Cited by 107Genomics and Chromatin DynamicsRNA Research and SplicingRNA and protein synthesis mechanisms

The DOI matches its Crossref record; 0 of the 34 references it cites were found in a registry or an index.

The increment of SII-facilitated transcript cleavage varies dramatically between elongation competent and incompetent RNA polymerase II ternary complexes

Open access

Izban, M.G., Luse, D.S.·1993·Journal of Biological Chemistry

Open this paper in CoChat — free account

Abstract

Elongation factor SII is required to increase the efficiency of transcription by RNA polymerase II through intrinsic arrest sites. RNA polymerase II ternary complexes exhibit a ribonuclease activity in the presence of SII, truncating nascent transcripts in a 3'-->5' direction. We show here that transcript cleavage is an obligatory step in re-establishing the elongation competency of complexes that have become blocked in elongation at an intrinsic arrest site. SII-facilitated transcript cleavage by these arrested complexes released 7-14 nucleotide RNA fragments. In contrast, SII-facilitated transcript cleavage by elongation competent complexes, which are stalled because of the absence of a nucleoside triphosphate from the reaction mixture, occurred primarily in dinucleotide increments. We can partially recreate the arrested phenotype and the preference for the large cleavage increment by stalling ternary complexes such that the 3'-end of the transcript contains consecutive U residues, which mimics the sequence of the 3'-ends of transcripts in arrested complexes.

Integrity signals

Registry

Crossref · 10.1016/s0021-9258(18)31468-6

Cites

0 of 34 references verified0 citation errors · 34 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

We couldn’t retrieve this paper’s full text, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

FASEB J
Kerppola (1991)
Unresolved
Oncogene
Spencer (1990)
Unresolved
J. Biol. Chem
Dedrick (1987)
Unresolved
Biochemistry
Kerppola (1990)
Unresolved
J. Mol. Biol
Reines (1987)
Unresolved
J. Biol. Chem
Reines (1989)
Unresolved
Mol. Cell. Biol
Bengal (1991)
Unresolved
J. Biol. Chem
Izban (1992)
Unresolved
J. Biol. Chem
Wiest (1992)
Unresolved
J. Biol. Chem
Resnekov (1989)
Unresolved

