Transposable Elements: A Guide to the Perplexed and the Novice With Appendices on RNAi, Chromatin Remodeling and Gene Tagging

342 Pages·2003·15 MB·English

by  Esra Galun (auth.)

Transposable Elements
Transposable Elements
A Guide to the Perplexed and the Novice
With Appendices on RNAi, Chromatin Remodeling
and Gene Tagging
by
Esra Galun
The Weizmann Institute of Science,
Rehovot, Israel
SPRINGER-SCIENCE+BUSINESS MEDIA, B.V.
A C.I.P. Catalogue record for this book is available from the Library of Congress.
ISBN 978-90-481-6357-1 ISBN 978-94-017-3582-7 (eBook)
DOI 10.1007/978-94-017-3582-7
Printed on acid-free paper
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© 2003 Springer Science+Business Media Dordrecht
Originally published by Kluwer Academic Publishers in 2003
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CONTENTS
Preface xi
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 .. 0 0 0 0 0 0. 0. 0 0 0 0 0 0 0 0 0 0 0 0 0. 0 0 0 0 .. 0 0 0 0 0. 00 00 ......... 0....
Chapter 1 Introduction
Chapter 2 Historical Background 5
00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
1 Hybridization and inheritance before Mendel ... 5
00 00 00 •• 00. 00.00 •••••••• 00......
2 Mendel's revolution 8
00 00 00 00.00 00 00 00 •• 00.00 00 •• 00 00 00 00 00 00 00.00 00 00.00 00 00.00 ••• 00 00..
3 Between Mendel and genetics 11
00 00. 00 00 00. 00. 00. 00 00 00. 00 00 00 00 .. 00 00 00. 00 00. 00 00 00 00.
4 From static genes to mobility 14
ooOoooo .. oo ................................ 00 .. 00.......
Chapter 3 Bacterial Insertion Sequences ............................... 25
1 Simple bacterial Insertion Sequences ............................... 26
00..............
2 General features and properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
2.1 The IRs ............................................... 27
0000 .........................
2.2 The structure of Tpases 27
00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 .. 00 .. 00 00 ... 00 00 00..
2.3 Direct repeats (DRs) 27
00 00 00 00 00 .. 00 00 00 00 00 00 00 00 00 00.00 00 00 00 00 ........ 00 00 00..
2.4 Effect on neighboring genes 28
00 00 00 ...... 00 00 00.00 00 00 00 00 00 00 00.00 .. 00 00 00 00.
2.5 Tpase expression and transposition ....................... 28
00...............
2.6 Host factors ...... 28
00 •••••••••••••••••••••• 00 00 •••••••••••• 00 •••••• 00..............
2. 7 The reaction mechanism of transposition 28
00 00 00 00 00 00 00 00 00 00 .. 00 00 00 00 00
2.8 The DDE motif ...... 29
oooooooo•ooooooOooOoooooooooooo ... oooooo ... oooooooo .. oooooo
2.9 Transposition "immunity" . 31
00 .... 00 ........... 00 00.00 00 00 00 00 00 ..... 00 00 00...
2.10 Target specificity .............. 32
00 ••••••• 00 00 •••••••••••••• 00 •••• 00..............
3 The families of bacterial Insertion Sequences 3 3
00 00 .. 00 00 00 00 00 ... 00 .. 00 00 00 00 00 00.
4 The lSI family 33
00 00 .. 00 .. 00 00 00 00 .. 00 00 00 .............. 00 00 .. 00 ............ 00.00. 00 00 .. 00.
5 The IS3 family 35
oooooooooooooooooooooooooooooooooooooooooooo .. oooooooooooooo.,ooooooooooo"
6 IS9II 36
ooooooooooooooOoooooooooooooooooooooooooooooooooooooooooooooooooooooooOooo.,oooooooooooo
6.1 General organization ofiS9II 3 7
00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 .. 00 00 00
6.2 The expression of encoded proteins 3 7
00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 .. 00.....
6. 3 The transposition of IS9II 3 7
00 00 00 00 00 00 00 00 00 .. 00 00 00 00 00 00 00 00 00 00 00 .. 00 00 00
7 The IS2 I family 40
00 00 00 00 00 00 00 00 00 00 00 .. 00 .. 00 00 .... 00 .. 00 .. 00 .... 00 ...... 00 ...... 00......
