Epigenetic mechanisms during ageing and neurogenesis as novel therapeutic avenues in human brain disorders

Delgado-Morales, Raúl; Agís-Balboa, Roberto Carlos; Esteller, Manel; Berdasco, María

doi:10.1186/s13148-017-0365-z

Clinical Epigenetics

Table 2 Epigenetic dysregulation in schizophrenia, PTSD (post-traumatic stress disorders) and Alzheimer’s disease

From: Epigenetic mechanisms during ageing and neurogenesis as novel therapeutic avenues in human brain disorders

Disorder	Molecular effect	Specie	Method	References
Schizophrenia
EPHA4, PKNOX1, ESR1, among others	DNA methylation, hsa-miR-219a-5p	Human	Gene set enrichment analysis	[206]
NUBP1, PRKCE, HLA-DQA1, HLA-B, FRK, IL12RB1, among others	DNA methylation	Human	DNA methylation array	[74]
FAM63B, among others	DNA methylation	Human	Methylome-wide association study, targeted pyrosequencing of bisulfite-converted DNA	[207]
GAD67	DNA methylation, H3 acetylation	Mouse	MeDIP, ChIP, qPCR, Western Blotting	[75, 77, 85]
REELIN	DNA methylation, H3 acetylation	Mouse, Human	MeDIP, ChIP, qPCR, Western Blotting, Gel Shift Binding Assays, Methylome-wide association study, targeted pyrosequencing of bisulfite-converted DNA	[77, 85, 207, 208]
BDNF	DNA methylation, H3 acetylation	Mouse, Human	MeDIP, ChIP, qPCR, Microarray-based DNA methylation profiling	[76, 209]
mGlu2	DNA methylation, H3 acetylation	Mouse	Bisulfite sequencing, ChIP, qPCR	[210]
HLA genes, among others	Histone acetylation	Mouse	Microarray studies, qRT-PCR, Western Blotting	[114]
COMT	DNA methylation	Human	Bisulfite, DNA sequencing, Methylated SpecificPCR and bisulfite sequencing, qRT-PCR	[211, 212]
S-COMT	DNA methylation	Human	Pyrosequencing	[213]
FOSP2	DNA methylation	Human	Bisulfite DNA sequencing	[214]
HTR2A	DNA methylation	Human	Bisulfite DNA sequencing	[215]
SOX10	DNA methylation	Human	Bisulfite DNA sequencing	[216]
5HTR1A	DNA methylation	Human	High-resolution melt assay	[217]
MAOA	DNA methylation	Human	Methylated Specific PCR	[218]
MEK1	DNA methylation	Human	Microarray-based DNA methylation profiling	[219]
CAMKIIγ	miR-129	Mouse	miRNA array profiling, miRNA specific RT-PCR	[220]
PTSD
BDNF	H4 acetylation	Mouse, Rat	Western Blotting, ChIP, qPCR	[221, 222]
FKBP5	DNA methylation/hydroxymethylation	Mouse	Bisulfite sequencing, Pyrosequencing	[34, 223]
HDAC1, cFos	H3 acetylation and methylation	Mouse	ChIP, qPCR	[224]
NR2B	H3 and H4 acetylation	Rat	Western Blotting, ChIP, RT-PCR	[225]
CBP, p300, PCAF	H2B and H4 acetylation	Rat	Western Blotting, ChIP, PCR	[226]
Calcineurin (CaN)	DNA methylation	Rat	Bisulfite sequencing	[227]
PP1	DNA methylation	Rat	DNA methylation assay	[228]
REELIN	DNA demethylation	Rat	DNA methylation assay	[228]
IGF2, cFOS, ARC	H3 acetylation	Mouse	ChIP, qPCR	[229]
TLR1, IL8, CNTN2, among others	DNA methylation	Human	DNA methylation array	[230, 231]
MAN2C1	DNA methylation	Human	DNA methylation array	[232]
IGF2, H19, IL8, IL16, IL18	DNA methylation	Human	Pyrosequencing	[233]
