biomedical Engineering and McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
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2
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Karttunen K, Patel D, Sahu B. Transposable elements as drivers of dedifferentiation: Connections between enhancers in embryonic stem cells, placenta, and cancer. Bioessays 2024:e2400059. [PMID: 39073128 DOI: 10.1002/bies.202400059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/12/2024] [Indexed: 07/30/2024]
Abstract
Transposable elements (TEs) have emerged as important factors in establishing the cell type-specific gene regulatory networks and evolutionary novelty of embryonic and placental development. Recently, studies on the role of TEs and their dysregulation in cancers have shed light on the transcriptional, transpositional, and regulatory activity of TEs, revealing that the activation of developmental transcriptional programs by TEs may have a role in the dedifferentiation of cancer cells to the progenitor-like cell states. This essay reviews the recent evidence of the cis-regulatory TEs (henceforth crTE) in normal development and malignancy as well as the key transcription factors and regulatory pathways that are implicated in both cell states, and presents existing gaps remaining to be studied, limitations of current technologies, and therapeutic possibilities.
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Affiliation(s)
- Konsta Karttunen
- Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Divyesh Patel
- Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Biswajyoti Sahu
- Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
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3
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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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4
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Chang NC, Wells JN, Wang AY, Schofield P, Huang YC, Truong VH, Simoes-Costa M, Feschotte C. Gag proteins encoded by endogenous retroviruses are required for zebrafish development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586437. [PMID: 38585793 PMCID: PMC10996621 DOI: 10.1101/2024.03.25.586437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Transposable elements (TEs) make up the bulk of eukaryotic genomes and examples abound of TE-derived sequences repurposed for organismal function. The process by which TEs become coopted remains obscure because most cases involve ancient, transpositionally inactive elements. Reports of active TEs serving beneficial functions are scarce and often contentious due to difficulties in manipulating repetitive sequences. Here we show that recently active TEs in zebrafish encode products critical for embryonic development. Knockdown and rescue experiments demonstrate that the endogenous retrovirus family BHIKHARI-1 (Bik-1) encodes a Gag protein essential for mesoderm development. Mechanistically, Bik-1 Gag associates with the cell membrane and its ectopic expression in chicken embryos alters cell migration. Similarly, depletion of BHIKHARI-2 Gag, a relative of Bik-1, causes defects in neural crest development in zebrafish. We propose an "addiction" model to explain how active TEs can be integrated into conserved developmental processes.
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Affiliation(s)
- Ni-Chen Chang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Jonathan N Wells
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Andrew Y Wang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Phillip Schofield
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Yi-Chia Huang
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Vinh H Truong
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Marcos Simoes-Costa
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
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5
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Kojima KK. Helenus and Ajax, Two Groups of Non-Autonomous LTR Retrotransposons, Represent a New Type of Small RNA Gene-Derived Mobile Elements. BIOLOGY 2024; 13:119. [PMID: 38392337 PMCID: PMC10886601 DOI: 10.3390/biology13020119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/06/2024] [Accepted: 02/10/2024] [Indexed: 02/24/2024]
Abstract
Terminal repeat retrotransposons in miniature (TRIMs) are short non-autonomous long terminal repeat (LTR) retrotransposons found from various eukaryotes. Cassandra is a unique TRIM lineage which contains a 5S rRNA-derived sequence in its LTRs. Here, two new groups of TRIMs, designated Helenus and Ajax, are reported based on bioinformatics analysis and the usage of Repbase. Helenus is found from fungi, animals, and plants, and its LTRs contain a tRNA-like sequence. It includes two LTRs and between them, a primer-binding site (PBS) and polypurine tract (PPT) exist. Fungal and plant Helenus generate 5 bp target site duplications (TSDs) upon integration, while animal Helenus generates 4 bp TSDs. Ajax includes a 5S rRNA-derived sequence in its LTR and is found from two nemertean genomes. Ajax generates 5 bp TSDs upon integration. These results suggest that despite their unique promoters, Helenus and Ajax are TRIMs whose transposition is dependent on autonomous LTR retrotransposon. These TRIMs can originate through an insertion of SINE in an LTR of TRIM. The discovery of Helenus and Ajax suggests the presence of TRIMs with a promoter for RNA polymerase III derived from a small RNA gene, which is here collectively termed TRIMp3.
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Affiliation(s)
- Kenji K Kojima
- Genetic Information Research Institute, Cupertino, CA 95014, USA
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6
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Michalak TI. The Initial Hepatitis B Virus-Hepatocyte Genomic Integrations and Their Role in Hepatocellular Oncogenesis. Int J Mol Sci 2023; 24:14849. [PMID: 37834296 PMCID: PMC10573506 DOI: 10.3390/ijms241914849] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/30/2023] [Accepted: 09/30/2023] [Indexed: 10/15/2023] Open
Abstract
Hepatitis B virus (HBV) remains a dominant cause of hepatocellular carcinoma (HCC). Recently, it was shown that HBV and woodchuck hepatitis virus (WHV) integrate into the hepatocyte genome minutes after invasion. Retrotransposons and transposable sequences were frequent sites of the initial insertions, suggesting a mechanism for spontaneous HBV DNA dispersal throughout the hepatocyte genome. Several somatic genes were also identified as early insertional targets in infected hepatocytes and woodchuck livers. Head-to-tail joints (HTJs) dominated amongst fusions, indicating their creation by non-homologous end-joining (NHEJ). Their formation coincided with the robust oxidative damage of hepatocyte DNA. This was associated with the activation of poly(ADP-ribose) polymerase 1 (PARP1)-mediated dsDNA repair, as reflected by the augmented transcription of PARP1 and XRCC1; the PARP1 binding partner OGG1, a responder to oxidative DNA damage; and increased activity of NAD+, a marker of PARP1 activation, and HO1, an indicator of cell oxidative stress. The engagement of the PARP1-mediated NHEJ repair pathway explains the HTJ format of the initial merges. The findings show that HBV and WHV are immediate inducers of oxidative DNA damage and hijack dsDNA repair to integrate into the hepatocyte genome, and through this mechanism, they may initiate pro-oncogenic processes. Tracking initial integrations may uncover early markers of HCC and help to explain HBV-associated oncogenesis.
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Affiliation(s)
- Tomasz I Michalak
- Molecular Virology and Hepatology Research Group, Division of BioMedical Science, Faculty of Medicine, Health Science Center, Memorial University of Newfoundland, St. John's, NL A1B 3V6, Canada
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7
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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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8
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Petrzilek J, Pasulka J, Malik R, Horvat F, Kataruka S, Fulka H, Svoboda P. De novo emergence, existence, and demise of a protein-coding gene in murids. BMC Biol 2022; 20:272. [PMID: 36482406 PMCID: PMC9733328 DOI: 10.1186/s12915-022-01470-5] [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: 09/30/2022] [Accepted: 11/15/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Genes, principal units of genetic information, vary in complexity and evolutionary history. Less-complex genes (e.g., long non-coding RNA (lncRNA) expressing genes) readily emerge de novo from non-genic sequences and have high evolutionary turnover. Genesis of a gene may be facilitated by adoption of functional genic sequences from retrotransposon insertions. However, protein-coding sequences in extant genomes rarely lack any connection to an ancestral protein-coding sequence. RESULTS We describe remarkable evolution of the murine gene D6Ertd527e and its orthologs in the rodent Muroidea superfamily. The D6Ertd527e emerged in a common ancestor of mice and hamsters most likely as a lncRNA-expressing gene. A major contributing factor was a long terminal repeat (LTR) retrotransposon insertion carrying an oocyte-specific promoter and a 5' terminal exon of the gene. The gene survived as an oocyte-specific lncRNA in several extant rodents while in some others the gene or its expression were lost. In the ancestral lineage of Mus musculus, the gene acquired protein-coding capacity where the bulk of the coding sequence formed through CAG (AGC) trinucleotide repeat expansion and duplications. These events generated a cytoplasmic serine-rich maternal protein. Knock-out of D6Ertd527e in mice has a small but detectable effect on fertility and the maternal transcriptome. CONCLUSIONS While this evolving gene is not showing a clear function in laboratory mice, its documented evolutionary history in Muroidea during the last ~ 40 million years provides a textbook example of how a several common mutation events can support de novo gene formation, evolution of protein-coding capacity, as well as gene's demise.
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Affiliation(s)
- Jan Petrzilek
- grid.418827.00000 0004 0620 870XInstitute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic ,grid.22937.3d0000 0000 9259 8492Present address: Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Josef Pasulka
- grid.418827.00000 0004 0620 870XInstitute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Radek Malik
- grid.418827.00000 0004 0620 870XInstitute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Filip Horvat
- grid.418827.00000 0004 0620 870XInstitute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic ,grid.4808.40000 0001 0657 4636Bioinformatics Group, Division of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Shubhangini Kataruka
- grid.418827.00000 0004 0620 870XInstitute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic ,grid.47100.320000000419368710Present address: Department of Genetics, Yale School of Medicine, New Haven, CT 06510 USA
| | - Helena Fulka
- grid.418827.00000 0004 0620 870XInstitute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic ,grid.418095.10000 0001 1015 3316Current address: Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Petr Svoboda
- grid.418827.00000 0004 0620 870XInstitute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
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9
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Ponting CP, Haerty W. Genome-Wide Analysis of Human Long Noncoding RNAs: A Provocative Review. Annu Rev Genomics Hum Genet 2022; 23:153-172. [PMID: 35395170 DOI: 10.1146/annurev-genom-112921-123710] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Do long noncoding RNAs (lncRNAs) contribute little or substantively to human biology? To address how lncRNA loci and their transcripts, structures, interactions, and functions contribute to human traits and disease, we adopt a genome-wide perspective. We intend to provoke alternative interpretation of questionable evidence and thorough inquiry into unsubstantiated claims. We discuss pitfalls of lncRNA experimental and computational methods as well as opposing interpretations of their results. The majority of evidence, we argue, indicates that most lncRNA transcript models reflect transcriptional noise or provide minor regulatory roles, leaving relatively few human lncRNAs that contribute centrally to human development, physiology, or behavior. These important few tend to be spliced and better conserved but lack a simple syntax relating sequence to structure and mechanism, and so resist simple categorization. This genome-wide view should help investigators prioritize individual lncRNAs based on their likely contribution to human biology.
