2023年9月 – 转座子实验室

Video

TE keynote lectures

*Part 1: Introduction to transposable elements (38 minutes) by Susan Wessler

*Part 2: How transposable elements amplify throughout genomes (70 minutes) by Susan Wessler

*Transposable Element-mediated Structural Variation: From McClintock to Pangenomes – YouTube by Susan Wessler, department of Botany and Plant Sciences, University of California (55 minutes)

The Dynamic Genome: Unintelligent Design – YouTube by Susan Wessler department of Botany and Plant Sciences, University of California (60 minutes)

LINE1 by Haig Kazazian Jr – YouTube 43′

Zebrafish link

斑马鱼胚胎显微注射视频下载

Zebrafish development stages 下载

ZFIN The Zebrafish Information Network

DANIO-CODE programme (birmingham.ac.uk)

转座子科普: RepBase

一、转座元件介绍

TE education: RepBase (girinst.org)

转座元件（Transposable element，TE）

转座元件（Transposable element，简称TE），又称转座子或移动元件，是一类DNA片段的集合，可以通过转座作用在基因组中从一个位置移动或复制到另一个位置。TE的长度范围从小于100个碱基对到超过20,000个碱基对不等。转座之后，很多类型TE两侧都含有短的（约1-20个碱基对）直接重复序列，这些直接重复序列是转座过程中从靶序列中衍生出来的靶位点重复序列（target site duplications，TSDs)。然而，一些TE类型，例如Helitron、几个Harbinger家族和CR1逆转座子，不产生TSDs。TSD的长度通常是一组TE及其相关物种的特征，但在不同家族和超家族中可能有所变化。在多数真核生物基因组中，TE是重复序列的主要成份。其他重复序列包括串联重复序列（卫星序列或微卫星）、零星的基因组重复以及一些多拷贝宿主基因（如rRNA、tRNA、组蛋白基因等）。事实上，TE可以被视为基因组内的寄生元件。同样地，细胞间病毒也可以被视为TE，因为它们可以整合到宿主基因组中，例如LTR-逆转录病毒。TE对宿主基因组具有多样化的进化影响。

转座子科普：维基百科

Transposable element – Wikipedia

Transposable_element-2023-8-26-generated from Wiki 下载

转座元件

转座元件（TE），也称为转座子或跳跃基因，是DNA中的一种核酸序列，可以在基因组内改变其位置，有时会介导产生突变或逆转突变，从而改变细胞的遗传特征和基因组大小。转座往往导致相同遗传物质的复制。在人类基因组中，L1和Alu转座子是两个典型例子。巴巴拉·麦克林托克在1983年因发现转座子而获得了诺贝尔奖。转座子在个性化医学中的重要性日益凸显；在多维大数据组学分析中，转座子也越来越受到关注。

在真核生物中，转座子占据了基因组的很大一部分，是真核细胞中DNA质量的主要决定因素。尽管转座子是自私的遗传元件，但许多转座子在基因组功能和进化中都发挥重要作用。转座子对于科学研究人员来说也非常有用，可以利用转座子对活有机体进行体内DNA遗传修饰。

转座子至少可以分为两大类：I类转座子（也称逆转录转座子），通常需要通过逆转录方式介导转座，而II类转座子（也称DNA转座子），能编码转座酶，介导转座（包括转座子在原有位置的切除和和新位置的插入），有些转座子也编码其他蛋白质。

转座子分类表

Copy-out–Paste-in IS elements identifed in prokaryotes

Families	groups	Size-range	DR	Ends	IRs	Nb ORF	Frameshift	Chemistry

IS1	IS1	740-1180	8-9	GGnnnTG	Y	2	ORFAB	DDE
	ISMhu11	900-4600	0-10		Y	2	ORFAB
IS3	IS911	1250			Y	2	ORFAB
	IS150	1200-1600	3-4	TG	Y	2	ORFAB	DDE
	IS407	1100-1400	4	TG
	IS51	1000-1400	3-4	TG
	IS3	1150-1750	3-4	TGa/g
	IS2	1300-1400	5	TG
IS481	–	950-1300	4-15	TGT	Y	1
IS30	–	1000-1700	2-3		Y	1		DDE
IS110	IS110	1200-1550	0		N			DEDD
	IS1111				Y *			DEDD
IS256	–	1200-1500	8-9	Ga/g	Y	1		DDE
ISL3	–	1300-2300	8	GG	Y	1
IS21	–	1750-2600	4-8	TG	Y	2 *		DDE
ISLre2

Based on reference: Copy-out–paste-in transposition of IS911: a major transposition pathway. Microbiol Spectrum 3(4):MDNA3-0031-2014 Reference

Classification, terminal features, TSD features and the number of entries of DNA transposons in Repbase

