Restricting retrotransposons: a review

Goodier, John L.

doi:10.1186/s13100-016-0070-z

Mobile DNA

Table 1 Cellular factors associated with mammalian non-LTR retrotransposon activity

From: Restricting retrotransposons: a review

Protein Symbol (Hs) (1)	Alternative Name (Hs or Mm) (1)	Protein Name	Source species of factor (1)	Comment	Altered retrotransposition reported	References
Post-transcriptional
AICDA	AID	Activation-induced cytidine deaminase	various	RNA-editing cytidine deaminase	Y	[142, 144]
APOBEC1		Apolipoprotein B mRNA editing enzyme catalytic subunit 1	various	RNA-editing cytidine deaminase	Y	[143, 145]
APOBEC3		Apolipoprotein B mRNA editing enzyme catalytic subunit 3	Hs	RNA-editing cytidine deaminase	Y	[136, 145, 149, 152, 153, 160, 515–521]
ATG5		Autophagy related 5	Hs	Autophagy E1-like activating enzyme	Y	[52]
BECN1	ATG6	Beclin 1	Mm	Autophagy factor	Y	[52]
CALCOCO2	NDP52	Calcium binding and coiled-coil domain 2	Hs	Macroautophagy receptor	Y	[52]
HNRNPL		Heterogeneous nuclear ribonucleoprotein L	Hs		Y	[56, 236, 240, 261]
KIAA0430	MARF1, LKAP	Meiosis arrest female protein 1	Hs	Regulator of oogenesis		[266, 267]
MOV10		Mov10 RISC complex RNA helicase	Hs	Putative ATP-dependent RNA helicase	Y	[232, 234–237]
MTNR1A	MT1	Melatonin receptor 1A	Hs		Y	[258]
PABPC1	PABP1	Poly(A) binding protein cytoplasmic 1	Hs		Y	[259]
RNASEL		Ribonuclease L	Hs	Endoribonuclease/component of 2-5A system	Y	[254]
SAMHD1		SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1	Hs,Mm		Y	[168, 169, 171, 172]
SQSTM1	P62	Sequestosome 1	Hs	Macroautophagy receptor	Y	[52]
TEX19	TEX19.1	Testis expressed 19	Mm			[264, 265]
TREX1	AGS1	Three prime repair exonuclease 1	Mm	3' exonuclease	Y	[257]
ZC3HAV1	PARP13, ZAP	Zinc finger CCCH-type containing, antiviral 1	Hs	Antiviral protein	Y	[236, 240, 250]
piRNA/RNAi-Pathways
ASZ1	GASZ	Ankyrin repeat, SAM and basic leucine zipper domain containing 1	Mm			[206, 217]
DDX4	MVH, VASA	DEAD-box helicase 4	Mm	ATP-dependent RNA helicase		[210, 217]
DGCR8	pasha	DGCR8 microprocessor complex subunit	Hs	Subunit of microprocessor	Y	[196, 197]
DICER1	DCR1	Dicer 1, ribonuclease type III	Hs	dsRNA endoribonuclease	Y	[191, 194]
DROSHA	RNASEN	Drosha ribonuclease type III	Hs	dsRNA-specific endoribonuclease/subunit of microprocessor	Y	[197]
EXD1		Exonuclease 3'-5' domain containing 1	Mm	3'-5' exonuclease activity		[223]
FKBP6		FK506 binding protein 6	Mm	Cis-trans peptidyl-prolyl isomerase		[215]
GTSF1	CUE110	Gametocyte specific factor 1	Mm	UPF0224 (FAM112) family member		[209]
HENMT1		HEN1 methyltransferase homolog 1	Mm	2'-O-methylation pf piRNAs		[221]
HSP90AA1	HSP90N	Heat shock protein 90 alpha family class A member 1	Mm	Molecular chaperone		[220]
MAEL		Maelstrom spermatogenic transposon silencer	Mm			[204]
MIR128-1		microRNA 128-1	Hs		Y	[192]
MOV10L1		Mov10 RISC complex RNA helicase like 1	Mm	Putative ATP-dependent RNA helicase		[244, 245]
	Nct1/2	Non-coding in testis 1/2	Mm	piRNA encoding non-coding RNAs		[205]
PIWIL1	MIWI	Piwi like RNA-mediated gene silencing 1	Mm	Argonaute family member		[212]
PIWIL2	MILI	Piwi like RNA-mediated gene silencing 2	Mm	Argonaute family member		[200, 211, 216, 217]
PIWIL4	MIWI2	Piwi like RNA-mediated gene silencing 4	Mm	Argonaute family member		[202, 203, 211, 212, 222]
PLD6	MITOPLD	Phospholipase D family member 6	Mm			[213]
TDRD1		Tudor domain containing 1	Mm			[207]
TDRD5		Tudor domain containing 5	Mm			[214]
TDRD9		Tudor domain containing 9	Mm	Putative ATP-dependent RNA helicase		[208, 217]
TDRD12		Tudor domain containing 12	Mm	Putative ATP-dependent RNA helicase		[218]
TDRKH	TDRD2	Tudor and KH domain containing	Mm			[219]
Epigenetic/Nuclear Factors
