High-resolution transcription atlas of the mitotic cell cycle in budding yeast

Granovskaia, Marina; Jensen, Lars Juhl; Ritchie, Matthew E.; Toedling, Joern; Ye, Ning; Bork, Peer; Huber, Wolfgang; Steinmetz, Lars M.

doi:10.1186/gb-2010-11-3-r24

Cited by 107 publications

(161 citation statements)

References 58 publications

Supporting

Mentioning

151

Contrasting

Order By: Relevance

“…This includes repression of mitotic genes incompatible with meiotic development, activation of genes specifically needed for meiosis and gametogenesis, and adaptation of cell cycle-regulated loci to the meiotic divisions. Although such regulatory functions have typically been attributed to DNA binding transcriptional activators and repressors (27,28), a number of mitotic ncRNAs were recently shown to positively or negatively influence gene expression via changes of histone modification or transcriptional interference (17,(29)(30)(31)(32). It is therefore conceivable that developmentally regulated ncRNAs such as MUTs contribute to the control of genes required for, for example, cytokinesis (CHS2) and the mitotic cell cycle (CLN3, HUG1) through similar mechanisms.…”

Section: Discussionmentioning

confidence: 99%

Execution of the meiotic noncoding RNA expression program and the onset of gametogenesis in yeast require the conserved exosome subunit Rrp6

Lardenois

Liu

Walther

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

126

217

View full text Add to dashboard Cite

Budding yeast noncoding RNAs (ncRNAs) are pervasively transcribed during mitosis, and some regulate mitotic protein-coding genes. However, little is known about ncRNA expression during meiotic development. Using high-resolution profiling we identified an extensive meiotic ncRNA expression program interlaced with the protein-coding transcriptome via sense/antisense transcript pairs, bidirectional promoters, and ncRNAs that overlap the regulatory regions of genes. Meiotic unannotated transcripts (MUTs) are mitotic targets of the conserved exosome component Rrp6, which itself is degraded after the onset of meiosis when MUTs and other ncRNAs accumulate in successive waves. Diploid cells lacking Rrp6 fail to initiate premeiotic DNA replication normally and cannot undergo efficient meiotic development. The present study demonstrates a unique function for budding yeast Rrp6 in degrading distinct classes of meiotically induced ncRNAs during vegetative growth and the onset of meiosis and thus points to a critical role of differential ncRNA expression in the execution of a conserved developmental program.

show abstract

Section: Discussionmentioning

confidence: 99%

Execution of the meiotic noncoding RNA expression program and the onset of gametogenesis in yeast require the conserved exosome subunit Rrp6

Lardenois

Liu

Walther

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

126

217

View full text Add to dashboard Cite

show abstract

“…Antisense transcription is emerging as an important means by which sense transcription is repressed (Camblong et al 2007;Granovskaia et al 2010). For instance, IME4, a proposed master regulator of the entry into meiosis, is repressed in mitotically growing cells via antisense transcription (Hongay et al 2006).…”

Section: Antisense Repression Of Meiotic Genesmentioning

confidence: 99%

Stable and dynamic nucleosome states during a meiotic developmental process

Zhang

Mā²,

Pugh³

2011

Genome Res.

View full text Add to dashboard Cite

The plasticity of chromatin organization as chromosomes undergo a full compendium of transactions including DNA replication, recombination, chromatin compaction, and changes in transcription during a developmental program is unknown. We generated genome-wide maps of individual nucleosome organizational states, including positions and occupancy of all nucleosomes, and H3K9 acetylation and H3K4, K36, K79 tri-methylation, during meiotic spore development (gametogenesis) in Saccharomyces. Nucleosome organization was remarkably constant as the genome underwent compaction. However, during an acute meiotic starvation response, nucleosomes were repositioned to alter the accessibility of select transcriptional start sites. Surprisingly, the majority of the meiotic programs did not use this nucleosome repositioning, but was dominated by antisense control. Histone modification states were also remarkably stable, being abundant at specific nucleosome positions at three-quarters of all genes, despite most genes being rarely transcribed. Our findings suggest that, during meiosis, the basic features of genomic chromatin organization are essentially a fixed property of chromosomes, but tweaked in a restricted and program-specific manner.

