Roles of cofactors and chromatin accessibility in Hox protein target specificity.

Background: The regulation of specific target genes by transcription factors is central to our understanding of gene network control in developmental and physiological processes yet how target specificity is achieved is still poorly understood. This is well illustrated by the Hox family of transcription factors as their limited in vitro DNA-binding specificity contrasts with their clear in vivo functional specificity.

Results: We generated genome-wide binding profiles for three Hox proteins, Ubx, Abd-A and Abd-B, following transient expression in Drosophila Kc167 cells, revealing clear target specificity and a striking influence of chromatin accessibility.

Characterisation of Drosophila Ubx CPTI000601 and hth CPTI000378 protein trap lines.

In Drosophila, protein trap strategies provide powerful approaches for the generation of tagged proteins expressed under endogenous control. Here, we describe expression and functional analysis to evaluate new Ubx and hth protein trap lines generated by the Cambridge Protein Trap project. Both protein traps exhibit spatial and temporal expression patterns consistent with the reported endogenous pattern in the embryo.

VibrioBase: a model for next-generation genome and annotation database development.

To facilitate the ongoing research of Vibrio spp., a dedicated platform for the Vibrio research community is needed to host the fast-growing amount of genomic data and facilitate the analysis of these data. We present VibrioBase, a useful resource platform, providing all basic features of a sequence database with the addition of unique analysis tools which could be valuable for the Vibrio research community.

MabsBase: a Mycobacterium abscessus genome and annotation database.

Mycobacterium abscessus is a rapidly growing non-tuberculous mycobacterial species that has been associated with a wide spectrum of human infections. As the classification and biology of this organism is still not well understood, comparative genomic analysis on members of this species may provide further insights on their taxonomy, phylogeny, pathogenicity and other information that may contribute to better management of infections. The MabsBase described in this paper is a user-friendly database providing access to whole-genome sequences of newly discovered M.

Whole-Genome Shotgun Sequencing of Mycobacterium abscessus M156, an Emerging Clinical Pathogen in Malaysia.

Mycobacterium abscessus is an emerging clinical pathogen commonly associated with non-tuberculous mycobacterial infections. We report herein the draft genome of M. abscessus strain M156.