The functions of the SAGA and SWI/SNF complexes are interrelated and can form stable “epigenetic ... more The functions of the SAGA and SWI/SNF complexes are interrelated and can form stable “epigenetic marks” on promoters in vivo. Here we show that stable promoter occupancy by SWI/SNF and SAGA in the absence of transcription activators requires the bromodomains of the Swi2/Snf2 and Gcn5 subunits, respectively, and nucleosome acetylation. This acetylation can be brought about by either the SAGA or NuA4 HAT complexes. The bromodomain in the Spt7 subunit of SAGA is dispensable for this activity but will anchor SAGA if it is swapped into Gcn5, indicating that specificity of bromodomain function is determined in part by the subunit it occupies. Thus, bromodomains within the catalytic subunits of SAGA and SWI/SNF anchor these complexes to acetylated promoter nucleosomes.
SWI/SNF complexes have been shown to participate in the transdisplacement of histone octamers fro... more SWI/SNF complexes have been shown to participate in the transdisplacement of histone octamers from DNA fragments (Owen-Hughes and Workman, 1996; Lorch et al., 1999; Phelan et al., 2000) and to promote the sliding Summary of histones octamers along DNA in cis (Whitehouse et al. , 1999). Through these mechanisms the SWI/SNF To investigate the function of SWI/SNF in site-specific chromatin remodeling at promoters, we have used a complex is thought to participate in the formation of nucleosome-free regions or regions of altered nucleo-purified system to analyze its distribution, function, and retention following recruitment by a sequence-somes at the promoters of specific genes. Sequence-specific transcription activators can ac-specific transcription activator. Activator recruitment of SWI/SNF bound the complex to promoter proximal complish targeting of the SWI/SNF complex to specific promoters. Both the yeast and human SWI/SNF com-nucleosomes and led to localized nucleosome disruption. However, retention of SWI/SNF on the promoter plexes have been shown to interact directly with transcription activators Natarajan et al., 1999; Neely et al., required either the continued binding of the transcription activator or acetylated histones. Histone acetyla-1999; Yudkovsky et al., 1999; Kadam et al., 2000; Wallberg et al., 2000). The yeast SWI/SNF complex interacts tion by either the SAGA or NuA4 HAT complexes increased the retention of SWI/SNF on the promoter. with the activation domains of numerous transcription activators (Natarajan et al., 1999; Neely et al., 1999; These data illustrate a functional link between HAT complexes and the SWI/SNF chromatin remodeling Yudkovsky et al., 1999; Wallberg et al., 2000). Activator recruitment of SWI/SNF allows its participation in the complex and provide a mechanistic basis for the ordered recruitment of these complexes. transcription of specific promoters in a milieu of competing chromatin (Neely et al., 1999; Wallberg et al., 2000). In vivo crosslinking/chromatin immunoprecipita-by adding 4 l of 5 M NaCl in 100 l binding buffer and incubated at 65ЊC overnight. DNA was extracted from the beads with 50 l of We thank L. Howe for advice in designing experiments and M. Vignali 1% SDS, 0.1 M NaHCO 3 solution twice followed by proteinase K for assistance in quantifying data and editing this manuscript. We digestion, phenol-chloroform extraction, and ethanol precipitation thank C. Peterson for suggesting the experiment shown in Figure of the unbound and bound materials. Denatured samples were ap-5. We are grateful to B. Cairns for providing ␣ Swp61/Arp7 and other plied to Zeta-Probe membranes by slot blot. The membranes were antibodies against SWI/SNF subunits. We thank M. Carey for the then hybridized successively with probes of 250-300 bp generated pG5E4T plasmid, and K. Ikeda for pG5E4-5S. We also thank F. Pugh by PCR and labeled by random hexanucleotide primer extension for a Gal4-proline expression plasmid and R. Utley for Gal4-VP16 (Boehringer Mannheim) as described (Vignali et al., 2000b) and purification. We are grateful to J. Cote, T. Owen-Hughes, A. Ebershown in . The membranes were exposed to harter, and members of the Workman, Simpson, and Reese labs at Phosphoimager and quantified. In , control or hyperacety-Penn State University for many helpful comments during this study. lated histones were used to reconstitute the templates and 1 g of This work was supported by a grant from NIGMS (to J. L. W.). Gal4 or LexA oligo was added where indicated and incubated for J. L. W. is an Associate Investigator with the Howard Hughes Medical 30 min to compete Gal4-VP16 prior to crosslinking. In , Institute. SAGA in the presence or absence of 2 M acetyl-CoA was targeted to the templates after the addition of 100 mM Gal4-VP16 as before. After a 30 min incubation and two washes with the binding buffer to remove the SAGA complex, SWI/SNF and competitor chromatin References was added and the experiment was continued as before.
