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348 results on '"Bussemaker, Harmen J."'

7. Classification of Saccharomyces cerevisiae promoter regions into distinct chromatin classes reveals the existence of nucleosome-depleted hotspots of transcription factor occupancy

Author

Wang, Junbai, Ward, Lucas D., and Bussemaker, Harmen J.

Subjects
Quantitative Biology - Genomics
Abstract

Transcription factors (TF) play an essential role in the cell as locus- and condition-specific recruiters of transcriptional machinery or chromatin-modifying complexes. However, predicting the in vivo profile of TF occupancy along the genome, which depends on complex interactions with other chromatin-associated proteins, from the DNA sequence remains a major challenge. Through careful reanalysis of ChIP-chip data for 138 TFs obtained in rich media, we were able to classify the upstream promoter regions of S. cerevisiae into 15 distinct chromatin types. One of these encompasses 5% of all promoters and is unique in that it is highly occupied by (essentially) all TFs expressed in rich media. These "hotspots" of TF occupancy are strongly nucleosome-depleted and preferentially targeted by chromatin-remodeling complexes and the origin-of-replication complex (ORC). They are also the only chromatin type enriched for predicted Rap1p and Pdr1p binding sites, which we found to work cooperatively with AAA/TTT motifs, known to affect local DNA structure, to reduce nucleosome occupancy. Taken together, our results reveal and characterize a new type of local chromatin structure in yeast., Comment: This paper has been withdrawn by the author due to a crucial error in the text

Published
2010

17. Optimisation of TP53 reporters by systematic dissection of synthetic TP53 response elements

Author

Trauernicht, Max, Rastogi, Chaitanya, Manzo, Stefano, Bussemaker, Harmen J., and van Steensel, Bas

Subjects
TP53, MPRA, Reporter, Transcription, Sensitivity
Abstract

This deposition contains supplementary data files and laboratory notebooks of the manuscript 'Systematic dissection of the regulatory logic of transcriptional activation by TP53 binding sites'. In this study, thousands of barcoded TP53 reporters were systematically designed and probed in MCF7 and TP53-KO MCF7 cells upon stimulation with Nutlin-3a. Barcodes in the cDNA were quantified by high-throughput sequencing. Among others, the results demonstrate that TP53 drives transcription cooperatively from adjacent TP53 binding sites, and that the positioning of the TP53 binding sites is crucial for transcriptional activation. The files deposited here include: Laboratory notebooks (pdfs printedfrom labguru). This includes the generation of the plasmid pools, the library transfection protocols, and the western blotting procedure. Raw gel images etc. are available in this folder. Clustered barcode count files. These are the raw barcode counts that were extracted from the sequencing files and clustered using starcode. A reporter information sheet. This file includes a table containing all relevant reporter information and reporter sequences. A reporter activity sheet. This file includes the calculated reporter activities and can be used to recreate the figures presented in the manuscript. A supplementary table containing the primer sequences used in this study. &nbsp

Published
2023
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18. Comparative genome sequencing of drosophila pseudoobscura: Chromosomal, gene and cis-element evolution

Author

Richards, Stephen, Liu, Yue, Bettencourt, Brian R., Hradecky, Pavel, Letovsky, Stan, Nielsen, Rasmus, Thornton, Kevin, Todd, Melissa J., Chen, Rui, Meisel, Richard P., Couronne, Olivier, Hua, Sujun, Smith, Mark A., Bussemaker, Harmen J., van Batenburg, Marinus F., Howells, Sally L., Scherer, Steven E., Sodergren, Erica, Matthews, Beverly B., Crosby, Madeline A., Schroeder, Andrew J., Ortiz-Barrientos, Daniel, Rives, Catherine M., Metzker, Michael L., Muzny, Donna M., Scott, Graham, Steffen, David, Wheeler, David A., Worley, Kim C., Havlak, Paul, Durbin, K. James, Egan, Amy, Gill, Rachel, Hume, Jennifer, Morgan, Margaret B., Miner, George, Hamilton, Cerissa, Huang, Yanmei, Waldron, Lenee, Verduzco, Daniel, Blankenburg, Kerstin P., Dubchak, Inna, Noor, Mohamed A.F., Anderson, Wyatt, White, Kevin P., Clark, Andrew G., Schaeffer, Stephen W., Gelbart, William, Weinstock, George M., and Gibbs, Richard A.

