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Status |
Public on Oct 30, 2017 |
Title |
Transfer RNA Genes Affect Chromosome Architecture and Function |
Organism |
Saccharomyces cerevisiae |
Experiment type |
Other
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Summary |
Chromosomes are packaged and organized in the nucleus in an ordered, non-random manner. This organization influences many nuclear processes such as transcription, gene silencing and mitosis. While transfer RNA genes (tDNAs) are essential for the generation of tRNAs these gene loci are also binding sites for transcription factors and chromosomal architectural proteins. In the yeast Saccharomyces cerevisiae, tDNAs are dispersed along all sixteen chromosomes. In this study, we investigated the role of tDNAs in genomic organization and nuclear function by editing a chromosome so that it lacks any tDNAs. Our analyses of this tDNA-less chromosome show that loss of tDNAs affect nucleosome positioning, binding of SMC proteins, centromere clustering, long-range chromosome folding and epigenetic gene silencing. We propose that these effects are primarily mediated via changes in local interactions between tDNAs and other regulatory sequences that then manifest as alterations in long-range chromosome architecture with effects on gene regulation over large distances.
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Overall design |
Chromatin is fragmented by MNase, subsequenct nucleosomal end repair, and a modified two-step method for purfiying ligation products. Using Illumina paired-end sequencing maps Micro-C library and generates nucleosome resolution contact maps.
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Contributor(s) |
Rando OJ, Hsieh TS |
Citation(s) |
30718362 |
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Submission date |
May 04, 2017 |
Last update date |
Jul 25, 2021 |
Contact name |
Xavier Darzacq |
E-mail(s) |
darzacq@berkeley.edu
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Phone |
510-642-0884
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Organization name |
University of California, Berkeley
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Department |
Molecular and Cell Biology
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Lab |
Darzacq Lab
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Street address |
475D Li Ka Shing Center
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City |
Berkeley |
State/province |
CA |
ZIP/Postal code |
94720 |
Country |
USA |
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Platforms (1) |
GPL19756 |
Illumina NextSeq 500 (Saccharomyces cerevisiae) |
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Samples (4)
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Relations |
BioProject |
PRJNA385483 |
SRA |
SRP106463 |
Supplementary file |
Size |
Download |
File type/resource |
GSE98543_RAW.tar |
983.5 Mb |
(http)(custom) |
TAR (of BED, TAR) |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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