Promoters of germline transposon silencing genes evolve rapidly accompanied by diverging gene expression DOI Creative Commons
David W. J. McQuarrie, Azad Alizada, Benjamin Czech Nicholson

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Ноя. 2, 2023

Abstract Background The piRNA pathway in animal gonads functions as an ‘RNA-based immune system’, serving to silence transposable elements and prevent inheritance of novel invaders. In Drosophila , this relies on three gonad-specific Argonaute proteins (Argonaute-3, Aubergine Piwi) that associate with 23-28 nucleotide piRNAs, directing the silencing transposon-derived transcripts. Transposons constitute a primary driver genome evolution, yet evolution factors has not received in-depth exploration. Specifically, channel nuclear pore proteins, which impact processing, exhibit regions rapid their promoters. Consequently, question arises whether such mode is general feature transposon pathways. Results By employing genomic analysis coding promoter within genes function we demonstrate promoters germ cell-specific are undergoing evolution. Our findings indicate common trait among engaged germline across insect species, potentially contributing gene expression divergence closely related taxa. Furthermore, observe exclusively expressed cells generally some expression. Conclusion results suggest increased partnership other factors, could contribute species through differential driven by invading transposons.

Язык: Английский

Impact of a horizontally transferred Helitron family on genome evolution in Xenopus laevis DOI Creative Commons
Zhen Li, Nicolas Pollet

Mobile DNA, Год журнала: 2025, Номер 16(1)

Опубликована: Апрель 16, 2025

Язык: Английский

Процитировано

0
SVA Regulation of Transposable Element Clustered Transcription within the Major Histocompatibility Complex Genomic Class II Region of the Parkinson’s Progression Markers Initiative DOI Open Access
Jerzy K. Kulski, Abigail L. Pfaff,

Sulev Kõks

и другие.

Genes, Год журнала: 2024, Номер 15(9), С. 1185 - 1185

Опубликована: Сен. 9, 2024

SINE-VNTR-Alu (SVA) retrotransposons can regulate expression quantitative trait loci (eQTL) of coding and noncoding genes including transposable elements (TEs) distributed throughout the human genome. Previously, we reported that expressed SVAs leucocyte antigen (HLA) class II genotypes on chromosome 6 were associated significantly with Parkinson’s disease (PD). Here, our aim was to follow-up previous study evaluate SVA associations their regulatory effects transcription TEs within HLA genomic region. We reanalyzed transcriptome data peripheral blood cells from Progression Markers Initiative (PPMI) for 1530 subjects TE gene RNAs publicly available computing packages. Four structurally polymorphic 20 distinct clusters 235 represented by LINES (37%), SINES (28%), LTR/ERVs (23%), ancient transposon DNA (12%) are located in close proximity genes. The transcribed mostly short length, an average size 389 nucleotides. numbers, types profiles positive negative regulation varied markedly between four SVAs. appear be enhancer-like coordinated differentially Future work mechanisms underlying potential impact is essential elucidating roles normal cellular processes pathogenesis.

Язык: Английский

Процитировано

2
rDNA magnification is a unique feature of germline stem cells DOI Creative Commons
Jonathan O. Nelson, Tomohiro Kumon, Yukiko Yamashita

и другие.

Proceedings of the National Academy of Sciences, Год журнала: 2023, Номер 120(47)

Опубликована: Ноя. 15, 2023

Ribosomal DNA (rDNA) encodes ribosomal RNA and exists as tandem repeats of hundreds copies in the eukaryotic genome to meet high demand ribosome biogenesis. Tandemly repeated elements are inherently unstable; thus, mechanisms must exist maintain rDNA copy number (CN), particular germline that continues through generations. A phenomenon called magnification was discovered over 50 y ago Drosophila a process recovers CN on chromosomes harbor minimal CN. Our recent studies indicated is mechanism under physiological conditions counteract spontaneous loss occurs during aging. previous explored implied asymmetric division stem cells (GSCs) may be particularly suited achieve magnification. However, it remains elusive whether GSCs unique cell type undergoes or differentiating germ also capable In this study, we provide empirical evidence suggests operates uniquely GSCs, but not cells. We further computer simulation only achievable GSC divisions. propose despite known plasticity transcriptomic similarity between cells, GSCs’ ability divide asymmetrically serves critical role maintaining generations, supporting immortality.

Язык: Английский

Процитировано

6
Rapid evolution of promoters from germline-specifically expressed genes including transposon silencing factors DOI Creative Commons
David W. J. McQuarrie, Azad Alizada, Benjamin Czech Nicholson

и другие.