We have identified two Gcn5-dependent histone acetyltransferase (HAT) complexes from Saccharomyce... more We have identified two Gcn5-dependent histone acetyltransferase (HAT) complexes from Saccharomyces cerevisiae, the 0.8-MDa ADA complex and the 1.8-MDa SAGA complex. The SAGA (Spt-Ada-Gcn5-acetyltransferase) complex contains several subunits which also function as part of other protein complexes, including a subset of TATA box binding protein-associated factors (TAFIIs) and Tra1. These observations raise the question of whether the 0.8-MDa ADA complex is a subcomplex of SAGA or whether it is a distinct HAT complex that also shares subunits with SAGA. To address this issue, we sought to determine if the ADA complex contained subunits that are not present in the SAGA complex. In this study, we report the purification of the ADA complex over 10 chromatographic steps. By a combination of mass spectrometry analysis and immunoblotting, we demonstrate that the adapter proteins Ada2, Ada3, and Gcn5 are indeed integral components of ADA. Furthermore, we identify the product of the S. cerevisiae gene YOR023C as a novel subunit of the ADA complex and name it Ahc1 for ADA HAT complex component 1. Biochemical functions of YOR023C have not been reported. However, AHC1 in high copy numbers suppresses the cold sensitivity caused by particular mutations in HTA1 (I. Pinto and F. Winston, personal communication), which encodes histone H2A (J. N. Hirschhorn et al., Mol. Cell. Biol. 15:1999-2009. Deletion of AHC1 disrupted the integrity of the ADA complex but did not affect SAGA or give rise to classic Ada ؊ phenotypes. These results indicate that Gcn5, Ada2, and Ada3 function as part of a unique HAT complex (ADA) and represent shared subunits between this complex and SAGA.
We have previously shown that the yeast SWI/SNF complex stimulates in vitro transcription from ch... more We have previously shown that the yeast SWI/SNF complex stimulates in vitro transcription from chromatin templates in an ATP-dependent manner. SWI/SNF function in this regard requires the presence of an activator with which it can interact directly, linking activator recruitment of SWI/SNF to transcriptional stimulation. In this study, we determine the SWI/SNF subunits that mediate its interaction with activators. Using a photocross-linking label transfer strategy, we show that the Snf5, Swi1, and Swi2/Snf2 subunits are contacted by the yeast acidic activators, Gcn4 and Hap4, in the context of the intact native SWI/SNF complex. In addition, we show that the same three subunits can interact individually with acidic activation domains, indicating that each subunit contributes to binding activators. Furthermore, mutations that reduce the activation potential of these activators also diminish its interaction with each of these SWI/SNF subunits. Thus, three distinct subunits of the SWI/SNF complex contribute to its interactions with activation domains.