Show all 34 references

Sorted by citations

Metazoan promoters: emerging characteristics and insights into transcriptional regulation
Lenhard, B., Sandelin, A., & Carninci, P. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3163 · Cited by 566
BASIC MECHANISMS OF TRANSCRIPT ELONGATION AND ITS REGULATION
Uptain, S. M., Kane, C. M., & Chamberlin, M. J. (1997) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.66.1.117 · Cited by 445
The RNA–DNA Hybrid Maintains the Register of Transcription by Preventing Backtracking of RNA Polymerase
Nudler, E., MUSTAEV, A. A., Goldfarb, A., & LUKHTANOV, E. A. (1997) · Cell · doi:10.1016/s0092-8674(00)80180-4 · Cited by 441
Structural basis of RNA polymerase II backtracking, arrest and reactivation
Cheung, A. C. M., & Cramer, P. (2011) · Nature · doi:10.1038/nature09785 · Cited by 373
Transcript cleavage by RNA polymerase II arrested by a cyclobutane pyrimidine dimer in the DNA template.
Donahue, B. A., Yin, S., Taylor, J., Reines, D., & Hanawalt, P. C. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.18.8502 · Cited by 358
Architecture of the RNA Polymerase II-TFIIS Complex and Implications for mRNA Cleavage
Kettenberger, H., Armache, K., & Cramer, P. (2003) · Cell · doi:10.1016/s0092-8674(03)00598-1 · Cited by 355
Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3′ end of the RNA intact and extruded
Komissarova, N. V., & Kashlev, M. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.5.1755 · Cited by 341
Recycling of the general transcription factors during RNA polymerase II transcription.Preprint
Zawel, L. S., Kumar, K. P., & Reinberg, D. (1995) · Genes & Development · doi:10.1101/gad.9.12.1479 · Cited by 320
Exchange of RNA Polymerase II Initiation and Elongation Factors during Gene Expression In Vivo
Pokholok, D., Hannett, N. M., & Young, R. A. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00502-6 · Cited by 311
Nucleosomes Can Form a Polar Barrier to Transcript Elongation by RNA Polymerase II
Bondarenko, V. A., Steele, L. M., Újvári, A., Gaykalova, D. A., Kulaeva, O. I., Polikanov, Y. S., Luse, D. S., & Studitsky, V. M. (2006) · Molecular Cell · doi:10.1016/j.molcel.2006.09.009 · Cited by 272
Self-citation
RNA Polymerase Switches between Inactivated and Activated States By Translocating Back and Forth along the DNA and the RNA
Komissarova, N., & Kashlev, M. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.24.15329 · Cited by 269
The RNA Polymerase II Elongation Complex
Shilatifard, A., Conaway, R. C., & Conaway, J. W. (2003) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.72.121801.161551 · Cited by 253
Transcriptional Fidelity and Proofreading by RNA Polymerase II
Thomas, M. J., Platas, A. A., & Hawley, D. K. (1998) · Cell · doi:10.1016/s0092-8674(00)81191-5 · Cited by 252
Structural Basis of Transcription: Backtracked RNA Polymerase II at 3.4 Angstrom Resolution
Wang, D., Bushnell, D. A., Huang, X., Westover, K. D., Levitt, M., & Kornberg, R. D. (2009) · Science · doi:10.1126/science.1168729 · Cited by 241
Promoting elongation with transcript cleavage stimulatory factors
Fish, R. N., & Kane, C. M. (2002) · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression · doi:10.1016/s0167-4781(02)00459-1 · Cited by 236
Nature of the Nucleosomal Barrier to RNA Polymerase II
Kireeva, M. L., Hancock, B., Cremona, G. H., Walter, W., Studitsky, V. M., & Kashlev, M. (2005) · Molecular Cell · doi:10.1016/j.molcel.2005.02.027 · Cited by 227
“This notion agreed with a previously observed correlation between longer backtracking distance and irreversible catalytic inactivation of the TEC (Izban and Luse, 1993).”
Background
To be or not to be active: the stochastic nature of enhancer action
Fiering, S., Whitelaw, E., & Martin, D. I. K. (2000) · BioEssays · doi:10.1002/(sici)1521-1878(200004)22:4 · Cited by 161
Intrinsic transcript cleavage activity of RNA polymerase.
Orlova, M. O., Newlands, J. T., Das, A., et al. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.10.4596 · Cited by 209
RNA polymerase II speed: a key player in controlling and adapting transcriptome composition
Muniz, L., Nicolas, E., & Trouche, D. (2021) · The EMBO Journal · doi:10.15252/embj.2020105740 · Cited by 198
“RNA Pol II cleaves the nascent RNA 3 0 end, releasing an RNA fragment of 2 – 14 bases long (Izban & Luse, 1993) and producing a new 3 0 end perfectly aligned with its active site.”
Unified two‐metal mechanism of RNA synthesis and degradation by RNA polymerase