ALKBH1		alkB homolog 1, histone H2A dioxygenase	Mm	3-methylcytosine demethylase		[366]
ATM		ATM serine/threonine kinase	Hs,Mm	PI3/PI4-kinase family member	Y	[369–371]
CHAF1	CAF1	Chromatin assembly factor 1	Mm	Assembles histone octamer		[297]
DCLRE1C	ARTEMIS	DNA cross-link repair 1C	Gg	Roles in NHEJ DNA repair and V(D)J recombination	Y	[367]
DNMT1		DNA methyltransferase 1	Hs,Mm			[313, 340]
DNMT3A		DNA methyltransferase 3 alpha	Hs,Mm			[313, 340, 342, 344]
DNMT3B		DNA methyltransferase 3 beta	Hs,Mm			[313, 340, 342, 344]
DNMT3L		DNA methyltransferase 3 like	Mm	DNA methyltransferase cofactor		[222, 342, 345]
EHMT2	G9A	Euchromatic histone lysine methyltransferase 2	Mm	Histone H3K9me1 and H3K9me2 methyltransferase		[289]
ERCC1	RAD10	ERCC excision repair 1, endonuclease non-catalytic subunit	Cg	Nucleotide excision repair	Y	[368]
ERCC4	XPF	ERCC excision repair 4, endonuclease catalytic subunit	Hs,Cg	Nucleotide excision repair (heterodimer with ERCC1)	Y	[368]
KDM1A	LSD1	Lysine demethylase 1A	Mm	Histone H3K4me and H3K9me demethylase		[363]
LIG4		DNA ligase 4	Gg	Roles in NHEJ DNA repair and V(D)J recombination	Y	[367]
MECP2		Methyl CpG binding protein 2	Hs,Mm	Binds methylated DNA	Y	[355–357]
MORC1		MORC family CW-type zinc finger 1	Mm	Role in early spermatogenesis		[352]
PRKDC	XRCC7, DNA-PKcs	Protein kinase, DNA-activated, catalytic polypeptide	Cg	NHEJ DNA double-strand break repair	Y	[68, 72]
SIRT6		Sirtuin 6	Mm	NAD-dependent protein deacetylase	Y	[473]
SUV39H		Suppressor of variegation 3–9 homolog 1	Hs,Mm	Histone H3-K9 methyltransferase 1		[286, 288, 291]
TRIM28	KAP1	Tripartite motif containing 28	Hs,Mm	Nuclear corepressor for KRAB-ZFPs		[313]
UHRF1	NP95, ICBP90	Ubiquitin-like with PHD and ring finger domains 1	Mm	RING-finger type E3 ubiquitin ligases		[351]
XRCC4		X-ray repair cross complementing 4	Cg	DNA single-strand break repair	Y	[68, 72]
XRCC6	KU70	X-ray repair cross complementing 6	Gg	ssDNA-dependent ATP-dependent helicase	Y	[367]
Krüppel-associated box domain-containing zinc finger proteins (KRAB-ZFPs)
	GM6871	Predicted gene 6871	Mm			[313]
ZBTB16	PLZF	Zinc finger and BTB domain containing 16	Hs,Mm		Y	[317]
	ZFP819	Zinc finger protein 819	Mm			[314]
ZNF91		Zinc finger protein 91	Hominidae			[315]
ZNF93		Zinc finger protein 93	Hominidae		Y	[315]
Other transcription factors
AHR		Aryl hydrocarbon receptor	Mm,Dr	Ligand-activated transcription factor		[109, 114]
CTCF		CCCTC-binding factor	various	BORIS + CTCF gene family member		[108, 116]
ETS1		ETS proto-oncogene 1, transcription factor	Hs	ETS transcription family member		[102]
RAR		Retinoic acid receptor	Hs	Thyroid-steroid hormone receptor superfamily member		[107, 115]
	RB/E2F1	RB transcriptional corepressor proteins/E2F transcription factor 1	Hs,Mm	Transcription repressor complex		[112, 298]
RUNX3		Runt-related transcription factor 3	Hs	Runt domain-containing transcription family member	Y	[104]
SNAI2	SLUG	Snail family transcriptional repressor 2	Mm,Dr	Snail C2H2-type zinc finger transcription family member		[109, 114]
SOX2		SRY-box 2	Hs,Mm	SRY-related HMG-box (SOX) transcription family member		[103, 106, 111]
SP1		Sp1 transcription factor	Hs	zinc finger transcription factor		[102]
	TCF-LEF	T-cell factor/lymphoid enhancer factor	Rn	Wnt transcription factors		[111]
TP53	p53	tumor protein p53	Dr,Hs,Mm	tumor suppressor protein	Y	[110, 299, 300]
YY1		YY1 transcription factor	Hs,Mm	GLI-Kruppel zinc finger transcription family member		[101, 105, 113]

(1) Cg, Cricetulus griseus; Cl, Canis lupus; Dr, Danio rerio; Gg, Gallus gallus; Hs, Homo sapiens; Mm, Mus musculus, Rn, Rattus norvegicus

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