volves a perturbation of histone DNA interactions that alters the path and length of DNA bent aro... more volves a perturbation of histone DNA interactions that alters the path and length of DNA bent around the histone octamer (Cô té et al., 1998; Bazett-Jones et al., 1999). The altered conformation of nucleosome cores generated by the action of SWI/SNF or the related RSC complex (Cairns et al., 1996c) persists after depletion ). The action of the SWI/SNF complex can facilitate the sliding of histone octamers on DNA in cis University of Utah School of Medicine Salt Lake City, Utah 84108 (Whitehouse et al., 1999) as well as the displacement of histone octamers from DNA in trans (Owen-Hughes et ‡ Department of Biosciences Karolinska Institute al., 1996; Lorch et al., 1999). Consequences of SWI/SNF action include increased accessibility of nucleosomal NOVUM, S-141 57 Huddinge and Sö dertö rns hö gskola DNA to transcription factors and restriction enzymes (Cô té et al., 1994; Kwon et al., 1994; Logie and Peterson, Box 4101, S-141 04 Huddinge Sweden 1997; Logie et al., 1999) and the release of nucleosomeinduced paused RNA polymerase II (Brown et al., 1996). An important question regarding SWI/SNF function is how the complex might be targeted to specific promoter Summary regions in chromatin. The possibility that SWI/SNF is targeted by transcription activators is consistent with The yeast SWI/SNF complex is required for the transeveral results. Interactions between the SWI/SNF comscription of several yeast genes and has been shown plex and the glucocorticoid receptor (Yoshinaga et al., to alter nucleosome structure in an ATP-dependent 1992; Fryer and Archer, 1998) and the lymphoid-specific reaction. In this study, we show that the complex stim-Ikaros DNA-binding proteins (Kim et al., 1999) have been ulated in vitro transcription from nucleosome temreported in cell extracts. A SWI/SNF-related complex plates in an activation domain-dependent manner. was purified as an essential cofactor for the erythroid Transcription stimulation by SWI/SNF required an actitranscription activator EKLF (Armstrong et al., 1998). vation domain with which it directly interacts. The Moreover, recent chromatin immunoprecipitation studacidic activation domains of VP16, Gcn4, Swi5, and ies in yeast suggest that interaction of the SWI/SNF Hap4 interacted directly with the purified SWI/SNF complex with the HO endonuclease gene promoter folcomplex and with the SWI/SNF complex in whole-cell lows the binding of the Swi5 transcription activator extracts. The similarity of activation domain interac-(Cosma et al., 1999; Krebs et al., 1999). Transcription tions and transcriptional stimulation between SWI/ activation via a Swi5-binding site in yeast is highly de-SNF and the SAGA histone acetyltransferase complex pendent on components of the SWI/SNF complex may account for their apparent overlapping functions (Cairns et al., 1996b). in vivo. In this study, we show activation of Gal4-VP16-driven transcription from chromatin templates by the yeast Introduction SWI/SNF complex. Transcription activation by SWI/SNF is attributed to recruitment of the SWI/SNF complex by The SWI/SNF complex is a multisubunit complex that acidic activation domains. These results and those in alters the conformation of nucleosomal DNA via an ATPthe accompanying manuscript (Natarajan et al., 1999 dependent reaction (for review, see Imbalzano, 1998; [this issue of Molecular Cell]) reveal the role of se-Workman and Kingston, 1998). The genes encoding subquence-specific transcription activators in targeting the units of the SWI/SNF complex were discovered in yeast SWI/SNF chomatin remodeling complex to promoters. genetic screens as genes that are required for HO and for SUC2 gene expression (Neigeborn and Carlson, 1984; Stern et al., 1984; Breeden and Nasmyth, 1987; Results Laurent et al., 1990; Peterson and Herskowitz, 1992). The SWI/SNF complex contains 11 known subunits, one Stimulation of Gal4-VP16-Driven Transcription of which is a highly conserved DNA-dependent ATPase, by the SWI/SNF Complex the Swi2/Snf2 subunit (Laurent et al., 1993). To test the transcriptional activities of SWI/SNF, we utilized a purified in vitro chromatin reconstitution system, which generates spaced nucleosome arrays, to form § To whom correspondence should be addressed (e-mail: jlw10@ transcription templates. This approach has demonpsu.edu). strated acetyl-CoA-dependent transcription activation Present address: by histone acetyltransferase complexes (Steger et al., its detachment, enhancing subsequent transcription factor binding. Proc. Natl. Acad. Sci. USA 95, 4947-4952. We thank D. Stillman, M. Green, J. Reese, S. Berger, B. F. Pugh, Cress, W.D., and Treizenberg, S.J. (1991). Critical structural eleand K. Ikeda for providing expression plasmids, J. Reese for an ments of the VP16 transcriptional activation domain. Science 251, ␣Taf30 antibody, T. Owen-Hughes, J. Cô té , and R. Utley for prepar-87-90. ing Gal4-VP16 and Gal4-glutamine, and M. Vignali for assistance Fryer, C.J., and Archer, T.K. (1998). Chromatin remodeling by the in preparing figures. We thank K. Natarajan and A. Hinnebusch for glucocorticoid receptor requires the BRG1 complex. Nature 393, testing SWI fractions for mediator subunits and sharing unpublished 88-91. information. We thank the members of the Workman, Simpson, and Reese labs at Penn State for many valuable discussions. This work Ikeda, K., Steger, D.J., Eberharter, A., and Workman, J.L. (1999). was supported by a grant from NIGMS to J. L. W. A grant was Activation domain-specific and general transcription stimulation by awarded to A. P. H. W. from the Swedish Natural Sciences Research native histone acetyltransferase complexes. Mol. Cell. Biol. 19, 855-863. Council. A. E. W. was awarded fellowships by the Swedish Medical Research Council (K98-03RM-12413) and the Erik and Edith Ferns-Imbalzano, A.N. (1998). Energy-dependent chromatin remodelers: trö m Foundation. D. J. S. was a Postdoctoral Associate of HHMI, complex complexes and their components. Crit. Rev. Eukaryot. and J. L. W. is an HHMI Associate Investigator. Gene Exp. 8, 225-255. . some disruption by human SWI/SNF is maintained in the absence of continued ATP hydrolysis. J. Biol. Chem. 271, 20726-20733.
