Long non-coding MEG3 is a marker for skeletal muscle development and meat production traits in pigs

Full text

Long non-coding MEG3 is a marker for skeletal muscle development
and meat production traits in pigs
X. Yu*
†1
, Z. Wang
‡1
, H. Sun*, Y. Yang*, K. Li* and Z. Tang*
†
*Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
†
Group of Pig Genomic Design and
Breeding, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
‡
Department of
Computer Science, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong.
Summary Long non-coding RNA maternally expressed gene 3 (lncRNA MEG3) plays an important role
in mammalian muscle development. Our previous transcriptome study showed that lncRNA
MEG3 is differentially expressed during postnatal skeletal muscle development in pigs. The
objective of the present study was to analyse the role of lncRNA MEG3 in prenatal and
postnatal skeletal muscle development and investigate the association of MEG3 with meat
production traits in pigs. We investigated the sequence conservation and temporal-spatial
expression of lncRNA MEG3 and identified its core promoter and single nucleotide
polymorphisms (SNPs). Our results show that MEG3 is conserved among pig, human and
mouse and is expressed in a tissue-specific manner with high expression levels in kidney and
leg and dorsal muscles. In addition, MEG3 is more abundant in prenatal muscle compared
to postnatal muscle, and its expression peaks at gestational day 60. Notably, we observed
almost no expression 40 days after birth. The core promoter of MEG3 is located upstream of
the transcription initiation site between 447 and 40 bp. In our SNP linkage
disequilibrium and association analyses, four of the 10 potential polymorphism sites were
found to be associated with corrected back fat thickness and age to reach 100 kg
(rs325797437, rs344501106, rs81286029 and rs318656749). In addition, three
haplotypes were found to be associated with differences in corrected age to reach 100 kg
(AAAT, AAAT/GGGC, GAAT/GGGC). Our results indicate that MEG3 regulates skeletal
muscle development and is a candidate gene for improving meat production traits in pigs.
Keywords lncRNA, maternally expressed gene 3, swine, association analysis, muscle
growth
Introduction
Advances in high-throughput sequencing platforms have
revealed an astounding number of noncoding RNAs that
play critical roles in gene regulation and developmental
processes (Mattick 2004). Long noncoding RNAs (lncRNAs)
are a class of RNA molecules of more than 200 nucleotides
that lack protein-coding capacity. Many lncRNAs, including
H19 (Kallen et al. 2013), linc-MD1 (Legnini et al. 2014),
lncmyod (Gong et al. 2015), lnc-31 (Ballarino et al. 2015),
linc-YY1 (Zhou et al. 2015) and lnc-mg (Zhu et al. 2017),
play crucial roles in skeletal muscle development.
Maternally expressed gene 3 (MEG3), a lncRNA first
identified in mice, is the orthologue of the trap locus 2
(GTL2) gene (Schuster-Gossler et al. 1998). The human
orthologue of MEG3,DLK1/MEG3, is located on chromo-
some 14q32.3 (da Rocha et al. 2008). The pig MEG3 gene,
located on chromosome 7, encodes for multiple alterna-
tively spliced transcripts and is expressed from the mater-
nally inherited chromosome. Although the role of MEG3 in
regulating autophagy in cancer is known (Wang et al.
2012), the function of MEG3 in livestock is unclear. MEG3
is involved in callipyge, a muscle hypertrophy phenotype in
sheep that causes significant changes in muscle develop-
ment, carcass composition, shape and meat quality
(Koohmaraie et al. 1995; Freking et al. 1998, 1999). These
studies imply that MEG3 is associated with livestock meat
production traits.
The pig is an important protein source for humans, and
meat production traits are economically significant traits.
Although development, growth and function of skeletal
Address for correspondence
Z. Tang, Institute of Animal Sciences, Chinese Academy of Agricultural
Sciences, Beijing 100193, China.
E-mail: tangzhonglin@caas.cn
1
These authors contributed equally to this work.
