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Thematische Bibliographien / PiRNA clusters / Zeitschriftenartikel

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Zeitschriftenartikel zum Thema „PiRNA clusters“

Autor: Grafiati

Veröffentlicht am 25. Mai 2024

Zuletzt aktualisiert am 25. Juli 2025

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1

Komarov, Pavel A., Olesya Sokolova, Natalia Akulenko, Emilie Brasset, Silke Jensen, and Alla Kalmykova. "Epigenetic Requirements for Triggering Heterochromatinization and Piwi-Interacting RNA Production from Transgenes in the Drosophila Germline." Cells 9, no. 4 (2020): 922. http://dx.doi.org/10.3390/cells9040922.

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Transgenes containing a fragment of the I retrotransposon represent a powerful model of piRNA cluster de novo formation in the Drosophila germline. We revealed that the same transgenes located at different genomic loci form piRNA clusters with various capacity of small RNA production. Transgenic piRNA clusters are not established in piRNA pathway mutants. However, in the wild-type context, the endogenous ancestral I-related piRNAs heterochromatinize and convert the I-containing transgenes into piRNA-producing loci. Here, we address how the quantitative level of piRNAs influences the heterochro

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Radion, Elizaveta, Olesya Sokolova, Sergei Ryazansky, Pavel Komarov, Yuri Abramov, and Alla Kalmykova. "The Integrity of piRNA Clusters is Abolished by Insulators in the Drosophila Germline." Genes 10, no. 3 (2019): 209. http://dx.doi.org/10.3390/genes10030209.

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Piwi-interacting RNAs (piRNAs) control transposable element (TE) activity in the germline. piRNAs are produced from single-stranded precursors transcribed from distinct genomic loci, enriched by TE fragments and termed piRNA clusters. The specific chromatin organization and transcriptional regulation of Drosophila germline-specific piRNA clusters ensure transcription and processing of piRNA precursors. TEs harbour various regulatory elements that could affect piRNA cluster integrity. One of such elements is the suppressor-of-hairy-wing (Su(Hw))-mediated insulator, which is harboured in the ret

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Bespalova, Alina V., Dina A. Kulikova, Elena S. Zelentsova, et al. "Paramutation-Like Behavior of Genic piRNA-Producing Loci in Drosophila virilis." International Journal of Molecular Sciences 26, no. 9 (2025): 4243. https://doi.org/10.3390/ijms26094243.

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Piwi-interacting RNAs (piRNAs) play a crucial role in silencing transposable elements (TEs) in the germ cells of Metazoa by acting as sequence-specific guides. Originating from distinct genomic loci, called piRNA clusters, piRNA can trigger an epigenetic conversion of TE insertions into piRNA clusters by means of a paramutation-like process. However, the variability in piRNA clusters’ capacity to induce such conversions remains poorly understood. Here, we investigated two Drosophila virilis strains with differing capacities to produce piRNAs from the subtelomeric RhoGEF3 and Adar gene loci. We

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Chen, Peiwei, Yicheng Luo, and Alexei A. Aravin. "RDC complex executes a dynamic piRNA program during Drosophila spermatogenesis to safeguard male fertility." PLOS Genetics 17, no. 9 (2021): e1009591. http://dx.doi.org/10.1371/journal.pgen.1009591.

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piRNAs are small non-coding RNAs that guide the silencing of transposons and other targets in animal gonads. In Drosophila female germline, many piRNA source loci dubbed “piRNA clusters” lack hallmarks of active genes and exploit an alternative path for transcription, which relies on the Rhino-Deadlock-Cutoff (RDC) complex. RDC was thought to be absent in testis, so it remains to date unknown how piRNA cluster transcription is regulated in the male germline. We found that components of RDC complex are expressed in male germ cells during early spermatogenesis, from germline stem cells (GSCs) to

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Assis, Raquel, and Alexey S. Kondrashov. "Rapid repetitive element-mediated expansion of piRNA clusters in mammalian evolution." Proceedings of the National Academy of Sciences 106, no. 17 (2009): 7079–82. http://dx.doi.org/10.1073/pnas.0900523106.