Subjects
Applied life sciences
Abstract

The genome sequence of a second fruit fly, D. pseudoobscura, presents an opportunity for comparative analysis of a primary model organism D. melanogaster. The vast majority of Drosophila genes have remained on the same arm, but within each arm gene order has been extensively reshuffled leading to the identification of approximately 1300 syntenic blocks. A repetitive sequence is found in the D. pseudoobscura genome at many junctions between adjacent syntenic blocks. Analysis of this novel repetitive element family suggests that recombination between offset elements may have given rise to many paracentric inversions, thereby contributing to the shuffling of gene order in the D. pseudoobscura lineage. Based on sequence similarity and synteny, 10,516 putative orthologs have been identified as a core gene set conserved over 35 My since divergence. Genes expressed in the testes had higher amino acid sequence divergence than the genome wide average consistent with the rapid evolution of sex-specific proteins. Cis-regulatory sequences are more conserved than control sequences between the species but the difference is slight, suggesting that the evolution of cis-regulatory elements is flexible. Overall, a picture of repeat mediated chromosomal rearrangement, and high co-adaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila.

Published
2004

20. Emerging questions in transcriptional regulation

Author

Nora, Elphège P., primary, Aerts, Stein, additional, Wittkopp, Patricia J., additional, Bussemaker, Harmen J., additional, Bulyk, Martha, additional, Sinha, Saurabh, additional, Zeitlinger, Julia, additional, Crocker, Justin, additional, and Fuxman Bass, Juan Ignacio, additional

Published
2023
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21. Defining the fine structure of promoter activity on a genome-wide scale with CISSECTOR

Author

Fitzpatrick, Vincent D., Leemans, Christ, Van Arensbergen, Joris, Van Steensel, Bas, Bussemaker, Harmen J., Fitzpatrick, Vincent D., Leemans, Christ, Van Arensbergen, Joris, Van Steensel, Bas, and Bussemaker, Harmen J.

Abstract

Classic promoter mutagenesis strategies can be used to study how proximal promoter regions regulate the expression of particular genes of interest. This is a laborious process, in which the smallest sub-region of the promoter still capable of recapitulating expression in an ectopic setting is first identified, followed by targeted mutation of putative transcription factor binding sites. Massively parallel reporter assays such as survey of regulatory elements (SuRE) provide an alternative way to study millions of promoter fragments in parallel. Here we show how a generalized linear model (GLM) can be used to transform genome-scale SuRE data into a high-resolution genomic track that quantifies the contribution of local sequence to promoter activity. This coefficient track helps identify regulatory elements and can be used to predict promoter activity of any sub-region in the genome. It thus allows in silico dissection of any promoter in the human genome to be performed. We developed a web application, available at cissector.nki.nl, that lets researchers easily perform this analysis as a starting point for their research into any promoter of interest.

Published
2023

25. Systematic dissection of the regulatory logic of transcriptional activation by TP53 binding sites

Author

Trauernicht, Max, Rastogi, Chaitanya, Bussemaker, Harmen J., and van Steensel, Bas

Subjects
TP53, MPRA, Reporter, Transcription, Sensitivity
Abstract

This deposition contains supplementary data files and laboratory notebooks of the manuscript 'Systematic dissection of the regulatory logic of transcriptional activation by TP53 binding sites'. In this study, thousands of barcoded TP53 reporters were systematically designed and probed in MCF7 and TP53-KO MCF7 cells upon stimulation with Nutlin-3a. Barcodes in the cDNA were quantified by high-throughput sequencing. Among others, the results demonstrate that TP53 drives transcription cooperatively from adjacent TP53 binding sites, and that the positioning of the TP53 binding sites is crucial for transcriptional activation. The files deposited here include: Laboratory notebooks (pdfs printedfrom labguru). This includes the generation of the plasmid pools, the library transfection protocols, and the western blotting procedure. Raw gel images etc. are available in this folder. Clustered barcode count files. These are the raw barcode counts that were extracted from the sequencing files and clustered using starcode. A reporter information sheet. This file includes a table containing all relevant reporter information and reporter sequences. A reporter activity sheet. This file includes the calculated reporter activities and can be used to recreate the figures presented in the manuscript. A supplementary table containing the primer sequences used in this study. &nbsp

