Abstract：
During spaceflight, multiple unique hazardous factors, particularly microgravity and space radiation, can induce different types of DNA damage, which pose a constant threat to genomic integrity and stability of living organisms. Although organisms have evolved different kinds of conserved DNA repair pathways to eliminate this DNA damage on Earth, the impact of space microgravity on the expressions of these DNA repair genes and their regulatory miRNAs has not been fully explored. In this study, we integrated all existing datasets, including both transcriptional and miRNA microarrays in wild-type (WT) Caenorhabditis elegans that were exposed to the treatments of spaceflight (SF), spaceflight control with a 1g centrifugal device (SC), and ground control (GC) in three space experiments with the periods of 4, 8 and 16.5 days. The results of principal component analysis showed the gene expression patterns for five major DNA repair pathways (i.e., non-homologous end joining (NHEJ), homologous recombination (HR), mismatch repair (MMR), nucleotide excision repair (NER), and base excision repair (BER)) were well separated and clustered between SF/GC and SC/GC treatments after three spaceflights. In the 16.5-days space experiment, we also selected the datasets of dys-1 mutant and ced-1 mutant of C. elegans, which respectively presented microgravity-insensitivity and radiosensitivity. Compared to the WT C. elegans flown in the 16.5-days spaceflight, the separation distances between SF and SC samples were significantly reduced in the dys-1 mutant, while greatly enhanced in the ced-1 mutant for five DNA repair pathways. By comparing the results of differential expression analysis in SF/GC versus SC/GC samples, we found the DNA repair genes annotated in the pathways of BER and NER were prominently down-regulated under microgravity during both the 4- and 8-days spaceflights. While, under microgravity, the genes annotated in MMR were dominatingly up-regulated during the 4-days spaceflight, and those annotated in HR were mainly up-regulated during the 8-days spaceflight. And, most of the DNA repair genes annotated in the pathways of BER, NER, MMR, and HR were up-regulated under microgravity during the 16.5-days spaceflight. Using miRNA-mRNA integrated analysis, we determined the regulatory networks of differentially expressed DNA repair genes and their regulatory miRNAs in WT C. elegans after three spaceflights. Compared to GC conditions, the differentially expressed miRNAs were analyzed under SF and SC treatments of three spaceflights, and some altered miRNAs that responded to SF and SC could regulate the expressions of corresponding DNA repair genes annotated in different DNA repair pathways. In summary, these findings indicate that microgravity can significantly alter the expression patterns of DNA repair genes and their regulatory miRNAs in space-flown C. elegans. The alterations of the expressions of DNA repair genes and the dominating DNA repair pathways under microgravity are possibly related to the spaceflight period. In addition, the key miRNAs are identified as the post-transcriptional regulators to regulate the expressions of various DNA repair genes under microgravity. These altered miRNAs that responded to microgravity can be implicated in regulating diverse DNA repair processes in space-flown C. elegans.
摘要：
在太空飞行期间，多种独特的危险因素，特别是微重力和空间辐射，可以诱导不同类型的DNA损伤，这对生物体的基因组完整性和稳定性构成了持续的威胁。尽管生物体已经进化出不同种类的保守DNA修复途径来消除地球上的这种DNA损伤，空间微重力对这些DNA修复基因及其调控miRNA表达的影响尚未得到充分探索。在这项研究中,我们整合了所有现有的数据集，包括暴露于太空飞行（SF）治疗的野生型（WT）秀丽隐杆线虫中的转录和miRNA微阵列，使用1g离心装置（SC）进行航天控制，和地面控制（GC）在三个空间实验中分别进行了4天、8天和16.5天。主成分分析结果显示了五种主要DNA修复途径的基因表达模式(即非同源末端连接（NHEJ），同源重组（HR），失配修复(MMR),核苷酸切除修复（NER），和碱基切除修复（BER））在三次太空飞行后，在SF/GC和SC/GC处理之间很好地分离和聚集。在16.5天的太空实验中,我们还选择了秀丽隐杆线虫的dys-1突变体和ced-1突变体的数据集，分别呈现微重力不敏感性和放射敏感性。与在16.5天的太空飞行中飞行的WTC.elegans相比，在Dys-1突变体中，SF和SC样品之间的分离距离显着减小，同时在ced-1突变体中对五种DNA修复途径的增强。通过比较SF/GC和SC/GC样品的差异表达分析结果，我们发现在4天和8天的太空飞行中，在微重力作用下，BER和NER途径中注释的DNA修复基因显着下调。同时,在微重力下,在为期4天的太空飞行中，MMR中注释的基因主要上调，在8天的太空飞行中，HR中注释的那些主要是上调的。And,大部分的DNA修复基因注释在BER的途径，NER,MMR,在16.5天的太空飞行中，在微重力下HR上调。使用miRNA-mRNA整合分析，我们确定了三次太空飞行后WTC.elegans中差异表达DNA修复基因的调控网络及其调控miRNA。与GC条件相比，在三个太空飞行的SF和SC处理下分析差异表达的miRNA，一些对SF和SC有反应的改变的miRNA可以调节不同DNA修复途径中注释的相应DNA修复基因的表达。总之,这些发现表明，微重力可以显著改变DNA修复基因及其调节miRNAs在太空飞行C.elegans中的表达模式。微重力下DNA修复基因表达的改变和主要的DNA修复途径可能与太空飞行时期有关。此外,关键miRNAs被鉴定为转录后调节因子,在微重力条件下调节各种DNA修复基因的表达。这些响应微重力的改变的miRNA可能与调节太空飞行的C.elegans中的不同DNA修复过程有关。
