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Table 1 The 60 genes involved in lipid metabolism and their associated publication

From: Long noncoding RNAs in lipid metabolism: literature review and conservation analysis across species

Name in article

Database name (feature)

Normalized name

Sp.

Experiment

Tissue/Cell type

Action

Ref.

ANRIL

CDKN2B-AS1 (h: 28tr; 3837 bp; 19ex)

ANRIL

h

Co-effects (6 yr-adiposity)

Umbilical cord

lnc & fat mass

[40]

APOA1-AS

APOA1-AS (h: 2tr; 956 bp; 3ex)

APOA1-AS

h

KD (lnc)

HepG2

APO gene cluster: APOA1, APOC3, APOA4

[41]

APOA4-AS

Gm10680 (m: 1tr; 702 bp; 2ex)

APOA4-ASa

m

KD (lnc)

Liver

APOA4 & TG, Chol.

[42]

FLRL5

m

Co-effects (NAFLD)

Liver

lnc, FADS2, FABP5, LPL, ACMSD,

[43]

AT102202

HMGCR

h

KD (lnc)

HepG2

HMGCR

[39]

AT115872

SOD2-OT1 (h: 1tr; 1718 bp; 2ex)

SOD2-OT1a

h

KD (lnc)

HepG2

HMGCR

[39]

Blnc1

Blnc1a

m

Ov. (lnc)

Primary hepatocytes

SREBP1c, FASN, SCD, DGAT2, FABP4, ABCA1, ABCG5, LPCAT3

[44]

CASIMO1

SMIM22b

SMIM22a

h

Ov. (lnc)

MCF-7

Lipid droplet formation

[45]

CRNDE

CRNDE (h: 24tr; 6325 bp; 2ex)

CRNDE

h

KD (lnc)

HCT116, HT29

FASN, DGKA, CDS1, PLCB3, PLCG1, ACADVL, ACOT9, PI4KB

[46]

ORat7

c

Co-effects (Se-deficient diet)

Vein

lnc, ACADS

[47]

E330013P06

Carmn (m: 2tr; 1778 bp; 3ex)

CARMN

m

Ov. (lnc)

RAW 264.7

lipid uptake

[48]

FLRL3

Gm11832 (m: 1tr; 432 bp; 3ex)

RAD54B-AS1a

m

Co-effects (NAFLD)

Liver

lnc, FADS2, FABP5, LPL, ACMSD,

[43]

FLRL8

1700067K01Rikb

-a

m

Co-effects (NAFLD)

Liver

lnc, FADS2, FABP5, LPL, ACMSD,

[43]

Gm16551

Gm16551 (m: 5tr; 3162 bp; 3ex)

LINCxxxxa

m

KD (lnc)

Liver

ACLY, FASN, SCD & TG

[49]

H19

H19 (m: 7tr; 2286 bp; 5ex)

H19

m

Co-effects (FA)

Liver

lnc, PTBP1

[50]

HAGLR

HAGLR (h: 17tr; 4095; 3ex)

HAGLRa

h

KD (lnc)

NSCLC cells

FASN & FA

[51]

HOTAIR

HOTAIR (h: 5tr; 2421 bp; 7ex)

HOTAIRa

h

KD (lnc)

CNE2, 5-8F

FASN & FA

[52]

HOXC-AS1

HOXC-AS1 (h: 2tr; 548 bp; 2ex)

HOXC-AS1a

h

Ov. (lnc)

THP-1

HOXC6 & Chol.

[53]

HULC

HULC

h

Co-effects (HCC)

HepG2

lnc, ACSL1, PPARA & TG, Chol.

[54]

LeXis

4930412L05Rik (m: 2tr; 1241 bp; 8ex)

LeXis

m

KO, KD, Ov. (lnc)

Liver

CYP51A1, FDPS, MVK, MVD, SQLE, IDI1, LSS, PMVK & Chol.

[55]

LINC01138

LINC01138 (h: 14tr; 2212 bp; 4ex)

LINC01138a

h

KD, Ov. (lnc)

Renal cell carcinoma

SREBP1 activity & lipid desaturation

[56]

linc-ADAL

LINCADL (h: 1tr; 521 bp; 2ex)

LINCADLa

h

KD (lnc)

ASC

PPARG, CEBPA, SREBF1, FASN, ELOVL6, ATGL & TG

[57]

lincRNA-DYNLRB2–2

LINC01228 (h:1tr; 623 bp; 2ex)

LINC01228

h

Co-effects (Ox-LDL)

THP-1

lnc, GPR119, ABCA1 & Chol., Efflux

[58]

LINK-A

LINC01139 (h: 7tr; 1579; 2ex)