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Affiliation(s)
- Chris P Ponting
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom;
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10
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Ai Z, Xiang X, Xiang Y, Szczerbinska I, Qian Y, Xu X, Ma C, Su Y, Gao B, Shen H, Bin Ramli MN, Chen D, Liu Y, Hao JJ, Ng HH, Zhang D, Chan YS, Liu W, Liang H. Krüppel-like factor 5 rewires NANOG regulatory network to activate human naive pluripotency specific LTR7Ys and promote naive pluripotency. Cell Rep 2022; 40:111240. [PMID: 36001968 DOI: 10.1016/j.celrep.2022.111240] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/06/2022] [Accepted: 07/27/2022] [Indexed: 12/01/2022] Open
Abstract
Endogenous retroviruses (ERVs) have been reported to participate in pre-implantation development of mammalian embryos. In early human embryogenesis, different ERV sub-families are activated in a highly stage-specific manner. How the specificity of ERV activation is achieved remains largely unknown. Here, we demonstrate the mechanism of how LTR7Ys, the human morula-blastocyst-specific HERVH long terminal repeats, are activated by the naive pluripotency transcription network. We find that KLF5 interacts with and rewires NANOG to bind and regulate LTR7Ys; in contrast, the primed-specific LTR7s are preferentially bound by NANOG in the absence of KLF5. The specific activation of LTR7Ys by KLF5 and NANOG in pluripotent stem cells contributes to human-specific naive pluripotency regulation. KLF5-LTR7Y axis also promotes the expression of trophectoderm genes and contributes to the expanded cell potential toward extra-embryonic lineage. Our study suggests that HERVs are activated by cell-state-specific transcription machinery and promote stage-specific transcription network and cell potency.
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Affiliation(s)
- Zhipeng Ai
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Xinyu Xiang
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining 314400, China
| | - Yangquan Xiang
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Iwona Szczerbinska
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Yuli Qian
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China
| | - Xiao Xu
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Chenyang Ma
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Yaqi Su
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining 314400, China
| | - Bing Gao
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining 314400, China
| | - Hao Shen
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Muhammad Nadzim Bin Ramli
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Di Chen
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining 314400, China
| | - Yue Liu
- Guangzhou Laboratory, No. 9 Xing Dao Huan Bei Road, Guangzhou International Bio Island, Guangzhou 510005, China
| | - Jia-Jie Hao
- Guangzhou Laboratory, No. 9 Xing Dao Huan Bei Road, Guangzhou International Bio Island, Guangzhou 510005, China
| | - Huck Hui Ng
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117597, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 639798, Singapore
| | - Dan Zhang
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou 310006, China.
| | - Yun-Shen Chan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; Guangzhou Laboratory, No. 9 Xing Dao Huan Bei Road, Guangzhou International Bio Island, Guangzhou 510005, China.
| | - Wanlu Liu
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining 314400, China; Department of Orthopedic Surgery of the Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310029, China; Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Hongqing Liang
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310006, China.
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11
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Lee Y, Ha U, Moon S. Ongoing endeavors to detect mobilization of transposable elements. BMB Rep 2022. [PMID: 35725016 PMCID: PMC9340088 DOI: 10.5483/bmbrep.2022.55.7.088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transposable elements (TEs) are DNA sequences capable of mobilization from one location to another in the genome. Since the discovery of ‘Dissociation (Dc) locus’ by Barbara McClintock in maize (1), mounting evidence in the era of genomics indicates that a significant fraction of most eukaryotic genomes is composed of TE sequences, involving in various aspects of biological processes such as development, physiology, diseases and evolution. Although technical advances in genomics have discovered numerous functional impacts of TE across species, our understanding of TEs is still ongoing process due to challenges resulted from complexity and abundance of TEs in the genome. In this mini-review, we briefly summarize biology of TEs and their impacts on the host genome, emphasizing importance of understanding TE landscape in the genome. Then, we introduce recent endeavors especially in vivo retrotransposition assays and long read sequencing technology for identifying de novo insertions/TE polymorphism, which will broaden our knowledge of extraordinary relationship between genomic cohabitants and their host.
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Affiliation(s)
- Yujeong Lee
- Department of Biological Sciences, Kangwon National University, Chuncheon 24341, Korea
| | - Una Ha
- Department of Biological Sciences, Kangwon National University, Chuncheon 24341, Korea
| | - Sungjin Moon
- Department of Biological Sciences, Kangwon National University, Chuncheon 24341, Korea
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12
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Campitelli LF, Yellan I, Albu M, Barazandeh M, Patel ZM, Blanchette M, Hughes TR. Reconstruction of full-length LINE-1 progenitors from ancestral genomes. Genetics 2022; 221:6584822. [PMID: 35552404 PMCID: PMC9252281 DOI: 10.1093/genetics/iyac074] [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: 03/25/2022] [Accepted: 04/27/2022] [Indexed: 11/24/2022] Open
Abstract
Sequences derived from the Long INterspersed Element-1 (L1) family of retrotransposons occupy at least 17% of the human genome, with 67 distinct subfamilies representing successive waves of expansion and extinction in mammalian lineages. L1s contribute extensively to gene regulation, but their molecular history is difficult to trace, because most are present only as truncated and highly mutated fossils. Consequently, L1 entries in current databases of repeat sequences are composed mainly of short diagnostic subsequences, rather than full functional progenitor sequences for each subfamily. Here, we have coupled 2 levels of sequence reconstruction (at the level of whole genomes and L1 subfamilies) to reconstruct progenitor sequences for all human L1 subfamilies that are more functionally and phylogenetically plausible than existing models. Most of the reconstructed sequences are at or near the canonical length of L1s and encode uninterrupted ORFs with expected protein domains. We also show that the presence or absence of binding sites for KRAB-C2H2 Zinc Finger Proteins, even in ancient-reconstructed progenitor L1s, mirrors binding observed in human ChIP-exo experiments, thus extending the arms race and domestication model. RepeatMasker searches of the modern human genome suggest that the new models may be able to assign subfamily resolution identities to previously ambiguous L1 instances. The reconstructed L1 sequences will be useful for genome annotation and functional study of both L1 evolution and L1 contributions to host regulatory networks.
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Affiliation(s)
- Laura F Campitelli
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada.,Donnelly Centre, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Isaac Yellan
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada.,Donnelly Centre, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Mihai Albu
- Donnelly Centre, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Marjan Barazandeh
- Donnelly Centre, University of Toronto, Toronto, ON M5S 1A1, Canada.,Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Zain M Patel
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada.,Donnelly Centre, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Mathieu Blanchette
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.,Department of Computer Science, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Timothy R Hughes
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A1, Canada.,Donnelly Centre, University of Toronto, Toronto, ON M5S 1A1, Canada
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13
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Viviani A, Ventimiglia M, Fambrini M, Vangelisti A, Mascagni F, Pugliesi C, Usai G. Impact of transposable elements on the evolution of complex living systems and their epigenetic control. Biosystems 2021; 210:104566. [PMID: 34718084 DOI: 10.1016/j.biosystems.2021.104566] [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: 10/01/2021] [Revised: 10/21/2021] [Accepted: 10/21/2021] [Indexed: 10/20/2022]
Abstract
Transposable elements (TEs) contribute to genomic innovations, as well as genome instability, across a wide variety of species. Popular designations such as 'selfish DNA' and 'junk DNA,' common in the 1980s, may be either inaccurate or misleading, while a more enlightened view of the TE-host relationship covers a range from parasitism to mutualism. Both plant and animal hosts have evolved epigenetic mechanisms to reduce the impact of TEs, both by directly silencing them and by reducing their ability to transpose in the genome. However, TEs have also been co-opted by both plant and animal genomes to perform a variety of physiological functions, ranging from TE-derived proteins acting directly in normal biological functions to innovations in transcription factor activity and also influencing gene expression. Their presence, in fact, can affect a range of features at genome, phenotype, and population levels. The impact TEs have had on evolution is multifaceted, and many aspects still remain unexplored. In this review, the epigenetic control of TEs is contextualized according to the evolution of complex living systems.
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Affiliation(s)
- Ambra Viviani
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Maria Ventimiglia
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Marco Fambrini
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Alberto Vangelisti
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Flavia Mascagni
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy.
| | - Gabriele Usai
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
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14
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Nicolau M, Picault N, Moissiard G. The Evolutionary Volte-Face of Transposable Elements: From Harmful Jumping Genes to Major Drivers of Genetic Innovation. Cells 2021; 10:cells10112952. [PMID: 34831175 PMCID: PMC8616336 DOI: 10.3390/cells10112952] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/20/2021] [Accepted: 10/20/2021] [Indexed: 12/25/2022] Open
Abstract
Transposable elements (TEs) are self-replicating DNA elements that constitute major fractions of eukaryote genomes. Their ability to transpose can modify the genome structure with potentially deleterious effects. To repress TE activity, host cells have developed numerous strategies, including epigenetic pathways, such as DNA methylation or histone modifications. Although TE neo-insertions are mostly deleterious or neutral, they can become advantageous for the host under specific circumstances. The phenomenon leading to the appropriation of TE-derived sequences by the host is known as TE exaptation or co-option. TE exaptation can be of different natures, through the production of coding or non-coding DNA sequences with ultimately an adaptive benefit for the host. In this review, we first give new insights into the silencing pathways controlling TE activity. We then discuss a model to explain how, under specific environmental conditions, TEs are unleashed, leading to a TE burst and neo-insertions, with potential benefits for the host. Finally, we review our current knowledge of coding and non-coding TE exaptation by providing several examples in various organisms and describing a method to identify TE co-option events.