Sosunov, V. V., Sosunova, E., Mustaev, A., Bass, I., Nikiforov, V., & Goldfarb, A. (2003) · The EMBO Journal · doi:10.1093/emboj/cdg193 · Cited by 198
The RNA cleavage activity of RNA polymerase III is mediated by an essential TFIIS-like subunit and is important for transcription terminationPreprint
Chédin, S., Riva, M., Schultz, P., Sentenac, A., & Carles, C. (1998) · Genes & Development · doi:10.1101/gad.12.24.3857 · Cited by 175
Fidelity of RNA polymerase II transcription controlled by elongation factor TFIIS
Jeon, C., & Agarwal, K. L. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.24.13677 · Cited by 134
Coupling between transcription termination and RNA polymerase inchworming
Nudler, E., Kashlev, M., Nikiforov, V., et al. (1995) · Cell · doi:10.1016/0092-8674(95)90388-7 · Cited by 131
Promoter Proximal Sequences Modulate RNA Polymerase II Elongation by a Novel Mechanism
Reeder, T., & Hawley, D. K. (1996) · Cell · doi:10.1016/s0092-8674(00)81395-1 · Cited by 126
Widespread Backtracking by RNA Pol II Is a Major Effector of Gene Activation, 5′ Pause Release, Termination, and Transcription Elongation Rate
Sheridan, R. M., Fong, N., D’Alessandro, A., & Bentley, D. L. (2019) · Molecular Cell · doi:10.1016/j.molcel.2018.10.031 · Cited by 123
“TFIIS-stimulated endonucleolytic cleavage releases RNA fragments 2 – 14 bases long (Izban and Luse, 1993).”
DNA Bending and Wrapping around RNA Polymerase: a “Revolutionary” Model Describing Transcriptional Mechanisms
Coulombe, B., & Burton, Z. F. (1999) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.63.2.457-478.1999 · Cited by 118
Transcription elongation: structural basis and mechanisms
Nudler, E. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2641 · Cited by 117
The active site of RNA polymerase II participates in transcript cleavage within arrested ternary complexes.
Rudd, M. D., Izban, M. G., & Luse, D. S. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.17.8057 · Cited by 113
Self-citation
Regulation of transcriptional elongation by RNA polymerase II
Bentley, D. L. (1995) · Current Opinion in Genetics & Development · doi:10.1016/0959-437x(95)80010-7 · Cited by 111
Contending with transcriptional arrest during RNAPII transcript elongation
Svejstrup, J. Q. (2007) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2007.02.005 · Cited by 107
Identification of a Decay in Transcription Potential That Results in Elongation Factor Dependence of RNA Polymerase II
Gu, W., & Reines, D. (1995) · Journal of Biological Chemistry · doi:10.1074/jbc.270.19.11238 · Cited by 108
GreA-induced transcript cleavage in transcription complexes containing Escherichia coli RNA polymerase is controlled by multiple factors, including nascent transcript location and structure.
Feng, G. H., Lee, D. N., Wang, D., et al. (1994) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)31788-x · Cited by 106
Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes
Valen, E., Preker, P., Andersen, P. R., Zhao, X., Chen, Y., Ender, C., Dueck, A., Meister, G., Sandelin, A., & Jensen, T. H. (2011) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2091 · Cited by 99
General Transcription Factors for RNA Polymerase II1
Conaway, R., & Conaway, J. W. (1997) · Progress in nucleic acid research and molecular biology · doi:10.1016/s0079-6603(08)61009-0 · Cited by 99
Interaction of Elongation Factors TFIIS and Elongin A with a Human RNA Polymerase II Holoenzyme Capable of Promoter-specific Initiation and Responsive to Transcriptional Activators
Pan, G., Aso, T., & Greenblatt, J. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.39.24563 · Cited by 96
Roles of RNA:DNA hybrid stability, RNA structure, and active site conformation in pausing by human RNA polymerase II
Palangat, M., & Landick, R. C. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4842 · Cited by 93
Mutations in the Second Largest Subunit of RNA Polymerase II Cause 6-Azauracil Sensitivity in Yeast and Increased Transcriptional Arrest in Vitro
Powell, W. H., & Reines, D. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.12.6866 · Cited by 93
Transcription Factor S, a Cleavage Induction Factor of the Archaeal RNA Polymerase
Hausner, W., Lange, U., & Musfeldt, M. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.275.17.12393 · Cited by 91
Nascent RNA cleavage by arrested RNA polymerase II does not require upstream translocation of the elongation complex on DNA.