Software systems contain entities, such as functions and variables, which are related to each oth... more Software systems contain entities, such as functions and variables, which are related to each other. As a software system evolves to accommodate new features and repair bugs, changes occur to these entities. Developers must ensure that related entities are updated to be consistent with these changes.
A reference software architecture for a domain defines the fundamental components of the domain a... more A reference software architecture for a domain defines the fundamental components of the domain and the relations between them. Research has shown the benefits of having a reference architecture for product development, software reuse, and maintenance. Many mature domains, such as compilers and operating systems, have well-known reference architectures.
To remain competitive in the fast paced world of software development, managers must optimize the... more To remain competitive in the fast paced world of software development, managers must optimize the usage of their limited resources to deliver quality products on time and within budget. In this paper, we present an approach (The Top Ten List) which highlights to managers the ten most susceptible subsystems to have a fault. The list is updated dynamically as the development of the system progresses. Manager can focus testing resources to the subsystems suggested by the list.
Software systems become progressively more complex and difficult to maintain. To facilitate maint... more Software systems become progressively more complex and difficult to maintain. To facilitate maintenance tasks, project managers and developers often turn to the evolution history of the system to recover various kinds of useful information, such as anomalous phenomena and lost design decisions. An informative visualization of the evolution history can help cope with this complexity by highlighting conspicuous evolution events using strong visual cues. In this paper, we present a scalable visualization technique called evolution spectrographs (ESG). An evolution spectrograph portrays the evolution of a spectrum of components based on a particular property measurement. We describe several special-purpose spectrographs and discuss their use in understanding and supporting software evolution through the case studies of three large software systems (OpenSSH, KOffice and FreeBSD).
Web applications are the legacy software of the future. Developed under tight schedules, with hig... more Web applications are the legacy software of the future. Developed under tight schedules, with high employee turn over, and in a rapidly evolving environment, these systems are often poorly structured and poorly documented. Maintaining such systems is problematic.
Software evolution is commonly characterized as a slow process of incremental change. Researchers... more Software evolution is commonly characterized as a slow process of incremental change. Researchers have observed that software systems also exhibit characteristics of punctuation (sudden and discontinuous change) during their evolution. In this paper, we analyze punctuated evolution from the perspective of structural change. We developed a colorcoded visualization technique called the Evolution Spectrograph (ESG). ESG can be applied to highlight conspicuous changes across a historical sequence of software releases. We describe evolution spectrographs and present the empirical results from our studies of three open source software systems: OpenSSH, PostgreSQL, and Linux. We show that punctuated change occurred in the evolution of these three systems, and we validate our empirical results by examining related software documents such as change logs and release notes.
In this paper we present a new perspective on the problem of complexity in software, using sound ... more In this paper we present a new perspective on the problem of complexity in software, using sound mathematical concepts from information theory such as Shannon's Entropy . We study the complexity of the development process by examining the logs of the source control repository for large software projects. We hypothesize that the process of developing code is a good indicator of the current and future problems in the code and the project. A complex process will have negative affects on its outcome, such as producing a complex system or delaying releases. We validate our work by studying the evolution of six large open source projects (three operating systems, a window manager, an office productivity suite, and a database).