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Affiliation(s)
- Melody Nicolau
- LGDP-UMR5096, CNRS, 66860 Perpignan, France; (M.N.); (N.P.)
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Nathalie Picault
- LGDP-UMR5096, CNRS, 66860 Perpignan, France; (M.N.); (N.P.)
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Guillaume Moissiard
- LGDP-UMR5096, CNRS, 66860 Perpignan, France; (M.N.); (N.P.)
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
- Correspondence:
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15
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Hermant C, Torres-Padilla ME. TFs for TEs: the transcription factor repertoire of mammalian transposable elements. Genes Dev 2021; 35:22-39. [PMID: 33397727 PMCID: PMC7778262 DOI: 10.1101/gad.344473.120] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this review, Hermant and Torres-Padilla summarize and discuss the transcription factors known to be involved in the sequence-specific recognition and transcriptional activation of specific transposable element families or subfamilies. Transposable elements (TEs) are genetic elements capable of changing position within the genome. Although their mobilization can constitute a threat to genome integrity, nearly half of modern mammalian genomes are composed of remnants of TE insertions. The first critical step for a successful transposition cycle is the generation of a full-length transcript. TEs have evolved cis-regulatory elements enabling them to recruit host-encoded factors driving their own, selfish transcription. TEs are generally transcriptionally silenced in somatic cells, and the mechanisms underlying their repression have been extensively studied. However, during germline formation, preimplantation development, and tumorigenesis, specific TE families are highly expressed. Understanding the molecular players at stake in these contexts is of utmost importance to establish the mechanisms regulating TEs, as well as the importance of their transcription to the biology of the host. Here, we review the transcription factors known to be involved in the sequence-specific recognition and transcriptional activation of specific TE families or subfamilies. We discuss the diversity of TE regulatory elements within mammalian genomes and highlight the importance of TE mobilization in the dispersal of transcription factor-binding sites over the course of evolution.
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Affiliation(s)
- Clara Hermant
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377 München, Germany
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377 München, Germany.,Faculty of Biology, Ludwig-Maximilians Universität München, D-82152 Planegg-Martinsried, Germany
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16
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Zhou SS, Yan XM, Zhang KF, Liu H, Xu J, Nie S, Jia KH, Jiao SQ, Zhao W, Zhao YJ, Porth I, El Kassaby YA, Wang T, Mao JF. A comprehensive annotation dataset of intact LTR retrotransposons of 300 plant genomes. Sci Data 2021; 8:174. [PMID: 34267227 PMCID: PMC8282616 DOI: 10.1038/s41597-021-00968-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/07/2021] [Indexed: 12/11/2022] Open
Abstract
LTR retrotransposons (LTR-RTs) are ubiquitous and represent the dominant repeat element in plant genomes, playing important roles in functional variation, genome plasticity and evolution. With the advent of new sequencing technologies, a growing number of whole-genome sequences have been made publicly available, making it possible to carry out systematic analyses of LTR-RTs. However, a comprehensive and unified annotation of LTR-RTs in plant groups is still lacking. Here, we constructed a plant intact LTR-RTs dataset, which is designed to classify and annotate intact LTR-RTs with a standardized procedure. The dataset currently comprises a total of 2,593,685 intact LTR-RTs from genomes of 300 plant species representing 93 families of 46 orders. The dataset is accompanied by sequence, diverse structural and functional annotation, age determination and classification information associated with the LTR-RTs. This dataset will contribute valuable resources for investigating the evolutionary dynamics and functional implications of LTR-RTs in plant genomes.
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Affiliation(s)
- Shan-Shan Zhou
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xue-Mei Yan
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Kai-Fu Zhang
- College of Big data and Intelligent Engineering, Southwest Forestry University, Yunnan, 650224, China
| | - Hui Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jie Xu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shuai Nie
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Kai-Hua Jia
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Si-Qian Jiao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Wei Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - You-Jie Zhao
- College of Big data and Intelligent Engineering, Southwest Forestry University, Yunnan, 650224, China
| | - Ilga Porth
- Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval Québec, Québec, QC, G1V 0A6, Canada
| | - Yousry A El Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Tongli Wang
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Jian-Feng Mao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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17
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Mobility connects: transposable elements wire new transcriptional networks by transferring transcription factor binding motifs. Biochem Soc Trans 2021; 48:1005-1017. [PMID: 32573687 PMCID: PMC7329337 DOI: 10.1042/bst20190937] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/01/2020] [Accepted: 06/03/2020] [Indexed: 12/28/2022]
Abstract
Transposable elements (TEs) constitute major fractions of plant genomes. Their potential to be mobile provides them with the capacity to cause major genome rearrangements. Those effects are potentially deleterious and enforced the evolution of epigenetic suppressive mechanisms controlling TE activity. However, beyond their deleterious effects, TE insertions can be neutral or even advantageous for the host, leading to long-term retention of TEs in the host genome. Indeed, TEs are increasingly recognized as major drivers of evolutionary novelties by regulating the expression of nearby genes. TEs frequently contain binding motifs for transcription factors and capture binding motifs during transposition, which they spread through the genome by transposition. Thus, TEs drive the evolution and diversification of gene regulatory networks by recruiting lineage-specific targets under the regulatory control of specific transcription factors. This process can explain the rapid and repeated evolution of developmental novelties, such as C4 photosynthesis and a wide spectrum of stress responses in plants. It also underpins the convergent evolution of embryo nourishing tissues, the placenta in mammals and the endosperm in flowering plants. Furthermore, the gene regulatory network underlying flower development has also been largely reshaped by TE-mediated recruitment of regulatory elements; some of them being preserved across long evolutionary timescales. In this review, we highlight the potential role of TEs as evolutionary toolkits in plants by showcasing examples of TE-mediated evolutionary novelties.
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18
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Ali A, Han K, Liang P. Role of Transposable Elements in Gene Regulation in the Human Genome. Life (Basel) 2021; 11:118. [PMID: 33557056 PMCID: PMC7913837 DOI: 10.3390/life11020118] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 01/28/2021] [Accepted: 02/02/2021] [Indexed: 02/07/2023] Open
Abstract
Transposable elements (TEs), also known as mobile elements (MEs), are interspersed repeats that constitute a major fraction of the genomes of higher organisms. As one of their important functional impacts on gene function and genome evolution, TEs participate in regulating the expression of genes nearby and even far away at transcriptional and post-transcriptional levels. There are two known principal ways by which TEs regulate the expression of genes. First, TEs provide cis-regulatory sequences in the genome with their intrinsic regulatory properties for their own expression, making them potential factors for regulating the expression of the host genes. TE-derived cis-regulatory sites are found in promoter and enhancer elements, providing binding sites for a wide range of trans-acting factors. Second, TEs encode for regulatory RNAs with their sequences showed to be present in a substantial fraction of miRNAs and long non-coding RNAs (lncRNAs), indicating the TE origin of these RNAs. Furthermore, TEs sequences were found to be critical for regulatory functions of these RNAs, including binding to the target mRNA. TEs thus provide crucial regulatory roles by being part of cis-regulatory and regulatory RNA sequences. Moreover, both TE-derived cis-regulatory sequences and TE-derived regulatory RNAs have been implicated in providing evolutionary novelty to gene regulation. These TE-derived regulatory mechanisms also tend to function in a tissue-specific fashion. In this review, we aim to comprehensively cover the studies regarding these two aspects of TE-mediated gene regulation, mainly focusing on the mechanisms, contribution of different types of TEs, differential roles among tissue types, and lineage-specificity, based on data mostly in humans.
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Affiliation(s)
- Arsala Ali
- Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1, Canada;
| | - Kyudong Han
- Department of Microbiology, Dankook University, Cheonan 31116, Korea;
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea
| | - Ping Liang
- Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1, Canada;
- Centre of Biotechnologies, Brock University, St. Catharines, ON L2S 3A1, Canada
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19
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Wang Y, Dai A, Tang T. Weak Effect of Gypsy Retrotransposon Bursts on Sonneratia alba Salt Stress Gene Expression. FRONTIERS IN PLANT SCIENCE 2021; 12:830079. [PMID: 35111190 PMCID: PMC8801733 DOI: 10.3389/fpls.2021.830079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 12/27/2021] [Indexed: 05/07/2023]
Abstract
Transposable elements (TEs) are an important source of genetic diversity and can be co-opted for the regulation of host genes. However, to what extent the pervasive TE colonization of plant genomes has contributed to stress adaptation remains controversial. Plants inhabiting harsh environments in nature provide a unique opportunity to answer this question. We compared TE compositions and their evolutionary dynamics in the genomes of two mangrove species: the pioneer Sonneratia alba and its less salt-tolerant relative S. caseolaris. Age distribution, strength of purifying selection and the removal rate of LTR (long terminal repeat) retrotransposons were estimated. Phylogenetic analysis of LTR retrotransposons and their distribution in the genome of S. alba were surveyed. Small RNA sequencing and whole-genome bisulfite sequencing was conducted using leaves of S. alba. Expression pattern of LTR retrotransposons and their nearby genes were examined using RNA-seq data of S. alba under different salt treatments. S. alba possesses more TEs than S. caseolaris. Particularly, many more young Gypsy LTR retrotransposons have accumulated in S. alba than in S. caseolaris despite an increase in purifying selection against TE insertions. The top two most abundant Gypsy families in S. alba preferentially insert in gene-poor regions. They are under relaxed epigenetic repression, probably due to the presence of CHROMO domains in their 3'-ends. Although a considerable number of TEs in S. alba showed differential expression under salt stress, only four copies were significantly correlated with their nearby genes in expression levels. One such TE-gene pair involves Abscisic acid 8'-hydroxylase 3 functioning in abscisic acid catabolism. This study sheds light on the evolutionary dynamics and potential function of TEs in an extremophile. Our results suggest that the conclusion on co-option of TEs should be cautious even though activation of TEs by stress might be prevalent.
