SWI/SNF is a chromatin-remodeling complex and Brahma (BRM) is the ATPase subunit of SWI/SNF. BRM regulates transcription by remodeling the nucleosomes at promoter regions. BRM is also associated with RNA and affects pre-mRNA processing together with other SWI/SNF subunits. In this thesis, I will discuss the roles of BRM in both transcription and pre-mRNA processing. In Paper I, we showed that BRM, as well as other SWI/SNF subunits SNR1 and MOR, affects the alternative processing of a subset of pre-mRNAs, as shown by microarray analysis. This observation was validated by RNAi experiments both in Drosophila S2 cells and in vivo. In Paper II, we characterized the trans-splicing of transcripts derived from the mod(mdg4) gene. RNA interference (RNAi) and overexpression experiments revealed that BRM regulates the trans-splicing of mod(mdg4)-RX in an ATPase independent manner. In Paper III, we analyzed the expression of two BRM-target genes identified in Paper I, CG44250 and CG44251. RNAi and overexpression experiments showed that the expression levels of these two genes were affected by BRM in a manner that is independent of its ATPase activity. Transcriptome analysis further proved that BRM affects gene expression both in ATPase dependent and independent manners. In Paper IV, we showed that BRM is present at the 3’-end of two analyzed genes, CG5174 and CG2051. BRM facilitates the recruitment of the cleavage and polyadenylation machinery to the cleavage sites through protein-protein interactions that do not require the ATPase activity of BRM. Morevoer, BRM promotes the cleavage of the CG5174 and CG2051 pre-mRNAs. To sum up, SWI/SNF plays important roles not only in transcription but also in pre-mRNA processing. To regulate transcription, BRM can either act as an ATPase-dependent chromatin remodeler or in a manner that does not involve ATPase activity. Additionally, BRM interacts with RNA-binding proteins to regulate the processing of a subset of pre-mRNAs, and this function of BRM is independent of its chromatin remodeling activity. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript.</p>

The human auditory perception system is much more noise-robust than any state-of the art automatic speech recognition (ASR) system. It is expected that the noise-robustness of speech feature can be improved by employing the human auditory based feature extraction procedure. In this thesis, we investigate modifying the commonly-used feature extraction process for automatic speech recognition systems. A novel frequency masking curve, which is based on modeling the basilar membrane as a cascade system of damped simple harmonic oscillators, is used to replace the critical-band masking curve to compute the masking threshold. We mathematically analyze the coupled motion of the oscillator system (basilar membrane) when they are driven by short-time stationary (speech) signals. Based on the analysis, we derive the relation between the amplitudes of neighboring oscillators, and accordingly insert a masking module in the front-end signal processing stage to modify the speech spectrum. We evaluate the proposed method on the Aurora 2.0 noisy-digit speech database. When combined with the commonly-used cepstral mean subtraction post-processing, the proposed auditory front-end module achieves a significant improvement. The method of correlational masking effect curve combine with CMS can achieves relative improvements of 25.9% over the baseline respectively. After applying the methods iteratively, the relative improvement improves from 25.9% to 30.3%.

Thesis (Ph.D. in Molecular Biology) -- University of Colorado at Denver and Health Sciences Center, 2005. / Typescript. Includes bibliographical references (leaves 126-149). Free to UCDHSC affiliates. Online version available via ProQuest Digital Dissertations;

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3’-end modification by polyadenylation is a ubiquitous feature of almost all eukaryotic mRNA species and is catalyzed by a consortium of enzymes, the polyadenylation factors. Poly(A) polymerase (PAP), the enzyme catalyzing the addition of adenosine residues during the polyadenylation stage, exists in four isoforms within Arabidopsis. In silico and yeast two-hybrid studies showed that PAP1 has unique expression and interaction pattern in Arabidopsis, suggesting non-canonical functions of PAP1. Its exclusive interaction with PAP4 has not been reported in other living systems until now and hints at a difference in polyadenylation in plants with respect to mammals and yeast. Cleavage Stimulation Factor (CstF), a heterotrimeric complex of the polyadenylation factors CstF50, CstF64 and CstF77, plays a role largely in cleavage of pre-mRNA. This study highlights some aspects of the Arabidopsis homologs of CstF64 and CstF77, central to various cellular processes other than nuclear polyadenylation. In silico studies showed an elevated expression of CstF64 in the pollen while that of CstF77 remained fairly low. Yeast two-hybrid assays indicated a novel kind of interaction of CstF64 with Fip1(V). It is also speculated from sub-cellular localization techniques by agroinfiltration in tobacco leaves that CstF64 localizes in the cytoplasm and CstF77 in the nucleus, as found for the orthologs of CstF77 in other systems.

