Promoting developmental transcription

Ohler, Uwe; Wassarman, David A.

doi:10.1242/dev.035493

Cited by 78 publications

(69 citation statements)

References 132 publications

(64 reference statements)

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“…Core promoter elements use a number of motifs (e.g. TATA, Initiator [INR], and downstream promoter element [DPE]) that are often precisely positioned relative to transcription starts in Drosophila (FitzGerald et al 2006;Ohler 2006;Ohler and Wassarman 2010). These elements direct RNA polymerase to the promoter, but such simple sequence motifs will also appear in random sequence and might be easily generated de novo by mutation.…”

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confidence: 99%

Comparative validation of the D. melanogaster modENCODE transcriptome annotation

et al. 2014

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Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the Drosophila phylogeny by generating draft genomes for eight new species. For comparative transcriptome analysis, we generated mRNA expression profiles on 81 samples from multiple tissues and developmental stages of 15 Drosophila species, and we performed cap analysis of gene expression in D. melanogaster and D. pseudoobscura. We also describe conservation of four distinct core promoter structures composed of combinations of elements at three positions. Overall, each type of genomic feature shows a characteristic divergence rate relative to neutral models, highlighting the value of multispecies alignment in annotating a target genome that should prove useful in the annotation of other high priority genomes, especially human and other mammalian genomes that are rich in noncoding sequences. We report that the vast majority of elements in the annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community.

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confidence: 99%

Comparative validation of the D. melanogaster modENCODE transcriptome annotation

et al. 2014

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“…anticipated diversity of core promoter types and features, which suggests differential core promoter usage by subsets of genes (for reviews, see Müller et al 2007;Goodrich and Tjian 2010;Juven-Gershon and Kadonaga 2010;Ohler and Wassarman 2010;Lenhard et al 2012). The diversity of core promoters may reflect alternative integration points for developmental signals and plays a role in differential transcription regulation (D'Alessio et al 2009;Müller et al 2010).…”

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confidence: 99%

Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

et al. 2013

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Spatiotemporal control of gene expression is central to animal development. Core promoters represent a previously unanticipated regulatory level by interacting with cis-regulatory elements and transcription initiation in different physiological and developmental contexts. Here, we provide a first and comprehensive description of the core promoter repertoire and its dynamic use during the development of a vertebrate embryo. By using cap analysis of gene expression (CAGE), we mapped transcription initiation events at single nucleotide resolution across 12 stages of zebrafish development. These CAGE-based transcriptome maps reveal genome-wide rules of core promoter usage, structure, and dynamics, key to understanding the control of gene regulation during vertebrate ontogeny. They revealed the existence of multiple classes of pervasive intra- and intergenic post-transcriptionally processed RNA products and their developmental dynamics. Among these RNAs, we report splice donor site-associated intronic RNA (sRNA) to be specific to genes of the splicing machinery. For the identification of conserved features, we compared the zebrafish data sets to the first CAGE promoter map of Tetraodon and the existing human CAGE data. We show that a number of features, such as promoter type, newly discovered promoter properties such as a specialized purine-rich initiator motif, as well as sRNAs and the genes in which they are detected, are conserved in mammalian and Tetraodon CAGE-defined promoter maps. The zebrafish developmental promoterome represents a powerful resource for studying developmental gene regulation and revealing promoter features shared across vertebrates.

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“…Together, these factors create a chromatin environment that allows the synthesis of the primary transcript (2). If the transcriptional machinery is defective or challenged due to e.g., transcription-blocking DNA lesions, the process of RNA synthesis halts.…”

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Defective transcription initiation causes postnatal growth failure in a mouse model of nucleotide excision repair (NER) progeria

Kamileri

Karakasilioti

Sideri

et al. 2012

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

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Nucleotide excision repair (NER) defects are associated with cancer, developmental disorders and neurodegeneration. However, with the exception of cancer, the links between defects in NER and developmental abnormalities are not well understood. Here, we show that the ERCC1-XPF NER endonuclease assembles on active promoters in vivo and facilitates chromatin modifications for transcription during mammalian development. We find that Ercc1 −/− mice demonstrate striking physiological, metabolic and gene expression parallels with Taf10 −/− animals carrying a liver-specific transcription factor II D (TFIID) defect in transcription initiation. Promoter occupancy studies combined with expression profiling in the liver and in vitro differentiation cell assays reveal that ERCC1-XPF interacts with TFIID and assembles with POL II and the basal transcription machinery on promoters in vivo. Whereas ERCC1-XPF is required for the initial activation of genes associated with growth, it is dispensable for ongoing transcription. Recruitment of ERCC1-XPF on promoters is accompanied by promoter-proximal DNA demethylation and histone marks associated with active hepatic transcription. Collectively, the data unveil a role of ERCC1/XPF endonuclease in transcription initiation establishing its causal contribution to NER developmental disorders.DNA damage | genetics | metabolism

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Promoting developmental transcription

Cited by 78 publications

References 132 publications

Comparative validation of the D. melanogaster modENCODE transcriptome annotation

Comparative validation of the D. melanogaster modENCODE transcriptome annotation

Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

Defective transcription initiation causes postnatal growth failure in a mouse model of nucleotide excision repair (NER) progeria

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