Group	Superfamily	Termini	Mechanism	TSD	Entries
IS630/Mariner	Mariner/Tc1	YR..YR	Cut-and-paste	TA	2,539
	Zator	GG..CC	Cut-and-paste	3	54
IS481/Ginger	Ginger1	TGT..ACA	Cut-and-paste	4	39
	Ginger2/TDD	TGT..ACA	Cut-and-paste	4–5	20
IS3/IS3EU	IS3EU	TAY..RTA	Copy-out–Paste-in?	6	23
IS1016/Merlin	Merlin	GG..CC	Cut-and-paste	8–9	75
IS256/DxxH	hAT	YA..TR	Cut-and-paste	5–8	2,955
	MuDR	GR..YC	Cut-and-paste	8–9	1,345
	P	CA..TG	Cut-and-paste	7–8	189
	Kolobok	RR..YY	Cut-and-paste	TTAA	286
	Dada	?		6–7	36
IS1380/piggyBac	piggyBac	YY..RR	Cut-and-paste	TTAA	377
IS5/PHIS	Harbinger	RR..YY	Cut-and-paste	3	1,097
	ISL2EU	RR..YY	Cut-and-paste?	2	88
	Spy		Cut-and-paste	no
	NuwaI
	NuwaII
	Pangu
CCHH	EnSpm/CACTA	CAC..GTG	Cut-and-paste	2–4	715
	Transib	CAC..GTG	Cut-and-paste	5	123
KDZP	Zisupton	?	?	8	18
Sola	Sola		Cut-and-paste
	Sola1	?	Cut-and-paste	4	100
	Sola2	GRG..CYC	Cut-and-paste	4	90
	Sola3	GAG..CTC	Cut-and-paste	TTAA	28
	Unclassified Sola		Cut-and-paste		1
?	Academ	YR..YR	Cut-and-paste	3–4	90
?	Novosib	CA..TG	Cut-and-paste	8	9
Crypton	Crypton		Copy-out–Paste-in
	CryptonF		Copy-out–Paste-in	0	23
	CryptonA	TTA..	Copy-out–Paste-in	0	17
	CryptonI	?	Copy-out–Paste-in	0	9
	CryptonS	TATGG..	Copy-out–Paste-in	0	59
	CryptonV	?	Copy-out–Paste-in	0	46
	Unclassified Crypton		Copy-out–Paste-in		80
Helitron	Helitron	TC..CTRR	Rolling circle	0	955
Polinton	Polinton	AG..CT	Self-synthesizing	6	108
	Unclassified DNA transposon				2,357
	Total				13,960

Eukaryotic cut-and-paste transposase superfamilies

Fig. 2. An unrooted consensus tree of the transposase superfamilies inferred from the presence or absence of the highly conserved residues in the signature strings. Bootstrap values are at the nodes. The arrows with labels indicate superfamily clusters merged in our revised classification. Shown on the right is a schematic representation of the DDE/D domain and the signature string for each superfamily. Conserved blocks are highlighted in blue, variable regions are in gray. White gaps are regions not drawn to scale. The DDE triads are highlighted in red. Alternative residues are marked by slashes; lowercase indicates that a residue occurs in <10% of the sequences in the alignment profile. The C/DH motif is highlighted in orange; the C(2)C, [M/L]H, and H(3-4)H motifs are highlighted in green.

DDE-domain-sequences (fasta): The-catalytic-domain-of-all-eukaryotic-cut-and-paste-transposase-superfamilies-dataset1 下载

List of Copy-out–Paste-in IS elements

List of mobile elements whose transposases have been examined by secondary structure prediction programs