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Piwi-interacting RNAs (piRNAs) are ≈30 nucleotide noncoding RNAs that may be involved in transposon silencing in mammalian germline cells. Most piRNA sequences are found in a small number of genomic regions referred to as clusters, which range from 1 to hundreds of kilobases. We studied the evolution of 140 rodent piRNA clusters, 103 of which do not overlap protein-coding genes. Phylogenetic analysis revealed that 14 clusters were acquired after rat–mouse divergence and another 44 after rodent–primate divergence. Most clusters originated in a process analogous to the duplication of protein-cod

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Story, Benjamin, Xing Ma, Kazue Ishihara, et al. "Defining the expression of piRNA and transposable elements in Drosophila ovarian germline stem cells and somatic support cells." Life Science Alliance 2, no. 5 (2019): e201800211. http://dx.doi.org/10.26508/lsa.201800211.

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Piwi-interacting RNAs (piRNAs) are important for repressing transposable elements (TEs) and modulating gene expression in germ cells, thereby maintaining genome stability and germ cell function. Although they are also important for maintaining germline stem cells (GSCs) in the Drosophila ovary by repressing TEs and preventing DNA damage, piRNA expression has not been investigated in GSCs or their early progeny. Here, we show that the canonical piRNA clusters are more active in GSCs and their early progeny than late germ cells and also identify more than 3,000 new piRNA clusters from deep seque

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Iyer, Shantanu S., Yidan Sun, Janine Seyfferth, et al. "The NSL complex is required for piRNA production from telomeric clusters." Life Science Alliance 6, no. 9 (2023): e202302194. http://dx.doi.org/10.26508/lsa.202302194.

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The NSL complex is a transcriptional activator. Germline-specific knockdown of NSL complex subunits NSL1, NSL2, and NSL3 results in reduced piRNA production from a subset of bidirectional piRNA clusters, accompanied by widespread transposon derepression. The piRNAs most transcriptionally affected by NSL2 and NSL1 RNAi map to telomeric piRNA clusters. At the chromatin level, these piRNA clusters also show decreased levels of H3K9me3, HP1a, and Rhino after NSL2 depletion. Using NSL2 ChIP-seq in ovaries, we found that this protein specifically binds promoters of telomeric transposonsHeT-A,TAHRE,

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Wang, Sheng, Xiaohua Lu, Ding Qiu, and Yang Yu. "To export, or not to export: how nuclear export factor variants resolve Piwi's dilemma." Biochemical Society Transactions 49, no. 5 (2021): 2073–79. http://dx.doi.org/10.1042/bst20201171.

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Piwi-interacting RNAs (piRNAs) defend animal gonads by guiding PIWI-clade Argonaute proteins to silence transposons. The nuclear Piwi/piRNA complexes confer transcriptional repression of transposons, which is accompanied with heterochromatin formation at target loci. On the other hand, piRNA clusters, genomic loci that transcribe piRNA precursors composed of transposon fragments, are often recognized by piRNAs to define their heterochromatic identity. Therefore, Piwi/piRNA complexes must resolve this conundrum of silencing transposons while allowing the expression of piRNA precursors, at least

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Wang, Jiajia, Yirong Shi, Honghong Zhou, et al. "piRBase: integrating piRNA annotation in all aspects." Nucleic Acids Research 50, no. D1 (2021): D265—D272. http://dx.doi.org/10.1093/nar/gkab1012.

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Abstract Piwi-interacting RNAs are a type of small noncoding RNA that have various functions. piRBase is a manually curated resource focused on assisting piRNA functional analysis. piRBase release v3.0 is committed to providing more comprehensive piRNA related information. The latest release covers &gt;181 million unique piRNA sequences, including 440 datasets from 44 species. More disease-related piRNAs and piRNA targets have been collected and displayed. The regulatory relationships between piRNAs and targets have been visualized. In addition to the reuse and expansion of the content in

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Kofler, Robert. "piRNA Clusters Need a Minimum Size to Control Transposable Element Invasions." Genome Biology and Evolution 12, no. 5 (2020): 736–49. http://dx.doi.org/10.1093/gbe/evaa064.

