ORIGINAL ARTICLE3D disorganization and rearrangement of genome provide insights into pathogenesis of NAFLD by integrated Hi-C, Nanopore, and RNA sequencing
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Graphical abstract
A high-resolution 3D genome interaction resource for NAFLD investigations is provided that can reveal the relationship among genetic rearrangements, spatial organization disruption, and gene regulation, and identified candidate genes associated with these variations implicated in the pathogenesis of NAFLD.
Key words
3D genome
Chromatin looping
Topologically associated domain
Transcriptome
Whole-genome sequencing
Abbreviations
3C
chromosome conformation capture
3D
three-dimensional
Abcg5
ATP-binding cassette sub-family G member 5
ALT
alanine aminotransferase
AST
aspartate aminotransferase
BWA
Burrows-Wheeler Aligner
Camk1d
calcium/calmodulin-dependent protein kinase type 1D
Chr
chromosome
CNV
copy number variation
DEG
differentially expressed gene
DEL
deletion
DI
directionality index
DUP
duplication
Elovl6
elongation of very long chain fatty acids protein 6
FDR
false discovery rate
FFA
free fatty acid
Fgfr2
fibroblast growth factor receptor 2
Gadd45g
growth arrest and DNA damage-inducible protein GADD45 gamma
GCKR
glucokinase regulator
GO
gene ontology
Grm8
metabotropic glutamate receptor 8
GSH
glutathione
Gsta1
glutathione S-transferase A1
H&E
hematoxylin-eosin
HFD
high-fat diet
Hi-C
high-throughput chromosome conformation capture
HSD17B13
hydroxysteroid 17-beta dehydrogenase 13
IDE
interaction decay exponent
INS
insertion
INV
inversion
IR
inclusion ratio
IRGM
immunity related GTPase M
IRS4
insulin receptor substrate 4
Kcnma1
calcium-activated potassium channel subunit alpha-1
KEGG
Kyoto Encyclopedia of Genes and Genomes
LPIN1
lipin 1
MBOAT7
membrane bound O-acyltransferase domain containing 7
MDA
malondialdehyde
NAFLD
non-alcoholic fatty liver disease
NF1
neurofibromin 1
NGS
next-generation sequencing
NOTCH1
notch receptor 1
ONT
Oxford Nanopore Technologies
PCA
principal component analysis
Pde4b
phosphodiesterase 4B
Plce1
1-phosphat-idylinositol 4,5-bisphosphate phosphodiesterase epsilon-1
Plxnb1
Plexin-B1
PNPLA3
patatin like phospholipase domain containing 3
PPP1R3B
protein phosphatase 1 regulatory subunit 3B
PTEN
phosphatase and tensin homolog
RB1
RB transcriptional corepressor 1
RNA-seq
RNA-sequencing
Scd1
acyl-CoA desaturase 1
SD
standard deviation
SOD
superoxide dismutase
Sugct
succinate-hydroxymethylglutarate CoA-transferase
SV
structural variation
TAD
topologically associated domain
TC
total cholesterol
TG
triglyceride
TM6SF2
transmembrane 6 superfamily member 2
TP53
tumor protein p53
TRA
translocation
WGS
whole-genome sequencing
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Peer review under responsibility of Chinese Pharmaceutical Association and Institute of Materia Medica, Chinese Academy of Medical Sciences.
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