Mobile DNA最新文献_第4页

Proceedings of the inaugural Dark Genome Symposium: November 2022. 首届黑暗基因组研讨会论文集:2022年11月。

IF 4.7 2区生物学

Mobile DNA Pub Date : 2023-11-21 DOI: 10.1186/s13100-023-00306-5

Jef D Boeke, Kathleen H Burns, Katherine B Chiappinelli, Marie Classon, John M Coffin, Daniel D DeCarvalho, Joseph D Dukes, Benjamin Greenbaum, George Kassiotis, Sarah K Knutson, Arnold J Levine, Avindra Nath, Sophie Papa, Daniel Rios, John Sedivy, David T Ting

引用次数: 0

Long noncoding RNAs emerge from transposon-derived antisense sequences and may contribute to infection stage-specific transposon regulation in a fungal phytopathogen. 长非编码rna来自转座子衍生的反义序列，可能有助于真菌植物病原体感染阶段特异性转座子调控。

IF 4.9 2区生物学

Mobile DNA Pub Date : 2023-11-15 DOI: 10.1186/s13100-023-00305-6

Jiangzhao Qian, Heba M M Ibrahim, Myriam Erz, Florian Kümmel, Ralph Panstruga, Stefan Kusch

{"title":"Long noncoding RNAs emerge from transposon-derived antisense sequences and may contribute to infection stage-specific transposon regulation in a fungal phytopathogen.","authors":"Jiangzhao Qian, Heba M M Ibrahim, Myriam Erz, Florian Kümmel, Ralph Panstruga, Stefan Kusch","doi":"10.1186/s13100-023-00305-6","DOIUrl":"10.1186/s13100-023-00305-6","url":null,"abstract":"Background: The genome of the obligate biotrophic phytopathogenic barley powdery mildew fungus Blumeria hordei is inflated due to highly abundant and possibly active transposable elements (TEs). In the absence of the otherwise common repeat-induced point mutation transposon defense mechanism, noncoding RNAs could be key for regulating the activity of TEs and coding genes during the pathogenic life cycle.Results: We performed time-course whole-transcriptome shotgun sequencing (RNA-seq) of total RNA derived from infected barley leaf epidermis at various stages of fungal pathogenesis and observed significant transcript accumulation and time point-dependent regulation of TEs in B. hordei. Using a manually curated consensus database of 344 TEs, we discovered phased small RNAs mapping to 104 consensus transposons, suggesting that RNA interference contributes significantly to their regulation. Further, we identified 5,127 long noncoding RNAs (lncRNAs) genome-wide in B. hordei, of which 823 originated from the antisense strand of a TE. Co-expression network analysis of lncRNAs, TEs, and coding genes throughout the asexual life cycle of B. hordei points at extensive positive and negative co-regulation of lncRNAs, subsets of TEs and coding genes.Conclusions: Our work suggests that similar to mammals and plants, fungal lncRNAs support the dynamic modulation of transcript levels, including TEs, during pivotal stages of host infection. The lncRNAs may support transcriptional diversity and plasticity amid loss of coding genes in powdery mildew fungi and may give rise to novel regulatory elements and virulence peptides, thus representing key drivers of rapid evolutionary adaptation to promote pathogenicity and overcome host defense.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"14 1","pages":"17"},"PeriodicalIF":4.9,"publicationDate":"2023-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10648671/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"107591771","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Co-expression of distinct L1 retrotransposon coiled coils can lead to their entanglement. 不同L1反转录转座子盘绕线圈的共同表达可以导致它们的纠缠。