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20
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Abstract
Multicellular eukaryotic genomes show enormous differences in size. A substantial part of this variation is due to the presence of transposable elements (TEs). They contribute significantly to a cell's mass of DNA and have the potential to become involved in host gene control. We argue that the suppression of their activities by methylation of the C-phosphate-G (CpG) dinucleotide in DNA is essential for their long-term accommodation in the host genome and, therefore, to its expansion. An inevitable consequence of cytosine methylation is an increase in C-to-T transition mutations via deamination, which causes CpG loss. Cytosine deamination is often needed for TEs to take on regulatory functions in the host genome. Our study of the whole-genome sequences of 53 organisms showed a positive correlation between the size of a genome and the percentage of TEs it contains, as well as a negative correlation between size and the CpG observed/expected (O/E) ratio in both TEs and the host DNA. TEs are seldom found at promoters and transcription start sites, but they are found more at enhancers, particularly after they have accumulated C-to-T and other mutations. Therefore, the methylation of TE DNA allows for genome expansion and also leads to new opportunities for gene control by TE-based regulatory sites.
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21
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Gao B, Sang Y, Zong W, Diaby M, Shen D, Wang S, Wang Y, Chen C, Song C. Evolution and domestication of Tc1/mariner transposons in the genome of African coelacanth ( Latimeria chalumnae). Genome 2020; 63:375-386. [PMID: 32268072 DOI: 10.1139/gen-2019-0216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Here, we comprehensively analysed the abundance, diversity, and activity of Tc1/mariner transposons in African coelacanth (Latimeria chalumnae). Fifteen Tc1/mariner autonomous transposons were identified and grouped into six clades: DD34E/Tc1, DD34D/mariner, DD35D/Fot, DD31D/pogo, DD30-31D/pogo-like, and DD32-36D/Tigger, belonging to three known families: DD34E/Tc1, DD34D/mariner, and DD×D/pogo (DD35D/Fot, DD31D/pogo, DD30-31D/pogo-like, and DD32-36D/Tigger). Thirty-one miniature inverted-repeat transposable element (MITE) transposons of Tc1/mariner were also identified, and 20 of them display similarity to the identified autonomous transposons. The structural organization of these full Tc1/mariner elements includes a transposase gene flanked by terminal inverted repeats (TIRs) with TA dinucleotides. The transposases contain N-terminal DNA binding domain and a C-terminal catalytic domain characterized by the presence of a conservative D(Asp)DE(Glu)/D triad that is essential for transposase activity. The Tc1/mariner superfamily in coelacanth exhibited very low genome coverage (0.3%), but it experienced an extraordinary difference of proliferation dynamics among the six clades identified; moreover, most of them exhibited a very recent and current proliferation, suggesting that some copies of these transposons are putatively active. Additionally, at least four functional genes derived from Tc1/mariner transposons were found. We provide an up-to-date overview of Tc1/mariner in coelacanth, which may be helpful in determining genome and gene evolution in this living fossil.
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Affiliation(s)
- Bo Gao
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China.,Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Yatong Sang
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China.,Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Wencheng Zong
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China.,Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Mohamed Diaby
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China.,Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Dan Shen
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China.,Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Saisai Wang
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China.,Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Yali Wang
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China.,Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Cai Chen
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China.,Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Chengyi Song
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China.,Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
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22
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Goubert C, Zevallos NA, Feschotte C. Contribution of unfixed transposable element insertions to human regulatory variation. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190331. [PMID: 32075552 PMCID: PMC7061991 DOI: 10.1098/rstb.2019.0331] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2019] [Indexed: 12/11/2022] Open
Abstract
Thousands of unfixed transposable element (TE) insertions segregate in the human population, but little is known about their impact on genome function. Recently, a few studies associated unfixed TE insertions to mRNA levels of adjacent genes, but the biological significance of these associations, their replicability across cell types and the mechanisms by which they may regulate genes remain largely unknown. Here, we performed a TE-expression QTL analysis of 444 lymphoblastoid cell lines (LCL) and 289 induced pluripotent stem cells using a newly developed set of genotypes for 2743 polymorphic TE insertions. We identified 211 and 176 TE-eQTL acting in cis in each respective cell type. Approximately 18% were shared across cell types with strongly correlated effects. Furthermore, analysis of chromatin accessibility QTL in a subset of the LCL suggests that unfixed TEs often modulate the activity of enhancers and other distal regulatory DNA elements, which tend to lose accessibility when a TE inserts within them. We also document a case of an unfixed TE likely influencing gene expression at the post-transcriptional level. Our study points to broad and diverse cis-regulatory effects of unfixed TEs in the human population and underscores their plausible contribution to phenotypic variation. This article is part of a discussion meeting issue 'Crossroads between transposons and gene regulation'.
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Affiliation(s)
| | | | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Road, Ithaca, NY 14853, USA
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Abstract
Retroviruses infect a broad range of vertebrate hosts that includes amphibians, reptiles, fish, birds and mammals. In addition, a typical vertebrate genome contains thousands of loci composed of ancient retroviral sequences known as endogenous retroviruses (ERVs). ERVs are molecular remnants of ancient retroviruses and proof that the ongoing relationship between retroviruses and their vertebrate hosts began hundreds of millions of years ago. The long-term impact of retroviruses on vertebrate evolution is twofold: first, as with other viruses, retroviruses act as agents of selection, driving the evolution of host genes that block viral infection or that mitigate pathogenesis, and second, through the phenomenon of endogenization, retroviruses contribute an abundance of genetic novelty to host genomes, including unique protein-coding genes and cis-acting regulatory elements. This Review describes ERV origins, their diversity and their relationships to retroviruses and discusses the potential for ERVs to reveal virus-host interactions on evolutionary timescales. It also describes some of the many examples of cellular functions, including protein-coding genes and regulatory elements, that have evolved from ERVs.
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Maquat LE. Short interspersed nuclear element (SINE)-mediated post-transcriptional effects on human and mouse gene expression: SINE-UP for active duty. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190344. [PMID: 32075563 DOI: 10.1098/rstb.2019.0344] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Primate-specific Alu short interspersed nuclear elements (SINEs) and rodent-specific B and ID (B/ID) SINEs are non-autonomous and generally non-coding retrotransposons that have been copied and pasted into the respective genomes so as to constitute what is estimated to be a remarkable 13% and 8% of those genomes. In the context of messenger RNAs (mRNAs), those residing within 3'-untranslated regions (3'UTRs) can influence mRNA export from the nucleus to the cytoplasm, mRNA translation and/or mRNA decay via proteins with which they associate either individually or base-paired in cis or in trans with a partially complementary SINE. Each of these influences impinges on the primary function of mRNA, which is to serve as a template for protein synthesis. This review describes how human cells have used 3'UTR Alu elements to mediate post-transcriptional gene regulation and also describes examples of convergent evolution between human and mouse 3'UTR SINEs. This article is part of a discussion meeting issue 'Crossroads between transposons and gene regulation'.
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Affiliation(s)
- Lynne E Maquat
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.,Center for RNA Biology, University of Rochester, Rochester, NY, USA
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Piggin CL, Roden DL, Law AMK, Molloy MP, Krisp C, Swarbrick A, Naylor MJ, Kalyuga M, Kaplan W, Oakes SR, Gallego-Ortega D, Clark SJ, Carroll JS, Bartonicek N, Ormandy CJ. ELF5 modulates the estrogen receptor cistrome in breast cancer. PLoS Genet 2020; 16:e1008531. [PMID: 31895944 PMCID: PMC6959601 DOI: 10.1371/journal.pgen.1008531] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 01/14/2020] [Accepted: 11/20/2019] [Indexed: 11/28/2022] Open
Abstract
Acquired resistance to endocrine therapy is responsible for half of the therapeutic failures in the treatment of breast cancer. Recent findings have implicated increased expression of the ETS transcription factor ELF5 as a potential modulator of estrogen action and driver of endocrine resistance, and here we provide the first insight into the mechanisms by which ELF5 modulates estrogen sensitivity. Using chromatin immunoprecipitation sequencing we found that ELF5 binding overlapped with FOXA1 and ER at super enhancers, enhancers and promoters, and when elevated, caused FOXA1 and ER to bind to new regions of the genome, in a pattern that replicated the alterations to the ER/FOXA1 cistrome caused by the acquisition of resistance to endocrine therapy. RNA sequencing demonstrated that these changes altered estrogen-driven patterns of gene expression, the expression of ER transcription-complex members, and 6 genes known to be involved in driving the acquisition of endocrine resistance. Using rapid immunoprecipitation mass spectrometry of endogenous proteins, and proximity ligation assays, we found that ELF5 interacted physically with members of the ER transcription complex, such as DNA-PKcs. We found 2 cases of endocrine-resistant brain metastases where ELF5 levels were greatly increased and ELF5 patterns of gene expression were enriched, compared to the matched primary tumour. Thus ELF5 alters ER-driven gene expression by modulating the ER/FOXA1 cistrome, by interacting with it, and by modulating the expression of members of the ER transcriptional complex, providing multiple mechanisms by which ELF5 can drive endocrine resistance.
