14 Result(s)
within
A Maxwell Burroughs
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Article
Open AccessThe prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like β-grasp domains
Ubiquitin (Ub)-mediated signaling is one of the hallmarks of all eukaryotes. Prokaryotic homologs of Ub (ThiS and MoaD) and E1 ligases have been studied in relation to sulfur incorporation reactions in thiamin...
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Article
Open AccessA novel superfamily containing the β-grasp fold involved in binding diverse soluble ligands
Domains containing the β-grasp fold are utilized in a great diversity of physiological functions but their role, if any, in soluble or small molecule ligand recognition is poorly studied.
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Article
Open AccessSmall but versatile: the extraordinary functional and structural diversity of the β-grasp fold
The β-grasp fold (β-GF), prototyped by ubiquitin (UB), has been recruited for a strikingly diverse range of biochemical functions. These functions include providing a scaffold for different enzymatic active si...
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Article
Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila
RNA interference (RNAi) is generally associated with post-transcriptional gene silencing, but there is growing evidence that small RNAs and RNAi components also have a role in transcriptional gene silencing in...
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Protocol
Structure and Evolution of Ubiquitin and Ubiquitin-Related Domains
Since its discovery over three decades ago, it has become abundantly clear that the ubiquitin (Ub) system is a quintessential feature of all aspects of eukaryotic biology. At the heart of the system lies the c...
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Chapter
Targeted Methods to Improve Small RNA Profiles Generated by Deep Sequencing
Several recent reviews expertly address the relative merits of different approaches to preparation and analysis of deep-sequenced small RNA libraries. Here, we focus on an array of protocols and tools with the...
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Article
Open AccessTwo novel PIWI families: roles in inter-genomic conflicts in bacteria and Mediator-dependent modulation of transcription in eukaryotes
The PIWI module, found in the PIWI/AGO superfamily of proteins, is a critical component of several cellular pathways including germline maintenance, chromatin organization, regulation of splicing, RNA interfer...
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Article
Open AccessComprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing
The major role of enzymatic toxins that target nucleic acids in biological conflicts at all levels has become increasingly apparent thanks in large part to the advances of comparative genomics. Typically, toxi...
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Article
An atlas of active enhancers across human cell types and tissues
Enhancers control the correct temporal and cell-type-specific activation of gene expression in multicellular eukaryotes. Knowing their properties, regulatory activity and targets is crucial to understand the r...
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Article
Open AccessThe eukaryotic translation initiation regulator CDC123 defines a divergent clade of ATP-grasp enzymes with a predicted role in novel protein modifications
Deciphering the origin of uniquely eukaryotic features of sub-cellular systems, such as the translation apparatus, is critical in reconstructing eukaryogenesis. One such feature is the highly conserved, but po...
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Article
An atlas of human long non-coding RNAs with accurate 5′ ends
Long non-coding RNAs (lncRNAs) are largely heterogeneous and functionally uncharacterized. Here, using FANTOM5 cap analysis of gene expression (CAGE) data, we integrate multiple transcript collections to gener...
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Article
An integrated expression atlas of miRNAs and their promoters in human and mouse
An atlas of microRNA expression patterns and regulators is produced by deep sequencing of short RNAs in human and mouse cells.
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Article
Vms1 and ANKZF1 peptidyl-tRNA hydrolases release nascent chains from stalled ribosomes
Ribosomal surveillance pathways scan for ribosomes that are transiently paused or terminally stalled owing to structural elements in mRNAs or nascent chain sequences1, 2. Some stalls in budding yeast are sensed b...
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Article
Ribosome collisions induce mRNA cleavage and ribosome rescue in bacteria
Ribosome rescue pathways recycle stalled ribosomes and target problematic mRNAs and aborted proteins for degradation1,2. In bacteria, it remains unclear how rescue pathways distinguish ribosomes stalled in the mi...