Family	Element (or protein) analyzed	Active or # copies in genome1	From secondary structure, type of DDE/D motif2	Relevant references3
IS1	IS1NISSto9	>40*5	DD(24)EDD(20)E	* Nyman et al., 1981; Ohta et al., 2002, 2004; Siguier et al., 2009
IS1595	1. ISPna2	?,DD(36)N”	Siguier et al., 2009
	2. ISH4	?,DD(36)E”	Siguier et al., 2009
	3. IS1016C	?,DD(34)E”	Siguier et al., 2009
	4. IS1595	?,DD(35)N”	Siguier et al., 2009
	5. ISSod11	13	DD(34)H	Siguier et al., 2009
	6. ISNWi1	?,DD(35)E”	Siguier et al., 2009
	7. ISNha5	?,DD(33)E”	Siguier et al., 2009
	Merlin: MERLIN1_SM	Consensus	DD(36)E	Feschotte, 2004
IS3	IS911	Active	DD(35)E	Polard and Chandler, 1995; Rousseau et al., 2002
IS481	IS481	?00*	DD(35)E	*Glare et al., 1990; Chandler and Mahillon, 2002
IS4	IS50R	Active	PDB ID: 1muhDD(-strand)E	Rezshazy et al., 1993; Davies et al., 2000
IS701	IS701ISRso17	Active (15*)7	DD(-strand)E	*Mazel et al., 1991
ISH3	ISC1359ISC1439A	513	DD(-strand)E
IS1634	IS1634ISMac5ISPlu4	Active (?0*)77	DD(-strand)E	*Vilei et al., 1999
IS5	IS903	Active	DD(65)E	Derbyshire et al., 1987; Rezshazy et al., 1993; Tavakoli et al., 1997
	PIF/Harbinger: PIFa (Z. mays)	Active	DD(59)E	Zhang et al., 2001; Kapitonov and Jurka, 2004; Sinzelle et al., 2008
IS1182	IS660ISPsy6	314	DD(-strand)E	Takami et al., 2001
IS6	IS6100	Active	DD(34)E	Martin et al., 1990; Mahillon and Chandler, 1998
IS21	IS21	Active	DD(45)E	Mahillon and Chandler, 1998; Berger and Haas, 2001
IS30	IS30	Active	DD(33)E	Caspers et al., 1984; Mahillon and Chandler, 1998
IS66	IS679ISPsy5ISMac8	Active333	DD(-helical?)E	Han et al., 2001
IS110	IS492IS1111	Active20	DEDDDEDD	Perkins-Balding et al., 1999; Buchner et al., 2005
IS256	IS256	Active	DD(-helical)E	Mahillon and Chandler, 1998; Prudhomme et al., 2002
	MuDr/Foldback (Mutator)	Active	DD(-helical)E	Eisen et al., 1994; Babu et al., 2006; Hua-Van and Capy, 2008
IS630	ISY100	Active	DD(34)E	Doak et al., 1994; Feng and Colloms, 2007
	Tc1/mariner: Mos1 (D. mauritiana)	Active	PDB ID: 2f7tDD(34)D	Plasterk et al., 1999; Richardson et al., 2006
	Zator: Zator-1_HM	36*	DD(43)E	*Bao et al., 2009
IS982	ISPfu3	5	DD(47)E	Mahillon and Chandler, 1998
IS1380	IS1380A	?00*	DD(-strand)E	*Takemura et al., 1991; Chandler and Mahillon, 2002
	piggyBac (T. ni)	Active	DD(-strand)D	Cary et al., 1989; Sarkar et al., 2003; Mitra et al., 2008
ISAs1	ISAzo3	7	DD(-strand)E/D?
ISL3	IS31831IS651	Active22	DD(-helical)E	Suzuki et al., 2006
Tn3	Tn3 (E. coli)	Active	DD(-helical?)E	Grindley, 2002
hAT	Hermes (M. domestica)	Active	PDB ID: 2bw3 DD(-helical)E insertion	Warren et al., 1994; Rubin et al., 2001; Hickman et al., 2005
CACTA	CACTA1 (A. thaliana) En/Spm ZM	Active	DD(-helical?)E/D?	Miura et al., 2001; DeMarco et al., 2006
P	Drosophila	Active	?	Rio, 2002
Transib	Transib1_AG	Consensus	DD(-helical)E	Kapitonov and Jurka, 2005; Chen and Li, 2008
	RAG1 (M. musculus)	Active	DD(-helical)E	Kim et al., 1999; Landree et al., 1999; Lu et al., 2006
Sola	Sola3-3_HM	Multiple copies*	DD(40)E	*Bao et al., 2009

Hickman AB, Chandler M, Dyda F. Integrating prokaryotes and eukaryotes: DNA transposases in light of structure. Crit Rev Biochem Mol Biol. 2010 Feb;45(1):50-69. doi: 10.3109/10409230903505596.

Classification, distribution and the number of entries of LTR retrotransposons in Repbase

Superfamily	Total
Copia	10,595
Gypsy	6,694
BEL	1,855
ERV
ERV1	1,967
ERV2	1,266
ERV3	657
ERV4	187
Lentivirus	4
Unclassified ERV	325
Unclassified LTR	719
DIRS	418

Classification, and the number of entries of non-LTR retrotransposons in Repbase

Group	Clade	Total
CRE	CRE	43
R2	R4	46
	Hero	23
	NeSL	106
	R2	159
Dualen	RandI/Dualen	13
L1	Proto1	6
	L1	1,690
	Tx1	273
RTE	RTETP	1
	Proto2	47
	RTEX	138
	RTE	487
I	Outcast	23
	Ingi	17
	Vingi	141
	I	195
	Nimb	108
	Tad1	141
	Loa	74
	R1	237
	Jockey	243
CR1	Rex1	95
	CR1	803
	Kiri	91
	L2	285
	L2A	5
	L2B	27
	Crack	140
	Daphne	227
Ambal	Ambal	8
Penelope	Penelope	477
SINE	SINE1/7SL	95
	SINE2/tRNA	539
	SINE3/5S	30
	SINEU	17
	Unclassified SINE	112
	Unclassified non-LTR retrotransposon	179
	Total	7,341

