DNA damage repair and G2/M arrest are the key factors regulating the survival of cancer cells exposed to radiation. Recent studies have shown that long noncoding RNAs (lncRNAs) play important roles in a variety of biological processes, including DNA repair, cell cycle regulation, differentiation, and epigenetic regulation. However, the knowledge about the genome scale of lncRNAs and their potential biological functions in tumor cells exposed to radiation are still unclear. In this study, we used LncRNA + mRNA Human Gene Expression Microarray V4.0 to profile lncRNA and messenger RNA (mRNA) from HeLa, MCF-7, and A549 cells after irradiation with 4 Gy of γ-radiation. We identified 230, 227, and 274 differentially expressed lncRNAs and 150, 214, and 274 differentially expressed mRNAs in HeLa, MCF-7, and A549 cells, respectively, among which there are 14 common differentially expressed lncRNAs and 22 common differentially expressed mRNAs in all of the 3 cell lines. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that these differentially expressed mRNAs were mainly associated with cell cycle. Further, we also predicted the target genes and functions of these differentially expressed lncRNAs. Our study on lncRNAs has greatly expanded the field of gene research in the relationship of radiation, cell cycle, and DNA damage.
DNA damage repair and G2/M arrest are the key factors regulating the survival of cancer cells exposed to radiation. Recent studies have shown that long noncoding RNAs (lncRNAs) play important roles in a variety of biological processes, including DNA repair, cell cycle regulation, differentiation, and epigenetic regulation. However, the knowledge about the genome scale of lncRNAs and their potential biological functions in tumor cells exposed to radiation are still unclear. In this study, we used LncRNA + mRNA Human Gene Expression Microarray V4.0 to profile lncRNA and messenger RNA (mRNA) from HeLa, MCF-7, and A549 cells after irradiation with 4 Gy of γ-radiation. We identified 230, 227, and 274 differentially expressed lncRNAs and 150, 214, and 274 differentially expressed mRNAs in HeLa, MCF-7, and A549 cells, respectively, among which there are 14 common differentially expressed lncRNAs and 22 common differentially expressed mRNAs in all of the 3 cell lines. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that these differentially expressed mRNAs were mainly associated with cell cycle. Further, we also predicted the target genes and functions of these differentially expressed lncRNAs. Our study on lncRNAs has greatly expanded the field of gene research in the relationship of radiation, cell cycle, and DNA damage.
Radiotherapy is one of the most frequent methods used to treat carcinomas.[1] DNA damage repair and G2/M arrest are the key factors which regulate the
survival of cancer cells exposed to radiation.[2-5] The current models of the mechanism of DNA double-strand break (DSB) repair
and G2/M arrest are based on studies of proteins.[6,7]It is estimated that 98% of the human transcriptome is noncoding RNA, which is
limited with protein-coding capacity and was long thought to have no obvious
molecular function (MF).[8,9] Long noncoding RNAs (lncRNAs) are a group of noncoding RNAs with length
ranging from 200 nt to 100 kb.[10] The regulatory modes of lncRNAs can involve cis interactions
to affect the expression of nearby genes or protein complexes.[11] Furthermore, lncRNAs can interact with DNA, RNA, and proteins to either
activate or suppress gene expression, and they can bind to transcription factors or
chromosome-regulating complexes.[12-14] Long noncoding RNAs have lower levels of expression compared to the
protein-coding transcripts but exhibit more tissue-specific expression and
evolutionary conservation.[15] Recent studies have shown that lncRNAs play important roles in a variety of
biological processes (BPs), including DNA repair, cell cycle regulation,
differentiation, and epigenetic regulation.[16-19] Especially, a number of studies have shown that lncRNA expression can be
deregulated in humancancers.[20] However, the knowledge about the genome scale of lncRNAs and their potential
biological functions in tumor cells exposed to radiation are still far from
clear.In this study, we used LncRNA + mRNA Human Gene Expression Microarray V4.0 to profile
lncRNA and messenger RNA (mRNA) from HeLa, MCF-7, and A549 cells after irradiation
with 4 Gy of γ-radiation. We identified lncRNA and mRNA expression signatures after
irradiation in comparison to sham. Our results indicate that lncRNAs may exert a
partial or key role in the regulation of cell cycle regulation induced by
radiation.
