Search Results - "Müller, Carolin A."

DNA replication timing influences gene expression level by Müller, Carolin A, Nieduszynski, Conrad A

“…Eukaryotic genomes are replicated in a reproducible temporal order; however, the physiological significance is poorly understood. We compared replication…”
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A global profile of replicative polymerase usage by Daigaku, Yasukazu, Keszthelyi, Andrea, Müller, Carolin A, Miyabe, Izumi, Brooks, Tony, Retkute, Renata, Hubank, Mike, Nieduszynski, Conrad A, Carr, Antony M

“…Genome-wide DNA polymerase usage maps determined in fission yeast, using a new sequencing strategy based on ribonucleotide misincorporation, track the division…”
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Conservation of replication timing reveals global and local regulation of replication origin activity by Müller, Carolin A, Nieduszynski, Conrad A

“…DNA replication initiates from defined locations called replication origins; some origins are highly active, whereas others are dormant and rarely used…”
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Kinetochores Coordinate Pericentromeric Cohesion and Early DNA Replication by Cdc7-Dbf4 Kinase Recruitment by Natsume, Toyoaki, Müller, Carolin A., Katou, Yuki, Retkute, Renata, Gierliński, Marek, Araki, Hiroyuki, Blow, J. Julian, Shirahige, Katsuhiko, Nieduszynski, Conrad A., Tanaka, Tomoyuki U.

“…Centromeres play several important roles in ensuring proper chromosome segregation. Not only do they promote kinetochore assembly for microtubule attachment,…”
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Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads by Müller, Carolin A., Boemo, Michael A., Spingardi, Paolo, Kessler, Benedikt M., Kriaucionis, Skirmantas, Simpson, Jared T., Nieduszynski, Conrad A.

“…Replication of eukaryotic genomes is highly stochastic, making it difficult to determine the replication dynamics of individual molecules with existing…”
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DNA copy-number measurement of genome replication dynamics by high-throughput sequencing: the sort-seq, sync-seq and MFA-seq family by Batrakou, Dzmitry G., Müller, Carolin A., Wilson, Rosemary H. C., Nieduszynski, Conrad A.

“…Genome replication follows a defined temporal programme that can change during cellular differentiation and disease onset. DNA replication results in an…”
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Systematic Analysis of Copy Number Variations in the Pathogenic Yeast Candida parapsilosis Identifies a Gene Amplification in RTA3 That is Associated with Drug Resistance by Bergin, Sean A, Zhao, Fang, Ryan, Adam P, Müller, Carolin A, Nieduszynski, Conrad A, Zhai, Bing, Rolling, Thierry, Hohl, Tobias M, Morio, Florent, Scully, Jillian, Wolfe, Kenneth H, Butler, Geraldine

“…We analyzed the genomes of 170 C. parapsilosis isolates and identified multiple copy number variations (CNVs). We identified two genes, ( ) and ( ), each of…”
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Design, construction, and functional characterization of a tRNA neochromosome in yeast by Schindler, Daniel, Walker, Roy S K, Jiang, Shuangying, Brooks, Aaron N, Wang, Yun, Müller, Carolin A, Cockram, Charlotte, Luo, Yisha, García, Alicia, Schraivogel, Daniel, Mozziconacci, Julien, Pena, Noah, Assari, Mahdi, Sánchez Olmos, María Del Carmen, Zhao, Yu, Ballerini, Alba, Blount, Benjamin A, Cai, Jitong, Ogunlana, Lois, Liu, Wei, Jönsson, Katarina, Abramczyk, Dariusz, Garcia-Ruiz, Eva, Turowski, Tomasz W, Swidah, Reem, Ellis, Tom, Pan, Tao, Antequera, Francisco, Shen, Yue, Nieduszynski, Conrad A, Koszul, Romain, Dai, Junbiao, Steinmetz, Lars M, Boeke, Jef D, Cai, Yizhi

“…Here, we report the design, construction, and characterization of a tRNA neochromosome, a designer chromosome that functions as an additional, de novo…”
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The dynamics of genome replication using deep sequencing by Müller, Carolin A, Hawkins, Michelle, Retkute, Renata, Malla, Sunir, Wilson, Ray, Blythe, Martin J, Nakato, Ryuichiro, Komata, Makiko, Shirahige, Katsuhiko, de Moura, Alessandro P S, Nieduszynski, Conrad A

“…Eukaryotic genomes are replicated from multiple DNA replication origins. We present complementary deep sequencing approaches to measure origin location and…”
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Discovery of an Unconventional Centromere in Budding Yeast Redefines Evolution of Point Centromeres by Kobayashi, Norihiko, Suzuki, Yutaka, Schoenfeld, Lori W., Müller, Carolin A., Nieduszynski, Conrad, Wolfe, Kenneth H., Tanaka, Tomoyuki U.

“…Centromeres are the chromosomal regions promoting kinetochore assembly for chromosome segregation. In many eukaryotes, the centromere consists of up to mega…”
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Interspecies conservation of organisation and function between nonhomologous regional centromeres by Tong, Pin, Pidoux, Alison L., Toda, Nicholas R. T., Ard, Ryan, Berger, Harald, Shukla, Manu, Torres-Garcia, Jesus, Müller, Carolin A., Nieduszynski, Conrad A., Allshire, Robin C.

“…Despite the conserved essential function of centromeres, centromeric DNA itself is not conserved. The histone-H3 variant, CENP-A, is the epigenetic mark that…”
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High-Resolution Replication Profiles Define the Stochastic Nature of Genome Replication Initiation and Termination by Hawkins, Michelle, Retkute, Renata, Müller, Carolin A., Saner, Nazan, Tanaka, Tomoyuki U., de Moura, Alessandro P.S., Nieduszynski, Conrad A.