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Affiliation(s)
- Catherine L. Piggin
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - Daniel L. Roden
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - Andrew M. K. Law
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - Mark P. Molloy
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - Christoph Krisp
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
| | - Alexander Swarbrick
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - Matthew J. Naylor
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Maria Kalyuga
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - Warren Kaplan
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - Samantha R. Oakes
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - David Gallego-Ortega
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - Susan J. Clark
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - Jason S. Carroll
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre Robinson Way, Cambridge, United Kingdom
| | - Nenad Bartonicek
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
| | - Christopher J. Ormandy
- Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Victoria Street Darlinghurst Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Australia
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Drongitis D, Aniello F, Fucci L, Donizetti A. Roles of Transposable Elements in the Different Layers of Gene Expression Regulation. Int J Mol Sci 2019; 20:ijms20225755. [PMID: 31731828 PMCID: PMC6888579 DOI: 10.3390/ijms20225755] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/12/2019] [Accepted: 11/14/2019] [Indexed: 02/03/2023] Open
Abstract
The biology of transposable elements (TEs) is a fascinating and complex field of investigation. TEs represent a substantial fraction of many eukaryotic genomes and can influence many aspects of DNA function that range from the evolution of genetic information to duplication, stability, and gene expression. Their ability to move inside the genome has been largely recognized as a double-edged sword, as both useful and deleterious effects can result. A fundamental role has been played by the evolution of the molecular processes needed to properly control the expression of TEs. Today, we are far removed from the original reductive vision of TEs as “junk DNA”, and are more convinced that TEs represent an essential element in the regulation of gene expression. In this review, we summarize some of the more recent findings, mainly in the animal kingdom, concerning the active roles that TEs play at every level of gene expression regulation, including chromatin modification, splicing, and protein translation.
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Affiliation(s)
- Denise Drongitis
- Institute of Genetics and Biophysics “Adriano Buzzati Traverso”, Consiglio Nazionale delle Ricerche, 80131 Naples, Italy;
| | - Francesco Aniello
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (F.A.); (L.F.)
| | - Laura Fucci
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (F.A.); (L.F.)
| | - Aldo Donizetti
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (F.A.); (L.F.)
- Correspondence:
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27
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Bogan SN, Place SP. Accelerated evolution at chaperone promoters among Antarctic notothenioid fishes. BMC Evol Biol 2019; 19:205. [PMID: 31694524 PMCID: PMC6836667 DOI: 10.1186/s12862-019-1524-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 10/01/2019] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Antarctic fishes of the Notothenioidei suborder constitutively upregulate multiple inducible chaperones, a highly derived adaptation that preserves proteostasis in extreme cold, and represent a system for studying the evolution of gene frontloading. We screened for Hsf1-binding sites, as Hsf1 is a master transcription factor of the heat shock response, and highly-conserved non-coding elements within proximal promoters of chaperone genes across 10 Antarctic notothens, 2 subpolar notothens, and 17 perciform fishes. We employed phylogenetic models of molecular evolution to determine whether (i) changes in motifs associated with Hsf1-binding and/or (ii) relaxed purifying selection or exaptation at ancestral cis-regulatory elements coincided with the evolution of chaperone frontloading in Antarctic notothens. RESULTS Antarctic notothens exhibited significantly fewer Hsf1-binding sites per bp at chaperone promoters than subpolar notothens and Serranoidei, the most closely-related suborder to Notothenioidei included in this study. 90% of chaperone promoters exhibited accelerated substitution rates among Antarctic notothens relative to other perciformes. The proportion of bases undergoing accelerated evolution (i) was significantly greater in Antarctic notothens than in subpolar notothens and Perciformes in 70% of chaperone genes and (ii) increased among bases that were more conserved among perciformes. Lastly, we detected evidence of relaxed purifying selection and exaptation acting on ancestrally conserved cis-regulatory elements in the Antarctic notothen lineage and its major branches. CONCLUSION A large degree of turnover has occurred in Notothenioidei at chaperone promoter regions that are conserved among perciform fishes following adaptation to the cooling of the Southern Ocean. Additionally, derived reductions in Hsf1-binding site frequency suggest cis-regulatory modifications to the classical heat shock response. Of note, turnover events within chaperone promoters were less frequent in the ancestral node of Antarctic notothens relative to younger Antarctic lineages. This suggests that cis-regulatory divergence at chaperone promoters may be greater between Antarctic notothen lineages than between subpolar and Antarctic clades. These findings demonstrate that strong selective forces have acted upon cis-regulatory elements of chaperone genes among Antarctic notothens.
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Affiliation(s)
- Samuel N Bogan
- Department of Biology, Sonoma State University, Rohnert Park, CA, 94928, USA.
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, 93106, USA.
| | - Sean P Place
- Department of Biology, Sonoma State University, Rohnert Park, CA, 94928, USA
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Mustafin RN. The Role of Transposable Elements in the Differentiation of Stem Cells. MOLECULAR GENETICS MICROBIOLOGY AND VIROLOGY 2019. [DOI: 10.3103/s0891416819020071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Yang WR, Ardeljan D, Pacyna CN, Payer LM, Burns KH. SQuIRE reveals locus-specific regulation of interspersed repeat expression. Nucleic Acids Res 2019; 47:e27. [PMID: 30624635 PMCID: PMC6411935 DOI: 10.1093/nar/gky1301] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 12/18/2018] [Accepted: 01/03/2019] [Indexed: 12/13/2022] Open
Abstract
Transposable elements (TEs) are interspersed repeat sequences that make up much of the human genome. Their expression has been implicated in development and disease. However, TE-derived RNA-seq reads are difficult to quantify. Past approaches have excluded these reads or aggregated RNA expression to subfamilies shared by similar TE copies, sacrificing quantitative accuracy or the genomic context necessary to understand the basis of TE transcription. As a result, the effects of TEs on gene expression and associated phenotypes are not well understood. Here, we present Software for Quantifying Interspersed Repeat Expression (SQuIRE), the first RNA-seq analysis pipeline that provides a quantitative and locus-specific picture of TE expression (https://github.com/wyang17/SQuIRE). SQuIRE is an accurate and user-friendly tool that can be used for a variety of species. We applied SQuIRE to RNA-seq from normal mouse tissues and a Drosophila model of amyotrophic lateral sclerosis. In both model organisms, we recapitulated previously reported TE subfamily expression levels and revealed locus-specific TE expression. We also identified differences in TE transcription patterns relating to transcript type, gene expression and RNA splicing that would be lost with other approaches using subfamily-level analyses. Altogether, our findings illustrate the importance of studying TE transcription with locus-level resolution.
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Affiliation(s)
- Wan R Yang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daniel Ardeljan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,McKusick-Nathans Institute of Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Clarissa N Pacyna
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Lindsay M Payer
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kathleen H Burns
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,McKusick-Nathans Institute of Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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30
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Jung S, Venkatesh J, Kang MY, Kwon JK, Kang BC. A non-LTR retrotransposon activates anthocyanin biosynthesis by regulating a MYB transcription factor in Capsicum annuum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 287:110181. [PMID: 31481212 DOI: 10.1016/j.plantsci.2019.110181] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 06/24/2019] [Accepted: 06/28/2019] [Indexed: 05/20/2023]
Abstract
The flavonoid compound anthocyanin is an important plant metabolite with nutritional and aesthetic value as well as anti-oxidative capacity. MYB transcription factors are key regulators of anthocyanin biosynthesis in plants. In pepper (Capsicum annuum), the CaAn2 gene, encoding an R2R3 MYB transcription factor, regulates anthocyanin biosynthesis. However, no functional study or structural analysis of functional and dysfunctional CaAn2 alleles has been performed. Here, to elucidate the function of CaAn2, we generated transgenic Nicotiana benthamiana and Arabidopsis thaliana plants expressing CaAn2. All of the tissues in these plants were purple. Promoter analysis of CaAn2 in purple C. annuum 'KC00134' plants revealed the insertion of a non-long terminal repeat (LTR) retrotransposon designated Ca-nLTR-A. To determine the promoter activity and functional domain of Ca-nLTR-A, various constructs carrying different domains of Ca-nLTR-A fused with GUS were transformed into N. benthamiana. Promoter analysis showed that the 3' untranslated region (UTR) of the second open reading frame of Ca-nLTR-A is responsible for CaAn2 expression in 'KC00134'. Sequence analysis of Ca-nLTR-A identified transcription factor binding sites known to regulate anthocyanin biosynthesis. This study indicates that insertion of a non-LTR retrotransposon in the promoter may activate expression of CaAn2 by recruiting transcription factors at the 3' UTR and thus provides the first example of exaptation of a non-LTR retrotransposon into a new promoter in plants.
