-
2
-
-
0034268780
-
Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme
-
Muramatsu, M. et al. Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme. Cell 102, 553-563 (2000).
-
(2000)
Cell
, vol.102
, pp. 553-563
-
-
Muramatsu, M.1
-
3
-
-
0034264851
-
Activation-induced cytidine deaminase (AID) deficiency causes the autosomal recessive form of the Hyper-IgM syndrome (HIGM2)
-
Revy, P. et al. Activation-induced cytidine deaminase (AID) deficiency causes the autosomal recessive form of the Hyper-IgM syndrome (HIGM2). Cell 102, 565-575 (2000).
-
(2000)
Cell
, vol.102
, pp. 565-575
-
-
Revy, P.1
-
4
-
-
42649124572
-
The biochemistry of somatic hypermutation
-
DOI 10.1146/annurev.immunol.26.021607.090236
-
Peled, J. U. et al. The biochemistry of somatic hypermutation. Annu. Rev. Immunol. 26, 481-511 (2008). (Pubitemid 351600383)
-
(2008)
Annual Review of Immunology
, vol.26
, pp. 481-511
-
-
Peled, J.U.1
Fei, L.K.2
Iglesias-Ussel, M.D.3
Roa, S.4
Kalis, S.L.5
Goodman, M.F.6
Scharff, M.D.7
-
5
-
-
6344256944
-
Mismatch recognition and uracil excision provide complementary paths to both Ig switching and the A/T-focused phase of somatic mutation
-
DOI 10.1016/j.molcel.2004.10.011, PII S1097276504006136
-
Rada, C., Di Noia, J. M. & Neuberger, M. S. Mismatch recognition and uracil excision provide complementary paths to both Ig switching and the A/T-focused phase of somatic mutation. Mol. Cell 16, 163-171 (2004). (Pubitemid 39388832)
-
(2004)
Molecular Cell
, vol.16
, Issue.2
, pp. 163-171
-
-
Rada, C.1
Di Noia, J.M.2
Neuberger, M.S.3
-
6
-
-
42649123314
-
Mechanism and regulation of class switch recombination
-
DOI 10.1146/annurev.immunol.26.021607.090248
-
Stavnezer, J., Guikema, J. E. & Schrader, C. E. Mechanism and regulation of class switch recombination. Annu. Rev. Immunol. 26, 261-292 (2008). (Pubitemid 351600377)
-
(2008)
Annual Review of Immunology
, vol.26
, pp. 261-292
-
-
Stavnezer, J.1
Guikema, J.E.J.2
Schrader, C.E.3
-
7
-
-
0037388165
-
Activation-induced cytidine deaminase deaminates deoxycytidine on single-stranded DNA but requires the action of RNase
-
DOI 10.1073/pnas.0730835100
-
Bransteitter, R., Pham, P., Scharff, M. D. & Goodman, M. F. Activation-induced cytidine deaminase deaminates deoxycytidine on single-stranded DNA but requires the action of RNase. Proc. Natl Acad. Sci. USA 100, 4102-4107 (2003). (Pubitemid 36418164)
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.7
, pp. 4102-4107
-
-
Bransteitter, R.1
Pham, P.2
Scharfft, M.D.3
Goodman, M.F.4
-
8
-
-
77950955761
-
Origin of chromosomal translocations in lymphoid cancer
-
Nussenzweig, A. & Nussenzweig, M. C. Origin of chromosomal translocations in lymphoid cancer. Cell 141, 27-38 (2010).
-
(2010)
Cell
, vol.141
, pp. 27-38
-
-
Nussenzweig, A.1
Nussenzweig, M.C.2
-
9
-
-
84865193126
-
AID targeting is dependent on RNA polymerase II pausing
-
Kenter, A. L. AID targeting is dependent on RNA polymerase II pausing. Semin. Immunol. 24, 281-286 (2012).
-
(2012)
Semin. Immunol.
