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MicroRNAs Induced during Adipogenesis That Accelerate Fat Cell
Development Are Downregulated in Obesity
Huangming Xie1,2,3, Bing Lim2,3,4, *, Harvey F. Lodish1,2,5, *
1
Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge,
Massachusetts 02142, USA
2
Computation and Systems Biology, Singapore-MIT Alliance, National University of
Singapore, 4 Engineering Drive 3, Singapore 117576
3
Stem Cell and Developmental Biology, Genome Institute of Singapore, A*STAR
(Agency for Science, Technology and Research), 60 Biopolis Street, Singapore 138672
4
Beth Israel Deaconess Medical Center, Harvard Medical School, 77 Avenue Louis
Pasteur, Boston, Massachusetts 02215, USA
5
Departments of Biology and Biological Engineering, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, USA
* Correspondence:
Bing Lim: Email: [email protected]
Harvey F. Lodish: E-mail: [email protected]
miRNAs in adipogenesis and obesity
SUPPLEMENTAL DATA
Figure S1. Isolation scheme for the enrichment of mature primary adipocytes and
preadipocytes from mouse epididymal fat pads. Epididymal fat pads were minced and
digested with collagenase/dispase buffer (Invitrogen) at 37oC for about one hour and
filtered through a 100 m cell strainer (VWR). Enriched floating adipocytes were washed
and collected after centrifugation at 2000 rpm for 5 minutes. Stromal vascular cells (SVC)
were labeled with phycoerythrin (PE) conjugated antibodies against CD11b, CD90 and
CD31 (BD Pharmingen) and then anti-PE microbeads and fractionated on an
autoMACSTM Separator by negative separation according to the manufacturer’s
instruction (Miltenyi Biotec). Enriched preadipocytes (CD11b-CD90-CD31-) were further
treated with ammonium chloride solution (Stemcell Technologies) at room temperature
for 5 minutes to lyse contaminating red blood cells. More than 95% cells from the
negative fraction were PE negative based on FACS analysis.
Table S1. List of putative target genes of miR-103 at the early stage of 3T3-L1 differentiation. These genes meet all of the following
criteria: (1) Expressed in 3T3-L1 cells at day 0 or day 2 as defined by having an intensity >3000 for at least one probe mapping to the
gene on the Agilent microarray; (2) A lower mRNA expression level in day 2 cells in which miR-103 is ectopically expressed
compared to control cells at day 2, using the cut-off FDR<0.05; (3) Predicted targets based on Targetscan v4.2. Conserved =
conserved across human (H), mouse (M), rat (R), and dog (D).Context score is defined in the Targetscan database; a more negative
score is associated with a more favorable binding site for miR-103.
Gene
symbol
ACTG1
ACVR1
ADAMTS1
AFF1
AGRN
AIM2
AMMECR1L
APLP2
ARID5B
ARNT
ATP2B1
ATP7A
BACE1
BMF
CAMK2G
CAST
CAV1
CC2D1B
CD47
CDK6
CDKN2B
CDSN
Total
conserverd
sites
1
1
1
1
2
1
1
Total
nonconserverd
sites
1
0
1
2
1
1
1
1
1
1
0
1
2
1
0
1
1
2
1
1
1
2
Total context
score
-0.23
-0.13
0.00
-0.32
-0.06
-0.20
0.04
-0.05
-0.05
-0.43
-0.06
too close to ORF
-0.16
-0.08
-0.08
-0.19
-0.51
-0.27
-0.06
-0.20
-0.04
-0.24
Literature related to adipogenesis
pro-osteogenesis and pro-chondrogenesis
form a heterodimer with AhR, anti-adipogenic regulator
inhibitor of calpain, anti-adipogenic
miRNAs in adipogenesis and obesity
COL16A1
COL1A1
COL4A1
CSNK1G3
CSRP1
CTNNA1
CX3CL1