Accepted for publication 26 June 2018
doi: 10.1111/age.12712
571
©2018 Stichting International Foundation for Animal Genetics, 49, 571–578

muscle are dynamic processes critical to animal survival
(Sollero et al. 2011), the molecular mechanisms of skeletal
muscle development and meat production traits are largely
unknown. The role of lncRNA MEG3 in skeletal muscle
development and meat production traits in pigs is unde-
termined.
Previously, we performed comprehensive profiling of Sus
scrofa lncRNAs across nine organs and skeletal muscles
collected at three developmental stages. We identified 1405
lncRNAs that were differentially expressed during postnatal
skeletal muscle development (Tang et al. 2017). Of these,
MEG3, which shares homology with human and mouse,
was differentially expressed in postnatal skeletal muscle
development. To further explore the potential functions of
MEG3 in pigs, we investigated the sequence conservation
and temporal-spatial expression and identified the core
promoter and single nucleotide polymorphisms (SNPs) of
lncRNA MEG3. Our study indicates that lncRNA MEG3 is
highly conserved across mammals and is involved in
skeletal muscle development. We conclude from these
studies that lncRNA MEG3 is a valid target for improving
meat production traits in pigs.
Materials and methods
Animal and trait data collection
All animal procedures were performed according to the
guidelines of the Biological Studies Animal Care and Use
Committee, P. R. China. Longissimus dorsi muscles were
isolated from foetal Large White pigs on gestational days 33,
60, 65, 70, 75, 80, 95 and 105 (named E33, E60, E65, E70,
E75, E80, E95 and E105 respectively) and on postnatal days
20, 40, 60, 100, 140 and 160 (named D20, D40, D60, D100,
D140 and D160 respectively). Muscle samples collected at
the 14 different time points were used for expression
analysis. Each time point included independent biological
replicates from at least three individuals. In addition, nine
tissues—heart, liver, spleen, lung, kidney, intestine, stom-
ach, and leg and dorsal muscles—from three Large White
pigs at D160 were harvested. All samples were stored
immediately in liquid nitrogen for RNA extraction.
For SNP linkage disequilibrium and association studies,
blood samples were collected from 297 independent indi-
viduals from one farm in the Shunyi district of Beijing.
Traits of the 297 Large White pigs, including body weight,
age, back fat thickness, eye muscle area, piglet birth weight
and weaned piglets, were recorded. The following indicators
were corrected based on standard methods used in China
(GB 22283-2008), as follows:
Corrected back fat thickness ¼back fat thickness CF
Corrected age to reach 100 kg
¼measured age ½ðmeasured weight 100Þ=CF;
where CF is the correction factor for each trait.
Total RNA extraction, reverse transcription PCR and
real-time quantitative PCR (RT-qPCR)
Total RNA was extracted with TRIzol Reagent (Invitro-
gen). Total RNA concentration was determined using
spectrophotometry to ensure that the OD260/OD280
ratio was between 1.8 and 2.0. The integrity of the RNA
was assessed by gel electrophoresis. Total RNA was
reverse transcribed using a RevertAid First Strand cDNA
Synthesis Kit (ThermoFisher), according to the manu-
facturer’s instructions. RT-PCR was performed using
routine PCR programs (T
m
=60 °C) with 35 amplifica-
tion cycles. The RT-qPCR reaction was performed on a
7500 FAST Real-Time PCR System (Applied Biosystems)
accordingtotheSYBR
â
Premix Ex Taq
TM
instructions.
All reactions were replicated three times. Porcine glyc-
eraldehyde-3-phosphate dehydrogenase (GAPDH)wasused
as an endogenous control. The expression levels of all
genes of interest were normalized to those of GAPDH
using the 2
ΔΔCt
method. All primer sequences were
designed using PRIMER 5.0 software and are listed in
Table S1.
