Regulation of gene expression by alternative promoters

Ayoubi, Torik; Ven, Wim J.M. Van de

doi:10.1096/fasebj.10.4.8647344

Cited by 335 publications

(231 citation statements)

References 20 publications

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“…The traditional view of a gene with its precisely defined and fixed TSS has been first challenged by the findings that many genes can be transcribed from multiple promoters (alternative promoters) producing functionally diverse transcripts [98,99]. Differential utilization of alternative promoters plays a critical role in regulating gene expression in a spatial, temporal or lineage-specific manner.…”

Section: Promoter Usage Dynamics Across Cell Types and Developmental mentioning

confidence: 99%

Promoter architectures and developmental gene regulation

Haberle

Lenhard

2016

Seminars in Cell & Developmental Biology

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Core promoters are minimal regions sufficient to direct accurate initiation of transcription and are crucial for regulation of gene expression. They are highly diverse in terms of associated core promoter motifs, underlying sequence composition and patterns of transcription initiation.Distinctive features of promoters are also seen at the chromatin level, including nucleosome positioning patterns and presence of specific histone modifications. Recent advances in identifying and characterizing promoters using next-generation sequencing-based technologies have provided the basis for their classification into functional groups and have shed light on their modes of regulation, with important implications for transcriptional regulation in development.This review discusses the methodology and the results of genome-wide studies that provided insight into the diversity of RNA polymerase II promoter architectures in vertebrates and other Metazoa, and the association of these architectures with distinct modes of regulation in embryonic development and differentiation.

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Section: Promoter Usage Dynamics Across Cell Types and Developmental mentioning

confidence: 99%

Promoter architectures and developmental gene regulation

Haberle

Lenhard

2016

Seminars in Cell & Developmental Biology

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“…The few polymorphisms that do exist in basal promoters appear to contribute little to variable gene expression among strains of D. melanogaster (Brown and Feder, 2005). Genes can also contain multiple, alternative promoters that are active under different cellular conditions (Ayoubi and Van De Ven, 1996). The contribution of alternative promoters to regulatory divergence remains unclear.…”

Section: Enhancers Control Patterns Of Gene Expressionmentioning

confidence: 99%

Evolution of cis-regulatory sequence and function in Diptera

Wittkopp

2006

Heredity

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Cis-regulatory sequences direct patterns of gene expression essential for development and physiology. Evolutionary changes in these sequences contribute to phenotypic divergence. Despite their importance, cis-regulatory regions remain one of the most enigmatic features of the genome. Patterns of sequence evolution can be used to identify cisregulatory elements, but the power of this approach depends upon the relationship between sequence and function. Comparative studies of gene regulation among Diptera reveal that divergent sequences can underlie conserved expression, and that expression differences can evolve despite largely similar sequences. This complex structure-function relationship is the primary impediment for computational identification and interpretation of cis-regulatory sequences. Biochemical characterization and in vivo assays of cis-regulatory sequences on a genomic-scale will relieve this barrier.

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“…Like many other globin genes (24,31), the sequences of the TATA boxes of the N. coriiceps promoters deviate from the vertebrate canon, TATAAA (33). The use of alternative promoters and multiple transcription initiation sites to regulate gene expression in eukaryotes is now recognized to be a common phenomenon (37). For example, Hu et al (38) have shown that tissue-specific expression of prolactin receptors in the rat is controlled by three promoters, two of which contain noncanonical TATA elements.…”

Section: ␣-Globin Gene Remnants In Antarctic Icefishesmentioning

confidence: 99%

The Major Adult α-Globin Gene of Antarctic Teleosts and Its Remnants in the Hemoglobinless Icefishes

Zhao¹,

Ratnayake-Lecamwasam²,

Parker³

et al. 1998

Journal of Biological Chemistry

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The icefishes of the Southern Ocean (family Channichthyidae, suborder Notothenioidei) are unique among vertebrates in their inability to synthesize hemoglobin. We have shown previously (Cocca, E., Ratnayake-Lecamwasam, M., Parker, S. K., Camardella, L., Ciaramella, M., di Prisco, G., and Detrich, H. W., III (1995) Proc. Natl. Acad. Sci. U. S. A. 92, 1817-1821) that icefishes retain inactive genomic remnants of adult notothenioid ␣-globin genes but have lost the gene that encodes adult ␤-globin. Here we demonstrate that loss of expression of the major adult ␣-globin, ␣1, in two species of icefish (Chaenocephalus aceratus and Chionodraco rastrospinosus) results from truncation of the 5 end of the notothenioid ␣1-globin gene. The wild-type, functional ␣1-globin gene of the Antarctic yellowbelly rockcod, Notothenia coriiceps, contains three exons and two A ؉ T-rich introns, and its expression may be controlled by two or three distinct promoters. Retained in both icefish genomes are a portion of intron 2, exon 3, and the 3-untranslated region of the notothenioid ␣1-globin gene. The residual, nonfunctional ␣-globin gene, no longer under positive selection pressure for expression, has apparently undergone random mutational drift at an estimated rate of 0.12-0.33%/million years. We propose that abrogation of hemoglobin synthesis in icefishes most likely resulted from a single mutational event in the ancestral channichthyid that deleted the entire ␤-globin gene and the 5 end of the linked ␣1-globin gene.

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Regulation of gene expression by alternative promoters

Cited by 335 publications

References 20 publications

Promoter architectures and developmental gene regulation

Promoter architectures and developmental gene regulation

Evolution of cis-regulatory sequence and function in Diptera

The Major Adult α-Globin Gene of Antarctic Teleosts and Its Remnants in the Hemoglobinless Icefishes

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