, vol.24
, pp. 281-286
-
-
Kenter, A.L.1
-
10
-
-
0346362489
-
Transcription-coupled events associating with immunoglobulin switch region chromatin
-
DOI 10.1126/science.1092481
-
Nambu, Y. et al. Transcription-coupled events associating with immunoglobulin switch region chromatin. Science 302, 2137-2140 (2003). (Pubitemid 38017949)
-
(2003)
Science
, vol.302
, Issue.5653
, pp. 2137-2140
-
-
Nambu, Y.1
Sugai, M.2
Gonda, H.3
Lee, C.-G.4
Katakai, T.5
Agata, Y.6
Yokota, Y.7
Shimizu, A.8
-
11
-
-
77957239251
-
Activation-induced cytidine deaminase targets DNA at sites of RNA polymerase II stalling by interaction with Spt5
-
Pavri, R. et al. Activation-induced cytidine deaminase targets DNA at sites of RNA polymerase II stalling by interaction with Spt5. Cell 143, 122-133 (2010).
-
(2010)
Cell
, vol.143
, pp. 122-133
-
-
Pavri, R.1
-
12
-
-
84870204989
-
A role for the RNA pol II-associated PAF complex in AID-induced immune diversification
-
Willmann, K. L. et al. A role for the RNA pol II-associated PAF complex in AID-induced immune diversification. J. Exp. Med. 209, 2099-2111 (2012).
-
(2012)
J. Exp. Med.
, vol.209
, pp. 2099-2111
-
-
Willmann, K.L.1
-
13
-
-
79953779997
-
Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity
-
Martinez-Rucobo, F. W., Sainsbury, S., Cheung, A. C. & Cramer, P. Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity. EMBO J. 30, 1302-1310 (2011).
-
(2011)
EMBO J.
, vol.30
, pp. 1302-1310
-
-
Martinez-Rucobo, F.W.1
Sainsbury, S.2
Cheung, A.C.3
Cramer, P.4
-
14
-
-
84867160564
-
The RNA polymerase II CTD coordinates transcription and RNA processing
-
Hsin, J. P. & Manley, J. L. The RNA polymerase II CTD coordinates transcription and RNA processing. Genes Dev. 26, 2119-2137 (2012).
-
(2012)
Genes Dev.
, vol.26
, pp. 2119-2137
-
-
Hsin, J.P.1
Manley, J.L.2
-
15
-
-
84878315605
-
Global regulation of promoter melting in naive lymphocytes
-
Kouzine, F. et al. Global regulation of promoter melting in naive lymphocytes. Cell 153, 988-999 (2013).
-
(2013)
Cell
, vol.153
, pp. 988-999
-
-
Kouzine, F.1
-
16
-
-
27944493275
-
The very 5′ end and the constant region of Ig genes are spared from somatic mutation because AID does not access these regions
-
DOI 10.1084/jem.20051604
-
Longerich, S., Tanaka, A., Bozek, G., Nicolae, D. & Storb, U. The very 5' end and the constant region of Ig genes are spared from somatic mutation because AID does not access these regions. J. Exp. Med. 202, 1443-1454 (2005). (Pubitemid 41668746)
-
(2005)
Journal of Experimental Medicine
, vol.202
, Issue.10
, pp. 1443-1454
-
-
Longerich, S.1
Tanaka, A.2
Bozek, G.3
Nicolae, D.4
Storb, U.5
-
17
-
-
0142188274
-
Induction of somatic hypermutation is associated with modifications in immunoglobulin variable region chromatin
-
DOI 10.1016/S1074-7613(03)00261-9
-
Woo, C. J., Martin, A. & Scharff, M. D. Induction of somatic hypermutation is associated with modifications in immunoglobulin variable region chromatin. Immunity 19, 479-489 (2003). (Pubitemid 37311430)
-
(2003)
Immunity
, vol.19
, Issue.4
, pp. 479-489
-
-
Woo, C.J.1
Martin, A.2
Scharff, M.D.3
-
18
-
-
13444255004
-
An evolutionarily conserved target motif for immunoglobulin class-switch recombination
-
DOI 10.1038/ni1137
-
Zarrin, A. A. et al. An evolutionarily conserved target motif for immunoglobulin class-switch recombination. Nat. Immunol. 5, 1275-1281 (2004). (Pubitemid 41057743)
-
(2004)
Nature Immunology
, vol.5
, Issue.12
, pp. 1275-1281
-
-
Zarrin, A.A.1
Alt, F.W.2
Chaudhuri, J.3
Stokes, N.4
Kaushal, D.5
Du Pasquier, L.6
Tian, M.7
-
19
-
-
34547873538
-
Sequence dependence of chromosomal R-loops at the immunoglobulin heavy-chain Smu class switch region
-
Huang, F. T. et al. Sequence dependence of chromosomal R-loops at the immunoglobulin heavy-chain Smu class switch region. Mol. Cell Biol. 27, 5921-5932 (2007).