8 The IS2I ................................................................................... 41
8.1 Transposition of IS21 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
8.2 Phylogeny of the IS2J family 44
00 00 00 00 00 00 00 00 00 00 00 00 00 00 .... 00 00 00 .. 00 00..
9 Other simple bacterial Insertion Sequence families ............ 44
00...............
9.1 The IS4 family 45
00 00 00 00 00 00 00 00.00. 00.00 00 00 00 00 00 00 00 00.00 00 00 00 00 ... 00.00. 00...
9.2 The IS5 family 45
00 00 00 00 00 00 00 00 00 00 00 00 00 00 .. 00 00 00 00 .... 00 00 00 00 ... 00 00 00 .. 00 00.
10 Some remarks on recombinases 45
000000 .. 0000 .. 000000 .. 0000 ........ 000000 .... 00 .. 000000
11 The Tn transposons . 4 7
00 00. 00. 00 00 00 00 00 00 00 00. 00 00 00 00 00 00 00 00. 00 00 00 00 00 00 00 00 00. 00 00 00.
v
vi
12 The Tn3 family .. . . .... .... ..... ...... .... ....... ...... ..... .... .... .. .. ... ....... ..... .. . 48
12.1 Transposon organization ..... ... ........ ......... ............ .. ... ... . .. . .. ... 49
12.2 Transposition .. .. .. ... .. ... .... ..... .. ........ .. .. .. .. .. . ....... ..... .. . .. . . .. . .. 49
12.3 Transposon's terminals ........................................................ 50
12.4 Cointegration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
12.5 Co integrate resolution ................................................... ...... 50
12.6 The recombinational process . ...... .. .. ... .. . .. .. .. ..... ............ .. . .. . .. 52
13 The Tn5 and its transposition .. ...... ... .... .. .. ........ .. ..... .. .. ......... ... ... ... 53
13.1 The overall structure of Tn5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
13.2 Antibiotic resistance genes . . . . . . . . . . . .. . . . .. . . . .. . . . . . . . . . . . . . . . . .. . . . . . . . .. . 54
13.3 The structure of the IS50s .................................................... 54
13.4 An overview ofTn5 transposition ......................................... 55
13.5 The synaptic complex ......................................................... 56
13.6 Transposon backbone DNA cleavage ...................................... 59
13.7 Target DNA capture and strand transfer .................................. 59
13.8 Transposase release ............................................................. 59
13.9 The regulation of Tn5 transposition ....................................... 60
13.10 Tn5 as a genetic tool in bacteria and eukaryotes . . . . . . . . . . . . . . . . . . . . . . . 60
14 The Tn7 transposon ..................................................................... 61
14.1 The general structure of Tn7 ................................................. 61
14.2 The process of transposition ................................................. 63
14.3 TnsABC+E transposition .... ... ......... ... ............... ......... ... .. . ... 66
14.4 Target "immunity" .. ...... ...... .... ... .. ... ................ ......... ....... ... 66
14.5 The Tn7 as an experimental tool .... .. . ...... ... ... .................. ...... 66
14.6 A final general remark ......................................................... 67
15 Transposon TnlO ........................................................................ 67
15.1 Origin and overall structure . . . . . . . .. . .. . . . . . . . .. . . . . . . . . . . . . . . . . . .. . . . . . . . . . . 67
15.2 The biology of TnJ 0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
15.3 A summary of the transposition ............................................ 70
15.4 The mechanism of transposition ........................................... 70
15.5 The hairpin cleavage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
15.6 The TnJO transposase ......................................................... 72
Chapter 4 Retrotransposons .. . .. . . . .. . .. .. .. .. .. .. .. .. .. .. . .. .. . .. . .. . . .. . .. .. . . 75
1 General characteristics . . . . . . . . . . .. .. . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . 75
1.1 Terminology . . . . . . . . . . . . . .. . . . . . . . . . .. . . . . . .. . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . 75
1.2 Two, rather different, modes of integration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
2 The L TR retrotransposons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . 79
2.1 The transposable elements of the budding yeast
(Saccharomyces cerevisiae) ..... .. . ............ .. .. .. .... ... .......... ... .... 81
2.2 The structure ofTyl ........................................................... 81
2.3 Transcription and transcriptional regulation in Ty1 ................... 83
2.4 The transcript and the VLP of Ty 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