IF 4.9 2区生物学

Mobile DNA Pub Date : 2023-10-20 DOI: 10.1186/s13100-023-00303-8

Nikola A Mizgier, Charlie E Jones, Anthony V Furano

{"title":"Co-expression of distinct L1 retrotransposon coiled coils can lead to their entanglement.","authors":"Nikola A Mizgier, Charlie E Jones, Anthony V Furano","doi":"10.1186/s13100-023-00303-8","DOIUrl":"10.1186/s13100-023-00303-8","url":null,"abstract":"L1 (LINE1) non-LTR retrotransposons are ubiquitous genomic parasites and the dominant transposable element in humans having generated about 40% of their genomic DNA during their ~ 100 million years (Myr) of activity in primates. L1 replicates in germ line cells and early embryos, causing genetic diversity and defects, but can be active in some somatic stem cells, tumors and during aging. L1 encodes two proteins essential for retrotransposition: ORF2p, a reverse transcriptase that contains an endonuclease domain, and ORF1p, a coiled coil mediated homo trimer, which functions as a nucleic acid chaperone. Both proteins contain highly conserved domains and preferentially bind their encoding transcript to form an L1 ribonucleoprotein (RNP), which mediates retrotransposition. However, the coiled coil has periodically undergone episodes of substantial amino acid replacement to the extent that a given L1 family can concurrently express multiple ORF1s that differ in the sequence of their coiled coils. Here we show that such distinct ORF1p sequences can become entangled forming heterotrimers when co-expressed from separate vectors and speculate on how coiled coil entanglement could affect coiled coil evolution.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"14 1","pages":"16"},"PeriodicalIF":4.9,"publicationDate":"2023-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10588031/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49679845","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Plants acquired mitochondrial linear plasmids horizontally from fungi likely during the conquest of land. 植物可能在征服土地的过程中从真菌那里水平获得线粒体线性质粒。

IF 4.9 2区生物学

Mobile DNA Pub Date : 2023-10-17 DOI: 10.1186/s13100-023-00304-7

Yutong Wei, Zhen Gong, Guan-Zhu Han

引用次数: 0

Teleost genomic repeat landscapes in light of diversification rates and ecology. 根据多样化率和生态学，远隔基因组重复景观。

IF 4.9 2区生物学

Mobile DNA Pub Date : 2023-10-03 DOI: 10.1186/s13100-023-00302-9

William B Reinar, Ole K Tørresen, Alexander J Nederbragt, Michael Matschiner, Sissel Jentoft, Kjetill S Jakobsen

引用次数: 0

Parallel Pairwise Operations on Data Stored in DNA: Sorting, Shifting, and Searching 存储在DNA中的数据的并行成对操作:排序、移动和搜索

IF 4.9 2区生物学

Mobile DNA Pub Date : 2023-09-21 DOI: 10.4230/LIPIcs.DNA.27.11

Tonglin Chen, Arnav Solanki, Marc D. Riedel

引用次数: 4

Pan cancer characterization of genes whose expression has been associated with LINE-1 antisense promoter activity. 表达与LINE-1反义启动子活性相关的基因的泛癌症特征。

IF 4.9 2区生物学

Mobile DNA Pub Date : 2023-09-18 DOI: 10.1186/s13100-023-00300-x

Baohong Xu, Xueer Li, Shaoqi Zhang, Meina Lian, Wenbin Huang, Yin Zhang, Yudong Wang, Zhiquan Huang

{"title":"Pan cancer characterization of genes whose expression has been associated with LINE-1 antisense promoter activity.","authors":"Baohong Xu, Xueer Li, Shaoqi Zhang, Meina Lian, Wenbin Huang, Yin Zhang, Yudong Wang, Zhiquan Huang","doi":"10.1186/s13100-023-00300-x","DOIUrl":"10.1186/s13100-023-00300-x","url":null,"abstract":"Background: Long interspersed nuclear element-1 (LINE-1 or L1) comprises 17% of the human genome. As the only autonomous and active retrotransposons, L1 may take part in cancer initiation and progression in some ways. The studies of L1 in cancer mainly focus on the impact of L1 insertion into the new genome locus. The L1 5´ untranslated region (UTR) also contains antisense promoter (ASP) activity, generating L1-gene chimeric transcripts to a neighbor exon. Some of these ASP-associated genes have been reported to be overexpressed in cancer and promote cancer cell growth. However, little is known about overall expression patterns and the roles of L1 ASP-associated genes in human cancers.Results: L1 ASP-associated genes were frequently dysregulated in cancer and associated with the cell cycle, the PI3K/AKT pathway, and the GTPase signaling pathway. The expression of L1 ASP-associated genes was correlated with tumor patient prognosis. Hub L1 ASP-associated genes CENPU and MCM2 showed a correlation with immune infiltration, clinical T stage, and cancer stemness in pan-cancer. Knockdown of L1 ASP-associated gene LINC00491 resulted in a significant decrease in tumor growth and migration ability.Conclusions: The expression of L1 ASP-associated genes is significantly dysregulated at the pan-cancer level, which is closely related to the tumor microenvironment, progression, and patient prognosis. Hub genes CENPU and MCM2 are expected to be new tumor diagnostic markers and therapeutic targets.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"14 1","pages":"13"},"PeriodicalIF":4.9,"publicationDate":"2023-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10506190/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10314111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Retro-miRs: novel and functional miRNAs originating from mRNA retrotransposition. 逆转录mirs:源于mRNA逆转录转位的新型功能性mirna。