Materials and Methods
Cell Culture and Irradiation
HeLa, A549, and MCF-7 cells were used throughout the present study. HeLa cells
were cultured in RPM1640 medium supplemented with 10% fetal calf serum and A549
and MCF-7 cells were cultured in Dulbecco’s Modified Eagle’s Medium (Gibco,
Scotland, United Kingdom) supplemented with 10% fetal calf serum. All cells were
supplemented with appropriate penicillin and streptomycin and maintained at 37°C
in a humidified incubator supplied with 5% CO2.Cells were irradiated with γ-rays to a dose of 4 Gy using a cobalt-60 source
(Beijing Institute of Radiation Medicine, Beijing, China). After irradiation,
the cells were maintained at 37°C for 2 hours and then subjected to extract
total RNA or prepared for other analysis.
Cell Cycle Analysis
Two hours after irradiation, cells were fixed in 70% ethanol at −20°C overnight
and were washed with PBS and treated with 0.25% Triton X-100 for 15 minutes at
room temperature. Cell pellets were incubated with the p-H3 antibody (1:1000,
Bethyl, Montgomery, Texas) and goat anti-rabbit IgG (H+L) antibody labeled with
fluorescein isothiocyanate (FITC) (1:200, KPL, Milford, Massachusetts), which
was followed by incubation with RNase A and propidium iodide (PI). Stained cells
were analyzed by BD FACS Calibur flow cytometer (BD Biosciences, Sparks,
Maryland). Data were analyzed using CellQuest software (version 6.1).
Western Blotting
Two hours after irradiation, cells were lysed in lysis buffer (50 mmol/L Tris-HCl
pH8.0, 150 mmol/L NaCl, 1% TritonX-100, 100 μg/mL PMSF). Then, the lysates were
electrophoresed on sodium dodecyl sulfate–polyacrylamide gel electrophoresis
(12%) and transferred onto nitrocellulose membranes (Bio-Rad, Hercules,
California). Anti-γ-H2AX (Millipore, Burlington, Massachusetts), anti-β-actin
antibody (Proteintech, Rosemont, Illinois), and goat anti-mouse IgG (H+L)
secondary antibody (Sungene Biotech, Tianjin, China) were used for Western
blot.
Cell Colony Formation Assay
Cells were irradiated by 4 Gy and reseeded with 500 cells per well. After 12
days, cells were fixed with methanol for 30 minutes and stained with Giemsa for
30 minutes. The number of colonies with at least 50 cells was counted.
Array Data Production
Long noncoding RNA + mRNA Human Gene Expression Microarray V4.0 (cat No. 360069;
CapitalBio, Beijing, China) containing 41 000 human lncRNAs and 34 000 human
mRNAs was used in this study.[21] Sample preparation and microarray hybridization were performed by
CapitalBio Corporation according to the manufacturer’s protocol. Briefly, total
RNA was extracted using the TRIzol reagent (Invitrogen, Shanghai, China) and
purified with mirVanami RNA Isolation Kit (Ambion, Austin, Texas). The
quantification and quality of RNA were assessed using NanoDrop ND-1000
Spectrophotometer (Thermo Fisher Scientific, Waltham, Massachusetts). RNA
integrity and genomic DNA (gDNA) contamination were assessed by 1% formaldehyde
denaturing gel electrophoresis. The complementary RNA (cRNA) amplification and
labeling were performed using a CapitalBio cRNA Amplification and Labeling Kit
(CapitalBio, Beijing, China) according to the manufacturer’s protocol. Controls
and irradiated groups were labeled with Cy5-dCTP and Cy3-dCTP, respectively.
Then, each sample was hybridized to the LncRNA + mRNA Human Gene Expression
Microarray V4.0. Finally, the arrays were scanned with an Agilent DNA Microarray
Scanner G2505C (Agilent Technologies, Beijing, China).
Microarray Imaging and Data Analysis
Array images were acquired by Agilent Feature Extraction (v10.7; Agilent
Technologies, Beijing, China), and array data summarization, normalization, and
quality control were analyzed using the GeneSpring software V13.0 (Agilent
Technologies, Beijing, China). To select differentially expressed genes, we
normalized the raw data with the Lowess and used threshold values of ≥1.5 and
≤−1.5-fold changes (FCs). The probes that have flags in “Detected” were chosen
for further data analysis. Hierarchical clustering was performed using Adjust
Data function of CLUSTER 3.0 software then further analyzed with average
linkage.The functional enrichment of the differently expressed mRNAs was analyzed by Gene
Ontology (GO) enrichment analysis in the Database for Annotation, Visualization
and Integrated Discovery (DAVID, http://david.abcc.ncifcrf.gov/). Gene Ontology analysis was
divided into BP, cellular component (CC), and MF. The biological pathway was
analyzed using Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis
on DAVID.