Sequence conservation and core promoter analysis
Based on our previous transcriptome data (Gene Expres-
sion Omnibus database, GSE73763), we analysed gene
conservation across human, mouse, cow, opossum and
S. scrofa using the UCSC Comparative Genomics pipeline
(Washietl et al. 2014; Rosenbloom et al. 2015). We also
determined lncRNA sequences using pairwise alignment
with the S. scrofa 10.2 genome build to eliminate the
effects of genome assembly. We restricted the conservation
analysis of lncRNA to human or mouse by requiring that
50% of the nucleotides uniquely intersect with an align-
ment in the chain file. The conserved local secondary
structure of MEG3 was analysed via the Rfam model
(http://rfam.xfam.org/family/RF01872/alignment/html).
Primers were designed to amplify different segments of
MEG3 (Table S1) according to the 50flanking sequence
region of porcine lncRNA MEG3 in GenBank. Potential
transcription factors were predicted by TFSEARCH soft-
ware (available online: http://www.cbrc.jp/research/
db/TFSEARCH.html).
To identify the active promoter regions and determine
the DNA elements regulating lncRNA MEG3 expression,
we amplified eight short segments of different lengths
(2566, 2127, 1736, 1372, 951, 533, 217 and 126 bp)
using PCR. Recombinant vectors containing the amplified
segments, named PG-MEG3-1, PGL-MEG3-2, PGL-MEG3-
3, PG-MEG3-4, PG-MEG3-5, PG-MEG3-6, PG-MEG3-7
and PG-MEG3-8, were transfected into porcine kidney
cells (PK15) and premature intestinal epithelial cells
(PIEC). We detected changes in dual luciferase activity
48 h after transfection.
©2018 Stichting International Foundation for Animal Genetics, 49, 571–578
Yu et al.572

SNP identification
Potential polymorphism sites in lncRNA MEG3 were
identified by sequencing PCR products from 30 mixed Large
White pigs. Whole genomic DNA of lncRNA MEG3 was
amplified by PCR with four primer pairs, named segment 1–
4 (Table S1). The SNP sites were analysed by Beijing
Compass Biotechnology Co., Ltd. using mass spectrometry.
The primer pairs for genotyping the SNPs are displayed in
Table S1.
Statistical analyses
To compare gene frequencies, a chi-square analysis was
performed using Rversion 3.3.1 software (https://www.r-
project.org/). The meat production traits were analysed
using the GENERALIZED LINEAR MODELS (GLM) program within
R, according to the following linear mixed model (Ma et al.
2008):
Y¼XbþZb þe;
where Yrepresents the phenotype value, Xis the fixed
effects matrix for phenotype value, bis the fixed-effect
coefficients including two sexes (coded as 1 for male and 2
for female) and two parities (coded as 1 for primiparity and
2 for multiparity), Zis the design matrix for the random
effects of observations, bis the vector of random-effect
coefficients and ɛis the vector of errors for observations.
We also used HAPLOVIEW version 4.2 software with default
settings (Barrett et al. 2005) to analyse linkage disequilib-
rium of the regions with multiple significant SNPs clustered
around the peak SNP. A haplotype association study (Druet
& Farnir 2011) was also performed to identify genomic
regions associated with the correction of back fat thickness
value and correction of age to reach 100 kg value in 297
individuals.
Results
Sequence conservation among human, mouse and pig
We identified 10 813 putative lncRNAs from our previous
RNA-seq data in pigs. We analysed the pairwise alignments
between pig and four other species to explore the conser-
vation of lncRNAs. As shown in Fig. 1a, a large portion of
pig lncRNAs (>70%) aligned with closely related species
(cow, human and mouse), but the ratio dramatically
decreased (30%) when compared to distant species (opos-
sum). We found fewer conserved lncRNAs between pig and
cow compared to the number of conserved lncRNAs
between human or mouse and pig, although according to
the overall conservation of lncRNAs, cow is more closely
aligned with pig. We identified MEG3-like lncRNAs and
analysed their secondary structures, as shown in Fig. 1b.