Gu, W., Powell, W. H., Mote, J., & Reines, D. (1993) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)74433-0 · Cited by 81
Evolution of Two Modes of Intrinsic RNA Polymerase Transcript Cleavage
Ruan, W., Lehmann, E., Thomm, M., Kostrewa, D., & Cramer, P. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.222273 · Cited by 77
Amanitin Greatly Reduces the Rate of Transcription by RNA Polymerase II Ternary Complexes but Fails to Inhibit Some Transcript Cleavage Modes
Rudd, M. D., & Luse, D. S. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.35.21549 · Cited by 75
Self-citation
Complexes of yeast RNA polymerase II and RNA are substrates for TFIIS-induced RNA cleavage
Johnson, T., & Chamberlin, M. J. (1994) · Cell · doi:10.1016/0092-8674(94)90314-x · Cited by 73
FCP1, a Phosphatase Specific for the Heptapeptide Repeat of the Largest Subunit of RNA Polymerase II, Stimulates Transcription Elongation
Mandal, S. S., Cho, H. K., Kim, S., Cabane, K., & Reinberg, D. (2002) · Molecular and Cellular Biology · doi:10.1128/mcb.22.21.7543-7552.2002 · Cited by 67
“TFIIS stimulates a 3 -to-5 RNase activity present in RNAP II and is required to overcome arrest (20, 21, 45).”
Background
Hydrolytic cleavage of nascent RNA in RNA polymerase III ternary transcription complexes.
Whitehall, S. K., Bardeleben, C., & Kassavetis, G. A. (1994) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)42168-5 · Cited by 67
Processing of Nontelomeric 3′ Ends by Telomerase: Default Template Alignment and Endonucleolytic Cleavage
Melek, M., Greene, E. C., & Shippen, D. E. (1996) · Molecular and Cellular Biology · doi:10.1128/mcb.16.7.3437 · Cited by 67
“In response to transcription arrest, RNA polymerase on its own (41, 46) or in conjunction with trans-acting factors (5, 38) can endonucleolytically cleave phosphodiester bonds 17 nucleotides from a transcript 39 terminus (23, 41).”
Background
Increased accommodation of nascent RNA in a product site on RNA polymerase II during arrest.
Gu, W., Wind, M., & Reines, D. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.14.6935 · Cited by 63
Action of α-Amanitin during Pyrophosphorolysis and Elongation by RNA Polymerase II
Chafin, D. R., Guo, H., & Price, D. H. (1995) · Journal of Biological Chemistry · doi:10.1074/jbc.270.32.19114 · Cited by 58
Purified yeast RNA polymerase II reads through intrinsic blocks to elongation in response to the yeast TFIIS analogue, P37.
Christie, K., Awrey, D. E., Edwards, A. M., & Kane, C. M. (1994) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)42202-2 · Cited by 58
RNA cleavage and chain elongation by Escherichia coli DNA-dependent RNA polymerase in a binary enzyme.RNA complex.
Altmann, C. R., Solow-Cordero, D. E., & Chamberlin, M. J. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.9.3784 · Cited by 58
Purification of a human polyribosome-associated 3‘ to 5‘ exoribonuclease.
Caruccio, N., & Ross, J. (1994) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)31768-x · Cited by 56
Transcription Factors IIF and IIS and Nucleoside Triphosphate Substrates as Dynamic Probes of the Human RNA Polymerase II Mechanism
Zhang, C., & Burton, Z. F. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.07.070 · Cited by 58
“TFIIS stimulates dinucleotide cleavage from C40/U38 and from A43/A41, as previously shown by others and by us.(3,14,16,17,35) Notice the presence of the A41 and U38 gel bands in the presence of TFIIS (Figures 3 and 4).”
Method
Genetic Interactions of DST1 in Saccharomyces cerevisiae Suggest a Role of TFIIS in the Initiation-Elongation Transition
Malagón, F., Tong, A. H. Y., Shafer, B. K., & Strathern, J. N. (2004) · Genetics · doi:10.1534/genetics.166.3.1215 · Cited by 53
Transcriptional Properties of RNA Polymerase II within Triplet Repeat-containing DNA from the Human Myotonic Dystrophy and Fragile X Loci
Parsons, M. A., Sinden, R. R., & Izban, M. G. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.41.26998 · Cited by 49
Self-citation
In vitro characterization of mutant yeast RNA polymerase II with reduced binding for elongation factor TFIIS.
Wu, J., Awrey, D. E., Edwards, A. M., Archambault, J., & Friesen, J. D. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.21.11552 · Cited by 50
Promoter Clearance by RNA Polymerase II Is an Extended, Multistep Process Strongly Affected by Sequence
Pal, M., McKean, D. M., & Luse, D. S. (2001) · Molecular and Cellular Biology · doi:10.1128/mcb.21.17.5815-5825.2001 · Cited by 47