2.5 Reverse transcription in Ty1 . .. .. . . ...... .. .. . .. .. .. .. .. . .. ... ...... .. . . . ... 84
2.6 Recombination in Ty1 .. .. .. . . ......... ..... .. .. .. .. .. .. . .. .. ... .. ... . .. . .. . .. 85
2. 7 The reintegration of Ty 1 . . . . . . . . . . . . . .. . . . . . . . . . . .. . .. . . . . . . .. . . . . . . . . . . . . . . . . 86
2.8 Other Ty elements in yeast ..... .... .. ...... .. ... .... .. ... .. . . ... ....... .. . .. 88
2.9 The main features of Ty3 ..................................................... 89
vii
2.10 L TR retrotransposons in other fungal organisms . . . . . . . . . . . . . . . . . . . . 91
2.1 0.1 L TR retrotransposable elements of the fission yeast
(S.pombe) ........................................................... 91
2.10 .2 L TR transposons in the pathogenic yeast
Candida albicans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
2.1 0.3 Additional Ty3/gypsy-like retrotransposons in
hypha! fungi . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . .. . . .. . . . . . . . . . . . . . . 92
2.11 L TR retrotransposons of Drosophila .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. 93
2.11.1 Hybrid dysgenesis ........................................ ......... 93
2.12 The gypsy L TR retrotransposon .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. 96
2.12 .1 Basic features of gypsy .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. . 96
2.12.2 The effect of gypsy on gene expression .. .... .. ...... .... .... 98
2.12.3 The similarity of gypsy to retroviruses .. .... .. ...... .... .... 99
2.12.4 Flamenco and gypsy mobility ................................... 100
2.13 A brief overview of additional retrotransposons of Drosophila . . 102
2.14 A survey of L TR retrotransposons in metazoa .. .. .. .. .. .. .. .. .. .. .. .. 102
2.14.1 Insects other than Drosophila ................................... 103
2.14 .2 L TR retrotransposons of worms .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. 104
2.14.3 LTR retrotransposons in Echinoids ........................... 106
2.14.4 The emergence of the tail and a rich repertoire ofT.E.
in the urochordate Ciona intestinali s .. .. .. .. .. .. .. .. .. .. .. .. . 107
2.14.5 LTR retrotransposons in amphibia ............................ 108
2.15 Fishing for L TR retrotransposons in fishes . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
2.15 .1 The Sushi family of L TR retrotransposons from
the Fugu fish .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. 109
2.15 .2 Fishing for L TR retrotransposons in herring, salmon
and Xiphophorus .. . . . . . . . . .. .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . 110
2.16 L TR retrotransposons in plants ............................................ 112
2.16.1 LTR retrotransposons in Arabidopsis thaliana . . . . . . . . . . . . 113
2.16 .2 L TR retrotransposons of maize . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
2.16.3 LTR retrotransposons in wheat, barley and oats ........... 121
2.16 .4 L TR retrotransposons in rice .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. 123
2.16. 5 L TR retrotransposons in tobacco and other species
of Solanaceae .. .. .. . .. .. .. . .... .. . .. .. .. .. .. .. . .. .. .. .. .. .. .. . .. .. . .. 125
2.16.6 LTR retrotransposons in legumes .............................. 128
3 The DIRSJ retrotransposons ...................... ........ .... .......... ...... .. .. ... 129
4 Mobile introns ........................................................................... 131
5 Non-L TR retrotransposons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 2
5.1 The early studies on non-L TR retrotransposons of mammals .. .. . 13 3
5.2 SINE elements in animals ................................................... 137
5.3 SINE elements in plants ..................................................... 141
5.4 LINE elements in invertebrates ............................................ 142
5.5 A LINE element in an amphibian organism .......... ...... ........... 145
5.6 LINE elements in fishes ........ ...... .... .............................. ..... 146
5.7 LINE elements in mammals ................................................ 147
5. 7.1 The LINE elements of primates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14 7
5.7.2 The LINE elements in rodents .................................. 149
5.7.3 Ll elements transposition in cultured cells ................. 150
viii
5. 7.4 The impact of LINEs on the mammalian genome .... .. ... 151
5.7.5 Concluding remarks on mammalian LINEs and
a note on fungal LINEs .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. . 151
5.8 LINE-like elements in plants ............................................... 154
Chapter 5 Telomeres and Transposable Elements ............... 159
1 Characteristics of telomeres . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