-
(2007)
Mol. Cell Biol.
, vol.27
, pp. 5921-5932
-
-
Huang, F.T.1
-
20
-
-
0024279845
-
Transcription generates positively and negatively supercoiled domains in the template
-
Wu, H. Y., Shyy, S. H., Wang, J. C. & Liu, L. F. Transcription generates positively and negatively supercoiled domains in the template. Cell 53, 433-440 (1988).
-
(1988)
Cell
, vol.53
, pp. 433-440
-
-
Wu, H.Y.1
Shyy, S.H.2
Wang, J.C.3
Liu, L.F.4
-
21
-
-
57849109058
-
Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
-
Core, L. J., Waterfall, J. J. & Lis, J. T. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322, 1845-1848 (2008).
-
(2008)
Science
, vol.322
, pp. 1845-1848
-
-
Core, L.J.1
Waterfall, J.J.2
Lis, J.T.3
-
22
-
-
84871699564
-
Promoter-proximal pausing of RNA polymerase II: Emerging roles in metazoans
-
Adelman, K. & Lis, J. T. Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans. Nat. Rev. Genet. 13, 720-731 (2012).
-
(2012)
Nat. Rev. Genet.
, vol.13
, pp. 720-731
-
-
Adelman, K.1
Lis, J.T.2
-
24
-
-
68149158825
-
S region sequence RNA polymerase II, and histone modifications create chromatin accessibility during class switch recombination
-
Wang, L., Wuerffel, R., Feldman, S., Khamlichi, A. A. & Kenter, A. L. S region sequence, RNA polymerase II, and histone modifications create chromatin accessibility during class switch recombination. J. Exp. Med. 206, 1817-1830 (2009).
-
(2009)
J. Exp. Med.
, vol.206
, pp. 1817-1830
-
-
Wang, L.1
Wuerffel, R.2
Feldman, S.3
Khamlichi, A.A.4
Kenter, A.L.5
-
25
-
-
67449161835
-
Immunoglobulin switch mu sequence causes RNA polymerase II accumulation and reduces da hypermutation
-
Rajagopal, D. et al. Immunoglobulin switch mu sequence causes RNA polymerase II accumulation and reduces dA hypermutation. J. Exp. Med. 206, 1237-1244 (2009).
-
(2009)
J. Exp. Med.
, vol.206
, pp. 1237-1244
-
-
Rajagopal, D.1
-
26
-
-
84866366785
-
Microprocessor, Setx, Xrn2, and Rrp6 co-operate to induce premature termination of transcription by RNAPII
-
Wagschal, A. et al. Microprocessor, Setx, Xrn2, and Rrp6 co-operate to induce premature termination of transcription by RNAPII. Cell 150, 1147-1157 (2012).
