Nucleosome rotational setting is associated with transcriptional regulation in promoters of tissue-specific human genes

Human genes contain a 10 bp repeat of RR dinucleotides focused around the first nucleosome position suggesting a role in transcriptional control

Needed for completion of the human genome: hypothesis driven experiments and biologically realistic mathematical models

With the sponsorship of ``Fundacio La Caixa'' we met in Barcelona, November 21st and 22nd, to analyze the reasons why, after the completion of the human genome sequence, the identification all protein coding genes and their variants remains a distant goal. Here we report on our discussions and summarize some of the major challenges that need to be overcome in order to complete the human gene catalog.Comment: Report and discussion resulting from the `Fundacio La Caixa' gene finding meeting held November 21 and 22 2003 in Barcelon

Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes

Summary: Comparative genomics remains a pivotal strategy to study the evolution of gene organization, and this primacy is reinforced by the growing number of full genome sequences available in public repositories. Despite this growth, bioinformatic tools available to visualize and compare genomes and to infer evolutionary events remain restricted to two or three genomes at a time, thus limiting the breadth and the nature of the question that can be investigated. Here we present Genomicus, a new synteny browser that can represent and compare unlimited numbers of genomes in a broad phylogenetic view. In addition, Genomicus includes reconstructed ancestral gene organization, thus greatly facilitating the interpretation of the data

GC content shapes mRNA storage and decay in human cells.

mRNA translation and decay appear often intimately linked although the rules of this interplay are poorly understood. In this study, we combined our recent P-body transcriptome with transcriptomes obtained following silencing of broadly acting mRNA decay and repression factors, and with available CLIP and related data. This revealed the central role of GC content in mRNA fate, in terms of P-body localization, mRNA translation and mRNA stability: P-bodies contain mostly AU-rich mRNAs, which have a particular codon usage associated with a low protein yield; AU-rich and GC-rich transcripts tend to follow distinct decay pathways; and the targets of sequence-specific RBPs and miRNAs are also biased in terms of GC content. Altogether, these results suggest an integrated view of post-transcriptional control in human cells where most translation regulation is dedicated to inefficiently translated AU-rich mRNAs, whereas control at the level of 5' decay applies to optimally translated GC-rich mRNAs

Megasatellites: a peculiar class of giant minisatellites in genes involved in cell adhesion and pathogenicity in Candida glabrata

Minisatellites are DNA tandem repeats that are found in all sequenced genomes. In the yeast Saccharomyces cerevisiae, they are frequently encountered in genes encoding cell wall proteins. Minisatellites present in the completely sequenced genome of the pathogenic yeast Candida glabrata were similarly analyzed, and two new types of minisatellites were discovered: minisatellites that are composed of two different intermingled repeats (called compound minisatellites), and minisatellites containing unusually long repeated motifs (126–429 bp). These long repeat minisatellites may reach unusual length for such elements (up to 10 kb). Due to these peculiar properties, they have been named ‘megasatellites’. They are found essentially in genes involved in cell–cell adhesion, and could therefore be involved in the ability of this opportunistic pathogen to colonize the human host. In addition to megasatellites, found in large paralogous gene families, there are 93 minisatellites with simple shorter motifs, comparable to those found in S. cerevisiae. Most of the time, these minisatellites are not conserved between C. glabrata and S. cerevisiae, although their host genes are well conserved, raising the question of an active mechanism creating minisatellites de novo in hemiascomycetes

Definition of the Gene Content of the Human Genome: The Need for Deep Experimental Verification

Based on the analysis of the drafts of the human genome sequence, it is being speculated that our species may possess an unexpectedly low number of genes. The quality of the drafts, the impossibility of accurate gene prediction and the lack of sufficient transcript sequence data, however, render such speculations very premature. The complexity of human gene structure requires additional and extensive experimental verification of transcripts that may result in major revisions of these early estimates of the number of human genes