LINK-Aa

h

Co-effects (lipid-binding)

TNBC

lnc with highest lipid enrichment

[59]

LISPR1

S1PR1-DTa

h

KD (lnc)

HUVEC

S1PR1

[60]

lnc_DHCR24

DHCR24-DT (h: 4tr; 440 bp; 2ex)c

DHCR24-DTa

c

Co-effects (fat line)

Liver

lnc, DHCR24

[20]

lnc18q22.2

LIVAR (h: 1tr; 384 bp; 2ex)

LIVAR

h

Co-effects (NASH)

Liver

lnc, anti-apoptotic genes

[61]

lncACACA

LINCxxxxa

h

Co-effects (LXR agonist)

THP-1

lnc

[62]

lncARSR

LNCARSR d (h: 10tr; 2932 bp;2ex)

lncARSRa

m

Ov. (lnc)

Liver

SREBP1c, FASN, ACC1, SCD, CPT1A

[63]

m

Ov. (lnc)

Liver

HMGCR, HMGCS, SQLE, CYP7A1 & Chol.

[64]

lncFASN

LINC01970 (h: 1tr; 1810 bp; 2ex)

LINC01970a

h

Co-effects (LXR agonist)

THP-1

lnc

[62]

lnc-HC

lnc-HC

r

KD, Ov. (lnc)

Liver, CBRH-7919

CYP7A1, ABCA1 & TG, Chol.

[65]

lncHR1

AC023161.1 d (h: 1tr; 420 bp; 2ex)

lncHR1

m

Ov. (lnc)

Liver

SREBP1c, FASN, ACACA & TG

[66]

lnc-KDM5D-4

LINCxxxxa

h

KD (lnc)

HepG2

LPIN2 & Lipid droplet formation

[67]

lnc-leptin

lnc-leptina

m

KD (lnc)

Primary adipocyte

LEP

[68]

lncLSTR

C730036E19Rik (m: 1tr; 1102 bp; 5ex)

lncLSTR

m

KD (lnc)

Liver

APOC2, CYP8B1 & TG, Glucose

[69]

lncLTR

NONGGAG001747.2 (c: 1tr; 776 bp; NA)

lncLTRa

c

GWAS (serum TG content)

SNP in lncLTR locus

[70]

lncSHGL

B4GALT1-AS1 d (h: 3tr; 3752 bp; 4ex)

lncSHGLa

m

KD, Ov. (lnc)

Liver

ACACB, FASN, SREBP1 & FA, lipolyse

[71]

lncSREBF1

SMCR2 (h:1tr; 564 bp; 4ex)

SMCR2a

h

Co-effects (LXR agonist)

THP-1

lnc

[62]

LNMICC

AC009902.2 (h: 2tr; 620 bp; 2ex)

LNMICCa

h

KD, Ov. (lnc)

HeLa229

ACACA, FASN, FABP5, ACOX1, CPT1A & TG, PL

[72]

LOC100506036

CNNM3-DT (h: 1tr; 415 bp; 2ex)

CNNM3-DT

h

KD (lnc)

Jurkat cells

SMPD1, NFAT1

[73]

LOC157273

AC022784.6 (h: 1tr; 559 bp; 1ex)

LINCxxxxa

h

GWAS (lipid-traits)

lnc / SNP in the lncRNA locus

[74]

MALAT1

MALAT1 (h: 17tr; 1519 bp; 2ex)

MALAT1

h

KD (lnc)

HepG2

SREBP1c & TG, Chol.

[75]

MEG3

MEG3 (h: 50tr; 4867 bp; 2ex)

MEG3

h,m

Ov. (lnc)

Liver

HEK-293 T

CYP7A1, CYP8B1, FXR, SREBP1c, SHP

[76]

m

KD (lnc)

Liver

TG

[77]

m

Co-effects (NAFLD)

Liver

lnc, NRF2, miR-136 & serum lipid

[78]

MeXis

AI427809 (m: 4tr; 2033 bp; 2ex)

MeXis

m

KO, Ov. (lnc)

Liver, Macrophage

ABCA1 & Chol. efflux

[37]

NEAT1

NEAT1 (h: 9tr; 3341 bp; 2ex)

NEAT1

h

KD (lnc)

THP-1

TNFa, CD36, OLR1 & lipid uptake

[79]

h

KD (lnc)

HCC

ATGL, PPARa, miR-124-3p

[80]

OLMALINC

OLMALINC (h: 36tr; 5893 bp; 5ex)

OLMALINCa

h

Co-effects (obesity)

Adipose

lnc, lipid metabolism genes

[81]

h

KD (lnc)

HepG2

SREBP2-dependent gene, SREBP1 pathway genes

[82]

PLA2G1Bat1

ENSGALG00000041755 (c: 3tr; 2101 bp; 3ex)

LINCxxxxa

c

Co-effects (Se-deficient diet)

Vein

lnc, PLA2G1B

[47]

PVT1

PVT1 (h:182tr; 1699 bp; 8ex)

PVT1a

h

KD (lnc)

U2OS

MG-63

miR-195, FASN

[83]

RNCR3

Mir124a-hg (m: 4tr; 4103 bp; 4ex)

RNCR3a

m

KD (lnc)

Plasma

TG, Chol.