-
(2012)
Cell
, vol.150
, pp. 1147-1157
-
-
Wagschal, A.1
-
27
-
-
15244358670
-
Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo
-
DOI 10.1016/j.molcel.2005.02.017
-
Mason, P. B. & Struhl, K. Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo. Mol. Cell 17, 831-840 (2005). (Pubitemid 40386944)
-
(2005)
Molecular Cell
, vol.17
, Issue.6
, pp. 831-840
-
-
Mason, P.B.1
Struhl, K.2
-
28
-
-
0032571254
-
Role of the human homolog of the yeast transcription factor SPT5 in HIV-1 Tat-activation
-
DOI 10.1006/jmbi.1997.1601
-
Wu-Baer, F., Lane, W. S. & Gaynor, R. B. Role of the human homolog of the yeast transcription factor SPT5 in HIV-1 Tat-activation. J. Mol. Biol. 277, 179-197 (1998). (Pubitemid 28174961)
-
(1998)
Journal of Molecular Biology
, vol.277
, Issue.2
, pp. 179-197
-
-
Wu-Baer, F.1
Lane, W.S.2
Gaynor, R.B.3
-
29
-
-
0036150085
-
Spt5 cooperates with human immunodeficiency virus type 1 Tat by preventing premature RNA release at terminator sequences
-
DOI 10.1128/MCB.22.4.1079-1093.2002
-
Bourgeois, C. F., Kim, Y. K., Churcher, M. J., West, M. J. & Karn, J. Spt5 cooperates with human immunodeficiency virus type 1 Tat by preventing premature RNA release at terminator sequences. Mol. Cell Biol. 22, 1079-1093 (2002). (Pubitemid 34094845)
-
(2002)
Molecular and Cellular Biology
, vol.22
, Issue.4
, pp. 1079-1093
-
-
Bourgeois, C.F.1
Kim, Y.K.2
Churcher, M.J.3
West, M.J.4
Karn, J.5
-
30
-
-
0032435650
-
TdT-accessible breaks are scattered over the immunoglobulin V domain in a constitutively hypermutating B cell line
-
DOI 10.1016/S1074-7613(00)80651-2
-
Sale, J. E. & Neuberger, M. S. TdT-accessible breaks are scattered over the immunoglobulin V domain in a constitutively hypermutating B cell line. Immunity 9, 859-869 (1998). (Pubitemid 29024465)
-
(1998)
Immunity
, vol.9
, Issue.6
, pp. 859-869
-
-
Sale, J.E.1
Neuberger, M.S.2
-
31
-
-
80455129758
-
Recombinase-mediated cassette exchange as a novel method to study somatic hypermutation in Ramos cells
-
Baughn, L. B. et al. Recombinase-mediated cassette exchange as a novel method to study somatic hypermutation in Ramos cells. mBio 2, e00186-e00211 (2011).
-
(2011)
MBio
, vol.2
-
-
Baughn, L.B.1
-
32
-
-
84872393129
-
Transcription elongation factors DSIF and NELF: Promoter-proximal pausing and beyond
-
Yamaguchi, Y., Shibata, H. & Handa, H. Transcription elongation factors DSIF and NELF: promoter-proximal pausing and beyond. Biochim. Biophys. Acta 1829, 98-104 (2013).
-
(1829)
Biochim. Biophys. Acta
, pp. 98-104
-
-
Yamaguchi, Y.1
Shibata, H.2
Handa, H.3
-
33
-
-
33846424933
-
Detection of chromatin-associated single-stranded DNA in regions targeted for somatic hypermutation
-
DOI 10.1084/jem.20062032
-
Ronai, D. et al. Detection of chromatin-associated single-stranded DNA in regions targeted for somatic hypermutation. J. Exp. Med. 204, 181-190 (2007). (Pubitemid 46148768)
-
(2007)
Journal of Experimental Medicine
, vol.204
, Issue.1
, pp. 181-190
-
-
Ronai, D.1
Iglesias-Ussel, M.D.2
Fan, M.3
Li, Z.4
Martin, A.5
Scharff, M.D.6
-
34
-
-
84859166706
-
Negative supercoiling creates single-stranded patches of DNA that are substrates for AID-mediated mutagenesis
-
Parsa, J. Y. et al. Negative supercoiling creates single-stranded patches of DNA that are substrates for AID-mediated mutagenesis. PLoS Genet. 8, e1002518 (2012).
-
(2012)
PLoS Genet.