Published
2023
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34. Nuclear Pore Component Nup98 Is a Potential Tumor Suppressor and Regulates Posttranscriptional Expression of Select p53 Target Genes

Author

Singer, Stephan, Zhao, Ruiying, Barsotti, Anthony M., Ouwehand, Anette, Fazollahi, Mina, Coutavas, Elias, Breuhahn, Kai, Neumann, Olaf, Longerich, Thomas, Pusterla, Tobias, Powers, Maureen A., Giles, Keith M., Leedman, Peter J., Hess, Jochen, Grunwald, David, Bussemaker, Harmen J., Singer, Robert H., Schirmacher, Peter, and Prives, Carol

Published
2012
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46. Probing molecular specificity with deep sequencing and biophysically interpretable machine learning

Author

Tomas Rube, H., primary, Rastogi, Chaitanya, additional, Feng, Siqian, additional, Kribelbauer, Judith F., additional, Li, Allyson, additional, Becerra, Basheer, additional, Melo, Lucas A. N., additional, Do, Bach Viet, additional, Li, Xiaoting, additional, Adam, Hammaad H., additional, Shah, Neel H., additional, Mann, Richard S., additional, and Bussemaker, Harmen J., additional

Published
2021
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48. Profiling condition-specific, genome-wide regulation of mRNA stability in yeast

Author

Foat, Barrett C., Houshmandi, S. Sean, Olivas, Wendy M., and Bussemaker, Harmen J.

Subjects
Yeast fungi -- Genetic aspects, Messenger RNA -- Research, Gene expression -- Research, DNA microarrays -- Observations, Science and technology
Abstract

The steady-state abundance of an mRNA is determined by the balance between transcription and decay. Although regulation of transcription has been well studied both experimentally and computationally, regulation of transcript stability has received little attention. We developed an algorithm, MatrixREDUCE, that discovers the position-specific affinity matrices for unknown RNA-binding factors and infers their condition-specific activities, using only genomic sequence data and steady-state mRNA expression data as input. We identified and computationally characterized the binding sites for six mRNA stability regulators in Saccharomyces cerevisiae, which include two members of the Pumilio-homology domain (Puf) family of RNA-binding proteins, Puf3p and Puf4p. We provide computational and experimental evidence that regulation of mRNA stability by these factors is modulated in response to a variety of environmental stimuli. cis-regulatory element | gene expression | microarray | mRNA decay | Puf protein

Published
2005

49. Dissecting complex transcriptional responses using pathway-level scores based on prior information

Author

Ward Lucas D, Bussemaker Harmen J, and Boorsma Andre

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background The genomewide pattern of changes in mRNA expression measured using DNA microarrays is typically a complex superposition of the response of multiple regulatory pathways to changes in the environment of the cells. The use of prior information, either about the function of the protein encoded by each gene, or about the physical interactions between regulatory factors and the sequences controlling its expression, has emerged as a powerful approach for dissecting complex transcriptional responses. Results We review two different approaches for combining the noisy expression levels of multiple individual genes into robust pathway-level differential expression scores. The first is based on a comparison between the distribution of expression levels of genes within a predefined gene set and those of all other genes in the genome. The second starts from an estimate of the strength of genomewide regulatory network connectivities based on sequence information or direct measurements of protein-DNA interactions, and uses regression analysis to estimate the activity of gene regulatory pathways. The statistical methods used are explained in detail. Conclusion By avoiding the thresholding of individual genes, pathway-level analysis of differential expression based on prior information can be considerably more sensitive to subtle changes in gene expression than gene-level analysis. The methods are technically straightforward and yield results that are easily interpretable, both biologically and statistically.

Published
2007
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50. Identification of genes expressed in C. elegans touch receptor neurons

Author

Zhang, Yun, Ma, Charles, Delohery, Thomas, Nasipak, Brian, Foat, Barrett C., Bounoutas, Alexander, Bussemaker, Harmen J., Kim, Stuart K., and Chalfie, Martin

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Yun Zhang [1]; Charles Ma [1]; Thomas Delohery [2, 3]; Brian Nasipak [1]; Barrett C. Foat [1]; Alexander Bounoutas [1]; Harmen J. Bussemaker [1]; Stuart K. Kim [4]; Martin [...]

Published
2002
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