Quantitative Real-Time PCR
Total RNA was reverse transcribed into cDNA using a PrimeScript RT reagent Kit
with gDNA Eraser (Takara, Dalian, China) according to the manufacturer’s
protocol. Quantitative PCR (qPCR) was performed using a TaqMan probe Ex Taq
(TaKara, Dalian, China) on MyiQTM2 (Bio-Rad, Hercules, California). Relative
gene expression was analyzed using the 2−ΔΔ
CT method and normalized to β-actin. Specific primers and probes of
genes were shown in Supplementary Table S1.
Results
Radiation Induces G2/M Arrest and DNA Damage
It is well known that the G2/M checkpoint responds to radiation-induced DNA damage.[22,23] In order to detect G2/M arrest after radiation, we performed a flow
cytometric analysis of HeLa, MCF-7, and A549 cells treated with radiation. Two
hours after radiation at a dose of 4 Gy, cells were marked with the p-H3
antibody and PI and analyzed with flow cytometer. Figure 1A shows that the cells treated
with radiation significantly decreased in M phase. These results suggested that
treatment with radiation resulted in a cell cycle arrest in G2/M phase.
Figure 1.
Radiation induces G2/M arrest and DNA damage. Two hours after irradiation
by γ-ray, the percentages of Hela, MCF-7, and A549 cells in M phase were
analyzed by flow cytometer (A), and the γ-H2AX expression was analyzed
by Western blot (B). C, Two hours after irradiation, cells were
reseeded. After 12 days, the number of colonies was counted and the
survival rate was analysis. Representative results are shown, and mean ±
SD are presented. N = 3, *P < .05 versus control
group. SD indiates standard deviation.
Radiation induces G2/M arrest and DNA damage. Two hours after irradiation
by γ-ray, the percentages of Hela, MCF-7, and A549 cells in M phase were
analyzed by flow cytometer (A), and the γ-H2AX expression was analyzed
by Western blot (B). C, Two hours after irradiation, cells were
reseeded. After 12 days, the number of colonies was counted and the
survival rate was analysis. Representative results are shown, and mean ±
SD are presented. N = 3, *P < .05 versus control
group. SD indiates standard deviation.Phosphorylated H2AX (γ-H2AX) is a marker of DSBs.[24] To investigate the DNA damage, we analyzed γ-H2AX expression in cells 2
hours after exposure to IR by Western blotting. As shown in Figure 1B, the expression level of γ-H2AX
was markedly increased in cells treated with radiation compared with control
cells.The radiosensitivity of cells was examined by clonogenic assay after exposure to
radiation at dose of 4 Gy. After 12 days treated by radiation, colonies were
counted to determine the cell viability. As shown in Figure 1C, compared with the control
group, the survival cells treated with radiation were significantly reduced.
This suggested that HeLa, MCF-7, and A549 cells were relatively sensitive to
radiation.
Differentially Expressed LncRNAs and mRNA in Tumor Cell Lines After
Irradiation Exposure
To identify potential lncRNAs and mRNAs that may be involved in DNA damage and
G2/M checkpoint induced by radiation, Agilent Feature Extraction (version10.7,
Agilent Technologies) was utilized to analyze acquired array images to get raw
data. GeneSpring (version 13.0, Agilent Technologies) was employed to finish the
data summarization, normalization, and quality control with the raw data. To
begin with, the raw data were normalized with the Lowess. The probes that have
flags in “Detected” were chosen for further data analysis. Differentially
expressed lncRNAs or mRNAs were then identified through FC. The threshold set
for upregulated or downregulated RNAs was FC ≥1.5. We scanned 14 784 lncRNA
probes and 20 875 mRNA probes in 3 cell lines; 230, 227, and 274 differentially
expressed lncRNAs and 150, 214, and 274 differentially expressed mRNA were
identified in HeLa, MCF-7, and A549 cells, respectively (Supplementary Tables S2
and S3). The 10 most differentially expressed lncRNAs and mRNAs are shown in
Tables 1 and
2.