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Affiliation(s)
- Soyoung Jung
- Department of Plant Science, Plant Genomics & Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.
| | - Jelli Venkatesh
- Department of Plant Science, Plant Genomics & Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.
| | - Min-Young Kang
- Department of Plant Science, Plant Genomics & Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.
| | - Jin-Kyung Kwon
- Department of Plant Science, Plant Genomics & Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.
| | - Byoung-Cheorl Kang
- Department of Plant Science, Plant Genomics & Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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Mustafin RN, Kazantseva AV, Enikeeva RF, Davydova YD, Karunas AS, Malykh SB, Khusnutdinova EK. Epigenetics of Aggressive Behavior. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419090096] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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32
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Mustafin RN, Khusnutdinova EK. The Role of Reverse Transcriptase in the Origin of Life. BIOCHEMISTRY (MOSCOW) 2019; 84:870-883. [DOI: 10.1134/s0006297919080030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Barco B, Kim Y, Clay NK. Expansion of a core regulon by transposable elements promotes Arabidopsis chemical diversity and pathogen defense. Nat Commun 2019; 10:3444. [PMID: 31371717 PMCID: PMC6671987 DOI: 10.1038/s41467-019-11406-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 07/14/2019] [Indexed: 01/09/2023] Open
Abstract
Plants synthesize numerous ecologically specialized, lineage-specific metabolites through biosynthetic gene duplication and functional specialization. However, it remains unclear how duplicated genes are wired into existing regulatory networks. We show that the duplicated gene CYP82C2 has been recruited into the WRKY33 regulon and indole-3-carbonylnitrile (ICN) biosynthetic pathway through exaptation of a retroduplicated LINE retrotransposon (EPCOT3) into an enhancer. The stepwise development of a chromatin-accessible WRKY33-binding site on EPCOT3 has potentiated the regulatory neofunctionalization of CYP82C2 and the evolution of inducible defense metabolite 4-hydroxy-ICN in Arabidopsis thaliana. Although transposable elements (TEs) have long been recognized to have the potential to rewire regulatory networks, these results establish a more complete understanding of how duplicated genes and TEs contribute in concert to chemical diversity and pathogen defense. Arabidopsis plants can produce 4-hydroxyindole-3-carbonitrile (4OH-ICN) upon pathogen infection. Here, the authors show that EPCOT3, a retrotransposonderived enhancer, mediates WRKY33-binding, pathogen-responsive transcription of CYP82C2, and synthesis of 4OH-ICN.
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Affiliation(s)
- Brenden Barco
- Department of Molecular, Cellular and Developmental Biology, Yale University, Kline Biology Tower 734, 219 Prospect Street, New Haven, CT, 06511, USA. .,Seeds Research, Syngenta Crop Protection, 9 Davis Drive, Durham, NC, 27703, USA.
| | - Yoseph Kim
- Hopkins School, 986 Forest Road, New Haven, CT, 06515, USA
| | - Nicole K Clay
- Department of Molecular, Cellular and Developmental Biology, Yale University, Kline Biology Tower 734, 219 Prospect Street, New Haven, CT, 06511, USA.
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Wu C, Lu J. Diversification of Transposable Elements in Arthropods and Its Impact on Genome Evolution. Genes (Basel) 2019; 10:genes10050338. [PMID: 31064091 PMCID: PMC6562904 DOI: 10.3390/genes10050338] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/09/2019] [Accepted: 04/26/2019] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) are ubiquitous in arthropods. However, analyses of large-scale and long-term coevolution between TEs and host genomes remain scarce in arthropods. Here, we choose 14 representative Arthropoda species from eight orders spanning more than 500 million years of evolution. By developing an unbiased TE annotation pipeline, we obtained 87 to 2266 TE reference sequences in a species, which is a considerable improvement compared to the reference TEs previously annotated in Repbase. We find that TE loads are diversified among species and were previously underestimated. The highly species- and time-specific expansions and contractions, and intraspecific sequence diversification are the leading driver of long terminal repeat (LTR) dynamics in Lepidoptera. Terminal inverted repeats (TIRs) proliferated substantially in five species with large genomes. A phylogenetic comparison reveals that the loads of multiple TE subfamilies are positively correlated with genome sizes. We also identified a few horizontally transferred TE candidates across nine species. In addition, we set up the Arthropod Transposable Elements database (ArTEdb) to provide TE references and annotations. Collectively, our results provide high-quality TE references and uncover that TE loads and expansion histories vary greatly among arthropods, which implies that TEs are an important driving force shaping the evolution of genomes through gain and loss.
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Affiliation(s)
- Changcheng Wu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China.
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China.
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Feng M, Ren F, Zhou Y, Zhang N, Lu Q, Swevers L, Sun J. Correlation in Expression between LTR Retrotransposons and Potential Host Cis-Targets during Infection of Antherea pernyi with ApNPV Baculovirus. Viruses 2019; 11:v11050421. [PMID: 31064084 PMCID: PMC6563192 DOI: 10.3390/v11050421] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 05/04/2019] [Indexed: 12/14/2022] Open
Abstract
The published genome sequence of Antheraeayamamai (Saturnnidae) was used to construct a library of long terminal repeat (LTR)-retrotransposons that is representative of the wild silkmoth (Antherea) genus, and that includes 22,666 solo LTRs and 541 full-length LTRs. The LTR retrotransposons of Antheraeayamamai (AyLTRs) could be classified into the three canonical groups of Gypsy, Copia and Belpao. Eleven AyLTRs contained the env gene element, but the relationship with the env element of baculovirus, particularly A. yamamai and pernyi nucleopolyhedrovirus (AyNPV and ApNPV), was distant. A total of 251 “independent” full-length AyLTRs were identified that were located within 100 kb distance (downstream or upstream) of 406 neighboring genes in A. yamamai. Regulation of these genes might occur in cis by the AyLTRs, and the neighboring genes were found to be enriched in GO terms such as “response to stimulus”, and KEGG terms such as “mTOR signaling pathway” among others. Furthermore, the library of LTR-retrotransposons and the A. yamamai genome were used to identify and analyze the expression of LTR-retrotransposons and genes in ApNPV-infected and non-infected A. pernyi larval midguts, using raw data of a published transcriptome study. Our analysis demonstrates that 93 full-length LTR-retrotransposons are transcribed in the midgut of A. pernyi of which 12 significantly change their expression after ApNPV infection (differentially expressed LTR-retrotransposons or DELs). In addition, the expression of differentially expressed genes (DEGs) and neighboring DELs on the chromosome following ApNPV infection suggests the possibility of regulation of expression of DEGs by DELs through a cis mechanism, which will require experimental verification. When examined in more detail, it was found that genes involved in Notch signaling and stress granule (SG) formation were significantly up-regulated in ApNPV-infected A. pernyi larval midgut. Moreover, several DEGs in the Notch and SG pathways were found to be located in the neighborhood of particular DELs, indicating the possibility of DEG-DEL cross-regulation in cis for these two pathways.
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Affiliation(s)
- Min Feng
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences and Applications, National Centre for Scientific Research Demokritos, Aghia Paraskevi, Athens 15341, Greece.
| | - Feifei Ren
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Yaohong Zhou
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Nan Zhang
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Qiuyuan Lu
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - Luc Swevers
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences and Applications, National Centre for Scientific Research Demokritos, Aghia Paraskevi, Athens 15341, Greece.
| | - Jingchen Sun
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
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Chauhan R, Shimizu Y, Watashi K, Wakita T, Fukasawa M, Michalak TI. Retrotransposon elements among initial sites of hepatitis B virus integration into human genome in the HepG2-NTCP cell infection model. Cancer Genet 2019; 235-236:39-56. [PMID: 31064734 DOI: 10.1016/j.cancergen.2019.04.060] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/11/2019] [Accepted: 04/18/2019] [Indexed: 02/07/2023]
Abstract
Integration of hepatitis B virus (HBV) DNA into host's genome is evident in all stages and models of HBV infection. Investigations of the initial virus-host junctions have been just recently initiated since their nature may promote liver oncogenesis immediately following infection. We examined the time-frame and host sites at which HBV integrates in HepG2 cells overexpressing sodium taurocholate co-transporting polypeptide (NTCP) receptor mediating HBV entry. HepG2-NTCP cells were analyzed from 15 min to 13 days post-infection (p.i.). The results showed that except for 15 min p.i., HBV-host integrations were detected at all time points thereafter. At 30 min p.i., virus junctions with retrotransposon SINE and with neuroblastoma breakpoint family member 1 gene were detected. At one-hour p.i., HBV integration with retrotransposon THE-1B-LTR was identified, while virus insertions into proline-rich protein and protein kinase cGMP-dependent type 1 encoding genes were found at 3 h p.i. Fusion with runt-related transcription factor 1 was detected at 24 h p.i. and merges with 9 different genes at 13 day p.i. The data showed that retrotransposon elements are frequent among first-hit sites of HBV insertion. This may suggest a mechanism by which HBV DNA may spread across host's genome from earliest stages of infection.
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Affiliation(s)
- Ranjit Chauhan
- Molecular Virology and Hepatology Research Group, Division of BioMedical Sciences, Faculty of Medicine, Health Science Centre, Memorial University, St. John's, NL, Canada
| | - Yoshimi Shimizu
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Koichi Watashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takaji Wakita
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masayoshi Fukasawa
- Department of Biochemistry and Cell Biology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomasz I Michalak
- Molecular Virology and Hepatology Research Group, Division of BioMedical Sciences, Faculty of Medicine, Health Science Centre, Memorial University, St. John's, NL, Canada.