2 The telomeres of Drosophila .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. 161
Chapter 6 Class II Transposable Elements in Eukaryotes .. 163
1 General characteristics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
2 The Class II T.E. first discovered in maize ...................................... 164
2.1 The AciDs controlling elements of maize ............................... 165
2 .1.1 Sexual reproduction in maize .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. . 165
2.1.2 The main findings of McClintock on the
AciDs system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
2.1.3 The mutator function of Ac ...................... ...... ...... .... 167
2.1.4 Mechanism oftransposition ..................................... 167
2.1.5 Ac can undergo reversible inactivation and "mutate"
into aDs element ................................................... 169
2.2 Molecular-genetics of AciDs elements: Pioneering studies . . . . . . . . 169
2.3 Further molecular studies on AciDs elements . . . . . . . . . . . . . . . . . . . . . . . . . 171
2.4 Transposition of AciDs elements .......................................... 174
2.4.1 Sites of insertion ...... .......................... ...... ............. 174
2.4.2 Transposition and excision requirements .. . .... ...... .. .. .. . 175
2.4.3 Features of AciDs transposition .... .......... ...... ............ 176
2.4.4 The transposase of Ac .. .......................... .... ...... ....... 176
2.4.5 Is there an Ac transposome? ........................ ............. 177
2.4.6 Transposition frequency ...... .. ...... .. .......... .... .. .. .... .. .. 178
2.4. 7 A special note on the P gene of maize .. .. .. .. .. .. .. .. .. .. .. .. 178
2.5 The AciDs elements in transgenic plants ................................ 179
2.5.1 Transgenic tobacco and potato ... .. . .... .. . ........ ............. 179
2.5.2 Transgenic Arabidopsis thaliana .............................. 181
2.5.3 Transgenic tomato .................................................. 181
2.5.4 Insertion of AciDs into rice and other cereals ............... 182
2.5.5 The introduction of AciDs into other transgenic
plants .................................................................. 183
3 The Spm/En elements .................................................................. 183
3.1 Discovery and nomenclature .... .. .... .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. 184
3.2 Basic characteristics of the Spm family .................................. 185
3.3 Adding molecular methods to Spm research .. .. .. .. .. .. .. .. .. .. .. .. .. . 188
3.3.1 The overall structure ofthe autonomous Spm .............. 188
3.3 .2 The subterminal repetitive regions ............................. 189
3.3.3 Exons, introns and translation .................................. 190
3.3.4 Structure and function of Spm and dSpm .................... 190
3.3 .5 Transposition .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. 191
3. 3. 6 Methylation and the regulation of transposition .. .. .. .. .. . 194
ix
4 The family of MuDR!Mu transposable elements . . . . . . . . . . . . .. . . . . . . . . .. . . .. . . . 197
4.1 Early genetic studies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . 198
4.2 The structure of Mutator elements ........................................ 201
4.3 Transposition ................................................................... 204
4.3 .1 Germinal transposition in the MuDR system ............... 207
4.3 .2 The functions of MURA and MURB ........................... 208
4.3.3 The timing of transposition ..................................... 208
4.4 Epigenetic regulation of Mutator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 208
4.4.1 Silencing in somatic and germinal tissues .................. 209
4.4.2 Molecular mechanisms of silencing ........................... 209
4.5 Applications ofthe MuDR!Mu system .................................. 209
5 The transposable elements of snapdragon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209
5.1 The structures ofthe Tam elements ...................................... 212
5.2 Transposition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 214
5.2.1 Excision ............................................................... 214
5.2.2 Integration ............................................................ 215
5.3 No non-autonomous and mobile elements in the Tam system ... 216
5.4 Gene tagging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 217
6 Class II transposable elements in Arabidopsis thaliana ..................... 218
6.1 Class II elements that populate A. thaliana . . .. . ....... .. .. . . ... . . . . . .. 218
6.2 The Tagl transposable element ............................................ 219
