原生动物利什曼原虫中转录已灭绝的截短反转录子的进化分化群驱动低 mRNA 表达和发育调控。

IF 4.4 1区 生物学 Q1 BIOLOGY BMC Biology Pub Date : 2024-10-29 DOI:10.1186/s12915-024-02051-4
Gabriel Reis Ferreira, Jean-Guillaume Emond-Rheault, Lysangela Alves, Philippe Leprohon, Martin A Smith, Barbara Papadopoulou
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引用次数: 0

摘要

背景:利什曼原虫基因组中以前存在着活跃的短穿插变性逆转录子(SIDERs),是锥虫中最大的重复元件家族。它们在利什曼原虫中的大量扩增是重要生物学功能的有力预测。在这项研究中,我们将多层次生物信息学预测与高通量基因组和转录组分析相结合,对 SIDER2 亚家族的逆转录子在利什曼原虫基因组进化和表达中发挥的多样化作用有了新的认识:结果:我们发现SIDER2逆回子形成了各种进化分化的簇,每个簇都包含同源的SIDER2序列,这些序列通常位于染色体线性序列的附近。这种耐人寻味的基因组组织凸显了 SIDER2 邻近性在形成染色体动态和协同调控方面的重要性。因此,我们发现属于同一 SIDER2 簇的转录本可以表现出相似的表达水平。SIDER2 反转录子大多作为 3'UTR 的一部分被转录,占利什曼原虫转录组的 13%。全基因组表达谱分析研究强调了 SIDER2 通常与低 mRNA 表达有关。SIDER2 反转录子与基因表达下调的显著联系支持了它们作为 mRNA 丰度主要调节因子的共同作用。SIDER2 序列还增加了利什曼原虫基因表达库的多样性,因为约 35% 含 SIDER2 的转录本可在寄生虫的整个发育过程中受到不同的调控,其中一些编码关键的毒力因子。此外,我们还提供了含 SIDER2 转录本功能偏倚的证据,其中蛋白激酶和跨膜转运活性的转录本最多:总之,这些发现为转录灭绝的逆转录子作为主要 RNA 顺式调控因子的进化创新提供了重要的概念性进展。
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Evolutionary divergent clusters of transcribed extinct truncated retroposons drive low mRNA expression and developmental regulation in the protozoan Leishmania.

Background: The Leishmania genome harbors formerly active short interspersed degenerated retroposons (SIDERs) representing the largest family of repetitive elements among trypanosomatids. Their substantial expansion in Leishmania is a strong predictor of important biological functions. In this study, we combined multilevel bioinformatic predictions with high-throughput genomic and transcriptomic analyses to gain novel insights into the diversified roles retroposons of the SIDER2 subfamily play in Leishmania genome evolution and expression.

Results: We show that SIDER2 retroposons form various evolutionary divergent clusters, each harboring homologous SIDER2 sequences usually located nearby in the linear sequence of chromosomes. This intriguing genomic organization underscores the importance of SIDER2 proximity in shaping chromosome dynamics and co-regulation. Accordingly, we show that transcripts belonging to the same SIDER2 cluster can display similar levels of expression. SIDER2 retroposons are mostly transcribed as part of 3'UTRs and account for 13% of the Leishmania transcriptome. Genome-wide expression profiling studies underscore SIDER2 association generally with low mRNA expression. The remarkable link of SIDER2 retroposons with downregulation of gene expression supports their co-option as major regulators of mRNA abundance. SIDER2 sequences also add to the diversification of the Leishmania gene expression repertoire since ~ 35% of SIDER2-containing transcripts can be differentially regulated throughout the parasite development, with a few encoding key virulence factors. In addition, we provide evidence for a functional bias of SIDER2-containing transcripts with protein kinase and transmembrane transporter activities being most represented.

Conclusions: Altogether, these findings provide important conceptual advances into evolutionary innovations of transcribed extinct retroposons acting as major RNA cis-regulators.

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来源期刊
BMC Biology
BMC Biology 生物-生物学
CiteScore
7.80
自引率
1.90%
发文量
260
审稿时长
3 months
期刊介绍: BMC Biology is a broad scope journal covering all areas of biology. Our content includes research articles, new methods and tools. BMC Biology also publishes reviews, Q&A, and commentaries.
期刊最新文献
Novel function of single-target regulator NorR involved in swarming motility and biofilm formation revealed in Vibrio alginolyticus. Hibernation reduces GABA signaling in the brainstem to enhance motor activity of breathing at cool temperatures. A powerful and versatile new fixation protocol for immunostaining and in situ hybridization that preserves delicate tissues. Bridging chemical structure and conceptual knowledge enables accurate prediction of compound-protein interaction. Evolutionary divergent clusters of transcribed extinct truncated retroposons drive low mRNA expression and developmental regulation in the protozoan Leishmania.
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