, vol.8
-
-
Parsa, J.Y.1
-
35
-
-
0034813325
-
Clonal instability of V region hypermutation in the Ramos Burkitt's lymphoma cell line
-
Zhang, W. et al. Clonal instability of V region hypermutation in the Ramos Burkitt's lymphoma cell line. Int. Immunol. 13, 1175-1184 (2001). (Pubitemid 32899160)
-
(2001)
International Immunology
, vol.13
, Issue.9
, pp. 1175-1184
-
-
Zhang, W.1
Bardwell, P.D.2
Woo, C.J.3
Poltoratsky, V.4
Scharff, M.D.5
Martin, A.6
-
36
-
-
0037418279
-
De novo protein synthesis is required for the activation-induced cytidine deaminase function in class-switch recombination
-
DOI 10.1073/pnas.0437710100
-
Doi, T., Kinoshita, K., Ikegawa, M., Muramatsu, M. & Honjo, T. De novo protein synthesis is required for the activation-induced cytidine deaminase function in class-switch recombination. Proc. Natl Acad. Sci. USA 100, 2634-2638 (2003). (Pubitemid 36297550)
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.5
, pp. 2634-2638
-
-
Doi, T.1
Kinoshita, K.2
Ikegawa, M.3
Muramatsu, M.4
Honjo, T.5
-
37
-
-
77949312619
-
The C-terminal repeat domain of Spt5 plays an important role in suppression of Rad26-independent transcription coupled repair
-
Ding, B., LeJeune, D. & Li, S. The C-terminal repeat domain of Spt5 plays an important role in suppression of Rad26-independent transcription coupled repair. J. Biol. Chem. 285, 5317-5326 (2010).
-
(2010)
J. Biol. Chem.
, vol.285
, pp. 5317-5326
-
-
Ding, B.1
Lejeune, D.2
Li, S.3
-
38
-
-
84880650205
-
Changes in RNA polymerase II progression influence somatic hypermutation of Ig-related genes by AID
-
Kodgire, P., Mukkawar, P., Ratnam, S., Martin, T. E. & Storb, U. Changes in RNA polymerase II progression influence somatic hypermutation of Ig-related genes by AID. J. Exp. Med. 210, 1481-1492 (2013).
-
(2013)
J. Exp. Med.
, vol.210
, pp. 1481-1492
-
-
Kodgire, P.1
Mukkawar, P.2
Ratnam, S.3
Martin, T.E.4
Storb, U.5
-
39
-
-
39149099085
-
Two levels of protection for the B cell genome during somatic hypermutation
-
DOI 10.1038/nature06547, PII NATURE06547
-
Liu, M. et al. Two levels of protection for the B cell genome during somatic hypermutation. Nature 451, 841-845 (2008). (Pubitemid 351253166)
-
(2008)
Nature
, vol.451
, Issue.7180
, pp. 841-845
-
-
Liu, M.1
Duke, J.L.2
Richter, D.J.3
Vinuesa, C.G.4
Goodnow, C.C.5
Kleinstein, S.H.6
Schatz, D.G.7
-
40
-
-
79551681406
-
The RNA exosome targets the AID cytidine deaminase to both strands of transcribed duplex DNA substrates
-
Basu, U. et al. The RNA exosome targets the AID cytidine deaminase to both strands of transcribed duplex DNA substrates. Cell 144, 353-363 (2011).
-
(2011)
Cell
, vol.144
, pp. 353-363
-
-
Basu, U.1
-
41
-
-
67649910424
-
Origins and activities of the eukaryotic exosome
-
Lykke-Andersen, S., Brodersen, D. E. & Jensen, T. H. Origins and activities of the eukaryotic exosome. J. Cell Sci. 122(Pt 10): 1487-1494 (2009).
-
(2009)
J. Cell Sci.
, vol.122
, Issue.PART 10
, pp. 1487-1494
-
-
Lykke-Andersen, S.1
Brodersen, D.E.2
Jensen, T.H.3
-
42
-
-
41549094037
-
The nuclear RNA surveillance machinery: The link between ncRNAs and genome structure in budding yeast?