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Abstract piRNA clusters are thought to repress transposable element (TE) activity in mammals and invertebrates. Here, we show that a simple population genetics model reveals a constraint on the size of piRNA clusters: The total size of the piRNA clusters of an organism must exceed 0.2% of a genome to repress TE invasions. Moreover, larger piRNA clusters accounting for up to 3% of the genome may be necessary when populations are small, transposition rates are high, and TE insertions are recessive. If piRNA clusters are too small, the load of deleterious TE insertions that accumulate during a TE

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Huang, Xinya, Peng Cheng, Chenchun Weng, et al. "A chromodomain protein mediates heterochromatin-directed piRNA expression." Proceedings of the National Academy of Sciences 118, no. 27 (2021): e2103723118. http://dx.doi.org/10.1073/pnas.2103723118.

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PIWI-interacting RNAs (piRNAs) play significant roles in suppressing transposons, maintaining genome integrity, and defending against viral infections. How piRNA source loci are efficiently transcribed is poorly understood. Here, we show that in Caenorhabditis elegans, transcription of piRNA clusters depends on the chromatin microenvironment and a chromodomain-containing protein, UAD-2. piRNA clusters form distinct focus in germline nuclei. We conducted a forward genetic screening and identified UAD-2 that is required for piRNA focus formation. In the absence of histone 3 lysine 27 methylation

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Paniagua, Nancy, C. Jackson Roberts, Lauren E. Gonzalez, David Monedero-Alonso, and Valerie Reinke. "The Upstream Sequence Transcription Complex dictates nucleosome positioning and promoter accessibility at piRNA genes in the C. elegans germ line." PLOS Genetics 20, no. 7 (2024): e1011345. http://dx.doi.org/10.1371/journal.pgen.1011345.

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The piRNA pathway is a conserved germline-specific small RNA pathway that ensures genomic integrity and continued fertility. In C. elegans and other nematodes, Type-I piRNAs are expressed from >10,000 independently transcribed genes clustered within two discrete domains of 1.5 and 3.5 MB on Chromosome IV. Clustering of piRNA genes contributes to their germline-specific expression, but the underlying mechanisms are unclear. We analyze isolated germ nuclei to demonstrate that the piRNA genomic domains are located in a heterochromatin-like environment. USTC (Upstream Sequence Transcription Com

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Ji, Qun, Zhengli Xie, Wu Gan, Lumin Wang, and Wei Song. "Identification and Characterization of PIWI-Interacting RNAs in Spinyhead Croakers (Collichthys lucidus) by Small RNA Sequencing." Fishes 7, no. 5 (2022): 297. http://dx.doi.org/10.3390/fishes7050297.

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PIWI-interacting RNAs (piRNAs) are an emerging class of small RNAs which protect the animal germline genome against deleterious transposable elements. Nevertheless, the characteristics and sex-related expression patterns of piRNA in Collichthys lucidus remain unknown. In this study, we first performed systematic next-generation high-throughput sequencing in C. lucidus ovaries and testes. We identified 3,027,834 piRNAs across six gonad libraries. Of these, 2225 piRNAs were differently expressed between testes and ovaries; 1195 were upregulated and 1030 downregulated in the testes. Interestingly

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Shoji, Keisuke, Yusuke Umemura, Susumu Katsuma, and Yukihide Tomari. "The piRNA cluster torimochi is an expanding transposon in cultured silkworm cells." PLOS Genetics 19, no. 2 (2023): e1010632. http://dx.doi.org/10.1371/journal.pgen.1010632.

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PIWI proteins and PIWI-interacting RNAs (piRNAs) play a central role in repressing transposable elements in animal germ cells. It is thought that piRNAs are mainly produced from discrete genomic loci named piRNA clusters, which often contain many “dead” transposon remnants from past invasions and have heterochromatic features. In the genome of silkworm ovary-derived cultured cells called BmN4, a well-established model for piRNA research, torimochi was previously annotated as a unique and specialized genomic region that can capture transgenes and produce new piRNAs bearing a trans-silencing act

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Tsai, Shih-Ying, and Fu Huang. "Acetyltransferase Enok regulates transposon silencing and piRNA cluster transcription." PLOS Genetics 17, no. 2 (2021): e1009349. http://dx.doi.org/10.1371/journal.pgen.1009349.