Table 1.
The 10 Most Differentially Expressed LncRNAs (5 Upregulated and 5
Downregulated lncRNAs) in Different Cells.
LncRNA ID
FC (abs)
Regulation
Probe Name
Cell Lines
TCONS_00024285
3.65
Up
p20002
HeLa
ENST00000511029.1
3.50
Up
p13114
HeLa
uc031rxs.1
2.83
Up
p44599_v4
HeLa
TCONS_00016514
2.75
Up
p24393
HeLa
ENST00000517408.1
2.63
Up
p13506
HeLa
ENST00000566143.1
2.74
Down
p5937
HeLa
TCONS_00019202
2.53
Down
p18409
HeLa
TCONS_00011775
2.33
Down
p23427
HeLa
nc-HOXC11-113
2.28
Down
p28042
HeLa
int-HOXA3-11
2.25
Down
p28119
HeLa
ENST00000517408.1
2.59
Up
p13506
MCF-7
ENST00000601826.1
2.43
Up
p1783
MCF-7
TCONS_00024285
2.21
Up
p20002
MCF-7
ENST00000511029.1
2.19
Up
p13114
MCF-7
RNA95930|RNS_1012_94
2.14
Up
RNA95930|RNS_1012_94
MCF-7
TCONS_00003905
2.41
Down
p21243
MCF-7
ENST00000566143.1
2.38
Down
p5937
MCF-7
RNA147360|p0464_imsncRNA7
2.33
Down
RNA147360|p0464_imsncRNA7
MCF-7
TCONS_00019202
2.29
Down
p18409
MCF-7
ENST00000608981.1
2.20
Down
p38518_v4
MCF-7
ENST00000544710.1
3.66
Up
p3736
A549
ASO1912
2.72
Up
p28351
A549
XR_428457.1
2.55
Up
p41738_v4
A549
ENST00000430471.1
2.41
Up
p599
A549
ENST00000599209.1
2.27
Up
p8807
A549
TCONS_00013667
2.18
Down
p23601
A549
ENST00000566770.1
2.18
Down
p6007
A549
ENST00000606250.1
2.14
Down
p38285_v4
A549
ENST00000535817.1
2.11
Down
p2778
A549
ENST00000604760.1
2.10
Down
p38689_v4
A549
Abbreviations: FC, fold change; lncRNA, long noncoding RNA.
Table 2.
The 10 Most Differentially Expressed mRNAs (5 Upregulated and 5
Downregulated mRNAs) in Different Cells.
The 10 Most Differentially Expressed LncRNAs (5 Upregulated and 5
Downregulated lncRNAs) in Different Cells.Abbreviations: FC, fold change; lncRNA, long noncoding RNA.The 10 Most Differentially Expressed mRNAs (5 Upregulated and 5
Downregulated mRNAs) in Different Cells.Abbreviations: FC, fold change; mRNA, messenger RNA.
Validation of Differential LncRNA or mRNA Expression by Quantitative
Real-Time PCR
To verify the results of microarray, we detected the expression of 9 lncRNAs and
5 mRNAs selecting randomly from the differentially expressed transcripts using
qPCR. β-actin was used as a normalization control. As shown in Figure 2, the expression
dates of 67% were consistent with the lncRNA and mRNA array analysis, which
indicates the reliability of the microarray data.
Figure 2.
Validation of differential lncRNAs and mRNAs expression by qRT-PCR. Nine
differentially expressed lncRNAs and 5 differentially expressed mRNAs
were randomly selected and their expression in HeLa (A), MCF-7 (B), and
A549 (C) was analyzed by qRT-PCR. The qRT-PCR data are presented as the
mean ± SD. LncRNA indicates long noncoding RNA; mRNA, messenger RNA;
qRT-PCR, quantitative real-time polymerase chain reaction; SD, standard
deviation.
Validation of differential lncRNAs and mRNAs expression by qRT-PCR. Nine
differentially expressed lncRNAs and 5 differentially expressed mRNAs
were randomly selected and their expression in HeLa (A), MCF-7 (B), and
A549 (C) was analyzed by qRT-PCR. The qRT-PCR data are presented as the
mean ± SD. LncRNA indicates long noncoding RNA; mRNA, messenger RNA;
qRT-PCR, quantitative real-time polymerase chain reaction; SD, standard
deviation.