Bases shown in light green are conserved among pig,
human and mouse; bases shown in dark green are
covariance base pairs, which differ among species but do
not affect the local structure. Overall, these results suggest
that lncRNA MEG3 is conserved among pig, human and
mouse.
Temporal-spatial expression patterns
To explore the temporal and spatial expression patterns of
lncRNA MEG3 in S. scrofa, we measured expression distri-
bution in nine different tissues (heart, liver, spleen, lung,
kidney, intestine, stomach, and leg and dorsal muscles). To
determine dynamic changes, we measured MEG3 expres-
sion in skeletal muscle across 14 developmental stages
(embryonic E33, E60, E65, E70, E75, E80, E95 and E105
and postnatal D20, D40, D60, D100, D140 and D160) in
Large White pigs (Fig. 1c). We found that lncRNA MEG3
was expressed in all nine tissues, with the highest expres-
sion levels in skeletal muscle (including leg and dorsal
muscles) and kidney. Low expression levels of MEG3 were
observed in the stomach, and moderate expression levels
were observed in the remaining tissues (lung, heart, liver,
spleen and intestine). As shown in Fig. 1d, lncRNA MEG3
was detected mainly in prenatal and neonatal skeletal
muscle (from E33 to D40) and expression peaked at E60.
Identifying the core promoter of lncRNA MEG3
To further understand the temporal-spatial expression
restrictions of lncRNA MEG3, we cloned the porcine
lncRNA MEG3 promoter and analysed the sequence. The
pig lncRNA MEG3 promoter contains several putative
transcription factor binding sites, including binding sites
for MyoD, SP1, NFY, USF and E47. The relative activities of
the 50flanking region fragments expressed in PIEC (black)
and PK15 cells (grey) are shown in Fig. 2a. Luciferase
assays revealed that promoter activities of the truncated
fragments PGL-MEG3-1, PGL-MEG3-2, PGL-MEG3-3, PGL-
MEG3-4, PGL-MEG3-5, PGL-MEG3-6 and PGL-MEG3-7
were significantly higher than was pGL3-basic in both cell
types (Table S2). Promoter activity gradually increased
between PGL-MEG3-1 and PGL-MEG3-5. In contrast,
promoter activity gradually decreased between PGL-
MEG3-5 and PGL-MEG3-8. Promoter activity of PGL-
MEG3-8 decreased significantly. These results indicate that
the region between 447 and 40 bp, upstream of the
transcriptional start site, was sufficient for regulating
transcription activity (Fig. 2b).
SNP linkage disequilibrium and association with meat
production traits
Direct sequencing of the porcine MEG3 genome was
performed to detect potential polymorphisms in 30 Large
White pigs. The following SNPs were identified: rs322438324
(T/G) in the 50-UTR region; rs25 (C/T), rs24 (T/G) and rs23
©2018 Stichting International Foundation for Animal Genetics, 49, 571–578
lncRNA-MEG3 is a marker in pig meat production 573

(A/G) in the first intron; and rs318656749 (T/C),
rs81286029 (A/G), rs344501106 (A/G), rs325797437
(A/G), rs334059356 (T/A), rs323571592 (G/A) and
rs322802425 (T/G) in the second exon (rs identifications
were artificially assigned).
We examined polymorphisms in 297 Large White pigs.
Sequence comparative analysis revealed 10 polymorphic
sites. Unfortunately, rs24 was not detected. Genetic diver-
sity analysis showed that genotypic distribution for
rs322802425, rs323571592, rs334059356, rs23, rs25
and rs322438324 deviated from Hardy–Weinberg equilib-
rium (P
HW
<0.05 or P
HW
=1), whereas the distribution for
rs325797437, rs344501106, rs81286029 and rs318656749
was in accordance with Hardy–Weinberg equilibrium
(Table 1). Moreover, D0/r
2
linkage disequilibrium analysis
indicated that four SNPs (rs325797437, rs344501106,
rs81286029 and rs318656749) showed linkage inheritance
that led to six haplotypes (GGGC, GAAT, AAAT, AAAT/
GGGC, GAAT/GGGC and GAAT/AAAT) (Fig. 3). Thus, we
selected these four SNP sites for further association analysis
with meat production traits.