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The piRNA pathway is a highly conserved mechanism to repress transposon activation in the germline in Drosophila and mammals. This pathway starts from transcribing piRNA clusters to generate long piRNA precursors. The majority of piRNA clusters lack conventional promoters, and utilize heterochromatin- and HP1D/Rhino-dependent noncanonical mechanisms for transcription. However, information regarding the transcriptional regulation of piRNA clusters is limited. Here, we report that the Drosophila acetyltransferase Enok, which can activate transcription by acetylating H3K23, is critical for piRNA

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Geles, Konstantinos, Domenico Palumbo, Assunta Sellitto, et al. "WIND (Workflow for pIRNAs aNd beyonD): a strategy for in-depth analysis of small RNA-seq data." F1000Research 10 (May 14, 2021): 1. http://dx.doi.org/10.12688/f1000research.27868.2.

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Current bioinformatics workflows for PIWI-interacting RNA (piRNA) analysis focus primarily on germline-derived piRNAs and piRNA-clusters. Frequently, they suffer from outdated piRNA databases, questionable quantification methods, and lack of reproducibility. Often, pipelines specific to miRNA analysis are used for the piRNA research in silico. Furthermore, the absence of a well-established database for piRNA annotation, as for miRNA, leads to uniformity issues between studies and generates confusion for data analysts and biologists. For these reasons, we have developed WIND (Workflow for pIRNA

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Geles, Konstantinos, Domenico Palumbo, Assunta Sellitto, et al. "WIND (Workflow for pIRNAs aNd beyonD): a strategy for in-depth analysis of small RNA-seq data." F1000Research 10 (July 12, 2021): 1. http://dx.doi.org/10.12688/f1000research.27868.3.

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Current bioinformatics workflows for PIWI-interacting RNA (piRNA) analysis focus primarily on germline-derived piRNAs and piRNA-clusters. Frequently, they suffer from outdated piRNA databases, questionable quantification methods, and lack of reproducibility. Often, pipelines specific to miRNA analysis are used for the piRNA research in silico. Furthermore, the absence of a well-established database for piRNA annotation, as for miRNA, leads to uniformity issues between studies and generates confusion for data analysts and biologists. For these reasons, we have developed WIND (Workflow for pIRNA

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Geles, Konstantinos, Domenico Palumbo, Assunta Sellitto, et al. "WIND (Workflow for pIRNAs aNd beyonD): a strategy for in-depth analysis of small RNA-seq data." F1000Research 10 (January 4, 2021): 1. http://dx.doi.org/10.12688/f1000research.27868.1.

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Current bioinformatics workflows for PIWI-interacting RNA (piRNA) analysis focus primarily on germline-derived piRNAs and piRNA-clusters. Frequently, they suffer from outdated piRNA databases, questionable quantification methods, and lack of reproducibility. Often, pipelines specific to miRNA analysis are used for the piRNA research in silico. Furthermore, the absence of a well-established database for piRNA annotation, as for miRNA, leads to uniformity issues between studies and generates confusion for data analysts and biologists. For these reasons, we have developed WIND (Workflow for pIRNA

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Huang, Ying, and Bowen Yu. "Structural studies of Rhino protein in piRNA biogenesis." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C1589. http://dx.doi.org/10.1107/s2053273314084101.

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Small-RNA-guided gene regulation is a common biological process in eukaryotic cells. Animal germ cells are characterized by an intriguing small-RNA-mediated gene-silencing mechanism known as PIWI pathway. PIWI-interacting RNAs (piRNAs) are small, 21-30 nt single-stranded RNAs that associate with PIWI proteins. The function of piRNA is silencing transposon elements in germ line cells to keep the genome integrity since germ line cells are the only source for transmitting genetic information to the next generation. For a long time the biogenesis of piRNA and the mechanism of how it functions rema

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Abajorga, Milky, Leonid Yurkovetskiy, and Jeremy Luban. "piRNA Defense Against Endogenous Retroviruses." Viruses 16, no. 11 (2024): 1756. http://dx.doi.org/10.3390/v16111756.

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Infection by retroviruses and the mobilization of transposable elements cause DNA damage that can be catastrophic for a cell. If the cell survives, the mutations generated by retrotransposition may confer a selective advantage, although, more commonly, the effect of new integrants is neutral or detrimental. If retrotransposition occurs in gametes or in the early embryo, it introduces genetic modifications that can be transmitted to the progeny and may become fixed in the germline of that species. PIWI-interacting RNAs (piRNAs) are single-stranded, 21–35 nucleotide RNAs generated by the PIWI cl

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Kamenova, Saltanat, Aksholpan Sharapkhanova, Aigul Akimniyazova, et al. "piRNA and miRNA can Suppress the Expression of Multiple Sclerosis Candidate Genes." Nanomaterials 13, no. 1 (2022): 22. http://dx.doi.org/10.3390/nano13010022.

