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High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts

ABSTRACT: High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts

PROVIDER: PRJNA566357 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10144900.fastq.gz	Fastqsanger.gz
	SRR10145000_1.fastq.gz	Fastqsanger.gz
	SRR10145000_2.fastq.gz	Fastqsanger.gz
	SRR10145100.fastq.gz	Fastqsanger.gz
	SRR10144901.fastq.gz	Fastqsanger.gz

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High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts.

Project description:BackgroundThe start and end sites of messenger RNAs (TSSs and TESs) are highly regulated, often in a cell-type-specific manner. Yet the contribution of transcript diversity in regulating gene expression remains largely elusive. We perform an integrative analysis of multiple highly synchronized cell-fate transitions and quantitative genomic techniques in Saccharomyces cerevisiae to identify regulatory functions associated with transcribing alternative isoforms.ResultsCell-fate transitions feature widespread elevated expression of alternative TSS and, to a lesser degree, TES usage. These dynamically regulated alternative TSSs are located mostly upstream of canonical TSSs, but also within gene bodies possibly encoding for protein isoforms. Increased upstream alternative TSS usage is linked to various effects on canonical TSS levels, which range from co-activation to repression. We identified two key features linked to these outcomes: an interplay between alternative and canonical promoter strengths, and distance between alternative and canonical TSSs. These two regulatory properties give a plausible explanation of how locally transcribed alternative TSSs control gene transcription. Additionally, we find that specific chromatin modifiers Set2, Set3, and FACT play an important role in mediating gene repression via alternative TSSs, further supporting that the act of upstream transcription drives the local changes in gene transcription.ConclusionsThe integrative analysis of multiple cell-fate transitions suggests the presence of a regulatory control system of alternative TSSs that is important for dynamic tuning of gene expression. Our work provides a framework for understanding how TSS heterogeneity governs eukaryotic gene expression, particularly during cell-fate changes.

| S-EPMC7807719 | biostudies-literature

High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-12-15 | GSE137711 | GEO

An alternative transcriptome shapes cell fate transitions in yeast (TES-seq)

Project description:Alternative mRNA isoforms and long noncoding RNAs (lncRNA) make up a large fraction of the transcriptome and play key functions in cell-fate programming. These transcripts often initiate upstream of coding gene promoters from alternative transcription start sites (TSS) where they can regulate gene expression in cis through transcription-coupled chromatin alterations. How, when and where transcription of alternative cis-acting RNAs regulates local gene expression remains poorly understood. Here, we use a high-resolution quantitative approach to study alternative TSS and transcript end site (TES) usage during three different cell fate transitions in yeast: entry into gametogenesis, commitment to meiotic divisions and return to vegetative growth. We propose that an alternative transcriptome of mRNA isoforms and lncRNAs shapes local gene expression during cell fate transitions. Hence, changes in the types and proportions of different RNAs transcribed at a locus are important inputs for gene expression at distinct stages of development.

2020-12-15 | GSE137708 | GEO

An alternative transcriptome shapes cell fate transitions in yeast (TSS-seq)

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An alternative transcriptome shapes cell fate transitions in yeast (mRNA-seq)

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An alternative transcriptome shapes cell fate transitions in yeast (TIF-seq)

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An alternative transcriptome shapes cell fate transitions in yeast (MNase-seq)

2020-12-15 | GSE137709 | GEO

An alternative transcriptome shapes cell fate transitions in yeast (TSS-seq)

Project description:An alternative transcriptome shapes cell fate transitions in yeast (TSS-seq)

| PRJNA566359 | ENA