Unraveling the role of helicases in transcription

Proteins with seven conserved “helicase domains” play essential roles in all aspects of nucleic acid metabolism. Deriving energy from ATP hydrolysis, helicases alter the structure of DNA, RNA, or DNA:RNA duplexes, remodeling chromatin and modulating access to the DNA template by the transcriptional machinery. This review focuses on the diverse functions of these proteins in the process of RNA polymerase II transcription in eukaryotes. Known or putative helicases are required for general transcription initiation and for transcription‐coupled DNA repair, and may play important roles in elongation, termination, and transcript stability. Recent evidence suggests that helicase‐domain‐containing proteins are also involved in complexes that facilitate the activity of groups of seemingly unrelated genes. BioEssays 20:634–641, 1998. © 1998 John Wiley & Sons Inc.

[1]  R. Schwartz,et al.  Homologous Disease Reactivation by X-radiation , 1963, Science.

[2]  P. Hanawalt,et al.  DNA repair in an active gene: Removal of pyrimidine dimers from the DHFR gene of CHO cells is much more efficient than in the genome overall , 1985, Cell.

[3]  P. Sung,et al.  Mutation of lysine‐48 to arginine in the yeast RAD3 protein abolishes its ATPase and DNA helicase activities but not the ability to bind ATP. , 1988, The EMBO journal.

[4]  F. Homa,et al.  A specific 15-bp TATA box promoter element is required for expression of a herpes simplex virus type 1 late gene. , 1988, Genes & development.

[5]  J. Manley,et al.  A functional mRNA polyadenylation signal is required for transcription termination by RNA polymerase II. , 1988, Genes & development.

[6]  P. Hanawalt,et al.  Induction of the Escherichia coli lactose operon selectively increases repair of its transcribed DNA strand , 1989, Nature.

[7]  W. S. Hayward,et al.  The block to transcription elongation is promoter dependent in normal and Burkitt's lymphoma c-myc alleles. , 1990, Genes & development.

[8]  D. St Johnston,et al.  A conserved double-stranded RNA-binding domain. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[9]  I. Herskowitz,et al.  Roles of SWI1, SWI2, and SWI3 proteins for transcriptional enhancement by steroid receptors. , 1992, Science.

[10]  J. Hoeijmakers,et al.  RAD25 (SSL2), the yeast homolog of the human xeroderma pigmentosum group B DNA repair gene, is essential for viability. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[11]  S. Squires,et al.  The XPD complementation group. Insights into xeroderma pigmentosum, Cockayne's syndrome and trichothiodystrophy. , 1992, Mutation research.

[12]  F. Winston,et al.  Yeast SNF/SWI transcriptional activators and the SPT/SIN chromatin connection. , 1992, Trends in genetics : TIG.

[13]  Steven A. Brown,et al.  Evidence that SNF2/SWI2 and SNF5 activate transcription in yeast by altering chromatin structure. , 1992, Genes & development.

[14]  A. Bardwell,et al.  Dual roles of a multiprotein complex from S. cerevisiae in transcription and DNA repair , 1993, Cell.

[15]  P. Chambon,et al.  DNA repair helicase: a component of BTF2 (TFIIH) basic transcription factor. , 1993, Science.

[16]  A. Sancar,et al.  Molecular mechanism of transcription-repair coupling. , 1993, Science.

[17]  Eugene V. Koonin,et al.  Helicases: amino acid sequence comparisons and structure-function relationships , 1993 .

[18]  J. Hurwitz,et al.  Human RNA helicase A is homologous to the maleless protein of Drosophila. , 1993, The Journal of biological chemistry.

[19]  J. Lis,et al.  Polymerase processivity and termination on Drosophila heat shock genes. , 1993, The Journal of biological chemistry.

[20]  P. Moore,et al.  The type 1 human immunodeficiency virus Tat binding protein is a transcriptional activator belonging to an additional family of evolutionarily conserved genes. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[21]  M. Carlson,et al.  The yeast SNF2/SWI2 protein has DNA-stimulated ATPase activity required for transcriptional activation. , 1993, Genes & development.

[22]  S. Buratowski.  DNA repair and transcription: the helicase connection. , 1993, Science.

[23]  W. Tanner,et al.  A yeast gene encoding a putative RNA helicase of the “DEAD”‐box family , 1993, Yeast.

[24]  H. Chiba,et al.  Two human homologues of Saccharomyces cerevisiae SWI2/SNF2 and Drosophila brahma are transcriptional coactivators cooperating with the estrogen receptor and the retinoic acid receptor. , 1994, Nucleic acids research.