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Multiple sclerosis (MS) is a common inflammatory demyelinating disease with a high mortality rate. MS is caused by many candidate genes whose specific involvement has yet to be established. The aim of our study was to identify endogenous miRNAs and piRNAs involved in the regulation of MS candidate gene expression using bioinformatic methods. A program was used to quantify the interaction of miRNA and piRNA nucleotides with mRNA of the target genes. We used 7310 miRNAs from three databases and 40,000 piRNAs. The mRNAs of the candidate genes revealed miRNA binding sites (BSs), which were located

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Ahrend, Franziska, Parthena Konstantinidou, Zuzana Loubalova, et al. "Protocol for assembling, prioritizing, and characterizing piRNA clusters using the piRNA Cluster Builder." STAR Protocols 6, no. 2 (2025): 103759. https://doi.org/10.1016/j.xpro.2025.103759.

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Fromm, Bastian, Juan Pablo Tosar, Felipe Aguilera, Marc R. Friedländer, Lutz Bachmann, and Andreas Hejnol. "Evolutionary Implications of the microRNA- and piRNA Complement of Lepidodermella squamata (Gastrotricha)." Non-Coding RNA 5, no. 1 (2019): 19. http://dx.doi.org/10.3390/ncrna5010019.

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Gastrotrichs—'hairy bellies’—are microscopic free-living animals inhabiting marine and freshwater habitats. Based on morphological and early molecular analyses, gastrotrichs were placed close to nematodes, but recent phylogenomic analyses have suggested their close relationship to flatworms (Platyhelminthes) within Spiralia. Small non-coding RNA data on e.g., microRNAs (miRNAs) and PIWI-interacting RNAs (piRNA) may help to resolve this long-standing question. MiRNAs are short post-transcriptional gene regulators that together with piRNAs play key roles in development. In a ‘multi-omics’ approa

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Milyaeva, P. A., A. R. Lavrenov, I. V. Kuzmin, A. I. Kim, and L. N. Nefedova. "Regulation of Uni-Strand and Dual-Strand piRNA Clusters in Germ and Somatic Tissues in <i>Drosophila melanogaster</i> under Control of <i>rhino</i>." Генетика 59, no. 12 (2023): 1372–81. http://dx.doi.org/10.31857/s0016675823120056.

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Drosophila melanogaster is a common genetic object for research of RNA-interference pathways and mobile elements regulation. Nowadays taking a part in control of retrotransposon expression the system of piRNA-interfecence well studied in ovary tissues. It is strongly believed that D. melanogaster piRNA-interference is used for retrotransposon suppression only in gonads, and two distinct pathways of piRNA biogenesis exist. Both mechanisms use transcripts of piRNA-clusters (accumulations of truncated and defect mobile elements copies): from unstrand clusters in the first case and from dualstrand

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Altshuller, Yelena, Qun Gao, and Michael A. Frohman. "A C-Terminal Transmembrane Anchor Targets the Nuage-Localized Spermatogenic Protein Gasz to the Mitochondrial Surface." ISRN Cell Biology 2013 (July 15, 2013): 1–7. http://dx.doi.org/10.1155/2013/707930.

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Mitochondria, normally tubular and distributed throughout the cell, are instead found in spermatocytes in perinuclear clusters in close association with nuage, an amorphous organelle composed of RNA and RNA-processing proteins that generate piRNAs. piRNAs are a form of RNAi required for transposon suppression and ultimately fertility. MitoPLD, another protein required for piRNA production, is anchored to the mitochondrial surface, suggesting that the nuage, also known as intermitochondrial cement, needs to be juxtaposed there to bring MitoPLD into proximity with the remainder of the piRNA-gene

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Le Thomas, Adrien, Evelyn Stuwe, Sisi Li, et al. "Transgenerationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing." Genes & Development 28, no. 15 (2014): 1667–80. http://dx.doi.org/10.1101/gad.245514.114.