Chez les eucaryotes, la maturation de l’extrémité 3’ des ARNs messagers a lieu lors de la transcription et regroupe deux étapes : le clivage endonucléolytique du transcrit au niveau d’un site spécifique et l’ajout d’une queue poly(A) sur le fragment en amont du site de clivage. Chez S. cerevisiae, le complexe de polyadénylation est formé par 20 protéines, regroupées principalement en deux sous-complexes : CF IA et CPF. Nous nous intéressons plus spécifiquement à Pcf11, sous-unité du complexe CF IA. Pcf11 est formé de sept sous-domaines, mais la fonction d’une grande partie de la protéine n’est pour l’instant pas connue. Par exemple, aucune fonction n’est associée à la région située entre le domaine d’interaction avec le CTD de l’ARN polymérase II (CID) et une répétion de 20 résidus glutamines. Récemment, la structure de ce domaine, appelé 2nd NTD a été décrite. Pour essayer de comprendre la fonction du 2nd NTD et des motifs liant le zinc encadrant le domaine d’interaction avec Clp1, nous avons mis en place une stratégie systématique de mutagénèse, soit par délétions, soit par mutations ponctuelles. Le 2nd NTD est formé de trois hélices α et interagit avec l’ARN. La délétion de ce domaine conduit à un phénotype de croissance lente chez la levure et un défaut de terminaison de transcription des snoRNAs. Malgré une similarité de structure et de fonction, le 2nd NTD présenterait une fonction indépendante. La fonction des motifs liant le zinc n’est pour l’instant pas connue. Cependant, la mutation de l’un de ces deux motifs conduit à un défaut de clivage et de polyadénylation in vitro. La mutation des deux motifs est létale chez la levure. / In eukaryotes, poly (A) tails are added to nuclear pre-mRNA 3'-ends in the two steps of cleavage and polyadenylation. This co-transcriptional processing requires the activity of a large protein complex comprising at least 20 different polypeptides in yeast organized primarily into the two factors CF IA and CPF. We are interested in the functional characterization of Pcf11, a CF IA subunit. The Pcf11 protein is organized into seven different domains, but here is still a large portion of the polypeptide that has not yet been characterized. For example the region from the end of the CTD interaction domain (CID) to an uninterrupted stretch of 20 glutamine residues has no known function. Recently, the structure of this region, called the 2nd NTD have been characterized. To gain insight into the function of the 2nd NTD and the two zinc fingers motif surrounding the Clp1 interaction domain, we have employed a systematic strategy of mutagenesis, either by deletion or via point mutations. The 2nd NTD is a folded domain composed of three α-helices. The deletion of this domain induced a severe defect of growth in yeast and impaired transcription termination of snoRNAs. Despite its similarity in structure and function with the CID, the 2nd NTD seems to act like an independent RNA binding domain. We don’t know yet the real function of the two zinc fingers motif at the C-terminal region of Pcf11, but the mutation of Cystein residues into serine of one of the two motifs impaired cleavage and polyadenylation. The mutation of the first motif is less harmful than the mutation of the second motif. The simultaneous mutation is lethal in yeast.