The results of the association analysis between the four
SNP sites and meat production traits are shown in Table 2.
Three of the four SNP sites were significantly associated
with corrected back fat thickness. Specifically, individual
animals with the TT genotype in rs318656749 had
significantly thicker back fat than did those with the
CT genotype (P=0.0240). Animals with the AA geno-
type had significantly thicker back fat than did those
with the AG genotype in both rs81286029 (P=0.0487)
and rs344501106 (P=0.0471). For corrected age to
reach 100 kg, individuals with the GG genotype in
rs325797437 took approximately 3 days longer to reach
the target weight than did individuals with the AG
genotype (P=0.0341).
Further association analysis on haplotypes indicated that
corrected age to reach 100 kg differed significantly among
the haplotype classes. The homozygous AAAT individuals
took about 10 days less than did heterozygous GAAT/GGGC
individuals (P=0.0301) to reach the target weight;
heterozygous AAAT/GGGC individuals took approximately
4.6 days less than did the heterozygous GAAT/GGGC
individuals to reach the target weight (P=0.0184)
(Table 3).
Discussion
To understand the role of lncRNAs in skeletal muscle
development and meat production traits, we analysed the
pairwise alignments between pig and four other species
(human, mouse, cow and opossum). The results revealed
that lncRNAs were highly conserved among mammals.
Figure 1 Conservation and spatial-temporal expression analysis of porcine lncRNA-MEG3. (a) Pig lncRNAs aligned with multiple species. (b)
Structure conservation of the lncRNA MEG3 in Sus scrofa. (c) RT-PCR tissue expression analysis of lncRNA MEG3. (d) Relative expression quantity of
lncRNA MEG3 at different developmental stages. The values in the graphs represent means standard error expressed as the expression level
relative to GAPDH.
©2018 Stichting International Foundation for Animal Genetics, 49, 571–578
Yu et al.574

Thousands of lncRNAs are evolutionary conserved, though
not to the same extent as many protein-coding genes
(Ponjavic et al. 2007; Guttman et al. 2009). We identified
MEG3 as a conserved lncRNA sequence. In agreement with
previous reports, MEG3 is evolutionary conserved between
the pig and closely related species (e.g. cow, human and
mouse) (Li et al. 2008; Hezroni et al. 2015).
LncRNAs are involved in various biological processes via
diverse mechanisms (Moran et al. 2012). LncRNA MEG3 is
associated with human diseases such as cancers and
diabetes (Benetatos et al. 2008; Qiu et al. 2016). However,
there are no reports on the involvement of MEG3 in pig
skeletal muscle development. Fleming-Waddell et al. (2009)
identified a number of genes that are regulated by DLK1 and
RTL1 and exert control over postnatal skeletal muscle
growth, which provides an important clue to the role of
lncRNA MEG3 in muscle development. The secondary
structures of DLK1 and RTL1 are highly similar to MEG3,
indicating that they have similar functions in pigs, e.g.
regulation of postnatal skeletal muscle growth. For
Figure 2 Relative luciferase activity in porcine kidney cells (PK15) and premature intestinal epithelial cells (PIEC) for different truncated fragments. (a)
MEG3 gene promoter activity detection in PIEC (black) and PK15 (grey). (b) Promoter activity of each truncated fragment recombinant vector in PIEC
(black) and PK15 (grey). Luciferase activities were normalized to co-expressed b-gal. Data for both panels are shown as the mean SD of a
representative experiment performed in triplicate.