The functions of the SAGA and SWI/SNF complexes are interrelated and can form stable “epigenetic ... more The functions of the SAGA and SWI/SNF complexes are interrelated and can form stable “epigenetic marks” on promoters in vivo. Here we show that stable promoter occupancy by SWI/SNF and SAGA in the absence of transcription activators requires the bromodomains of the Swi2/Snf2 and Gcn5 subunits, respectively, and nucleosome acetylation. This acetylation can be brought about by either the SAGA or NuA4 HAT complexes. The bromodomain in the Spt7 subunit of SAGA is dispensable for this activity but will anchor SAGA if it is swapped into Gcn5, indicating that specificity of bromodomain function is determined in part by the subunit it occupies. Thus, bromodomains within the catalytic subunits of SAGA and SWI/SNF anchor these complexes to acetylated promoter nucleosomes.
SWI/SNF complexes have been shown to participate in the transdisplacement of histone octamers fro... more SWI/SNF complexes have been shown to participate in the transdisplacement of histone octamers from DNA fragments (Owen-Hughes and Workman, 1996; Lorch et al., 1999; Phelan et al., 2000) and to promote the sliding Summary of histones octamers along DNA in cis (Whitehouse et al. , 1999). Through these mechanisms the SWI/SNF To investigate the function of SWI/SNF in site-specific chromatin remodeling at promoters, we have used a complex is thought to participate in the formation of nucleosome-free regions or regions of altered nucleo-purified system to analyze its distribution, function, and retention following recruitment by a sequence-somes at the promoters of specific genes. Sequence-specific transcription activators can ac-specific transcription activator. Activator recruitment of SWI/SNF bound the complex to promoter proximal complish targeting of the SWI/SNF complex to specific promoters. Both the yeast and human SWI/SNF com-nucleosomes and led to localized nucleosome disruption. However, retention of SWI/SNF on the promoter plexes have been shown to interact directly with transcription activators Natarajan et al., 1999; Neely et al., required either the continued binding of the transcription activator or acetylated histones. Histone acetyla-1999; Yudkovsky et al., 1999; Kadam et al., 2000; Wallberg et al., 2000). The yeast SWI/SNF complex interacts tion by either the SAGA or NuA4 HAT complexes increased the retention of SWI/SNF on the promoter. with the activation domains of numerous transcription activators (Natarajan et al., 1999; Neely et al., 1999; These data illustrate a functional link between HAT complexes and the SWI/SNF chromatin remodeling Yudkovsky et al., 1999; Wallberg et al., 2000). Activator recruitment of SWI/SNF allows its participation in the complex and provide a mechanistic basis for the ordered recruitment of these complexes. transcription of specific promoters in a milieu of competing chromatin (Neely et al., 1999; Wallberg et al., 2000). In vivo crosslinking/chromatin immunoprecipita-by adding 4 l of 5 M NaCl in 100 l binding buffer and incubated at 65ЊC overnight. DNA was extracted from the beads with 50 l of We thank L. Howe for advice in designing experiments and M. Vignali 1% SDS, 0.1 M NaHCO 3 solution twice followed by proteinase K for assistance in quantifying data and editing this manuscript. We digestion, phenol-chloroform extraction, and ethanol precipitation thank C. Peterson for suggesting the experiment shown in Figure of the unbound and bound materials. Denatured samples were ap-5. We are grateful to B. Cairns for providing ␣ Swp61/Arp7 and other plied to Zeta-Probe membranes by slot blot. The membranes were antibodies against SWI/SNF subunits. We thank M. Carey for the then hybridized successively with probes of 250-300 bp generated pG5E4T plasmid, and K. Ikeda for pG5E4-5S. We also thank F. Pugh by PCR and labeled by random hexanucleotide primer extension for a Gal4-proline expression plasmid and R. Utley for Gal4-VP16 (Boehringer Mannheim) as described (Vignali et al., 2000b) and purification. We are grateful to J. Cote, T. Owen-Hughes, A. Ebershown in . The membranes were exposed to harter, and members of the Workman, Simpson, and Reese labs at Phosphoimager and quantified. In , control or hyperacety-Penn State University for many helpful comments during this study. lated histones were used to reconstitute the templates and 1 g of This work was supported by a grant from NIGMS (to J. L. W.). Gal4 or LexA oligo was added where indicated and incubated for J. L. W. is an Associate Investigator with the Howard Hughes Medical 30 min to compete Gal4-VP16 prior to crosslinking. In , Institute. SAGA in the presence or absence of 2 M acetyl-CoA was targeted to the templates after the addition of 100 mM Gal4-VP16 as before. After a 30 min incubation and two washes with the binding buffer to remove the SAGA complex, SWI/SNF and competitor chromatin References was added and the experiment was continued as before.
