Transcription of Two Long Noncoding RNAs Mediates Mating-Type Control of Gametogenesis in Budding Yeast

Werven, Folkert J. van; Neuert, Gregor; Hendrick, Natalie; Lardenois, Aurélie; Buratowski, Stephen; Oudenaarden, Alexander van; Primig, Michael; Amon, Angelika

doi:10.1016/j.cell.2012.06.049

Cited by 237 publications

(315 citation statements)

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“…108 Repression FLO11 Cell surface glycoprotein NO PWR1. 108 Upregulation FLO11 Cell surface glycoprotein NO IME4 AS RNA 109,110 Repression IME4 Meiosis regulator NO IRT1. 109 Repression IME1 Meiosis regulator NO "non-coding" with caution until a much larger subset of these molecules have been functionally validated.…”

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confidence: 99%

“…108 Upregulation FLO11 Cell surface glycoprotein NO IME4 AS RNA 109,110 Repression IME4 Meiosis regulator NO IRT1. 109 Repression IME1 Meiosis regulator NO "non-coding" with caution until a much larger subset of these molecules have been functionally validated. Aberrant expression of lncRNAs is associated with various diseases such as prostate cancer, 89 breast cancer, 90 HIV, 91 Type-2 diabetes, 92,93 and obesity, 93,94 underscoring a need for understanding the precise roles of lncRNAs.…”

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confidence: 99%

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LncRNAs: Bridging environmental sensing and gene expression

2016

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The survival of all organisms is dependent on complex, coordinated responses to environmental cues. Non-coding RNAs have been identified as major players in regulation of gene expression, with recent evidence supporting roles for long non-coding (lnc)RNAs in both transcriptional and post-transcriptional control. Evidence from our laboratory shows that lncRNAs have the ability to form hybridized structures called R-loops with specific DNA target sequences in S. cerevisiae, thereby modulating gene expression. In this Point of View, we provide an overview of the nature of lncRNA-mediated control of gene expression in the context of our studies using the GAL gene cluster as a model for controlling the timing of transcription.

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confidence: 99%

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LncRNAs: Bridging environmental sensing and gene expression

2016

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“…8). In addition, it is conceivable that SMA2 expression is partially inhibited during mitosis by SUT292 and XUT1538 via well-established antisense-and promoter interference mechanisms 32,33 ; for review see reference. 34 A new role for Ndt80 in the activation of a meiotic transcript isoform that inhibits translation One might expect ORC1 to be transcriptionally repressed when cells exit pre-meiotic DNA replication, because there is no further need for assembling an origin recognition complex at autonomously replicating sequence (ARS) elements.…”

Section: Establishing Developmental Stage-specific Middle Meiotic Isomentioning

confidence: 99%

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

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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.

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“…To answer this question, Amon and colleagues, in a study published in Cell [11], used the classical genetic model of mating-type control of sporulation in yeast. Upon nutrient deprivation, diploid yeast cells undergo meiosis resulting in the production of four haploid gametes housed in stress-resistant spores.…”

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“…Precisely how a transcription factor, known to activate gene transcription, is involved in the repression of a gene ~2 kb downstream was not clearly understood. van Werven et al [11] tackled this question in a systematic manner beginning with the identification of a stable un-annotated transcript (SUT), IRT1 (IME1 regulatory transcript 1) regulated by Rme1. The expression of IRT1 anti-correlated with that of IME1, and was reduced upon induction of sporulation in diploid cells.…”

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Non-coding transcription SETs up regulation

Venkatesh

Workman

2012

Cell Res

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npg An abundance of long non-coding RNA (lncRNA) present in most species from yeast to human are involved in transcriptional regulation, dosage compensation and imprinting. This underscores the importance of lncRNA as functional RNA despite the fact that they do not produce proteins. Two recent papers in Cell have demonstrated that transcription of the non-conserved lncRNAs, but not the RNAs themselves, is necessary to introduce co-transcriptional regulatory histone marks to regulate gene expression.Transcription over a chromatin template is modulated by a number of post-translational modifications. Histone acetylation is a key activating mark that facilitates access to the DNA not only by impairing the ability of nucleosomes to bind the DNA tightly, but also by recruiting factors that aid the movement of the nucleosomes in cis or in trans. Therefore, in order to achieve a tight control over gene expression, it is imperative that the acetylation marks must be removed by histone lysine deacetylases (KDACs). While promoter acetylation is removed by the targeted recruitment of KDACs by repressor proteins, acetylation over the gene body is removed in a co-transcriptional manner. Studies from several labs have identified two RNA polymerase II (RNAPII)-associated KDAC complexes [1] that act on the 5′ (SET3 complex) and 3′ (Rpd3S complex) ends of gene bodies ( Figure 1A), maintaining nucleosomes in a hypoacetylated state [2,3]. The specificity of targeting these deacetylases to specific regions of the gene body is achieved by the differential

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Transcription of Two Long Noncoding RNAs Mediates Mating-Type Control of Gametogenesis in Budding Yeast

Cited by 237 publications

References 54 publications

LncRNAs: Bridging environmental sensing and gene expression

LncRNAs: Bridging environmental sensing and gene expression

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

Non-coding transcription SETs up regulation

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