6.3 The "hidden" Class II elements of A. thaliana .. . . . .... ... . .. .... .. . .. 220
6.3.1 The resurrection by demethylation ............................. 221
6.3.2 Fishing for T.E. in the DNA sequence data
of A. thaliana . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222
6.4 Alien transposable elements inserted into A. thaliana . . . . . . . . . . . . . . 223
7 The Tel/Mariner superfamily of transposable elements ..................... 224
7.1 Discovery of transposable elements in C. elegans ................... 224
7.2 The transposition of Tel .................................................... 226
7.3 Discovery of the Mariner elements in Drosophila ................... 226
7.4 The main features of Mariner .............................................. 226
7.5 Structure and function of the Tel/Mariner superfamily ............ 229
7. 5 .1 Transposition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 229
7.5 .2 The transposases of the Tel !Mariner superfamily ......... 230
7.5.3 Regulation of transposition ...................................... 230
7.6 The Tel/Mariner elements as genetic and biotechnological
tools ............................................................................... 231
7.7 Examples of Tel/Mariner and other Class II T.E. in diverse
organisms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 232
7.7.1 MITEs and Tel/Mariner elements in angiosperm plants. 234
7.7.2 Class II transposable elements in hypha! fungi ............ 236
7.7.3 Tel/Mariner-like elements in protozoa ....................... 238
7.7.4 A note on Minos, Hobo, Pogo and other Class II T.E.
that reside in insects and in other invertebrate metazoa .. 239
7.7.5 Class II T.E. in non-mammalian vertebrates: Tel-like
transposable elements in amphibia . . . . . . . . . . . . . . . . . . . . . . . . . . . . 240
7. 7.6 Fishing for transposable elements in fishes . . . . . . . . . . . . . . . . . 241
7.7.7 Tel/Mariner-like transposons in man and
other mammals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243
x
8 The P element of Drosophila . . . . . . . . . . . . . . . . . . . . . . .. . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . 246
8.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 246
8.2 The discovery of the P element .... .......... ....... ......... ....... ....... 246
8.3 The structure of P and its truncated versions .......................... 247
8.4 Transcription and translation of P ........................................ 249
8.5 Transposition of P . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . 250
8.5.1 Additional information on hybrid dysgenesis .............. 250
8.5.2 Structural and biochemical aspects of P transposition ... 251
8.5.3 Transposition and gap repair .................................... 252
8.6 Regulation of transposition ................... ........ .. .. . ...... .. . ..... .. . 253
8.6.1 P and M cytotypes ................................................. 253
8.6.2 Transposition control by antisense and RNAi .............. 254
8.6.3 Pre-mRNA splicing ................................................ 254
8.7 The hobo elements ............................................................ 255
8.8 Use of the P element in Drosophila genetics .......................... 256
Chapter 7 Epilogue ................................................................... 259
Chapter 8 Appendices 261
Appendix I: RNA silencing .......................................................... 261
1.1 Early studies on RNAi ....................................................... 262
1.2 PTGS and RNA silencing in plants ...................................... 263
1.3 RNAi in animals .............................................................. 265
1.4 Selected reviews on RNAi and PTGS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 266
2 Appendix II: Chromatin remodeling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 266
2.1 Chromatin acetylation ........................................................ 268
2.2 Phosphorylation, methylation and ubiquitination .................... 268
2.3 Chromatin in plants and animals ......................................... 271
2.4 Heterochromatin and centromeres ......................................... 271
2.5 Recent reviews: The overall picture of chromatin remodeling .... 273
3 Appendix III: Gene tagging .......................................................... 275
3.1 General remarks on gene tagging .......................................... 275
3.2 Examples of gene tagging investigations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 278
Chapter 9 References . .. .. .. . .. .. .. .. . .. . . .. . .. .. .. .. .. .. .. . .. .. .. . .. .. . .. . .. .. . .. . . 283
Index ............................................................................................. 323