We have identified two Gcn5-dependent histone acetyltransferase (HAT) complexes from Saccharomyce... more We have identified two Gcn5-dependent histone acetyltransferase (HAT) complexes from Saccharomyces cerevisiae, the 0.8-MDa ADA complex and the 1.8-MDa SAGA complex. The SAGA (Spt-Ada-Gcn5-acetyltransferase) complex contains several subunits which also function as part of other protein complexes, including a subset of TATA box binding protein-associated factors (TAFIIs) and Tra1. These observations raise the question of whether the 0.8-MDa ADA complex is a subcomplex of SAGA or whether it is a distinct HAT complex that also shares subunits with SAGA. To address this issue, we sought to determine if the ADA complex contained subunits that are not present in the SAGA complex. In this study, we report the purification of the ADA complex over 10 chromatographic steps. By a combination of mass spectrometry analysis and immunoblotting, we demonstrate that the adapter proteins Ada2, Ada3, and Gcn5 are indeed integral components of ADA. Furthermore, we identify the product of the S. cerevisiae gene YOR023C as a novel subunit of the ADA complex and name it Ahc1 for ADA HAT complex component 1. Biochemical functions of YOR023C have not been reported. However, AHC1 in high copy numbers suppresses the cold sensitivity caused by particular mutations in HTA1 (I. Pinto and F. Winston, personal communication), which encodes histone H2A (J. N. Hirschhorn et al., Mol. Cell. Biol. 15:1999-2009. Deletion of AHC1 disrupted the integrity of the ADA complex but did not affect SAGA or give rise to classic Ada ؊ phenotypes. These results indicate that Gcn5, Ada2, and Ada3 function as part of a unique HAT complex (ADA) and represent shared subunits between this complex and SAGA.
We have previously shown that the yeast SWI/SNF complex stimulates in vitro transcription from ch... more We have previously shown that the yeast SWI/SNF complex stimulates in vitro transcription from chromatin templates in an ATP-dependent manner. SWI/SNF function in this regard requires the presence of an activator with which it can interact directly, linking activator recruitment of SWI/SNF to transcriptional stimulation. In this study, we determine the SWI/SNF subunits that mediate its interaction with activators. Using a photocross-linking label transfer strategy, we show that the Snf5, Swi1, and Swi2/Snf2 subunits are contacted by the yeast acidic activators, Gcn4 and Hap4, in the context of the intact native SWI/SNF complex. In addition, we show that the same three subunits can interact individually with acidic activation domains, indicating that each subunit contributes to binding activators. Furthermore, mutations that reduce the activation potential of these activators also diminish its interaction with each of these SWI/SNF subunits. Thus, three distinct subunits of the SWI/SNF complex contribute to its interactions with activation domains.