DCTN4
DKFZP434B0335
DLGAP4
DNAJC10
EIF4B
ENAH
EPHA4
EPN2
EPS15
ERBB2IP
EXT2
FAM107A
FBN1
FBXO10
FNIP1
FZD1
GALK2
GLCE
GLIS2
GOPC
GPR108
H6PD
HSD17B11
HYI
IGFBP3
1
1
1
1
1
1
1
0
1
1
2
1
1
0
1
1
2
1
1
1
2
1
1
2
0
1
2
1
1
1
2
1
2
1
1
1
-0.09
-0.21
-0.16
-0.20
-0.11
-0.12
-0.12
-0.08
-0.09
-0.10
-0.07
-0.20
0.00
-0.14
-0.10
-0.06
-0.11
too close to ORF
-0.19
-0.43
-0.34
-0.20
-0.34
-0.46
-0.06
-0.23
-0.40
-0.09
-0.19
-0.11
-0.09
-0.12
anti-adipogenic
miRNAs in adipogenesis and obesity
IL10RB
IL1R1
JAK1
KITLG
KLF4
LIMA1
LIMD2
LITAF
LPP
LRP1
MAF1
MAP3K14
MAP4
MAP4K3
MAP4K4
MASP1
MATN2
MEIS2
MMP11
MNT
NDEL1
NFAT5
NPEPPS
OGT
PDGFA
PDLIM2
PIK3R1
POLDIP2
POLM
PPP1R3C
PSD3
RAF1
1
1
1
1
1
1
1
1
1
1
1
1
0
1
1
1
4
0
0
1
1
1
2
1
1
1
1
1
0
0
1
0
1
1
0
0
1
1
3
1
-0.30
-0.07
-0.03
-0.09
-0.14
-0.11
-0.05
-0.12
-0.58
-0.06
-0.12
-0.05
-0.03
-0.09
-0.13
-0.09
-0.19
-0.06
-0.09
-0.02
-0.34
-0.14
-0.27
-0.19
-0.06
-0.25
-0.21
-0.15
-0.12
-0.14
-0.07
0.00
miRNAs in adipogenesis and obesity
RAI16
REV3L
RNF19
RPL22
RUNX1T1
SDC2
SDCBP
SENP6
SEPT11
SERINC3
SESN1
SLC25A17
SPARC
SPTBN1
STARD3NL
SYT13
TEP1
THBS1
TIMP2
TMEM123
TMEM49
TNS1
TNS3
TPP1
TRAFD1
TSC22D3
TSPAN9
UBE2B
UBE2H
UHRF2
VAMP5
VAT1
1
1
2
1
1
1
0
1
1
1
1
1
1
1
1
1
1
1
1
2
1
1
1
1
2
1
1
0
3
1
1
1
1
1
-0.22
-0.18
too close to ORF
-0.08
-0.35
-0.07
-0.38
-0.08
-0.08
-0.19
-0.06
-0.02
too close to ORF
-0.07
-0.16
-0.24
-0.18
-0.16
-0.10
-0.09
-0.18
-0.15
-0.22
-0.13
-0.14
-0.04
-0.10
-0.23
-0.08
-0.16
-0.06
-0.16
aka. ETO/MTG8, anti-adipogenic
aka. Dsip1
miRNAs in adipogenesis and obesity
VGLL3
WDFY2
WWC2
ZHX3
ZNF592
ZNRF1
ZYX
1
1
2
2
1
2
1
1
0
-0.09
-0.45
-0.10
-0.19
-0.29
-0.08
-0.10
miRNAs in adipogenesis and obesity
Table S2. List of putative target genes of miR-143 at the early stage of 3T3-L1 differentiation. These genes meet all of the following
criteria: (1) Expressed in 3T3-L1 cells at day 0 or day 2 as defined by having an intensity >3000 for at least one probe mapping to the
gene on the Agilent microarray; (2) A lower mRNA expression level in day 2 cells in which miR-143 is ectopically expressed
compared to control cells at day 2, using a the cut-off FDR<0.05; (3) Predicted targets based on Targetscan v4.2. Conserved =
conserved across human (H), mouse (M), rat (R), and dog (D).Context score is defined in the Targetscan database; a more negative
score is associated with a more favorable binding site for miR-143.
Gene
symbol
ADAMTS1
ADAMTS5
AFF1
AGTR2
ANXA3
APBB2
ARNT
ATP2B1
BACE1
CLIP3
CNN2
CRYZ
CXCL6
DPYSL3
FLJ10357
GHR
IGF1
IL17RD
ISLR
KIAA0556
MAF
MAPK7
Total
conserverd
sites
1
1
1
Total
nonconserverd
sites
3
1
2
1
0
1
1
1
3
1
1
1
1
1
1
1
1
2
1
1
0
0
Total
Contextscore
-0.46
-0.06
-0.35
-0.10
-0.20
-0.09
-0.25
-0.05
-0.44
-0.04
-0.24
-0.32
-0.28
0.01
-0.21
-0.19
-0.08
-0.13
-0.22
-0.16
-0.21
-0.29
Literature related to adipogenesis
form a heterodimer with AhR, anti-adipogenic regulator
downregulated during adipogenesis
aka. ERK5, validated target of miR-143
miRNAs in adipogenesis and obesity
MEST
NFIB
OCRL
PALLD
PDGFRA
PDLIM2
PRSS23
PSD3
SIAE
SOCS3
SRA1
SVEP1
SVIL
TIMP2
TMEM123
TMEM50A
TMSB10
TSC22D3
TSPAN9
VGLL3
ZNF618
1
1
1
1
1
1
1
1
1
0
1
1
1
1
1
2
0
1
1
1
1
1
0
1
1
1
-0.17
-0.07
-0.14
-0.04
-0.07
-0.35
-0.10
-0.26
-0.15
-0.13
-0.39
-0.18
-0.21
-0.12
-0.05
-0.19
-0.10
-0.26
-0.06
-0.27
-0.14
aka. Dsip1
aka. Zfp618