Reference: Kenji K. Kojima, Structural and sequence diversity of eukaryotic transposable elements, Genes & Genetic Systems, 2019, Volume 94, Issue 6, Pages 233-252

Proposal of TE classes with some members having a DNA transposon phenotype

Reference: Benoît Piégu, Solenne Bire, Peter Arensburger, Yves Bigot, A survey of transposable element classification systems – A call for a fundamental update to meet the challenge of their diversity and complexity,
Molecular Phylogenetics and Evolution, Volume 86, 2015, Pages 90-109,
ISSN 1055-7903, https://doi.org/10.1016/j.ympev.2015.03.009.

Major Features of Prokaryotes IS families (ISfinder)

Overview of common transposon annotation tools

	Approach			Class I			Class II
Name		Novo.	Struc.	Simil.	LTR	LINE	SINE	TIR	HEL	MITE
RepeatMasker		x		x	x	x	x	x	x	x
RepeatModeler		x			x	x	x	x	x	x
CLARI_TE	(107)	x	x	x	x	x	x	x	x	x
TESeeker	(41)			x	x	x	x	x	x	x
PILER	(40)	x			x	x	x	x	x	x
Censor	(108)	x			x	x	x	x	x	x
RepLong	(109)	x			x	x	x	x	x	x
EDTA	(44)	x	x	x	x	x	x	x	x	x
MGEScan	(110)	x	x	x	x	x	x
LTR_Finder	(111)		x		x
LtrDetector	(112)		x		x
LTRpred	(73)	x	x	x	x
LTRharvest	(66)	x	x	x	x
LTRdigest	(113)		x		x
SINE-Finder	(68)	x	x				x
SINE-Scan	(69)	x	x				x
TIRvish	(67)		x					x
HelitronScanner	(42)		x						x
MUSTv2	(70)		x							x
MiteFinderII	(71)		x							x
MITE-Tracker	(72)		x							x
detectMITE	(45)		x							x
MITE-Hunter	(47)		x							x
TransposonUltimate

Refernce

*Part 2: How transposable elements amplify throughout genomes (70 minutes) by Susan Wessler

*Transposable Element-mediated Structural Variation: From McClintock to Pangenomes – YouTube by Susan Wessler, department of Botany and Plant Sciences, University of California (55 minutes)

The Dynamic Genome: Unintelligent Design – YouTube by Susan Wessler department of Botany and Plant Sciences, University of California (60 minutes)

Group	Superfamily	Family	Identified in our Lab	Identified by other Lab
IS630-Tc1-mariner/ITm	Tc1/mariner	DD34E/ZB and ZB like	Y
		DD34E/SB and SB like	Y
		DD34E/Skipper (SK)	Y
		DD34E/Passport	?
		DD34E/Frog Prince	?
		DD35E/Traveler (TR)	Y
		DD36E/Incomer (IC)	Y
		DD37E/TRT		Y
		DD37E/Mosquito (MS)	Y
		DD38E/Intruder (IT)	Y
		DD34D/Mariner	Y (unpublished data)
		DD37D/maT	Y
		DD39D/Guest (GT)	Y
		DD41D/Visitor (VS)	Y
	pogo	Fot/Fot-like (DD35D)	Y
		Passer (PS)/DD35D	Y
		Tigger/DD29-36	Y
		pogoR/DD29-59D	Y
		Lemi/DD29D-42D	Y
		Mover/DD36E	Y
	DD82E/Sailor	DD82E/Sailor	Y
	DD34E/Gambol	DD34E/Gambol (GB)	Y
		DD35E/Hiker (HK)	Y
IS256/DxxH	hAT	TcBuster/TB	Y
		Ac		?
		Tip		?
		Cleaner/CN	Y (unpublished data)
		Dancer/DN	Y (unpublished data)
		Roamer/RM	Y (unpublished data)
	MuDR	MuDR		?
IS1380/piggyBac	piggyBac	Pokey	Y (unpublished data)
		?
IS5/PHIS	PHIS	PIF/Harbinger		Y
		ISL2EU		Y
		Spy	Y (unpublished data)
		Pangu		Y
		NuwaI		Y
		NuwaII		Y
CCHH	Transib	Transib		?
	EnSpm/CACTA	EnSpm/CACTA		?

Video

Zebrafish link

DNA 转座子研究进展

转座子科普: RepBase

转座子科普：维基百科

转座子分类表

转座子分布和结构

生物进化分类

科普视频

月度归档：9月 2023