“This emphasizes the fact that many halted RNA polymerase II transcription complexes exist in equilibrium among several template locations (11, 39, 40).”
BackgroundSelf-citation
A novel RNA polymerase I-dependent RNase activity that shortens nascent transcripts from the 3′ end
Tschochner, H. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.23.12914 · Cited by 46
Translocation and Transcriptional Arrest during Transcript Elongation by RNA Polymerase II
Samkurashvili, I., & Luse, D. S. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.38.23495 · Cited by 45
Self-citation
Transcriptional pause, arrest and termination sites for RNA polymerase II in mammalian N- and c-mycgenes
Keene, R. G., Mueller, A., Robert, L., & London, L. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.15.3173 · Cited by 46
RNA Polymerase II Transcription Complexes May Become Arrested If the Nascent RNA Is Shortened to Less than 50 Nucleotides
Uájvári, A., Pal, M., & Luse, D. S. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m201145200 · Cited by 45
Self-citation
Efficient and Rapid Nucleosome Traversal by RNA Polymerase II Depends on a Combination of Transcript Elongation Factors
Luse, D. S., Spangler, L. C., & Újvári, A. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.174722 · Cited by 44
Self-citation
Combinatorial Control of Human RNA Polymerase II (RNAP II) Pausing and Transcript Cleavage by Transcription Factor IIF, Hepatitis δ Antigen, and Stimulatory Factor II
Zhang, C., Honggao Yan, A., & Burton, Z. F. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m307590200 · Cited by 43
Structural Changes in the RNA Polymerase II Transcription Complex during Transition from Initiation to Elongation
Samkurashvili, I., & Luse, D. S. (1998) · Molecular and Cellular Biology · doi:10.1128/mcb.18.9.5343 · Cited by 43
“We have described several RNA polymerase II elongation complexes which show evidence of both conformations, either by exoIII footprinting (27) or by the presence of large (7 to 17 nucleotides [nt]) transcript cleavage products in the presence of SII (11).”
BackgroundInfluentialSelf-citation
Structure and Function of RNA Polymerase II
Cramer, P. (2004) · Advances in protein chemistry · doi:10.1016/s0065-3233(04)67001-x · Cited by 43
Cleavage of the nascent transcript induced by TFIIS is insufficient to promote read-through of intrinsic blocks to elongation by RNA polymerase II.
Cipres-Palacin, G., & Kane, C. M. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.17.8087 · Cited by 42
Variation in the Size of Nascent RNA Cleavage Products as a Function of Transcript Length and Elongation Competence
Gu, W., & Reines, D. (1995) · Journal of Biological Chemistry · doi:10.1074/jbc.270.51.30441 · Cited by 42
Transcription elongation factor S‐II maintains transcriptional fidelity and confers oxidative stress resistance
Koyama, H., Ito, T., Nakanishi, T., Kawamura, N., & Sekimizu, K. (2003) · Genes to Cells · doi:10.1046/j.1365-2443.2003.00677.x · Cited by 40
“After nascent RNA chain cleavage and re-alignment of the 3 ′ -end of the transcript with the catalytic centre, the RNA polymerase resumes transcription, which finally overcomes the transcriptional blocks (Izban & Luse 1992, 1993; Reines et al .”
Background
Transcription Factors TFIIF, ELL, and Elongin Negatively Regulate SII-induced Nascent Transcript Cleavage by Non-arrested RNA Polymerase II Elongation Intermediates
Elmendorf, B. J., Shilatifard, A., Yan, Q., Conaway, J. W., & Conaway, R. C. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m101445200 · Cited by 39
Intrinsic Transcript Cleavage in Yeast RNA Polymerase II Elongation Complexes
Weilbaecher, R. G., Awrey, D. E., Edwards, A. M., & Kane, C. M. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m211197200 · Cited by 36
Dissecting Chemical Interactions Governing RNA Polymerase II Transcriptional Fidelity
Kellinger, M. W., Ulrich, S., Chong, J. P. C., Kool, E. T., & Wang, D. (2012) · Journal of the American Chemical Society · doi:10.1021/ja302077d · Cited by 35
Nuclease Cleavage of the Upstream Half of the Nontemplate Strand DNA in an Escherichia coli Transcription Elongation Complex Causes Upstream Translocation and Transcriptional Arrest
Wang, D., & Landick, R. C. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.9.5989 · Cited by 33
Evidence that the Transcription Elongation Function of Rpb9 Is Involved in Transcription-Coupled DNA Repair in Saccharomyces cerevisiae
