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Bodea GO, Botto JM, Ferreiro ME, Sanchez-Luque FJ, de Los Rios Barreda J, Rasmussen J, Rahman MA, Fenlon LR, Jansz N, Gubert C, Gerdes P, Bodea LG, Ajjikuttira P, Da Costa Guevara DJ, Cumner L, Bell CC, Kozulin P, Billon V, Morell S, Kempen MJHC, Love CJ, Saha K, Palmer LM, Ewing AD, Jhaveri DJ, Richardson SR, Hannan AJ, Faulkner GJ. LINE-1 retrotransposons contribute to mouse PV interneuron development. Nat Neurosci 2024:10.1038/s41593-024-01650-2. [PMID: 38773348 DOI: 10.1038/s41593-024-01650-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 04/14/2024] [Indexed: 05/23/2024]
Abstract
Retrotransposons are mobile DNA sequences duplicated via transcription and reverse transcription of an RNA intermediate. Cis-regulatory elements encoded by retrotransposons can also promote the transcription of adjacent genes. Somatic LINE-1 (L1) retrotransposon insertions have been detected in mammalian neurons. It is, however, unclear whether L1 sequences are mobile in only some neuronal lineages or therein promote neurodevelopmental gene expression. Here we report programmed L1 activation by SOX6, a transcription factor critical for parvalbumin (PV) interneuron development. Mouse PV interneurons permit L1 mobilization in vitro and in vivo, harbor unmethylated L1 promoters and express full-length L1 mRNAs and proteins. Using nanopore long-read sequencing, we identify unmethylated L1s proximal to PV interneuron genes, including a novel L1 promoter-driven Caps2 transcript isoform that enhances neuron morphological complexity in vitro. These data highlight the contribution made by L1 cis-regulatory elements to PV interneuron development and transcriptome diversity, uncovered due to L1 mobility in this milieu.
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Affiliation(s)
- Gabriela O Bodea
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia.
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland, Australia.
| | - Juan M Botto
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Maria E Ferreiro
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Francisco J Sanchez-Luque
- Institute of Parasitology and Biomedicine 'López-Neyra', Spanish National Research Council, Granada, Spain
| | | | - Jay Rasmussen
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Muhammed A Rahman
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Laura R Fenlon
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Natasha Jansz
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland, Australia
| | - Carolina Gubert
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
| | - Patricia Gerdes
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland, Australia
| | - Liviu-Gabriel Bodea
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Prabha Ajjikuttira
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Darwin J Da Costa Guevara
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland, Australia
| | - Linda Cumner
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Charles C Bell
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland, Australia
| | - Peter Kozulin
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Victor Billon
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- Biology Department, École Normale Supérieure Paris-Saclay, Gif-sur-Yvette, France
| | - Santiago Morell
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland, Australia
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Marie-Jeanne H C Kempen
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Chloe J Love
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
| | - Karabi Saha
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, USA
| | - Lucy M Palmer
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
- Florey Department of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
| | - Adam D Ewing
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland, Australia
| | - Dhanisha J Jhaveri
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland, Australia
| | - Sandra R Richardson
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland, Australia
| | - Anthony J Hannan
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
| | - Geoffrey J Faulkner
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia.
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, Queensland, Australia.
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Workman S, Richardson SR. Every repeat is unique: Exploring the genomic impact of human L1 retrotransposons at locus-specific resolution. CELL GENOMICS 2024; 4:100504. [PMID: 38359785 PMCID: PMC10879126 DOI: 10.1016/j.xgen.2024.100504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/17/2024]
Abstract
Fully understanding the impact of the human retrotransposon L1 requires that each of ∼500,000 L1 copies be evaluated as a potentially unique genomic entity. In this issue of Cell Genomics, Lanciano et al.1 strive toward this goal, illuminating the reciprocal regulatory influence between individual L1s and their genomic integration sites.
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Affiliation(s)
- Stephanie Workman
- Mater Research Institute-University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Sandra R Richardson
- Mater Research Institute-University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia.
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Sakamoto M, Ishiuchi T. YY1-dependent transcriptional regulation manifests at the morula stage. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001108. [PMID: 38298464 PMCID: PMC10828890 DOI: 10.17912/micropub.biology.001108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/16/2024] [Accepted: 01/15/2024] [Indexed: 02/02/2024]
Abstract
YY1 plays multifaceted roles in various cell types. We recently reported that YY1 regulates nucleosome organization in early mouse embryos. However, despite the impaired nucleosome organization in the absence of YY1, the transcriptome was minimally affected in eight-cell embryos. We then hypothesized that YY1 might prepare a chromatin environment to regulate gene expression at later stages. To test this possibility, we performed a transcriptome analysis at the morula stage. We found that a substantial number of genes are aberrantly expressed in the absence of YY1. Furthermore, our analysis revealed that YY1 is required for the transcription of LINE-1 retrotransposons.
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Affiliation(s)
- Mizuki Sakamoto
- Faculty of Life and Environmental Sciences, University of Yamanashi, Kofu, Yamanashi, Japan
| | - Takashi Ishiuchi
- Faculty of Life and Environmental Sciences, University of Yamanashi, Kofu, Yamanashi, Japan
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Saha K, Nielsen GI, Nandani R, Kong L, Ye P, An W. YY1 is a transcriptional activator of mouse LINE-1 Tf subfamily. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.573552. [PMID: 38260579 PMCID: PMC10802269 DOI: 10.1101/2024.01.03.573552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Long interspersed element type 1 (LINE-1, L1) is an active autonomous transposable element (TE) in the human genome. The first step of L1 replication is transcription, which is controlled by an internal RNA polymerase II promoter in the 5' untranslated region (UTR) of a full-length L1. It has been shown that transcription factor YY1 binds to a conserved sequence motif at the 5' end of the human L1 5'UTR and dictates where transcription initiates but not the level of transcription. Putative YY1-binding motifs have been predicted in the 5'UTRs of two distinct mouse L1 subfamilies, Tf and Gf. Using site-directed mutagenesis, in vitro binding, and gene knockdown assays, we experimentally tested the role of YY1 in mouse L1 transcription. Our results indicate that Tf, but not Gf subfamily, harbors functional YY1-binding sites in its 5'UTR monomers. In contrast to its role in human L1, YY1 functions as a transcriptional activator for the mouse Tf subfamily. Furthermore, YY1-binding motifs are solely responsible for the synergistic interaction between monomers, consistent with a model wherein distant monomers act as enhancers for mouse L1 transcription. The abundance of YY1-binding sites in Tf elements also raise important implications for gene regulation at the genomic level.
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Affiliation(s)
- Karabi Saha
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD 57007, USA
| | - Grace I. Nielsen
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD 57007, USA
| | - Raj Nandani
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD 57007, USA
| | - Lingqi Kong
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD 57007, USA
| | - Ping Ye
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD 57007, USA
| | - Wenfeng An
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD 57007, USA
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