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Lee, SePil, Satomi Kuramochi-Miyagawa, Ippei Nagamori, and Toru Nakano. "Effects of transgene insertion loci and copy number on Dnmt3L gene silencing through antisense transgene-derived PIWI-interacting RNAs." RNA 28, no. 5 (2022): 683–96. http://dx.doi.org/10.1261/rna.078905.121.

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PIWI-interacting RNAs (piRNAs), which are germ cell-specific small RNAs, are essential for spermatogenesis. In fetal mouse germ cells, piRNAs are synthesized from sense and antisense RNAs of transposable element sequences for retrotransposon silencing. In a previous study, we reported that transgenic mice expressing antisense-Dnmt3L under the control of the Miwi2 promoter (Tg-Miwi2P-asDnmt3L) exhibited piRNA-mediated DNMT3L down-regulation. In this study, two transgene integration loci (B3 and E1) were identified on chromosome 18 of the Tg-Miwi2P-asDnmt3L mice; these loci were weak piRNA clust

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Yamanaka, Soichiro, Mikiko C. Siomi, and Haruhiko Siomi. "piRNA clusters and open chromatin structure." Mobile DNA 5, no. 1 (2014): 22. http://dx.doi.org/10.1186/1759-8753-5-22.

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Yu, Bowen, and Ying Huang. "Rhino defines H3K9me3-marked piRNA clusters." Oncotarget 6, no. 25 (2015): 20740–41. http://dx.doi.org/10.18632/oncotarget.5178.

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Kawaoka, Shinpei, Kahori Hara, Keisuke Shoji, et al. "The comprehensive epigenome map of piRNA clusters." Nucleic Acids Research 41, no. 3 (2012): 1581–90. http://dx.doi.org/10.1093/nar/gks1275.

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Rakhmetullina, Aizhan, Aigul Akimniyazova, Togzhan Niyazova, et al. "Interactions of piRNAs with the mRNA of Candidate Genes in Esophageal Squamous Cell Carcinoma." Current Issues in Molecular Biology 45, no. 7 (2023): 6140–53. http://dx.doi.org/10.3390/cimb45070387.

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Recently, a database of human piRNAs (piwi-interacting RNAs) was created, which allows the study of the binding of many piRNAs to the mRNAs of genes involved in many diseases, including cancer. In the present work, we identified the piRNAs that can interact with candidate esophageal squamous cell carcinoma (ESCC) genes. The binding of 480 thousand piRNAs with the mRNAs of 66 candidate ESCC genes was studied. Bioinformatic studies found that piRNAs bind only to the mRNAs of nine candidate genes: AURKA, BMP7, GCOM1, ERCC1, MTHFR, SASH1, SIX4, SULT1A1, and TP53. It has been shown that piRNAs can

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Firsov, Sergei Yu, Karina A. Kosherova, and Dmitry V. Mukha. "Identification and functional characterization of the German cockroach, Blattella germanica, short interspersed nuclear elements." PLOS ONE 17, no. 6 (2022): e0266699. http://dx.doi.org/10.1371/journal.pone.0266699.

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In recent decades, experimental data has accumulated indicating that short interspersed nuclear elements (SINEs) can play a significant functional role in the regulation of gene expression in the host genome. In addition, molecular markers based on SINE insertion polymorphisms have been developed and are widely used for genetic differentiation of populations of eukaryotic organisms. Using routine bioinformatics analysis and publicly available genomic DNA and small RNA-seq data, we first described nine SINEs in the genome of the German cockroach, Blattella germanica. All described SINEs have tR

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Kofler, Robert. "Dynamics of Transposable Element Invasions with piRNA Clusters." Molecular Biology and Evolution 36, no. 7 (2019): 1457–72. http://dx.doi.org/10.1093/molbev/msz079.

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Lipps, Northe, Figueiredo, et al. "Non-Invasive Approach for Evaluation of Pulmonary Hypertension Using Extracellular Vesicle-Associated Small Non-Coding RNA." Biomolecules 9, no. 11 (2019): 666. http://dx.doi.org/10.3390/biom9110666.