La maturation 3’ des pré-ARNm constitue une étape majeure dans la régulation post-transcriptionnelle de l’expression des gènes, indispensable à la stabilité, l’export vers le cytoplasme et la traduction des ARNm. Elle est composée de deux réactions : un clivage à l’extrémité 3’ suivie de l’addition d’une queue poly(A). Des études ont montré que la maturation en 3’ est inhibée en réponse aux dommages de l’ADN. Cependant, la cellule a mis en place des mécanismes compensatoires qui permettent à certains pré-ARNm d’être correctement maturés assurant ainsi le maintien de son intégrité. Les travaux que nous avons menés ont mis en évidence un mécanisme de résistance à l’inhibition de maturation en 3’ du pré-ARNm codant pour le suppresseur de tumeur p53. Ce mécanisme fait intervenir l’hélicase DHX36 qui déplie une structure secondaire appelée G-quadruplexe située en aval du site de clivage. Par ailleurs dans une deuxième étude, nous avons montré que la maturation en 3’ maintenue du pré-ARNm p53 en réponse aux dommages de l’ADN, est découplée du processus de transcription, contrairement au pré-ARNm TBP dont la maturation 3’ est inhibée en réponse aux dommage de l’ADN. Ce découplage a lieu grâce à un clivage co-transcriptionnelle du pré-ARNm p53 au niveau de la chromatine qui entraîne sa libération dans le nucléoplasme où il subit sa maturation en 3’. Une étude à grande échelle nous a permis de montrer que ce mécanisme de maturation en 3’ survenant dans le nucléoplasme est associé au maintien d'une maturation en 3’ efficace en réponse aux dommages de l’ADN. / The 3’-end processing of pre-mRNA, a key step in the post-transcriptional gene expression regulation, is essential for mRNA stability, export and translation. This process is a two-step reaction composed of a cleavage at the 3’-end followed by the addition of a poly(A) tail. Studies have shown that pre-mRNA 3’-end processing is inhibited in response to DNA damage. However, compensatory mechanisms exist to allow some pre-mRNA to be properly processed at their 3’-end in order to maintain cell integrity. For instance, in response to DNA damage, the 3’-end processing of the pre-mRNA coding for the tumor suppressor p53 is able to escape from its inhibition. In the present work, we have shown that the underlying mechanism involves the DHX36 helicase that unwinds a secondary structure called G-quadruplex located downstream of the cleavage site of the p53 pre-mRNA. Moreover, in a second study, we have shown that the maintained p53 pre-mRNA 3’-end processing in response to DNA damage is uncoupled from the transcription process, unlike the inhibited TBP pre-mRNA 3’-end processing. This uncoupling takes place through a co-transcriptional cleavage of p53 pre-mRNA from the chromatin and its release in the nucleoplasm where it undergoes its 3’-end processing. A genome-wide study allowed us to show that the pre-mRNA 3’-end processing occurring in the nucleoplasm is associated with a maintained 3’end processing in response to DNA damage

Cleavage and polyadenylation are essential pre-mRNA processing reactions maturing the 3’end of almost all protein encoding eukaryotic mRNAs. Analysis of the sequences required for cleavage and polyadenylation in the human melanocortin 4 receptor (MC4R) and the human transcription factors JUNB and JUND pre-mRNAs revealed that, at least for some mammalian genes, 3’end processing of the primary transcript is independent of previously described auxiliary sequence elements located upstream or downstream of the core poly(A) sequences. The analysis of the MC4R poly(A) site, contrary to the current understanding of mammalian poly(A) sites, showed that mutations of the AUUAAA hexamer sequence had no effect on 3’end processing levels while mutations in the short DSE severely reduced cleavage efficiency. The MC4R poly(A) site uses a potent DSE and to direct maximal cleavage efficiency requires only a short upstream adenosine rich sequence. Furthermore, analysis of the endogenous A-rich human JUNB poly(A) signal validated upstream A-rich core sequences as genuine 3’end formation directing sequences in human non-canonical 3’end formation signals. The results show that a minimal human poly(A) site, similar to yeast and plants, can be defined by an adenosine rich sequence adjacent to a U/GU-rich sequence element and a cleavage site. These findings further imply that some human non-canonical poly(A) sites may be recognised via a similar DSE-dependent mechanism and may not require additional auxiliary sequence elements. Finally, results on the analysis of the EDF1 poly(A) signal show that, in a spliced environment, A-rich sequences are also 3’end formation effectors but depend on an competent upstream splicing reaction for efficient definition of the 3’end processing site.

In 1990, Richard Jorgensen’s lab initiated a study to test if they could create a more vivid color petunia (Napoli et al. 1990). Their plan was to transform plants with the chalcone synthase transgene––the predicted rate limiting factor in the production of purple pigmentation. Much to their surprise, the transgenic plants, as well as their progeny, displayed a great reduction in pigmentation. This loss of endogenous function was termed “cosuppression” and it was thought that sequence-specific repression resulted from over-expression of the homologous transgene sequence. In 1998, Andrew Fire and Craig Mello described a phenomenon in which double stranded RNA (dsRNA) can trigger silencing of cognate sequences when injected into the nematode, Caenorhabditis elegans (Fire et al. 1998). This data explained observations seen years earlier by other worm researchers, and suggested that repression of pigmentation in plants was caused by a dsRNA-intermediate (Guo and Kemphues 1995; Napoli et al. 1990). The phenomenon––which soon after was coined RNA interference (RNAi)––was soon discovered to be a post-transcriptional surveillance system in plants and animals to remove foreign nucleic acids.