volves a perturbation of histone DNA interactions that alters the path and length of DNA bent aro... more volves a perturbation of histone DNA interactions that alters the path and length of DNA bent around the histone octamer (Cô té et al., 1998; Bazett-Jones et al., 1999). The altered conformation of nucleosome cores generated by the action of SWI/SNF or the related RSC complex (Cairns et al., 1996c) persists after depletion ). The action of the SWI/SNF complex can facilitate the sliding of histone octamers on DNA in cis University of Utah School of Medicine Salt Lake City, Utah 84108 (Whitehouse et al., 1999) as well as the displacement of histone octamers from DNA in trans (Owen-Hughes et ‡ Department of Biosciences Karolinska Institute al., 1996; Lorch et al., 1999). Consequences of SWI/SNF action include increased accessibility of nucleosomal NOVUM, S-141 57 Huddinge and Sö dertö rns hö gskola DNA to transcription factors and restriction enzymes (Cô té et al., 1994; Kwon et al., 1994; Logie and Peterson, Box 4101, S-141 04 Huddinge Sweden 1997; Logie et al., 1999) and the release of nucleosomeinduced paused RNA polymerase II (Brown et al., 1996). An important question regarding SWI/SNF function is how the complex might be targeted to specific promoter Summary regions in chromatin. The possibility that SWI/SNF is targeted by transcription activators is consistent with The yeast SWI/SNF complex is required for the transeveral results. Interactions between the SWI/SNF comscription of several yeast genes and has been shown plex and the glucocorticoid receptor (Yoshinaga et al., to alter nucleosome structure in an ATP-dependent 1992; Fryer and Archer, 1998) and the lymphoid-specific reaction. In this study, we show that the complex stim-Ikaros DNA-binding proteins (Kim et al., 1999) have been ulated in vitro transcription from nucleosome temreported in cell extracts. A SWI/SNF-related complex plates in an activation domain-dependent manner. was purified as an essential cofactor for the erythroid Transcription stimulation by SWI/SNF required an actitranscription activator EKLF (Armstrong et al., 1998). vation domain with which it directly interacts. The Moreover, recent chromatin immunoprecipitation studacidic activation domains of VP16, Gcn4, Swi5, and ies in yeast suggest that interaction of the SWI/SNF Hap4 interacted directly with the purified SWI/SNF complex with the HO endonuclease gene promoter folcomplex and with the SWI/SNF complex in whole-cell lows the binding of the Swi5 transcription activator extracts. The similarity of activation domain interac-(Cosma et al., 1999; Krebs et al., 1999). Transcription tions and transcriptional stimulation between SWI/ activation via a Swi5-binding site in yeast is highly de-SNF and the SAGA histone acetyltransferase complex pendent on components of the SWI/SNF complex may account for their apparent overlapping functions (Cairns et al., 1996b). in vivo. In this study, we show activation of Gal4-VP16-driven transcription from chromatin templates by the yeast Introduction SWI/SNF complex. Transcription activation by SWI/SNF is attributed to recruitment of the SWI/SNF complex by The SWI/SNF complex is a multisubunit complex that acidic activation domains. These results and those in alters the conformation of nucleosomal DNA via an ATPthe accompanying manuscript (Natarajan et al., 1999 dependent reaction (for review, see Imbalzano, 1998; [this issue of Molecular Cell]) reveal the role of se-Workman and Kingston, 1998). The genes encoding subquence-specific transcription activators in targeting the units of the SWI/SNF complex were discovered in yeast SWI/SNF chomatin remodeling complex to promoters. genetic screens as genes that are required for HO and for SUC2 gene expression (Neigeborn and Carlson, 1984; Stern et al., 1984; Breeden and Nasmyth, 1987; Results Laurent et al., 1990; Peterson and Herskowitz, 1992). The SWI/SNF complex contains 11 known subunits, one Stimulation of Gal4-VP16-Driven Transcription of which is a highly conserved DNA-dependent ATPase, by the SWI/SNF Complex the Swi2/Snf2 subunit (Laurent et al., 1993). To test the transcriptional activities of SWI/SNF, we utilized a purified in vitro chromatin reconstitution system, which generates spaced nucleosome arrays, to form § To whom correspondence should be addressed (e-mail: jlw10@ transcription templates. This approach has demonpsu.edu). strated acetyl-CoA-dependent transcription activation Present address: by histone acetyltransferase complexes (Steger et al., its detachment, enhancing subsequent transcription factor binding. Proc. Natl. Acad. Sci. USA 95, 4947-4952. We thank D. Stillman, M. Green, J. Reese, S. Berger, B. F. Pugh, Cress, W.D., and Treizenberg, S.J. (1991). Critical structural eleand K. Ikeda for providing expression plasmids, J. Reese for an ments of the VP16 transcriptional activation domain. Science 251, ␣Taf30 antibody, T. Owen-Hughes, J. Cô té , and R. Utley for prepar-87-90. ing Gal4-VP16 and Gal4-glutamine, and M. Vignali for assistance Fryer, C.J., and Archer, T.K. (1998). Chromatin remodeling by the in preparing figures. We thank K. Natarajan and A. Hinnebusch for glucocorticoid receptor requires the BRG1 complex. Nature 393, testing SWI fractions for mediator subunits and sharing unpublished 88-91. information. We thank the members of the Workman, Simpson, and Reese labs at Penn State for many valuable discussions. This work Ikeda, K., Steger, D.J., Eberharter, A., and Workman, J.L. (1999). was supported by a grant from NIGMS to J. L. W. A grant was Activation domain-specific and general transcription stimulation by awarded to A. P. H. W. from the Swedish Natural Sciences Research native histone acetyltransferase complexes. Mol. Cell. Biol. 19, 855-863. Council. A. E. W. was awarded fellowships by the Swedish Medical Research Council (K98-03RM-12413) and the Erik and Edith Ferns-Imbalzano, A.N. (1998). Energy-dependent chromatin remodelers: trö m Foundation. D. J. S. was a Postdoctoral Associate of HHMI, complex complexes and their components. Crit. Rev. Eukaryot. and J. L. W. is an HHMI Associate Investigator. Gene Exp. 8, 225-255. . some disruption by human SWI/SNF is maintained in the absence of continued ATP hydrolysis. J. Biol. Chem. 271, 20726-20733.