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Extracellular vesicles are released by numerous cell types of the human body under physiological but also under pathophysiological conditions. They are important for cell–cell communication and carry specific signatures of peptides and RNAs. In this study, we aimed to determine whether extracellular vesicles isolated from patients with pulmonary hypertension show a disease specific signature of small non-coding RNAs and thus have the potential to serve as diagnostic and prognostic biomarkers. Extracellular vesicles were isolated from the serum of 23 patients with chronic thromboembolic pulmona

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Aravin, A. A., R. Sachidanandam, A. Girard, K. Fejes-Toth, and G. J. Hannon. "Developmentally Regulated piRNA Clusters Implicate MILI in Transposon Control." Science 316, no. 5825 (2007): 744–47. http://dx.doi.org/10.1126/science.1142612.

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Zhang, Fan, Jie Wang, Jia Xu, et al. "UAP56 Couples piRNA Clusters to the Perinuclear Transposon Silencing Machinery." Cell 151, no. 4 (2012): 871–84. http://dx.doi.org/10.1016/j.cell.2012.09.040.

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Kotov, Alexei A., Vladimir E. Adashev, Ilia A. Kombarov, Sergei S. Bazylev, Aleksei S. Shatskikh, and Ludmila V. Olenina. "Molecular Insights into Female Hybrid Sterility in Interspecific Crosses between Drosophila melanogaster and Drosophila simulans." International Journal of Molecular Sciences 25, no. 11 (2024): 5681. http://dx.doi.org/10.3390/ijms25115681.

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Species of the genus Drosophila have served as favorite models in speciation studies; however, genetic factors of interspecific reproductive incompatibility are under-investigated. Here, we performed an analysis of hybrid female sterility by crossing Drosophila melanogaster females and Drosophila simulans males. Using transcriptomic data analysis and molecular, cellular, and genetic approaches, we analyzed differential gene expression, transposable element (TE) activity, piRNA biogenesis, and functional defects of oogenesis in hybrids. Premature germline stem cell loss was the most prominent d

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Lillestøl, Reidun, Peter Redder, Roger A. Garrett, and Kim Brügger. "A putative viral defence mechanism in archaeal cells." Archaea 2, no. 1 (2006): 59–72. http://dx.doi.org/10.1155/2006/542818.

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Clusters of regularly spaced direct repeats, separated by unconserved spacer sequences, are ubiquitous in archaeal chromosomes and occur in some plasmids. Some clusters constitute around 1% of chromosomal DNA. Similarly structured clusters, generally smaller, also occur in some bacterial chromosomes. Although early studies implicated these clusters in segregation/partition functions, recent evidence suggests that the spacer sequences derive from extrachromosomal elements, and, primarily, viruses. This has led to the proposal that the clusters provide a defence against viral propagation in cell

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Babenko, Vladimir, Anton Bogomolov, Roman Babenko, Elvira Galieva, and Yuriy Orlov. "CpG islands’ clustering uncovers early development genes in the human genome." Computer Science and Information Systems 15, no. 2 (2018): 473–85. http://dx.doi.org/10.2298/csis170523004b.

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We address the problem of the annotation of CpG islands (CGIs) clusters in the human genome. Upon analyzing gene content within CGIs clusters, piRNA, tRNA, and miRNA-encoding genes were found as well as CpG-rich homeobox genes reported previously. Chromosome-wide CGI density is positively correlated with replication timing, confirming that CGIs may serve as open chromatin markers. Early embryonic stage expressed KRAB-ZNF genes abundant at chromosome 19 were found to be interlinked with CGI clusters. We detected that a number of long CGIs and CGI clusters are, in fact, tandem copies with multip

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Mohamed, Mourdas, Nguyet Thi-Minh Dang, Yuki Ogyama, et al. "A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore." Cells 9, no. 8 (2020): 1776. http://dx.doi.org/10.3390/cells9081776.

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Transposable elements (TEs) are the main components of genomes. However, due to their repetitive nature, they are very difficult to study using data obtained with short-read sequencing technologies. Here, we describe an efficient pipeline to accurately recover TE insertion (TEI) sites and sequences from long reads obtained by Oxford Nanopore Technology (ONT) sequencing. With this pipeline, we could precisely describe the landscapes of the most recent TEIs in wild-type strains of Drosophila melanogaster and Drosophila simulans. Their comparison suggests that this subset of TE sequences is more

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Zhou, Hao, Jiajia Liu, Wei Sun, et al. "Differences in small noncoding RNAs profile between bull X and Y sperm." PeerJ 8 (September 18, 2020): e9822. http://dx.doi.org/10.7717/peerj.9822.