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Mustafin RN, Khusnutdinova EK. Prospects in the Search for Peptides for Specific Regulation of Aging. ADVANCES IN GERONTOLOGY 2019. [DOI: 10.1134/s2079057019020176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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38
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Sambamoorthy G, Sinha H, Raman K. Evolutionary design principles in metabolism. Proc Biol Sci 2019; 286:20190098. [PMID: 30836874 PMCID: PMC6458322 DOI: 10.1098/rspb.2019.0098] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 02/14/2019] [Indexed: 12/28/2022] Open
Abstract
Microorganisms are ubiquitous and adapt to various dynamic environments to sustain growth. These adaptations accumulate, generating new traits forming the basis of evolution. Organisms adapt at various levels, such as gene regulation, signalling, protein-protein interactions and metabolism. Of these, metabolism forms the integral core of an organism for maintaining the growth and function of a cell. Therefore, studying adaptations in metabolic networks is crucial to understand the emergence of novel metabolic capabilities. Metabolic networks, composed of enzyme-catalysed reactions, exhibit certain repeating paradigms or design principles that arise out of different selection pressures. In this review, we discuss the design principles that are known to exist in metabolic networks, such as functional redundancy, modularity, flux coupling and exaptations. We elaborate on the studies that have helped gain insights highlighting the interplay of these design principles and adaptation. Further, we discuss how evolution plays a role in exploiting such paradigms to enhance the robustness of organisms. Looking forward, we predict that with the availability of ever-increasing numbers of bacterial, archaeal and eukaryotic genomic sequences, novel design principles will be identified, expanding our understanding of these paradigms shaped by varied evolutionary processes.
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Affiliation(s)
- Gayathri Sambamoorthy
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
- Initiative for Biological Systems Engineering (IBSE), Indian Institute of Technology Madras, Chennai 600036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai 600036, India
| | - Himanshu Sinha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
- Initiative for Biological Systems Engineering (IBSE), Indian Institute of Technology Madras, Chennai 600036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai 600036, India
| | - Karthik Raman
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
- Initiative for Biological Systems Engineering (IBSE), Indian Institute of Technology Madras, Chennai 600036, India
- Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai 600036, India
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39
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Mustafin RN. Functional Dualism of Transposon Transcripts in Evolution of Eukaryotic Genomes. Russ J Dev Biol 2019. [DOI: 10.1134/s1062360418070019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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40
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Pirogov SA, Maksimenko OG, Georgiev PG. Transposable Elements in the Evolution of Gene Regulatory Networks. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419010113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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41
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Abstract
Transposable elements (TEs) are low-complexity elements (e.g., LINEs, SINEs, SVAs, and HERVs) that make up to two-thirds of the human genome. There is mounting evidence that TEs play an essential role in molecular functions that influence genomic plasticity and gene expression regulation. With the advent of next-generation sequencing approaches, our understanding of the relationship between TEs and psychiatric disorders will greatly improve. In this chapter, the Authors comprehensively summarize the state-of the-art of TE research in animal models and humans supporting a framework in which TEs play a functional role in mechanisms affecting a variety of behaviors, including neurodevelopmental, neuropsychiatric, and neurodegenerative disorders. Finally, the Authors discuss recent therapeutic applications raised from the increasing experimental evidence on TE functional mechanisms.
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Affiliation(s)
- G Guffanti
- McLean Hospital - Harvard Medical School, Belmont, MA, USA.
| | - A Bartlett
- Department of Psychology, University of Massachusetts, Boston, Boston, MA, USA
| | - P DeCrescenzo
- McLean Hospital - Harvard Medical School, Belmont, MA, USA
| | - F Macciardi
- Department of Psychiatry and Human Behavior, University of California, Irvine, Irvine, CA, USA
| | - R Hunter
- Department of Psychology, University of Massachusetts, Boston, Boston, MA, USA
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42
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Mustafin RN. The Relationship between Transposons and Transcription Factors in the Evolution of Eukaryotes. J EVOL BIOCHEM PHYS+ 2019. [DOI: 10.1134/s0022093019010022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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43
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Mustafin RN, Enikeeva RF, Davydova YD, Khusnutdinova EK. The Role of Epigenetic Factors in the Development of Depressive Disorders. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418120104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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44
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Exaptation at the molecular genetic level. SCIENCE CHINA-LIFE SCIENCES 2018; 62:437-452. [PMID: 30798493 DOI: 10.1007/s11427-018-9447-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 12/01/2018] [Indexed: 12/22/2022]
Abstract
The realization that body parts of animals and plants can be recruited or coopted for novel functions dates back to, or even predates the observations of Darwin. S.J. Gould and E.S. Vrba recognized a mode of evolution of characters that differs from adaptation. The umbrella term aptation was supplemented with the concept of exaptation. Unlike adaptations, which are restricted to features built by selection for their current role, exaptations are features that currently enhance fitness, even though their present role was not a result of natural selection. Exaptations can also arise from nonaptations; these are characters which had previously been evolving neutrally. All nonaptations are potential exaptations. The concept of exaptation was expanded to the molecular genetic level which aided greatly in understanding the enormous potential of neutrally evolving repetitive DNA-including transposed elements, formerly considered junk DNA-for the evolution of genes and genomes. The distinction between adaptations and exaptations is outlined in this review and examples are given. Also elaborated on is the fact that such distinctions are sometimes more difficult to determine; this is a widespread phenomenon in biology, where continua abound and clear borders between states and definitions are rare.
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Shaping Plant Adaptability, Genome Structure and Gene Expression through Transposable Element Epigenetic Control: Focus on Methylation. AGRONOMY-BASEL 2018. [DOI: 10.3390/agronomy8090180] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In plants, transposable elements (TEs) represent a large fraction of the genome, with potential to alter gene expression and produce genomic rearrangements. Epigenetic control of TEs is often used to stop unrestricted movement of TEs that would result in detrimental effects due to insertion in essential genes. The current review focuses on the effects of methylation on TEs and their genomic context, and how this type of epigenetic control affects plant adaptability when plants are faced with different stresses and changes. TEs mobilize in response to stress elicitors, including biotic and abiotic cues, but also developmental transitions and ‘genome shock’ events like polyploidization. These events transitionally lift TE repression, allowing TEs to move to new genomic locations. When TEs fall close to genes, silencing through methylation can spread to nearby genes, resulting in lower gene expression. The presence of TEs in gene promoter regions can also confer stress inducibility modulated through alternative methylation and demethylation of the TE. Bursts of transposition triggered by events of genomic shock can increase genome size and account for differences seen during polyploidization or species divergence. Finally, TEs have evolved several mechanisms to suppress their own repression, including the use of microRNAs to control genes that promote methylation. The interplay between silencing, transient TE activation, and purifying selection allows the genome to use TEs as a reservoir of potential beneficial modifications but also keeps TEs under control to stop uncontrolled detrimental transposition.
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46
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Shirai K, Matsuda F, Nakabayashi R, Okamoto M, Tanaka M, Fujimoto A, Shimizu M, Shinozaki K, Seki M, Saito K, Hanada K. A Highly Specific Genome-Wide Association Study Integrated with Transcriptome Data Reveals the Contribution of Copy Number Variations to Specialized Metabolites in Arabidopsis thaliana Accessions. Mol Biol Evol 2018; 34:3111-3122. [PMID: 28961930 DOI: 10.1093/molbev/msx234] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Lineage-specific gene duplications contribute to a large variation in specialized metabolites among different plant species. There is also considerable variability in the specialized metabolites within a single plant species. However, it is unclear whether copy number variations (CNVs) derived from gene duplication events contribute to the diversity of specialized metabolites within species. We identified metabolome quantitative trait genes (mQTGs) associated with quantitative metabolite variations and examined the relationship between mQTGs and CNVs. We obtained 1,335 specialized metabolite signals from 53 worldwide A. thaliana accessions using liquid chromatography-quadrupole time-of-flight mass spectrometry. In this study, genes associated with specialized metabolites were inferred by either a generally authorized genome-wide association study (GWAS) approach or a novel analysis of the association between gene expression and metabolite accumulation. Genes qualified by both analyses are defined to be mQTGs. The integrated method enabled us to detect mQTGs with a low false positive rate (=5.71 × 10-4). We also identified 5,654 genes associated with 1,335 specialized metabolites. Of these genes, 4.4% were affected by CNVs, which was more than expected (χ2 test: P < 0.01). This result suggests that CNVs contribute to variations in specialized metabolites within a species. To assess the contribution of CNVs to adaptive evolution in A. thaliana, we examined the selective sweeps around the mQTGs. We observed that the mQTGs with CNVs tended to undergo selective sweeps. These observations imply that variations in specialized metabolites caused by CNVs contribute to the adaptive evolution of A. thaliana.
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Affiliation(s)
- Kazumasa Shirai
- Frontier Research Academy for Young Researchers, Kyushu Institute of Technology, Fukuoka, Japan
| | - Fumio Matsuda
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan.,Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Ryo Nakabayashi
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
| | - Masanori Okamoto
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan.,Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Japan
| | - Maho Tanaka
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
| | - Akihiro Fujimoto
- Department of Drug Discovery Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan
| | - Minami Shimizu
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
| | - Kazuo Shinozaki
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
| | - Motoaki Seki
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
| | - Kazuki Saito
- Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan.,Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Kousuke Hanada
- Frontier Research Academy for Young Researchers, Kyushu Institute of Technology, Fukuoka, Japan.,Center for Sustainable Resource Science, RIKEN, Kanagawa, Japan
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47
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Fagnocchi L, Poli V, Zippo A. Enhancer reprogramming in tumor progression: a new route towards cancer cell plasticity. Cell Mol Life Sci 2018; 75:2537-2555. [PMID: 29691590 PMCID: PMC11105402 DOI: 10.1007/s00018-018-2820-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 04/11/2018] [Accepted: 04/17/2018] [Indexed: 12/13/2022]
Abstract
Cancer heterogeneity arises during tumor progression as a consequence of genetic insults, environmental cues, and reversible changes in the epigenetic state, favoring tumor cell plasticity. The role of enhancer reprogramming is emerging as a relevant field in cancer biology as it supports adaptation of cancer cells to those environmental changes encountered during tumor progression and metastasis seeding. In this review, we describe the cancer-related alterations that drive oncogenic enhancer activity, leading to dysregulated transcriptional programs. We discuss the molecular mechanisms of both cis- and trans-factors in overriding the regulatory circuits that maintain cell-type specificity and imposing an alternative, de-regulated enhancer activity in cancer cells. We further comment on the increasing evidence which implicates stress response and aging-signaling pathways in the enhancer landscape reprogramming during tumorigenesis. Finally, we focus on the potential therapeutic implications of these enhancer-mediated subverted transcriptional programs, putting particular emphasis on the lack of information regarding tumor progression and the metastatic outgrowth, which still remain the major cause of mortality related to cancer.