BMC Genomics, Год журнала: 2024, Номер 25(1)

Опубликована: Июль 8, 2024

Abstract Background The piRNA pathway in animal gonads functions as an ‘RNA-based immune system’, serving to silence transposable elements and prevent inheritance of novel invaders. In Drosophila , this relies on three gonad-specific Argonaute proteins (Argonaute-3, Aubergine Piwi) that associate with 23–28 nucleotide piRNAs, directing the silencing transposon-derived transcripts. Transposons constitute a primary driver genome evolution, yet evolution factors has not received in-depth exploration. Specifically, channel nuclear pore proteins, which impact processing, exhibit regions rapid their promoters. Consequently, question arises whether such mode is general feature transposon pathways. Results By employing genomic analysis coding promoter within genes function we demonstrate promoters germ cell-specific are undergoing evolution. Our findings indicate common trait among engaged germline across insect species, potentially contributing gene expression divergence closely related taxa. Furthermore, observe exclusively expressed cells generally some expression. Conclusion results suggest increased partnership other factors, could contribute species through differential driven by invading transposons.

Язык: Английский

Процитировано

1
Temporal and spatial niche partitioning in a retrotransposon community of the Drosophila genome DOI Open Access

Marion Varoqui,

Mourdas Mohamed, Bruno Mugat

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Авг. 16, 2024

Summary Transposable elements (TEs), widespread genetic parasites, pose potential threats to the stability of their host genomes. Hence, interactions observed today between TEs and genomes, as well among different TE species coexisting in same host, likely reflect those that did not lead extinction either or TEs. It is clear what extent expression integration steps replication cycles are involved this ‘peaceful’ coexistence. Here, we show four Drosophila LTR RetroTransposable Elements (LTR-RTEs), although sharing overall mechanism, preferentially integrate into distinct open chromatin domains germline. Notably, differential expressions gtwin ZAM LTR-RTEs ovarian embryonic somatic tissues, respectively, result timings targeting accessible landscapes differ early late nuclei, highlighting connections temporal spatial niche partitionings.

Язык: Английский

Процитировано

1
Heat stress drives transcription of LTR retrotransposons in the regenerative flatwormMacrostomum lignano DOI Creative Commons
Kirill Ustyantsev, Stijn Mouton, Mikhail V. Biryukov

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Дек. 21, 2024

Abstract The evolutionary arms race between transposable elements (TEs) and their hosts contributes to genomic complexity. As TEs mobilization is deleterious for individual cells organisms, activity restricted. During stress, can be reactivated; however, the exact mechanisms vary. We discovered that in flatworm Macrostomum lignano , LTR retrotransposons hijack heat shock response pathway boost transcription at elevated temperatures. While it has been well-described cruciferous plants, this first report of mechanism animal retrotransposons. Our results suggest a convergent evolution stress from animals plants.

Язык: Английский

Процитировано

0
Bi-directional Transcription, Double-Stranded RNA and the Implications on Genome Evolution DOI

Surar Al-Hashimi,

Shaymaa Sadeq,

Andreas Werner

и другие.

Опубликована: Янв. 1, 2024

Язык: Английский

Процитировано

0
Size evolution of gigantic genomes suggests stochastic outcomes of transposable element/host silencing interactions DOI Creative Commons
Jie Wang, Guangpu Zhang, Cheng Sun

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июль 23, 2024

Abstract Size evolution among gigantic genomes involves gain and loss of many gigabases transposable elements (TEs), sequences that parasitize host genomes. Animals suppress TEs using piRNA KRAB-ZFP pathways. hosts coevolve in an arms race, where suppression strength reflects TE fitness costs. In enormous genomes, additional costs become miniscule. How, then, do invoke further addition massive DNA amounts? We analyzed proliferation histories, deletion rates, community diversities six salamander (21.3 - 49.9 Gb), alongside gonadal expression activity is higher testes than ovaries, attributable to lower suppression. Unexpectedly, genome size/expansion uncorrelated with rate, history, expression, Also, diversity increases size, contrasting theoretical predictions. TE/host antagonism likely produces stochastic accumulation, determined by noisy intermolecular interactions huge genomes/cells.

Язык: Английский

Процитировано

0
Promoters of germline transposon silencing genes evolve rapidly accompanied by diverging gene expression DOI Creative Commons
David W. J. McQuarrie, Azad Alizada, Benjamin Czech Nicholson

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Ноя. 2, 2023

Abstract Background The piRNA pathway in animal gonads functions as an ‘RNA-based immune system’, serving to silence transposable elements and prevent inheritance of novel invaders. In Drosophila , this relies on three gonad-specific Argonaute proteins (Argonaute-3, Aubergine Piwi) that associate with 23-28 nucleotide piRNAs, directing the silencing transposon-derived transcripts. Transposons constitute a primary driver genome evolution, yet evolution factors has not received in-depth exploration. Specifically, channel nuclear pore proteins, which impact processing, exhibit regions rapid their promoters. Consequently, question arises whether such mode is general feature transposon pathways. Results By employing genomic analysis coding promoter within genes function we demonstrate promoters germ cell-specific are undergoing evolution. Our findings indicate common trait among engaged germline across insect species, potentially contributing gene expression divergence closely related taxa. Furthermore, observe exclusively expressed cells generally some expression. Conclusion results suggest increased partnership other factors, could contribute species through differential driven by invading transposons.

Язык: Английский

Процитировано

0