[25]  J. Hoeijmakers,et al.  The ERCC2/DNA repair protein is associated with the class II BTF2/TFIIH transcription factor. , 1994, The EMBO journal.

[26]  D. Reinberg,et al.  Binding of basal transcription factor TFIIH to the acidic activation domains of VP16 and p53 , 1994, Molecular and cellular biology.

[27]  J. Lis,et al.  Phosphorylation of RNA polymerase II C-terminal domain and transcriptional elongation , 1994, Nature.

[28]  Michael R. Green,et al.  Nucleosome disruption and enhancement of activator binding by a human SW1/SNF complex , 1994, Nature.

[29]  D. Reinberg,et al.  Dual role of TFIIH in DNA excision repair and in transcription by RNA polymerase II , 1994, Nature.

[30]  H. Timmers.  Transcription initiation by RNA polymerase II does not require hydrolysis of the beta‐gamma phosphoanhydride bond of ATP. , 1994, The EMBO journal.

[31]  P. Sung,et al.  RAD25 is a DMA helicase required for DNA repair and RNA polymerase II transcription , 1994, Nature.

[32]  F. Grosse,et al.  Nuclear DNA helicase II unwinds both DNA and RNA. , 1994, Biochemistry.

[33]  B. Cairns,et al.  A multisubunit complex containing the SWI1/ADR6, SWI2/SNF2, SWI3, SNF5, and SNF6 gene products isolated from yeast. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[34]  M. Scott,et al.  Five SWI/SNF gene products are components of a large multisubunit complex required for transcriptional enhancement. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[35]  T. Platt.  Rho and RNA: models for recognition and response , 1994, Molecular microbiology.

[36]  C. McCallum,et al.  Identification and characterization of Drosophila relatives of the yeast transcriptional activator SNF2/SWI2 , 1994, Molecular and cellular biology.

[37]  J. Thorner,et al.  Mot1, a global repressor of RNA polymerase II transcription, inhibits TBP binding to DNA by an ATP-dependent mechanism. , 1994, Genes & development.

[38]  R. Wood,et al.  Xeroderma pigmentosum and nucleotide excision repair of DNA. , 1994, Trends in biochemical sciences.

[39]  H. Qiu,et al.  DNA repair gene RAD3 of S. cerevisiae is essential for transcription by RNA polymerase II , 1994, Nature.

[40]  M. Meisterernst,et al.  Repression of basal transcription by HMG2 is counteracted by TFIIH-associated factors in an ATP-dependent process , 1994, Molecular and cellular biology.

[41]  M. Kuroda,et al.  Acetylated histone H4 on the male X chromosome is associated with dosage compensation in Drosophila. , 1994, Genes & development.

[42]  Michael R. Green,et al.  Facilitated binding of TATA-binding protein to nucleosomal DNA , 1994, Nature.

[43]  R. Tjian,et al.  Transcription factors IIE and IIH and ATP hydrolysis direct promoter clearance by RNA polymerase II , 1994, Cell.

[44]  J. Workman,et al.  Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex. , 1994, Science.

[45]  J. Conboy,et al.  Mouse erythroid cells express multiple putative RNA helicase genes exhibiting high sequence conservation from yeast to mammals. , 1994, Gene.

[46]  C. Sardet,et al.  A human protein with homology to Saccharomyces cerevisiae SNF5 interacts with the potential helicase hbrm. , 1995, Nucleic acids research.

[47]  D. Higgs,et al.  Mutations in a putative global transcriptional regulator cause X-linked mental retardation with α-thalassemia (ATR-X syndrome) , 1995, Cell.

[48]  M. Scott,et al.  The Drosophila snr1 and brm proteins are related to yeast SWI/SNF proteins and are components of a large protein complex. , 1995, Molecular biology of the cell.

[49]  R. Weinberg,et al.  Requirement for TFIIH kinase activity in transcription by RNA polymerase II , 1995, Nature.

[50]  D. Reinberg,et al.  Common themes in assembly and function of eukaryotic transcription complexes. , 1995, Annual review of biochemistry.

[51]  P. Sung,et al.  Lethality in Yeast of Trichothiodystrophy (TTD) Mutations in the Human Xeroderma Pigmentosum Group D Gene , 1995, The Journal of Biological Chemistry.

[52]  N. Ellis,et al.  The Bloom's syndrome gene product is homologous to RecQ helicases , 1995, Cell.

[53]  J. Lis,et al.  Short transcripts of the ternary complex provide insight into RNA polymerase II elongational pausing. , 1995, Journal of molecular biology.