Software systems contain entities, such as functions and variables, which are related to each oth... more Software systems contain entities, such as functions and variables, which are related to each other. As a software system evolves to accommodate new features and repair bugs, changes occur to these entities. Developers must ensure that related entities are updated to be consistent with these changes.
A reference software architecture for a domain defines the fundamental components of the domain a... more A reference software architecture for a domain defines the fundamental components of the domain and the relations between them. Research has shown the benefits of having a reference architecture for product development, software reuse, and maintenance. Many mature domains, such as compilers and operating systems, have well-known reference architectures.
To remain competitive in the fast paced world of software development, managers must optimize the... more To remain competitive in the fast paced world of software development, managers must optimize the usage of their limited resources to deliver quality products on time and within budget. In this paper, we present an approach (The Top Ten List) which highlights to managers the ten most susceptible subsystems to have a fault. The list is updated dynamically as the development of the system progresses. Manager can focus testing resources to the subsystems suggested by the list.
Software systems become progressively more complex and difficult to maintain. To facilitate maint... more Software systems become progressively more complex and difficult to maintain. To facilitate maintenance tasks, project managers and developers often turn to the evolution history of the system to recover various kinds of useful information, such as anomalous phenomena and lost design decisions. An informative visualization of the evolution history can help cope with this complexity by highlighting conspicuous evolution events using strong visual cues. In this paper, we present a scalable visualization technique called evolution spectrographs (ESG). An evolution spectrograph portrays the evolution of a spectrum of components based on a particular property measurement. We describe several special-purpose spectrographs and discuss their use in understanding and supporting software evolution through the case studies of three large software systems (OpenSSH, KOffice and FreeBSD).
Web applications are the legacy software of the future. Developed under tight schedules, with hig... more Web applications are the legacy software of the future. Developed under tight schedules, with high employee turn over, and in a rapidly evolving environment, these systems are often poorly structured and poorly documented. Maintaining such systems is problematic.
Software evolution is commonly characterized as a slow process of incremental change. Researchers... more Software evolution is commonly characterized as a slow process of incremental change. Researchers have observed that software systems also exhibit characteristics of punctuation (sudden and discontinuous change) during their evolution. In this paper, we analyze punctuated evolution from the perspective of structural change. We developed a colorcoded visualization technique called the Evolution Spectrograph (ESG). ESG can be applied to highlight conspicuous changes across a historical sequence of software releases. We describe evolution spectrographs and present the empirical results from our studies of three open source software systems: OpenSSH, PostgreSQL, and Linux. We show that punctuated change occurred in the evolution of these three systems, and we validate our empirical results by examining related software documents such as change logs and release notes.
In this paper we present a new perspective on the problem of complexity in software, using sound ... more In this paper we present a new perspective on the problem of complexity in software, using sound mathematical concepts from information theory such as Shannon's Entropy . We study the complexity of the development process by examining the logs of the source control repository for large software projects. We hypothesize that the process of developing code is a good indicator of the current and future problems in the code and the project. A complex process will have negative affects on its outcome, such as producing a complex system or delaying releases. We validate our work by studying the evolution of six large open source projects (three operating systems, a window manager, an office productivity suite, and a database).
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Papers by Ahmed Hassan