Losing DNA methylation at repetitive elements and breaking bad

Pappalardo, Xena Giada; Barra, Viviana

doi:10.1186/s13072-021-00400-z

Epigenetics & Chromatin

Table 1 Hypomethylated repetitive elements in human diseases

From: Losing DNA methylation at repetitive elements and breaking bad

	Disease	Type of RE	Cell type	References
Hereditary diseases	AGS	LINEs, LTRs, SINEs and DNA satellites	Fibroblasts	Lim et al. [112]
	ICF	Sat1 and 2	Fibroblasts, lymphoblasts	Hassan et al. [57]
			Leukocytes	Jeanpierre et al. [54]
			Lymphocytes	Ji et al. [56], Miniou et al. [55], Heyn et al. [58], Simo-Riudalbas et al. [72]
		Sat-α	Fibroblasts, leukocytes	Miniou et al. [63]
		Sat-α	Blood cells	Velasco et al. [62]
		Sub-telomeric repeats	Lymphoblastoid cell lines	Sagie et al. [67]
		D4Z4 and NBL2	Lymphoblastoid cell lines	Kondo et al. [71]
	FSHD	D4Z4 and NBL2	Several tissues including blood	van Overveld et al. [84], de Greef et al. [81], Lemmers et al. [85], Gaillard et al. [87]
	HSAN1E	Sat2, sat-α, LINEs and Alus	Blood cells	Klein et al. [99], Sun et al. [101]
	SLE	HERV-E	Blood cells	Wu et al. [107], Wang et al. [108]
Cancer	Breast cancer	Sat2, sat-α, LINEs and Alus	Tumoural cells	Narayan et al. [183]
	Bladder cancer	Sat2, LINE-1 and Alus, sat-α, NBL2	Tumoural cells	Si et al. [172]
	CLL	Alus, LINEs, LTRs, sat	Tumoural cells	Subhash et al. [173]
	Colon cancer	NBL2	Tumoural cells	Samuelsson et al. [187], Dumbović et al. [188]
	Colon cancer	LINE-1	Blood cells	Samuelsson et al. [187], Suter et al. [175]
	Extra-hepatic cholangiocarcinoma	LINE-1, sat2	Blood cells	Kim et al. [171]
	Gastrointestinal stromal tumour	AluYb8, sat-α, NBL2	Tumoural cells	Igarashi et al. [174]
	Gastrointestinal stromal tumour	LINE-1	Tumoural cells	Igarashi et al. [174], Shigaki et al. [179]
	Hepatocellular carcinoma	Alus and LINEs	Tumoural cells	Zheng et al. [170]
		Sat2		Wong et al. [186]
		NBL2		Nagai et al. [185]
	Neuroblastoma	NBL2	Tumoural cells	Thoraval et al. [184]
	Lung carcinoma	Alu	Tumoural cells	Ikeda et al. [176]
	Ovarian carcinoma	LINE-1	Tumoural cells	Notaro et al. [177], Zhang et al. [178]
	Ovarian carcinoma	sat2 and sat-α	Tumoural cells	Qu et al. [191], Widschwendter et al. [190]
	Thyroid cancer	Alus	Tumoural cells	Hesselink et al. [181]
	Wilms tumours	Sat2 and sat-α	Tumoural cells	Qu et al. [189]
Ageing	Ageing	Sat3	Fibroblasts	Enukashvily et al. [192]
		Alus	Blood cells	Bollati et al. [216]
		Alus	Blood cells	Jintaridth and Mutirangura [217]
		Alus and LINE-1	DNA-cell free	Erichsen et al. [219]
Brain diseases	Neurodevelopmental disorders
	ASD	LINE-1 s	Lymphocytes	Tangsuwansri et al. [135]
	ASD	Alus	Lymphocytes	Saeliw et al. [136]
	AT	LINE-1, sat2, sat-α	Lymphocytes	Almeida et al. [129]
	Neurodegenerative disorders
	AD	Alus, sat-α	Leukocytes	Bollati et al. [142]
	Neuropsychiatric disorders
	BP	LINE-1 S2 and S3	Blood cells	Li et al. [147]
	BP	AluYA3	Blood cells	Li et al. [148]
	ELS-related disorders	LINE-1	Leukocytes	Misiak et al. [126]
	ELS-related disorders	SINEs	Leukocytes	Nätt et al. [127]
	MDD	LINE-1	Blood cells	Liu et al. [157]
	MDD	AluJb	Blood cells	Schneider et al. [158]
	PTSD	Alus and LINE-1	Serum	Rusiecki et al. [163]
	SZ	LINE-1	Blood cells	Misiak et al. [126]
		LINE-1 S1 and S3		Li et al. [147]
		AluYA3		Li et al. [148]

AGS Aicardi–Goutières syndrome, AD Alzheimer's disease, ASD autism spectrum disorders, AT ataxia teleangectasia, BP bipolar disorder, CLL chronic lymphocytic leukaemia, ELS early life stress, ICF immunodeficiency with centromeric instability and facial anomalies syndrome, FSHD facioscapulohumeral muscular dystrophy, MDD major depressive disorder, PTSD post-traumatic stress disorder, SZ schizophrenia

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