Potential Function Identification of Differentially Expressed mRNAs
The differentially expressed mRNAs in the 3 cell lines were selected for
functional enrichment analysis. As shown in Figure 3 and Supplementary Table S4, we
found that the differentially expressed mRNAs were mostly enriched in
microtubule binding and protein binding in its MF, cell division, and mitotic
metaphase plate congression in its BP and midbody, microtubule cytoskeleton, and
microtubule in its CC. Kyoto Encyclopedia of Genes and Genomes pathway analysis
indicated that the mRNAs were mainly enriched in cell cycle pathway.
Figure 3.
Gene Ontology enrichment and KEGG pathway analysis of differentially
expressed mRNAs. The top 10 most enriched GO categories including
molecular function, biological process, cellular component, and pathways
of differentially expressed mRNAs were calculated and plotted. A, Hela,
(B) MCF-7, and (C) A549. GO indicates Gene Ontology; KEGG, Kyoto
Encyclopedia of Genes and Genomes; mRNA, messenger RNA.
Gene Ontology enrichment and KEGG pathway analysis of differentially
expressed mRNAs. The top 10 most enriched GO categories including
molecular function, biological process, cellular component, and pathways
of differentially expressed mRNAs were calculated and plotted. A, Hela,
(B) MCF-7, and (C) A549. GO indicates Gene Ontology; KEGG, Kyoto
Encyclopedia of Genes and Genomes; mRNA, messenger RNA.
Long Noncoding RNA Target Analysis of Differentially Expressed
LncRNAs
Long noncoding RNAs can regulate target genes in cis. The rationale for
identifying cis target genes was that the lncRNAs should be in relatively close
proximity to the protein-coding genes. Therefore, all genes in the proximity of
the lncRNA loci (10 kb upstream or downstream) were selected as target genes,
and the enrichment of specific MFs among the target genes was analyzed to
predict the functions of lncRNAs. In order to further identify the functions of
each individual lncRNA, we analyzed differentially expressed lncRNAs in each
cells. There were 150 genes in HeLa, 196 genes in A549, and 135 genes in MCF-7
predicted to be the targets of the lncRNAs (Supplementary Table S5). We also
conducted the GO enrichment and KEGG pathway analysis for these lncRNA-targeted
genes (Supplementary Table S6). Ten genes enriched in cell cycle are listed in
Table 3.
Table 3.
Target Genes of Differentially Expressed lncRNAs Enriched in Cell
Cycle.
lncRNA ID
Target
Cell Lines
ENST00000574212.1
NDE1
HeLa
ENST00000606853.1
MCPH1
HeLa
ENST00000583253.1
NDC80
HeLa
ENST00000604157.1
FBXW7
HeLa
ENST00000566143.1
PLK1
HeLa
ENST00000608572.1
SGSM3
A549
ENST00000566143.1
ERN2
A549
ENST00000588041.1
MAP2K6
A549
NR_044995.2
GAS6
A549
NR_037636.1
RRAGC
A549
Abbreviation: lncRNA, long noncoding RNA.
Target Genes of Differentially Expressed lncRNAs Enriched in Cell
Cycle.Abbreviation: lncRNA, long noncoding RNA.
Differentially Expressed LncRNAs and mRNAs in All of the 3 Cell Lines
Venn diagrams of the numbers of differentially expressed lncRNAs and mRNAs in
HeLa, MCF-7, and A549 cell are shown in Figure 4. The results showed that there
were 14 common differentially expressed lncRNAs and 22 common differentially
expressed mRNAs in the 3 cell lines (Figure 4A and B and Supplementary Table
S7). Hierarchical clustering of these common differentially expressed lncRNAs
and mRNAs was performed to display the same expression patterns of each lncRNA
or mRNA in different cell lines (Figure 4C and D). We also selected the 22
differentially expressed mRNAs for GO analysis. The results showed that these
mRNAs were enriched in cell cycle (Figure 4E and Supplementary Table
S8).
Figure 4.
Differentially expressed lncRNAs and mRNAs in all of in HeLa, MCF-7, and
A549. Venn diagrams of the numbers of differentially expressed lncRNAs
(A) and mRNAs (B) in HeLa, MCF-7, and A549. Hierarchical clustering of
common differentially expressed lncRNAs (C) and mRNAs (D) in HeLa, A549,
and MCF-7. E, GO enrichment analysis of common differentially expressed
mRNAs. GO indicates Gene Ontology; LncRNA, long noncoding RNA; mRNA,
messenger RNA.