Li, S., Ding, B., Chen, R., Ruggiero, C., & Chen, X. (2006) · Molecular and Cellular Biology · doi:10.1128/mcb.01656-06 · Cited by 31
“of the third category, stimulates RNase activity that is intrinsic to Pol II, and backtracks the elongation complex to rescue it from arrest (20, 21, 45).”
Background
Millisecond phase kinetic analysis of elongation catalyzed by human, yeast, and Escherichia coli RNA polymerase
Kireeva, M. L., Nedialkov, Y. A., Gong, X. Q., Zhang, C., Xiong, Y., Moon, W. J., Burton, Z. F., & Kashlev, M. (2009) · Methods · doi:10.1016/j.ymeth.2009.04.008 · Cited by 31
Human RNA Polymerase II Elongation in Slow Motion: Role of the TFIIF RAP74 α1 Helix in Nucleoside Triphosphate-Driven Translocation
Zhang, C., Zobeck, K. L., & Burton, Z. F. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.9.3583-3595.2005 · Cited by 32
“from previously backtracked and arrested ECs (15, 16, 19, 20).”
Background
Factor-dependent Release of Nascent RNA by Ternary Complexes of Vaccinia RNA Polymerase
Deng, L., Hagler, J., & Shuman, S. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.32.19556 · Cited by 29
Elongation Factor SII Contacts the 3′-End of RNA in the RNA Polymerase II Elongation Complex
Powell, W. H., Bartholomew, B., & Reines, D. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.37.22301 · Cited by 29
Substrate Specificity of the RNase Activity of Yeast RNA Polymerase III
Bobkova, E. V., & Hall, B. D. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.36.22832 · Cited by 28
Interaction of RNA Polymerase II Fork Loop 2 with Downstream Non-template DNA Regulates Transcription Elongation
Kireeva, M. L., Domecq, C., Coulombe, B., Burton, Z. F., & Kashlev, M. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.260844 · Cited by 26
RNA Polymerase II Ternary Complexes May Become Arrested after Transcribing to within 10 Bases of the End of Linear Templates
Izban, M. G., Samkurashvili, I., & Luse, D. S. (1995) · Journal of Biological Chemistry · doi:10.1074/jbc.270.5.2290 · Cited by 26
Self-citation
GreA-induced transcript cleavage is accompanied by reverse translocation to a different transcription complex conformation.
Lee, D. N., Feng, G., & Landick, R. C. (1994) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)31789-1 · Cited by 25
Activation and reactivation of the RNA polymerase II trigger loop for intrinsic RNA cleavage and catalysis
Čabart, P., Jin, H., Li, L., & Kaplan, C. D. (2014) · Transcription · doi:10.4161/trns.28869 · Cited by 23
“2F-G) illustrates the TFIIS-dependent dinucleotide cleavage of 1-bp backtracked complexes (cleavage of the second phosphodiester bond), as reported previously (lanes 5 and 6).(40,41) Both the intrinsic and TFIIS-mediated cleavage reactions appear to occur in parallel for H1085Y, suggesting that H1085Y can enter the TF…”
Background
Differential Blocking Effects of the Acetaldehyde-derived DNA Lesion N2-Ethyl-2′-deoxyguanosine on Transcription by Multisubunit and Single Subunit RNA Polymerases
Cheng, T., Hu, X., Gnatt, A. L., & Brooks, P. J. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m804086200 · Cited by 21
Flexible Positioning of the Telomerase-Associated Nuclease Leads to Preferential Elimination of Nontelomeric DNA
Greene, E. C., Bednenko, J., & Shippen, D. E. (1998) · Molecular and Cellular Biology · doi:10.1128/mcb.18.3.1544 · Cited by 20
“Hence, the cleavage and processive elongation may be mechanistically linked as is seen with RNA polymerase II (19, 34, 37).”
Background
Cockayne Syndrome Linked to Elevated R-Loops Induced by Stalled RNA Polymerase II during Transcription Elongation
Zhang, X., Xu, J., Hu, J., Zhang, S., Hao, Y., Zhang, D., Qian, H., Wang, D., & Fu, X. (2024) · Nature Communications · doi:10.1038/s41467-024-50298-w · Cited by 19
“Moreover, once the polymerase transitions into productive elongation, this chromatin remodeler becomes particularly important for over-coming transcription blockage at T-runs within GBs, which have been functionally linked to RNAPII backtrack and/or drop-off during elongation 38,39 .”
Comparative TFIIS-mediated transcript cleavage by mammalian RNA polymerase II arrested at a lesion in different transcription systems
Kalogeraki, V. S., Tornaletti, S., Cooper, P. K., & Hanawalt, P. C. (2005) · DNA repair · doi:10.1016/j.dnarep.2005.05.007 · Cited by 19
Mutational Analysis of the Hydrolytic Activity of Yeast RNA Polymerase III