-
DOI 10.1016/j.bbagrm.2007.12.008, PII S1874939907002015
-
Houseley, J. & Tollervey, D. The nuclear RNA surveillance machinery: the link between ncRNAs and genome structure in budding yeast? Biochim. Biophys. Acta 1779, 239-246 (2008). (Pubitemid 351474490)
-
(2008)
Biochimica et Biophysica Acta - Gene Regulatory Mechanisms
, vol.1779
, Issue.4
, pp. 239-246
-
-
Houseley, J.1
Tollervey, D.2
-
43
-
-
0034655640
-
Degradation of ribosomal RNA precursors by the exosome
-
Allmang, C., Mitchell, P., Petfalski, E. & Tollervey, D. Degradation of ribosomal RNA precursors by the exosome. Nucleic Acids Res. 28, 1684-1691 (2000). (Pubitemid 30199300)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.8
, pp. 1684-1691
-
-
Allmang, C.1
Mitchell, P.2
Petfalski, E.3
Tollervey, D.4
-
44
-
-
84860598427
-
The DSIF subunits Spt4 and Spt5 have distinct roles at various phases of immunoglobulin class switch recombination
-
Stanlie, A., Begum, N. A., Akiyama, H. & Honjo, T. The DSIF subunits Spt4 and Spt5 have distinct roles at various phases of immunoglobulin class switch recombination. PLoS Genet. 8, e1002675 (2012).
-
(2012)
PLoS Genet.
, vol.8
-
-
Stanlie, A.1
Begum, N.A.2
Akiyama, H.3
Honjo, T.4
-
45
-
-
0030006070
-
Clonal selection and learning in the antibody system
-
DOI 10.1038/381751a0
-
Rajewsky, K. Clonal selection and learning in the antibody system. Nature 381, 751-758 (1996). (Pubitemid 26243107)
-
(1996)
Nature
, vol.381
, Issue.6585
, pp. 751-758
-
-
Rajewsky, K.1
-
46
-
-
84882566900
-
E3-ubiquitin ligase Nedd4 determines the fate of AID-associated RNA polymerase II in B cells
-
Sun, J. et al. E3-ubiquitin ligase Nedd4 determines the fate of AID-associated RNA polymerase II in B cells. Genes Dev. 27, 1821-1833 (2013).
-
(2013)
Genes Dev.
, vol.27
, pp. 1821-1833
-
-
Sun, J.1
-
48
-
-
82755190634
-
Decrease in topoisomerase i is responsible for activation-induced cytidine deaminase (AID)-dependent somatic hypermutation
-
Kobayashi, M. et al. Decrease in topoisomerase I is responsible for activation-induced cytidine deaminase (AID)-dependent somatic hypermutation. Proc. Natl Acad. Sci. USA 108, 19305-19310 (2011).
-
(2011)
Proc. Natl Acad. Sci. USA
, vol.108
, pp. 19305-19310
-
-
Kobayashi, M.1
-
49
-
-
79955475464
-
Unravelling the means to an end: RNA polymerase II transcription termination
-
Kuehner, J. N., Pearson, E. L. & Moore, C. Unravelling the means to an end: RNA polymerase II transcription termination. Nat. Rev. Mol. Cell Biol. 12, 283-294 (2011).
-
(2011)
Nat. Rev. Mol. Cell Biol.
, vol.12
, pp. 283-294
-
-
Kuehner, J.N.1
Pearson, E.L.2
Moore, C.3
-
50
-
-
84869818088
-
Identification of core DNA elements that target somatic hypermutation
-
Kohler, K. M. et al. Identification of core DNA elements that target somatic hypermutation. J. Immunol. 189, 5314-5326 (2012).
-
(2012)
J. Immunol.
, vol.189
, pp. 5314-5326
-
-
Kohler, K.M.1
-
51
-
-
66349117823
-
Fluctuation analysis CalculatOR: A web tool for the determination of mutation rate using Luria-Delbruck fluctuation analysis
-
Hall, B. M., Ma, C. X., Liang, P. & Singh, K. K. Fluctuation analysis CalculatOR: a web tool for the determination of mutation rate using Luria-Delbruck fluctuation analysis. Bioinformatics 25, 1564-1565 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1564-1565
-
-
Hall, B.M.1
Ma, C.X.2
Liang, P.3
Singh, K.K.4
|