[54]  R. Conaway,et al.  Dissection of transcription factor TFIIF functional domains required for initiation and elongation. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[55]  M. Tsai,et al.  Molecular Characterization of the Rat Insulin Enhancer-binding Complex 3b2 , 1995, The Journal of Biological Chemistry.

[56]  P. Wade,et al.  Transcriptional corepression in vitro: a Mot1p-associated form of TATA-binding protein is required for repression by Leu3p , 1996, Molecular and cellular biology.

[57]  M. Wickens,et al.  A three-hybrid system to detect RNA-protein interactions in vivo. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[58]  T. Léveillard,et al.  Functional interactions between p53 and the TFIIH complex are affected by tumour‐associated mutations. , 1996, The EMBO journal.

[59]  L. Thompson,et al.  Defects in the DNA repair and transcription gene ERCC2(XPD) in trichothiodystrophy. , 1996, American journal of human genetics.

[60]  Craig L. Peterson,et al.  DNA-binding properties of the yeast SWI/SNF complex , 1996, Nature.

[61]  R. Conaway,et al.  A Role for ATP and TFIIH in Activation of the RNA Polymerase II Preinitiation Complex Prior to Transcription Initiation (*) , 1996, The Journal of Biological Chemistry.

[62]  L. Nelles,et al.  Characterization of a helicase-like transcription factor involved in the expression of the human plasminogen activator inhibitor-1 gene. , 1996, DNA and cell biology.

[63]  Paul Tempst,et al.  RSC, an Essential, Abundant Chromatin-Remodeling Complex , 1996, Cell.

[64]  M. Kuroda,et al.  RNA‐dependent association of the Drosophila maleless protein with the male X chromosome , 1996, Genes to cells : devoted to molecular & cellular mechanisms.

[65]  R. Conaway,et al.  The RNA polymerase II general elongation factors. , 1996, Trends in biochemical sciences.

[66]  F. Holstege,et al.  Opening of an RNA polymerase II promoter occurs in two distinct steps and requires the basal transcription factors IIE and IIH. , 1996, The EMBO journal.

[67]  R. Perry,et al.  CHD1 is concentrated in interbands and puffed regions of Drosophila polytene chromosomes. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[68]  D. Price,et al.  Drosophila Factor 2, an RNA Polymerase II Transcript Release Factor, Has DNA-dependent ATPase Activity* , 1997, The Journal of Biological Chemistry.

[69]  M. Gray,et al.  The Werner syndrome protein is a DNA helicase , 1997, Nature Genetics.

[70]  Mark Ellisman,et al.  A cellular cofactor for the constitutive transport element of type D retrovirus. , 1997, Science.

[71]  Jeffrey D. Parvin,et al.  RNA Helicase A Mediates Association of CBP with RNA Polymerase II , 1997, Cell.

[72]  F. Collins,et al.  Characterization of the CHD family of proteins. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[73]  T. Tsukiyama,et al.  Role of histone tails in nucleosome remodeling by Drosophila NURF , 1997, The EMBO journal.

[74]  J. Hoeijmakers,et al.  The Cockayne syndrome B protein, involved in transcription‐coupled DNA repair, resides in an RNA polymerase II‐containing complex , 1997, The EMBO journal.

[75]  Ronald L. Davis,et al.  roX1 RNA Paints the X Chromosome of Male Drosophila and Is Regulated by the Dosage Compensation System , 1997, Cell.

[76]  M. Kuroda,et al.  The NTPase/helicase activities of Drosophila maleless, an essential factor in dosage compensation , 1997, The EMBO journal.

[77]  Matthias Mann,et al.  Chromatin-remodelling factor CHRAC contains the ATPases ISWI and topoisomerase II , 1997, Nature.

[78]  Richard Axel,et al.  Genes Expressed in Neurons of Adult Male Drosophila , 1997, Cell.

[79]  Ryuji Kobayashi,et al.  ACF, an ISWI-Containing and ATP-Utilizing Chromatin Assembly and Remodeling Factor , 1997, Cell.

[80]  A. Sancar,et al.  Human Transcription-Repair Coupling Factor CSB/ERCC6 Is a DNA-stimulated ATPase but Is Not a Helicase and Does Not Disrupt the Ternary Transcription Complex of Stalled RNA Polymerase II* , 1997, The Journal of Biological Chemistry.

[81]  H. Mitsui,et al.  Dhh1p, a putative RNA helicase, associates with the general transcription factors Pop2p and Ccr4p from Saccharomyces cerevisiae. , 1998, Genetics.

[82]  S. Timsit,et al.  Specific interaction between the XNP/ATR-X gene product and the SET domain of the human EZH2 protein. , 1998, Human molecular genetics.