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Series GSE98543 Query DataSets for GSE98543
Status Public on Oct 30, 2017
Title Transfer RNA Genes Affect Chromosome Architecture and Function
Organism Saccharomyces cerevisiae
Experiment type Other
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.
 
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.
 
Contributor(s) Rando OJ, Hsieh TS
Citation(s) 30718362
Submission date May 04, 2017
Last update date Jul 25, 2021
Contact name Xavier Darzacq
E-mail(s) darzacq@berkeley.edu
Phone 510-642-0884
Organization name University of California, Berkeley
Department Molecular and Cell Biology
Lab Darzacq Lab
Street address 475D Li Ka Shing Center
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
 
Platforms (1)
GPL19756 Illumina NextSeq 500 (Saccharomyces cerevisiae)
Samples (4)
GSM2598434 tDNA2334_rep1
GSM2598435 tDNA690_rep1
GSM2598436 tDNA2334_rep2
Relations
BioProject PRJNA385483
SRA SRP106463

Download family Format
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Supplementary file Size Download File type/resource
GSE98543_RAW.tar 983.5 Mb (http)(custom) TAR (of BED, TAR)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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