COMT	DNA methylation	Human	DNA methylation array	[234]
ADCYAP1R1	DNA methylation	Human	DNA methylation array	[235]
NR3C1	DNA methylation	Human	Pyrosequencing and clonal sequencing	[236,237,238]
SLC6A3	DNA methylation	Human	DNA methylation array	[239]
SLC6A4	DNA methylation	Human	DNA methylation array	[240]
APC5, TPR, CLEC9A, ANXA2, TLR8	DNA methylation	Human	DNA methylation array	[241]
FKBP5	miR-511	Mouse	qPCR	[242]
Alzheimer’s disease
APP	DNA methylation	Human	MSRE-SB, pyrosequencing	[125,126,127]
BACE1	DNA methylation	Cell lines	HPLC	[129]
PSEN1	DNA methylation	Cell lines	HPLC	[129]
Neprylisin	DNA methylation	Cell lines	MS-PCR	[131]
DUSP22	DNA methylation	Human	BS-array, pyrosequencing	[117]
DUSP22	DNA hydroxymethylation	Human	WG 5-hmC-enriched seq	[117]
SORBS3	DNA methylation	Human	BS-array, pyrosequencing, MS-PCR	[116, 132]
NF-kB	DNA methylation	Human and Cell lines	Specific Methylation Assay	[133, 134]
COX2	DNA methylation	Human and Cell lines	Specific Methylation Assay	[134]
BDNF	DNA methylation	Human	MSRE-PCR	[133]
CREB	DNA methylation	Human	MSRE-PCR	[133]
TBXA2R	DNA methylation	Human	BS-array, pyrosequencing, MS-PCR	[116]
ANK1	DNA methylation	Human	WGBS, BS-array, pyrosequencing	[121, 122]
BACE1	H3 acetylation	Human	FAIRE/ChIP	[130]
Neprylisin	H4 acetylation	Cell lines	ChIP	[144]
miR-9	downregulation	Human	PCR	[179]
miR-26a	upregulation	Human	PCR	[161]
miR-29a/b-1	downregulation	Human	miRNA microarray	[164]
miR-29c	downregulation	Mouse	RT-PCR	[164, 168]
miR-34c	downregulation	Human	RNA sequencing	[178]
miR-101	downregulation	Cell lines	PCR	[158]
miR-106b	downregulation	Human	miRNA microarray, Northern blot	[157]
miR-107	downregulation	Human	miRNA microarray	[163]
miR-124	downregulation	Human	RT-PCR	[160]
miR-125	upregulation	Human	Northern blot	[161, 174, 183]
miR-132	downregulation	Human	Northern blot	[161, 174, 183]
miR-137	downregulation	Human	PCR	[162]
miR-153	downregulation	Human	PCR	[158]
miR-181c	downregulation	Human	PCR	[161, 162, 179]
miR-132	downregulation	Human	Northern blot	[174]
miiR-219	downregulation	Human	RNA sequencing	[170]
miR-339-5p	downregulation	Human and Cell lines	RT-PCR	[167]
BACE1-AS	upregulation	Human and Cell lines	RT-PCR	[169]
lnc-17A	upregulation	Human	RT-PCR	[184]

DNA methylation, histone alterations and microRNA expression is summarized. BS-array bisulfite-modified DNA based arrays, ChIP chromatin immunoprecipitation, FAIRE formaldehyde-assisted isolation of regulatory elements, HPLC high-performance liquid chromatography, MeDIP methylated DNA immunoprecipitation, MS-PCR methylation specific PCR, MSRE-PCR methylation-sensitive restriction enzyme-PCR, qPCR quantitative real-time PCR, WG 5-hmC-enriched seq whole-genome sequencing analysis of 5-hydroxymethylcytosine-enriched sequences, WGBS whole-genome bisulphite sequencing

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ISSN: 1868-7083

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