Table 1 Genetic diversity analysis results. SNPs Real He Expected He Ho Ae P
HW
%Geno MAF
rs322802425 0 0 1 1 1 99.7 0
rs323571592 0 0 1 1 1 99.7 0
rs334059356 0.017 0.03 0.983 1.0173 0.0021 100 0.0125
rs325797437 0.192 0.2 0.808 1.238 0.6197 100 0.117
rs344501106 0.354 0.392 0.646 1.548 0.1179 100 0.276
rs81286029 0.358 0.388 0.642 1.558 0.2268 99.7 0.269
rs318656749 0.358 0.391 0.642 1.558 0.1816 99.7 0.274
rs23 0 0 1 1 1 100 0
rs25 0.003 0.01 0.997 1.00 0.0102 99.7 0.0035
rs322438324 0.003 0.01 0.997 1.00 0.0101 100 0.007
Ae, effective number of alleles; He, heterozygosity; Ho, homogeneity; MAF, minor allele
frequency; P
HW
,P-value of Hardy-Weinberg balance.
©2018 Stichting International Foundation for Animal Genetics, 49, 571–578
lncRNA-MEG3 is a marker in pig meat production 575

example, MEG3 is abundantly expressed in the paraxial
mesoderm, suggesting a role in myogenesis (Schuster-
Gossler et al. 1998). MEG3-knockout mice acquire skeletal
muscle developmental defects, and perinatal death occurs,
indicating that MEG3 is a nuclear, cis-acting lncRNA
regulating muscle development (Zhou et al. 2010).
The spatial expression analysis showed that MEG3 was
expressed in a tissue-specific manner with high levels in the
kidney and dorsal and leg muscles. Temporal expression
analysis showed that MEG3 was expressed mainly in
prenatal and early postnatal skeletal muscle. These results
indicate that MEG3 is involved in myogenesis and con-
tributes to prenatal skeletal muscle development in pigs.
The promoter plays an important role in tissue-specific gene
expression (Xu et al. 2010), and the core promoter region of
lncRNA MEG3 in different tissues will be the subject of
future studies.
Skeletal muscle, composed mainly of myofibres, plays a
key role in the determination of meat production. During the
development of the pig, body segments develop on embryo
days 14–22. Primary myotubes are formed at E35, and cell
proliferation peaks at around E49. Secondary myotubes
begin to form when the primary myotubes proliferate, after
which the primary myotubes disappear. Secondary myo-
tubes proliferate at E90. The number of myofibres is
determined before birth during secondary myoduct forma-
tion, whereas the diameter and length of myofibres keep
increasing until D60 after birth (Ashmore et al. 1973; Tang
et al. 2007). According to our results, expression of MEG3
peaked at E60 (P<0.05), whereas almost no expression was
detected at postnatal D40. These results indicate that MEG3
is involved in the differentiation and maintenance of skeletal
muscle cells in early development.
Mutations in imprinting genes can directly or indirectly
affect important economic traits in livestock. In sheep, the
Figure 3 Linkage disequilibrium analysis of
lncRNA MEG3. Four (rs325797437,
rs344501106, rs81286029 and rs318656749)
of 10 potential polymorphism sites showed
linkage inheritance resulting in six haplotypes.
Table 2 Results of the relative analysis between the genotypes of the
SNPs.
SNPs
Geno-
type
Sample
size BFT CA100
rs318656749 CC 163 17.08 0.2737
ab
161.3 0.8843
TT 26 17.91 0.6124
a
157.7 1.630
CT 106 16.45 0.2617
b
160.7 0.9598
rs81286029 AA 25 17.71 0.6025
a
157.7 1.696
GG 164 17.07 0.2724
ab
161.3 0.8807
AG 106 16.46 0.2616
b
160.5 0.9567
rs344501106 AA 26 17.76 0.5808
a
157.4 1.649
GG 164 17.07 0.2724
ab
161.3 0.8807
AG 104 16.53 0.2704
b
160.7 0.9627
rs325797437 AA 7 18.15 1.240 152.4 2.871
ab
GG 233 17.00 0.2137 161.5 0.7123
a
AG 57 16.57 0.3992 158.2 1.158
b
BFT, corrected back fat thickness; CA100, corrected age to reach
100 kg.