IF 4.9 2区生物学

Mobile DNA Pub Date : 2023-09-08 DOI: 10.1186/s13100-023-00301-w

Rafael L V Mercuri, Helena B Conceição, Gabriela D A Guardia, Gabriel Goldstein, Maria D Vibranovski, Ludwig C Hinske, Pedro A F Galante

{"title":"Retro-miRs: novel and functional miRNAs originating from mRNA retrotransposition.","authors":"Rafael L V Mercuri, Helena B Conceição, Gabriela D A Guardia, Gabriel Goldstein, Maria D Vibranovski, Ludwig C Hinske, Pedro A F Galante","doi":"10.1186/s13100-023-00301-w","DOIUrl":"10.1186/s13100-023-00301-w","url":null,"abstract":"Background: Reverse-transcribed gene copies (retrocopies) have emerged as major sources of evolutionary novelty. MicroRNAs (miRNAs) are small and highly conserved RNA molecules that serve as key post-transcriptional regulators of gene expression. The origin and subsequent evolution of miRNAs have been addressed but not fully elucidated.Results: In this study, we performed a comprehensive investigation of miRNA origination through retroduplicated mRNA sequences (retro-miRs). We identified 17 retro-miRs that emerged from the mRNA retrocopies. Four of these retro-miRs had de novo origins within retrocopied sequences, while 13 retro-miRNAs were located within exon regions and duplicated along with their host mRNAs. We found that retro-miRs were primate-specific, including five retro-miRs conserved among all primates and two human-specific retro-miRs. All retro-miRs were expressed, with predicted and experimentally validated target genes except miR-10527. Notably, the target genes of retro-miRs are involved in key biological processes such as metabolic processes, cell signaling, and regulation of neurotransmitters in the central nervous system. Additionally, we found that these retro-miRs play a potential oncogenic role in cancer by targeting key cancer genes and are overexpressed in several cancer types, including liver hepatocellular carcinoma and stomach adenocarcinoma.Conclusions: Our findings demonstrated that mRNA retrotransposition is a key mechanism for the generation of novel miRNAs (retro-miRs) in primates. These retro-miRs are expressed, conserved, have target genes with important cellular functions, and play important roles in cancer.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"14 1","pages":"12"},"PeriodicalIF":4.9,"publicationDate":"2023-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10486083/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10253462","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

SARS-CoV-2 infection induces epigenetic changes in the LTR69 subfamily of endogenous retroviruses. SARS-CoV-2感染诱导内源性逆转录病毒LTR69亚家族的表观遗传变化。

IF 4.9 2区生物学

Mobile DNA Pub Date : 2023-09-04 DOI: 10.1186/s13100-023-00299-1

Ankit Arora, Jan Eric Kolberg, Smitha Srinivasachar Badarinarayan, Natalia Savytska, Daksha Munot, Martin Müller, Veronika Krchlíková, Daniel Sauter, Vikas Bansal

引用次数: 0

Themes and variations on piRNA-guided transposon control. pirna引导转座子控制的主题和变化。

IF 4.9 2区生物学

Mobile DNA Pub Date : 2023-09-02 DOI: 10.1186/s13100-023-00298-2

Zuzana Loubalova, Parthena Konstantinidou, Astrid D Haase

引用次数: 0