[84]

RP1-13D10.2

AL021407.3 (h: 1tr; 486 bp; 1ex)

LINCxxxxa

h

Ov. (lnc)

Huh7, HepG2

LDLR & LDL, ApoB

[85]

RP5-833A20.1

NFIA-AS1 (h: 7tr; 384 bp; 4ex)

NFIA-AS1

h

KD, Ov. (lnc)

THP-1

miR-382, NFIA & Chol.

[86]

SNHG14

Snhg14 (m: 15tr; 6861 bp;1 2ex)

SNHG14

m

KD, Ov. (lnc)

BV-2

PLA2G4A

[87]

SNHG16

SNHG16 (h: 13tr; 3607 bp; 3ex)

SNHG16a

h

KD (lnc)

HCT119

SCD, PCSK9, SQLE, ACLY, INPP5D, HSD17B7

[88]

SPRY4-IT1

SPRY4-AS1 (h: 7tr; 1293 bp; 5ex)

SPRY4-IT1a

h

KD (lnc)

HEM-1

DGAT2, GPAT3 & Acyl Carnitine, FA, TG

[89]

SRA

Sra1b (m: 2tr; 1299 bp; 4ex)

SRA1

m

KO (lnc)

Liver

ATGL

[90]

m

KO (lnc)

Liver

PPARA, PPARG, FABP4, SCD & TG, FA

[91]

TRIBAL

AC091114.1 (h: 2tr; 1272 bp; 3ex)

TRIBAL

h

GWAS (TG)

SNP in TRIBAL locus

[92]

uc.372

RALGAPA1-AS1a

h,m

Ov. (lnc)

Liver, HepG2

ACACA, FASN, SCD, CD36 & TG, Chol.

[93]

XLOC_011279

LINCxxxxa

p

Co-effects (fat line)

Adipose

lnc, LPIN1

[94]

XLOC_013639

LINCxxxxa

p

Co-effects (fat line)

Adipose

lnc, SCD

[94]

XLOC_014379

NF1-IT1a

p

Co-effects (fat line)

Adipose

lnc, SCD

[94]

XLOC_019518

RNF7-DTa

p

Co-effects (fat line)

Adipose

lnc, SCD

[94]

XLOC_064871

LINCxxxxa

p

Co-effects (fat line)

Adipose

lnc, TRIB3

[94]

  1. agenes that not described in previous reviews dedicated to lncRNA in lipid metabolism. Database name (feature): name used in the Ensembl database for human (h), mouse (m) or chicken(c) gene database depending on the species in which the lncRNA has been studied (see column “sp”), the database was NONCODE for lncLTR; between brackets, the following features are provided: transcript number; the size (in bp) and the exon number (ex) indicated only for the transcript having the highest size and noted in the database ‘genecode basic’ and/or ‘TSL1 or TSL2’ (indexes giving the transcript support level)); b: lncRNA with a double “protein coding-lncRNA” classification (see result section); c: human name for lncRNA discovered in chicken and for which a non ambigous 1-to-1 orthologue was found; d: human name if no mouse name was found in Ensembl database. Normalized name: new names according to the HUGO gene nomenclature committee [32]. “Sp.” column mentions the species studied: “h”, “m”, “r”, “p” and “c” for human, mouse, rat, pig and chicken, respectively. The “Experiment” column refers to three type of experiments: 1. a direct or indirect causative effect of the lnc on the lipid metabolism through either an invalidation of the lncRNA by knockout (KO) or knockdown (KD) or an overexpression (Ov.) performed in vitro in cells or in vivo in mice; in the “action” column, we have provided the effects of the lnc overexpression when there were Ov and KD/KO experiments; 2. a “Co-effect “refers to a modulation of the quantity of the lncRNA in parallel with the quantity of transcripts or metabolites known to be involved in lipid metabolism; this co-modulation being induced in response to a particular factor (given between brackets) as disease, genotype/line, diet or molecule known to modulate lipid metabolism; 3. a” genome-wide association study” analysis (GWAS). The information in the “Tissue/cell type” and “Action” columns correspond to the experiment