Bobkova, E. V., Habib, N. F., Alexander, G., et al. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.30.21342 · Cited by 19
Transcript Cleavage in an RNA Polymerase I Elongation Complex
Labhart, P. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.14.9055 · Cited by 19
Persistence of backtracking by human RNA polymerase II
Yang, K. B., Rasouly, A., Epshtein, V., Martinez, C., Nguyen, T. D., Shamovsky, I., & Nudler, E. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.01.019 · Cited by 16
The mechanism of nucleosome traversal by RNA polymerase II
Luse, D. S., & Studitsky, V. M. (2011) · RNA Biology · doi:10.4161/rna.8.4.15389 · Cited by 15
Self-citation
Restricted Expression of a Member of the Transcription Elongation Factor S-II Family in Testicular Germ Cells during and after Meiosis
Umehara, T., Kida, S., Hasegawa, S., et al. (1997) · The Journal of Biochemistry · doi:10.1093/oxfordjournals.jbchem.a021627 · Cited by 15
Mechanism of Action of RNA Polymerase II Elongation Factor Elongin
Moreland, R. J., Hanas, J. S., Conaway, J. W., & Conaway, R. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.41.26610 · Cited by 15
The Transition from Initiation to Elongation by RNA Polymerase IIPreprint
Luse, D. S., & Samkurashvili, I. (1998) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.1998.63.289 · Cited by 14
Self-citation
Rearrangement of the RNA polymerase subunit H and the lower jaw in archaeal elongation complexes
Grünberg, S., Reich, C., Zeller, M. E., Bartlett, M. S., & Thomm, M. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp1190 · Cited by 11
Genetic Interactions Between TFIIF and TFIIS
Fish, R. N., Ammerman, M. L., Davie, J. K., Lu, B., Pham, C. C., Howe, L. J., Ponticelli, A. S., & Kane, C. M. (2006) · Genetics · doi:10.1534/genetics.106.058834 · Cited by 11
“TFIIF (and mechanistically similar factors Elongin and ELL) increases the overall rate of elongation and suppresses pausing, whereas TFIIS acts upon stalled or arrested RNAPII elongation complexes in which the growing 39 end of the nascent transcript has lost register with the catalytic site of the polymerase (Izban a…”
Background
Assays for Investigating Transcription by RNA Polymerase IIin Vitro
Reines, D., Dvir, A., Conaway, J. W., & Conaway, R. C. (1997) · Methods · doi:10.1006/meth.1997.0471 · Cited by 8
RNA polymerase II complexes in the very early phase of transcription are not susceptible to TFIIS-induced exonucleolytic cleavage
Sijbrandi, R. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.11.2290 · Cited by 8
“Released cleavage products range from 2 to 14 nt and this may relate to the extent of backtracking (9,12).”
Background
Features of yeast RNA polymerase I with special consideration of the lobe binding subunits
Schwank, K., Schmid, C., Fremter, T., Engel, C., Milkereit, P., Griesenbeck, J., & Tschochner, H. (2023) · Biological Chemistry · doi:10.1515/hsz-2023-0184 · Cited by 7
“To overcome the backtracked state to restart transcription elongation, Pols have to realign the 3 ′ end of the RNA with the active site either by one dimensional di ﬀ usion or by RNA cleavage (Depken et al. 2009; Galburt et al. 2007; Izban and Luse 1993; Lisica et al. 2016; Reines 1992).”
Template End-to-End Transposition by RNA Polymerase II
Izban, M. G., Parsons, M. A., & Sinden, R. R. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.41.27009 · Cited by 7
Self-citation
Reversible Kinetics in Multi-nucleotide Addition Catalyzed by S. cerevisiae RNA polymerase II Reveal Slow Pyrophosphate Release
Fuller, K. B., Jacobs, R. Q., Schneider, D. A., et al. (2024) · Journal of Molecular Biology · doi:10.1016/j.jmb.2024.168606 · Cited by 5
Isolation and characterization of the gene encoding the Drosophila melanogaster transcriptional elongation factor, TFIIS
Oh, Y., Yoon, J., & Baek, K. (1995) · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression · doi:10.1016/0167-4781(95)00055-l · Cited by 4
Crystallization and preliminary X-ray crystallographic analyses ofThermus thermophilusbacktracked RNA polymerase
Murayama, Y., Sekine, S., & Yokoyama, S. (2013) · Acta Crystallographica Section F Structural Biology and Crystallization Communications · doi:10.1107/s1744309113000055 · Cited by 2
“In the latter case, RNAP hydrolyses the RNA at its catalytic site to remove the protruding 30-end residues, allowing it to resume RNA elongation from the newly formed 30 end (Izban & Luse, 1993; Reines, 1992).”
Background

