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A short ORF-encoded transcriptional regulator

ABSTRACT: A short ORF-encoded transcriptional regulator

PROVIDER: PRJNA689606 | ENA |

REPOSITORIES: ENA

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A short ORF-encoded transcriptional regulator

Project description:Recent technological advances have expanded the annotated protein coding content of mammalian genomes, as hundreds of previously unidentified, short open reading frame (ORF)-encoded peptides (SEPs) have now been found to be translated. Although several studies have identified important physiological roles for this emerging protein class, a general method to define their interactomes is lacking. Here, we demonstrate that genetic incorporation of the photo-crosslinking noncanonical amino acid AbK into SEP transgenes allows for the facile identification of SEP cellular interaction partners using affinity-based methods. From a survey of seven SEPs, we report the discovery of short ORF-encoded histone binding protein (SEHBP), a conserved microprotein that interacts with chromatin-associated proteins, localizes to discrete genomic loci, and induces a robust transcriptional program when overexpressed in human cells. This work affords a straightforward method to help define the physiological roles of SEPs and demonstrates its utility by identifying SEHBP as a short ORF-encoded transcription factor.

2021-01-11 | GSE164239 | GEO

A short ORF-encoded transcriptional regulator.

Project description: Not available

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Transcriptional response to overexpressing Vibrio Seventh Pandemic -II island encoded genes

Project description:Purpose: to characterize the regulatory targets of an AraC-like transcriptional regulator (VC0513) encoded on the Vibrio Seventh Pandemic Island -II (VSP-II) in V. cholerae O1 El Tor N16961 Methods: RNA was isolated from a wild-type N16961 carrying an IPTG-inducible copy of vc0513, vc0515, or an empty vector control Results: vc0513 induction significantly increased expression of other VSP-II encoded genes relative to the empty vector control Conclusions: our study represents the first analysis of a transcriptional regulator encoded on the VSP-II island

2021-05-08 | GSE174028 | GEO

Orf virus

Project description:Orf virus Genome sequencing

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Upstream ORF-encoded ASDURF is a novel prefoldin-like subunit of the PAQosome

Project description:The PAQosome is an eleven-subunit chaperone involved in the biogenesis of several human protein complexes. We show that ASDURF, a recently discovered upstream open reading frame (uORF) in the 5’ UTR of ASNSD1 mRNA, encodes the twelfth subunit of the PAQosome. ASDURF, displays significant structural homology to beta-prefoldins and assembles with the five known subunits of the prefoldin-like module of the PAQosome to form a heterohexameric prefoldin-like complex. A model of the PAQosome prefoldin-like module is presented. The data presented here provides an example of ana eukaryotic uORF-encoded polypeptide whose function is not limited to cis-acting translational regulation of downstream coding sequence and highlights the importance of including alternative ORF products in proteomic studies.

2019-11-25 | PXD015848 | Pride

Orf virus

Project description:Orf virus Genome sequencing and assembly

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Orf virus

Project description:Orf virus Genome sequencing and assembly

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ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF

Project description:Gene expression is orchestrated by transcription factors (TFs), which bind to DNA in a sequence-specific manner, and by spatial genome structure, which constrains and shapes TF activity. Zinc finger protein 143 (ZNF143/ZFP143) is a TF that has been implicated in both gene activation and 3D genome organisation. We have generated an acute ZNF143/ZFP143 depletion system to study its direct consequences on chromatin looping and gene transcription. The effects of ZNF143/ZFP143 depletion are inconsistent with it being a looping factor, which we further confirmed by systematic analysis of previous studies. However, degradation of ZNF143/ZFP143 led to the down-regulation of hundreds of its targets, which were found to be enriched in nuclear-encoded mitochondrial genes. By studying the consequences of ZNF143/ZFP143 loss in monoculture and in an in vitro embryonic development model, we establish ZNF143/ZFP143 as a conserved transcriptional regulator of cell proliferation and differentiation by modulating mitochondrial functions.

2024-03-08 | PXD049480 | Pride

The Msn2/4-like gene transcription factor Com2 (ORF YER130) is a key player of S. cerevisiae response and tolerance to sulphur dioxide

Project description:Sulphur dioxide (SO2) and its derivatives are widely used as preservatives in food and beverage industries to assure the maintenance of microbiological quality of their products. In this work it is shown, for the first time, the essential role played by the transcriptional regulator Com (ORF YER130c) in S. cerevisiae response and tolerance to SO2, this being the first biological function attributed for this regulator.

2019-11-04 | GSE117883 | GEO

Hemotin, a Regulator of Phagocytosis Encoded by a Small ORF and Conserved across Metazoans.

Project description: Not available

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