Differentially expressed lncRNAs and mRNAs in all of in HeLa, MCF-7, and
A549. Venn diagrams of the numbers of differentially expressed lncRNAs
(A) and mRNAs (B) in HeLa, MCF-7, and A549. Hierarchical clustering of
common differentially expressed lncRNAs (C) and mRNAs (D) in HeLa, A549,
and MCF-7. E, GO enrichment analysis of common differentially expressed
mRNAs. GO indicates Gene Ontology; LncRNA, long noncoding RNA; mRNA,
messenger RNA.
Discussion
Radiotherapy is one of the mainstream approaches for the treatment of carcinomas. The
purpose of radiotherapy is to kill tumor cells as efficiently as possible and reduce
recurrence. Radiation results in a series of changes in tumor, but which molecules
change and how these changes regulate tumor cells after radiation exposure is still
unclear. Basic research on these effects is urgently needed. DNA damage repair and
G2/M arrest are the important factors which regulate cell survival after radiation.
The current models of the mechanism of DNA damage repair and G2/M arrest are based
on studies of proteins. In order to screen the lncRNAs which involved in the
regulation DNA damage repair and G2/M arrest after radiation, we further carried out
a high-throughput lncRNA + mRNA microarray from HeLa, MCF-7, and A549 cells 2 hours
after 4 Gy radiation and discovered a series of differentially expressed mRNAs and
lncRNAs after radiation.One hundred fifty mRNAs in HeLa, 214 mRNAs in MCF-7, and 274 mRNAs in A549 were
identified as differentially expressed transcripts between the irradiated group and
the control group. Among these differentially expressed mRNA, some mRNAs have been
reported to be associated with radiation. Naito et al found that Cyclin G2 (CycG2)
is localized at DNA repair foci following DNA damage induced by ionizing radiation
and that CycG2 regulates the dephosphorylation of several factors necessary for DNA repair.[25] Wang et al proposed that the level of IL-8 may predict radiation-induced lung
toxicity in non-small cell lung cancer.[26] MDM2-p53 pathway is well known as a key factor in the protection against
cancer and confers radiosensitivty.[27] Series of other mRNAs such as SERHL2, PSRC1, BTG2, ATF3, and ARHGAP29 are
also considered to be related to radiation.[22,23,28-30] Meanwhile, many mRNAs such as KIAA1751, ERN1, and PIF1 are identified to be
related to radiation for the first time in our profile. These findings provide new
insights into relationship between radiation and cell survival.Gene Ontology term enrichment analysis showed that many mRNAs were involved in cell
division and cell cycle. It is well known that Aurora-A (AURKA) is a key regulator
in the G2/M transition and knocking down the expression of Aurora-A gene induces
G2/M phase arrest.[31,32] Brooks et al showed that the localization of G2E3 plays a role in cell cycle
regulation and the cellular response to DNA damage.[33] Other studies reported that BORA, AURKE, and PLK1 play important roles in the
regulation of mitosis.[34-37] These analyses indicated that radiation may regulate tumor process by
altering the expression of cell cycle–related molecules.Studies about the function of lncRNAs are difficult to carry out, for most of the
lncRNAs are not determined, and there is no existing database that could be used to
find their functional annotations. Long noncoding RNAs are well known to regulate
target genes in the proximity of its upstream or downstream by 10 kb. To predict the
potential functions of differently expressed lncRNAs after radiation, we identified
their targets and analyzed the function of these coding genes. The GO enrichment
analysis revealed that these targets were associated with different biological
progress in different cancer cells. Targets in HeLa were enriched in transcription,
targets in MCF-7 were enriched in regulation of cellular glucuronidation, and
targets in MCF-7 were enriched in regulation of gene expression. Ten targets were
found to be associated with cell cycle. Their matched lncRNAs include