The same superscript letter indicates no significant difference
(P>0.05); different superscript letters indicate significant differences
(P<0.05).
Table 3 Results of the relative analysis between the genotypes of the
haplotypes.
Haplotypes Sample size BFT CA100
GAAT 11 17.63 1.045 158.0 2.691
abc
AAAT 5 18.15 1.240 152.4 2.871
ac
GGGC 163 17.12 0.2703 161.4 0.8847
abc
AAAT/GGGC 46 16.47 0.4294 158.1 1.320
ac
GAAT/GGGC 59 18.49 1.953 162.7 1.322
b
GAAT/AAAT 10 17.69 0.8647 159.3 2.663
abc
BFT, corrected back fat thickness; CA100, corrected age to reach
100 kg.
The same superscript letter indicates no significant difference
(P>0.05); different superscript letters indicate significant differences
(P<0.05).
©2018 Stichting International Foundation for Animal Genetics, 49, 571–578
Yu et al.576

mutant MEG3 genotype, callipyge, is beneficial to muscle
development and lower fat content in the waist and
hindquarters (Cockett et al. 2005). In cattle, one SNP of
MEG3 influences production traits such as milk yield (Magee
et al. 2011). Another SNP, rs941576, is located in the sixth
intron of MEG3 and is associated with type 1 diabetes in
human beings, which is often accompanied by skeletal
muscle atrophy and recession (Wallace et al. 2010). In this
study, we identified four SNPs of MEG3 in Large White pigs.
Three of the SNPs were significantly associated with changes
in back fat thickness, and two of the SNPs were significantly
associated with changes in corrected age to reach 100 kg
(P<0.05). Haplotypes composed of four SNPs
(rs318656749, rs81286029, rs344501106 and
rs325797437) were associated with changes in corrected
age to reach 100 kg. Corrected back fat and corrected age to
reach 100 kg shows a genetic correlation with lean meat
percentage (Dube et al. 2013; Cabling et al. 2015). Therefore,
we conclude that SNPs can influence skeletal muscle devel-
opment and lead to significant production trait differences by
changing the secondary structure of MEG3. Although our
work shows that some SNP variants in lncRNA MEG3 have
strong associations with meat-producing traits in pigs, the
underlying mechanisms need further investigation.
Conclusions
We found that lncRNA MEG3 is conserved among mam-
mals and exhibits specific temporal-spatial expression pat-
terns. We identified the core promoter region, which can be
used for further functional studies of MEG3. Our data
indicate that lncRNA MEG3 is involved in the differentia-
tion and maintenance of early skeletal muscle development.
In addition, lncRNA MEG3 SNPs are associated with
changes in meat production traits and can be used as
biomarkers in pig breeding. This study increases our
knowledge about the biological function of MEG3 in muscle
growth. However, experiments focused on molecular mech-
anisms are needed.
Acknowledgements
This work was supported by the National Key Project
(2016ZX08009-003-006), the National Natural Science
Foundation of China (31372295) and the Agricultural
Science and Technology Innovation Program (ASTIP-
AGIS5).
Author contributions
Z.T. conceived and designed the experiments. Z.T., S.H.,
Z.W. and Y.Y. performed animal work and collected
biological samples. X.Y., Z.W. and H.S. contributed reagents
and materials and analysed data. H.S. and Y.Y. performed
cell culture and molecular experiments. Z.T., X.Y. and Z.W.
contributed to manuscript writing, and K.L. contributed to
manuscript revision. All authors read and agreed to the
final manuscript.
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Supporting information
Additional supporting information may be found online in
the Supporting Information section at the end of the article.
Table S1 Primer information for experiments.
Table S2 Electrophoresis charts for each truncated recom-
binant expression vector.
©2018 Stichting International Foundation for Animal Genetics, 49, 571–578
Yu et al.578