“…Eukaryotic genome replication is stochastic, and each cell uses a different cohort of replication origins. We demonstrate that interpreting high-resolution…”
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Tos4 mediates gene expression homeostasis through interaction with HDAC complexes independently of H3K56 acetylation by Cooke, Sophie L., Soares, Barbara L., Müller, Carolin A., Nieduszynski, Conrad A., Bastos de Oliveira, Francisco M., de Bruin, Robertus A.M.

“…Saccharomyces cerevisiae exhibits gene expression homeostasis, which is defined as the buffering of transcription levels against changes in DNA copy number…”
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A Link between ORC-origin binding mechanisms and origin activation time revealed in budding yeast by Hoggard, Timothy, Shor, Erika, Müller, Carolin A, Nieduszynski, Conrad A, Fox, Catherine A

“…Eukaryotic DNA replication origins are selected in G1-phase when the origin recognition complex (ORC) binds chromosomal positions and triggers molecular events…”
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Sir2 mitigates an intrinsic imbalance in origin licensing efficiency between early- and late-replicating euchromatin by Hoggard, Timothy, Müller, Carolin A., Nieduszynski, Conrad A., Weinreich, Michael, Fox, Catherine A.

“…A eukaryotic chromosome relies on the function of multiple spatially distributed DNA replication origins for its stable inheritance. The spatial location of an…”
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Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome by Shen, Yue, Wang, Yun, Chen, Tai, Gao, Feng, Gong, Jianhui, Abramczyk, Dariusz, Walker, Roy, Zhao, Hongcui, Chen, Shihong, Liu, Wei, Luo, Yisha, Müller, Carolin A., Paul-Dubois-Taine, Adrien, Alver, Bonnie, Stracquadanio, Giovanni, Mitchell, Leslie A., Luo, Zhouqing, Fan, Yanqun, Zhou, Baojin, Wen, Bo, Tan, Fengji, Wang, Yujia, Zi, Jin, Xie, Zexiong, Li, Bingzhi, Yang, Kun, Richardson, Sarah M., Jiang, Hui, French, Christopher E., Nieduszynski, Conrad A., Koszul, Romain, Marston, Adele L., Yuan, Yingjin, Wang, Jian, Bader, Joel S., Dai, Junbiao, Boeke, Jef D., Xu, Xun, Cai, Yizhi, Yang, Huanming

“…Here, we report the successful design, construction, and characterization of a 770-kilobase synthetic yeast chromosome II (synII). Our study incorporates…”
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Environment-dependent fitness gains can be driven by horizontal gene transfer of transporter-encoding genes by Milner, David S., Attah, Victoria, Cook, Emily, Maguire, Finlay, Savory, Fiona R., Morrison, Mark, Müller, Carolin A., Foster, Peter G., Talbot, Nicholas J., Leonard, Guy, Richards, Thomas A.

“…Many microbes acquire metabolites in a “feeding” process where complex polymers are broken down in the environment to their subunits. The subsequent uptake of…”
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Comparative Functional Genomics of the Fission Yeasts by Rhind, Nicholas, Chen, Zehua, Yassour, Moran, Thompson, Dawn A., Haas, Brian J., Habib, Naomi, Wapinski, Ilan, Roy, Sushmita, Lin, Michael F., Heiman, David I., Young, Sarah K., Furuya, Kanji, Guo, Yabin, Pidoux, Alison, Chen, Huei Mei, Robbertse, Barbara, Goldberg, Jonathan M., Aoki, Keita, Bayne, Elizabeth H., Berlin, Aaron M., Desjardins, Christopher A., Dobbs, Edward, Dukaj, Livio, Fan, Lin, FitzGerald, Michael G., French, Courtney, Gujja, Sharvari, Hansen, Klavs, Keifenheim, Dan, Levin, Joshua Z., Mosher, Rebecca A., Müller, Carolin A., Pfiffner, Jenna, Priest, Margaret, Russ, Carsten, Smialowska, Agata, Swoboda, Peter, Sykes, Sean M., Vaughn, Matthew, Vengrova, Sonya, Yoder, Ryan, Zeng, Qiandong, Allshire, Robin, Baulcombe, David, Birren, Bruce W., Brown, William, Ekwall, Karl, Kellis, Manolis, Leatherwood, Janet, Levin, Henry, Margalit, Hanah, Martienssen, Rob, Nieduszynski, Conrad A., Spatafora, Joseph W., Friedman, Nir, Dalgaard, Jacob Z., Baumann, Peter, Niki, Hironori, Regev, Aviv, Nusbaum, Chad

“…The fission yeast clade—comprising Schizosaccharomyces pombe, S. octosporus, S. cryophilus, and S. japonicus—occupies the basal branch of Ascomycete fungi and…”
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OriDB, the DNA replication origin database updated and extended by Siow, Cheuk C., Nieduszynska, Sian R., Müller, Carolin A., Nieduszynski, Conrad A.

“…OriDB (http://www.oridb.org/) is a database containing collated genome-wide mapping studies of confirmed and predicted replication origin sites. The original…”
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High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome by Liti, Gianni, Nguyen Ba, Alex N, Blythe, Martin, Müller, Carolin A, Bergström, Anders, Cubillos, Francisco A, Dafhnis-Calas, Felix, Khoshraftar, Shima, Malla, Sunir, Mehta, Neel, Siow, Cheuk C, Warringer, Jonas, Moses, Alan M, Louis, Edward J, Nieduszynski, Conrad A

“…Comparative genomics is a formidable tool to identify functional elements throughout a genome. In the past ten years, studies in the budding yeast…”
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