ENST00000574212.1, ENST00000606853.1, ENST00000583253.1, ENST00000604157.1,
ENST00000566143.1, ENST00000608572.1, ENST00000566143.1, ENST00000588041.1,
NR_044995.2, and NR_037636.1. It needs further study for the effect of these lncRNAs
on cell cycle after radiation.Furthermore, there were 14 common differentially expressed lncRNAs and 22 common
differentially expressed mRNAs in HeLa, MCF-7, and A549 cells. The expression
patterns of these differentially expressed mRNAs or lncRNAs are similar. Gene
Ontology analysis indicated that these common differential mRNAs were enriched in
cell cycle, consistent with the analysis in each cells. From these results, we
considered that the function of these common mRNAs and lncRNAs are independent of
cancer type.In summary, we discovered a profile of mRNAs and lncRNAs differentially expressed 2
hours after irradiation with 4 Gy. .Although the mechanisms of the discovered
lncRNAs in radiation damage regulation remain to be elucidated, our study on lncRNAs
has greatly expanded the field of gene research in the relationship of radiation,
cell cycle, and DNA damage.Click here for additional data file.Supplementary-Table-S1 for Screening of Long Noncoding RNAs Induced by Radiation
Using Microarray by Yilong Wang, Qi Wang, Shuangjing Chen, Yingchun Hu, Chang
Yu, Ruixue Liu and Zhidong Wang in Dose-ResponseClick here for additional data file.Supplementary-Table-S2 for Screening of Long Noncoding RNAs Induced by Radiation
Using Microarray by Yilong Wang, Qi Wang, Shuangjing Chen, Yingchun Hu, Chang
Yu, Ruixue Liu and Zhidong Wang in Dose-ResponseClick here for additional data file.Supplementary-Table-S3 for Screening of Long Noncoding RNAs Induced by Radiation
Using Microarray by Yilong Wang, Qi Wang, Shuangjing Chen, Yingchun Hu, Chang
Yu, Ruixue Liu and Zhidong Wang in Dose-ResponseClick here for additional data file.Supplementary-Table-S4 for Screening of Long Noncoding RNAs Induced by Radiation
Using Microarray by Yilong Wang, Qi Wang, Shuangjing Chen, Yingchun Hu, Chang
Yu, Ruixue Liu and Zhidong Wang in Dose-ResponseClick here for additional data file.Supplementary-Table-S5 for Screening of Long Noncoding RNAs Induced by Radiation
Using Microarray by Yilong Wang, Qi Wang, Shuangjing Chen, Yingchun Hu, Chang
Yu, Ruixue Liu and Zhidong Wang in Dose-ResponseClick here for additional data file.Supplementary-Table-S6 for Screening of Long Noncoding RNAs Induced by Radiation
Using Microarray by Yilong Wang, Qi Wang, Shuangjing Chen, Yingchun Hu, Chang
Yu, Ruixue Liu and Zhidong Wang in Dose-ResponseClick here for additional data file.Supplementary-Table-S7 for Screening of Long Noncoding RNAs Induced by Radiation
Using Microarray by Yilong Wang, Qi Wang, Shuangjing Chen, Yingchun Hu, Chang
Yu, Ruixue Liu and Zhidong Wang in Dose-ResponseClick here for additional data file.Supplementary-Table-S8 for Screening of Long Noncoding RNAs Induced by Radiation
Using Microarray by Yilong Wang, Qi Wang, Shuangjing Chen, Yingchun Hu, Chang
Yu, Ruixue Liu and Zhidong Wang in Dose-Response
Authors: Era L Pogosova-Agadjanyan; Wenhong Fan; George E Georges; Jeffrey L Schwartz; Crystal M Kepler; Hana Lee; Amanda L Suchanek; Michelle R Cronk; Ariel Brumbaugh; Julia H Engel; Michi Yukawa; Lue P Zhao; Shelly Heimfeld; Derek L Stirewalt Journal: Radiat Res Date: 2010-11-17 Impact factor: 2.841
Authors: Shulian Wang; Jeff Campbell; Matthew H Stenmark; Jing Zhao; Paul Stanton; Martha M Matuszak; Randall K Ten Haken; Feng-Ming Spring Kong Journal: Int J Radiat Oncol Biol Phys Date: 2017-03-14 Impact factor: 7.038
Authors: Christophe E Redon; Asako J Nakamura; Ksenia Gouliaeva; Arifur Rahman; William F Blakely; William M Bonner Journal: PLoS One Date: 2010-11-23 Impact factor: 3.240
Authors: Atanu Mondal; Apoorva Bhattacharya; Vipin Singh; Shruti Pandita; Albino Bacolla; Raj K Pandita; John A Tainer; Kenneth S Ramos; Tej K Pandita; Chandrima Das Journal: Mol Cell Biol Date: 2021-11-08 Impact factor: 5.069