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Affiliation(s)
- Luca Fagnocchi
- Laboratory of Chromatin Biology and Epigenetics, Center for Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy.
| | - Vittoria Poli
- Laboratory of Chromatin Biology and Epigenetics, Center for Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy
| | - Alessio Zippo
- Laboratory of Chromatin Biology and Epigenetics, Center for Integrative Biology (CIBIO), University of Trento, 38123, Trento, Italy.
- Department of Epigenetics, Fondazione Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi", Via F. Sforza 35, 20122, Milan, Italy.
- Division of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
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48
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Nikitin D, Penzar D, Garazha A, Sorokin M, Tkachev V, Borisov N, Poltorak A, Prassolov V, Buzdin AA. Profiling of Human Molecular Pathways Affected by Retrotransposons at the Level of Regulation by Transcription Factor Proteins. Front Immunol 2018; 9:30. [PMID: 29441061 PMCID: PMC5797644 DOI: 10.3389/fimmu.2018.00030] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/04/2018] [Indexed: 12/22/2022] Open
Abstract
Endogenous retroviruses and retrotransposons also termed retroelements (REs) are mobile genetic elements that were active until recently in human genome evolution. REs regulate gene expression by actively reshaping chromatin structure or by directly providing transcription factor binding sites (TFBSs). We aimed to identify molecular processes most deeply impacted by the REs in human cells at the level of TFBS regulation. By using ENCODE data, we identified ~2 million TFBS overlapping with putatively regulation-competent human REs located in 5-kb gene promoter neighborhood (~17% of all TFBS in promoter neighborhoods; ~9% of all RE-linked TFBS). Most of REs hosting TFBS were highly diverged repeats, and for the evolutionary young (0–8% diverged) elements we identified only ~7% of all RE-linked TFBS. The gene-specific distributions of RE-linked TFBS generally correlated with the distributions for all TFBS. However, several groups of molecular processes were highly enriched in the RE-linked TFBS regulation. They were strongly connected with the immunity and response to pathogens, with the negative regulation of gene transcription, ubiquitination, and protein degradation, extracellular matrix organization, regulation of STAT signaling, fatty acids metabolism, regulation of GTPase activity, protein targeting to Golgi, regulation of cell division and differentiation, development and functioning of perception organs and reproductive system. By contrast, the processes most weakly affected by the REs were linked with the conservative aspects of embryo development. We also identified differences in the regulation features by the younger and older fractions of the REs. The regulation by the older fraction of the REs was linked mainly with the immunity, cell adhesion, cAMP, IGF1R, Notch, Wnt, and integrin signaling, neuronal development, chondroitin sulfate and heparin metabolism, and endocytosis. The younger REs regulate other aspects of immunity, cell cycle progression and apoptosis, PDGF, TGF beta, EGFR, and p38 signaling, transcriptional repression, structure of nuclear lumen, catabolism of phospholipids, and heterocyclic molecules, insulin and AMPK signaling, retrograde Golgi-ER transport, and estrogen signaling. The immunity-linked pathways were highly represented in both categories, but their functional roles were different and did not overlap. Our results point to the most quickly evolving molecular pathways in the recent and ancient evolution of human genome.
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Affiliation(s)
- Daniil Nikitin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Dmitry Penzar
- The Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Andrew Garazha
- D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,OmicsWay Corp., Walnut, CA, United States
| | - Maxim Sorokin
- OmicsWay Corp., Walnut, CA, United States.,National Research Centre Kurchatov Institute, Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - Nicolas Borisov
- OmicsWay Corp., Walnut, CA, United States.,National Research Centre Kurchatov Institute, Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow, Russia
| | - Alexander Poltorak
- Program in Immunology, Sackler Graduate School, Tufts University, Boston, MA, United States
| | - Vladimir Prassolov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anton A Buzdin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,OmicsWay Corp., Walnut, CA, United States.,National Research Centre Kurchatov Institute, Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow, Russia
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Schartl M, Schories S, Wakamatsu Y, Nagao Y, Hashimoto H, Bertin C, Mourot B, Schmidt C, Wilhelm D, Centanin L, Guiguen Y, Herpin A. Sox5 is involved in germ-cell regulation and sex determination in medaka following co-option of nested transposable elements. BMC Biol 2018; 16:16. [PMID: 29378592 PMCID: PMC5789577 DOI: 10.1186/s12915-018-0485-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/11/2018] [Indexed: 12/21/2022] Open
Abstract
Background Sex determination relies on a hierarchically structured network of genes, and is one of the most plastic processes in evolution. The evolution of sex-determining genes within a network, by neo- or sub-functionalization, also requires the regulatory landscape to be rewired to accommodate these novel gene functions. We previously showed that in medaka fish, the regulatory landscape of the master male-determining gene dmrt1bY underwent a profound rearrangement, concomitantly with acquiring a dominant position within the sex-determining network. This rewiring was brought about by the exaptation of a transposable element (TE) called Izanagi, which is co-opted to act as a silencer to turn off the dmrt1bY gene after it performed its function in sex determination. Results We now show that a second TE, Rex1, has been incorporated into Izanagi. The insertion of Rex1 brought in a preformed regulatory element for the transcription factor Sox5, which here functions in establishing the temporal and cell-type-specific expression pattern of dmrt1bY. Mutant analysis demonstrates the importance of Sox5 in the gonadal development of medaka, and possibly in mice, in a dmrt1bY-independent manner. Moreover, Sox5 medaka mutants have complete female-to-male sex reversal. Conclusions Our work reveals an unexpected complexity in TE-mediated transcriptional rewiring, with the exaptation of a second TE into a network already rewired by a TE. We also show a dual role for Sox5 during sex determination: first, as an evolutionarily conserved regulator of germ-cell number in medaka, and second, by de novo regulation of dmrt1 transcriptional activity during primary sex determination due to exaptation of the Rex1 transposable element. Electronic supplementary material The online version of this article (10.1186/s12915-018-0485-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Manfred Schartl
- Physiological Chemistry, Biocenter, University of Würzburg, 97074, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Hospital, 97080, Würzburg, Germany.,Texas Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Susanne Schories
- Physiological Chemistry, Biocenter, University of Würzburg, 97074, Würzburg, Germany
| | - Yuko Wakamatsu
- Physiological Chemistry, Biocenter, University of Würzburg, 97074, Würzburg, Germany
| | - Yusuke Nagao
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Hisashi Hashimoto
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Chloé Bertin
- INRA, UR1037 Fish Physiology and Genomics, F-35000, Rennes, France
| | - Brigitte Mourot
- INRA, UR1037 Fish Physiology and Genomics, F-35000, Rennes, France
| | - Cornelia Schmidt
- Physiological Chemistry, Biocenter, University of Würzburg, 97074, Würzburg, Germany
| | - Dagmar Wilhelm
- Department of Anatomy & Neuroscience, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Lazaro Centanin
- Centre for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Yann Guiguen
- INRA, UR1037 Fish Physiology and Genomics, F-35000, Rennes, France
| | - Amaury Herpin
- Physiological Chemistry, Biocenter, University of Würzburg, 97074, Würzburg, Germany. .,INRA, UR1037 Fish Physiology and Genomics, F-35000, Rennes, France.
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50
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Evidence for convergent evolution of SINE-directed Staufen-mediated mRNA decay. Proc Natl Acad Sci U S A 2018; 115:968-973. [PMID: 29339519 DOI: 10.1073/pnas.1715531115] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Primate-specific Alu short interspersed elements (SINEs) as well as rodent-specific B and ID (B/ID) SINEs can promote Staufen-mediated decay (SMD) when present in mRNA 3'-untranslated regions (3'-UTRs). The transposable nature of SINEs, their presence in long noncoding RNAs, their interactions with Staufen, and their rapid divergence in different evolutionary lineages suggest they could have generated substantial modification of posttranscriptional gene-control networks during mammalian evolution. Some of the variation in SMD regulation produced by SINE insertion might have had a similar regulatory effect in separate mammalian lineages, leading to parallel evolution of the Staufen network by independent expansion of lineage-specific SINEs. To explore this possibility, we searched for orthologous gene pairs, each carrying a species-specific 3'-UTR SINE and each regulated by SMD, by measuring changes in mRNA abundance after individual depletion of two SMD factors, Staufen1 (STAU1) and UPF1, in both human and mouse myoblasts. We identified and confirmed orthologous gene pairs with 3'-UTR SINEs that independently function in SMD control of myoblast metabolism. Expanding to other species, we demonstrated that SINE-directed SMD likely emerged in both primate and rodent lineages >20-25 million years ago. Our work reveals a mechanism for the convergent evolution of posttranscriptional gene regulatory networks in mammals by species-specific SINE transposition and SMD.
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