Authors: Izban, M. G., & Luse, D. S.
Affiliations: University of Cincinnati (US)
ORCID: Izban, M.G.
Luse, D.S.
Venue: Journal of Biological Chemistry
Publisher: Elsevier BV
Published: 1993-06
Volume: 268
Issue: 17
Pages: 12874-12885
ISSN: 0021-9258 (ISSN-L)
DOI: 10.1016/s0021-9258(18)31468-6
OpenAlex: W1485158076
Cited by: 107
References: 34
Citations by year: 2026: 1 · 2025: 1 · 2024: 3 · 2023: 1 · 2021: 1 · 2018: 3 · 2014: 1 · 2013: 1 · 2012: 2
FWCI: 3.99
Type: journal article
Language: en
Open access: hybrid
doi.org
Licence: cc-by
www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
creativecommons.org/licenses/by/4.0/ (vor, 10013 d)
Locations: Journal of Biological Chemistry (publishedVersion, cc-by)
PubMed (publishedVersion)
Funders: National Institutes of Health (5f32gm014111-02)
National Institute of General Medical Sciences (GM 14111, R01GM029487, GM 29487)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords: RNA polymerase II, transcript cleavage, transcription elongation, ternary complex, 3' end processing
MeSH terms: Animals, Base Sequence, Cattle, Humans, Molecular Sequence Data, Oligodeoxyribonucleotides, Plasmids, Protein Binding, RNA Polymerase II, RNA, Messenger, Transcription Factors, Transcription, Genetic, Dinucleoside Phosphates, Transcription Factors, General, Transcriptional Elongation Factors

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

The increment of SII-facilitated transcript cleavage varies dramatically between elongation competent and incompetent RNA polymerase II ternary complexes

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Citations

Cites

Cited by

Related

Metadata

Record

About these checks