show abstract

“…Note that the data shown, which cover one mitotic cycle, are part of a larger experiment reported in reference. 24 (B) A heatmap shows RNA-Sequencing data for 3 wild type strains (WT S288C, W303 and SK1) and corresponding strains lacking Xrn1 activity (xrn1) given to the left. All strains are haploid unless their DNA content is indicated (2n).…”

Section: Divergent Promoters Driving Isoforms Pair Them With Ubiquitomentioning

confidence: 99%

“…9,23,24 Initially, we focused on meiotic lncRNAs and later on developmentally regulated transcript isoforms with extended 5 0 -UTRs. Published tiling array data are available at the ReproGenomics Viewer (RGV, rgv.genouest.org; Fig.…”

Section: Datasets and Experimental Rationalementioning

confidence: 99%

“…7 Published Sc_tlg GeneChip data from single samples of synchronized cells undergoing mitotic growth and division were obtained with the W101 MATa strain. 24 Mitotic gene expression is typically studied in haploid cells because of well-established cell synchronization protocols. 36,37 Graphical displays of tiling array data are available online at SGV (Saccharomyces Genome Viewer, sgv.genouest.org 26 ) and RGV (ReproGenomics Viewer, rgv.genouest.org 25 ).…”

Section: Yeast Sc_tlg Tiling Array Data and Rna-sequencing Datamentioning

confidence: 99%

See 1 more Smart Citation

Ndt80 activates the meiotic ORC1 transcript isoform and SMA2 via a bi-directional middle sporulation element in Saccharomyces cerevisiae

Xie

Horecka²,

Chu³

et al. 2016

RNA Biology

View full text Add to dashboard Cite

The origin of replication complex subunit ORC1 is important for DNA replication. The gene is known to encode a meiotic transcript isoform (mORC1) with an extended 5 0 -untranslated region (5 0 -UTR), which was predicted to inhibit protein translation. However, the regulatory mechanism that controls the mORC1 transcript isoform is unknown and no molecular biological evidence for a role of mORC1 in negatively regulating Orc1 protein during gametogenesis is available. By interpreting RNA profiling data obtained with growing and sporulating diploid cells, mitotic haploid cells, and a starving diploid control strain, we determined that mORC1 is a middle meiotic transcript isoform. Regulatory motif predictions and genetic experiments reveal that the activator Ndt80 and its middle sporulation element (MSE) target motif are required for the full induction of mORC1 and the divergently transcribed meiotic SMA2 locus. Furthermore, we find that the MSE-binding negative regulator Sum1 represses both mORC1 and SMA2 during mitotic growth. Finally, we demonstrate that an MSE deletion strain, which cannot induce mORC1, contains abnormally high Orc1 levels during post-meiotic stages of gametogenesis. Our results reveal the regulatory mechanism that controls mORC1, highlighting a novel developmental stage-specific role for the MSE element in bi-directional mORC1/SMA2 gene activation, and correlating mORC1 induction with declining Orc1 protein levels. Because eukaryotic genes frequently encode multiple transcripts possessing 5 0 -UTRs of variable length, our results are likely relevant for gene expression during development and disease in higher eukaryotes.

show abstract

High-resolution transcription atlas of the mitotic cell cycle in budding yeast

Abstract: A high resolution strand-specific transcriptional atlas of the budding yeast mitotic cell cycle, including both mRNA and non-coding RNA profiles.

Cited by 107 publications

References 58 publications

Execution of the meiotic noncoding RNA expression program and the onset of gametogenesis in yeast require the conserved exosome subunit Rrp6

Execution of the meiotic noncoding RNA expression program and the onset of gametogenesis in yeast require the conserved exosome subunit Rrp6

Stable and dynamic nucleosome states during a meiotic developmental process

Ndt80 activates the meiotic ORC1 transcript isoform and SMA2 via a bi-directional middle sporulation element in Saccharomyces cerevisiae

Contact Info

Product

Resources

About