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The differences in small noncoding RNAs (sncRNAs), including miRNAs, piRNAs, and tRNA-derived fragments (tsRNAs), between X and Y sperm of mammals remain unclear. Here, we employed high-throughput sequencing to systematically compare the sncRNA profiles of X and Y sperm from bulls (n = 3), which may have a wider implication for the whole mammalian class. For the comparison of miRNA profiles, we found that the abundance of bta-miR-652 and bta-miR-378 were significantly higher in X sperm, while nine miRNAs, including bta-miR-204 and bta-miR-3432a, had greater abundance in Y sperm (p < 0.05).

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Asif-Laidin, Amna, Valérie Delmarre, Jeanne Laurentie, Wolfgang J. Miller, Stéphane Ronsseray, and Laure Teysset. "Short and long-term evolutionary dynamics of subtelomeric piRNA clusters in Drosophila." DNA Research 24, no. 5 (2017): 459–72. http://dx.doi.org/10.1093/dnares/dsx017.

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Akulenko, Natalia, Sergei Ryazansky, Valeriya Morgunova, et al. "Transcriptional and chromatin changes accompanying de novo formation of transgenic piRNA clusters." RNA 24, no. 4 (2018): 574–84. http://dx.doi.org/10.1261/rna.062851.117.

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Olovnikov, I. A., and A. I. Kalmykova. "piRNA clusters as a main source of small RNAs in the animal germline." Biochemistry (Moscow) 78, no. 6 (2013): 572–84. http://dx.doi.org/10.1134/s0006297913060035.

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Chang, Timothy H., Eugenio Mattei, Ildar Gainetdinov, Cansu Colpan, Zhiping Weng, and Phillip D. Zamore. "Maelstrom Represses Canonical Polymerase II Transcription within Bi-directional piRNA Clusters in Drosophila melanogaster." Molecular Cell 73, no. 2 (2019): 291–303. http://dx.doi.org/10.1016/j.molcel.2018.10.038.

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Kotnova, A. P., and Yu V. Ilyin. "Comparative Analysis of the Structure of Three piRNA Clusters in the Drosophila melanogaster Genome." Molecular Biology 54, no. 3 (2020): 374–81. http://dx.doi.org/10.1134/s0026893320030085.

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Akimniyazova, Aigul, Oxana Yurikova, Anna Pyrkova, et al. "In Silico Study of piRNA Interactions with the SARS-CoV-2 Genome." International Journal of Molecular Sciences 23, no. 17 (2022): 9919. http://dx.doi.org/10.3390/ijms23179919.

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A prolonged pandemic with numerous human casualties requires a rapid search for means to control the various strains of SARS-CoV-2. Since only part of the human population is affected by coronaviruses, there are probably endogenous compounds preventing the spread of these viral pathogens. It has been shown that piRNA (PIWI-interacting RNAs) interact with the mRNA of human genes and can block protein synthesis at the stage of translation. Estimated the effects of piRNA on SARS-CoV-2 genomic RNA (gRNA) in silico. A cluster of 13 piRNA binding sites (BS) in the SARS-CoV-2 gRNA region encoding the

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Mohn, Fabio, Grzegorz Sienski, Dominik Handler, and Julius Brennecke. "The Rhino-Deadlock-Cutoff Complex Licenses Noncanonical Transcription of Dual-Strand piRNA Clusters in Drosophila." Cell 157, no. 6 (2014): 1364–79. http://dx.doi.org/10.1016/j.cell.2014.04.031.

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Devor, Eric J., Lingyan Huang, and Paul B. Samollow. "piRNA-like RNAs in the marsupial Monodelphis domestica identify transcription clusters and likely marsupial transposon targets." Mammalian Genome 19, no. 7-8 (2008): 581–86. http://dx.doi.org/10.1007/s00335-008-9109-x.

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Zanni, V., A. Eymery, M. Coiffet, et al. "Distribution, evolution, and diversity of retrotransposons at the flamenco locus reflect the regulatory properties of piRNA clusters." Proceedings of the National Academy of Sciences 110, no. 49 (2013): 19842–47. http://dx.doi.org/10.1073/pnas.1313677110.

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