Sequence simplicity and evolution of the 3′ untranslated region of the histone H1° Gene

The H1° gene has a long 3′ untranslated region (3′UTR) of 1,125 nucleotides in the rat and 1,310 in humans. Analysis of the sequences shows that they have features of simple DNA that suggest involvement of replication slippage in their evolution. These features include the length imbalance between the rat and human sequences; the abundance of single-base repeats, two-base runs and other simple motifs clustered along the sequence; and the presence of single-base repeat length polymorphisms in the rat and mouse sequences. Pairwise comparisons show numerous short insertions/deletions, often flanked by direct repeats. In addition, a proportion of short insertions/deletions results from length differences in conserved single-base repeats. Quantification of the sequence simplicity shows that simple sequences have been more actively incorporated in the human lineage than in the rodent lineage. The combination of insertions/deletions and nucleotide substitutions along the sequence gives rise to three main regions of homology: a highly variable central region flanked by more conserved regions nearest the coding region and the polyA addition site. Correspondence to: P. Suau     

Seasonal variations of changes in lipid and glucidic variables after bariatric surgery

Seasonality is a phenomenon that is characterized by changes over the year in sleep, mood, behaviour, appetite and body weight. In humans, seasonal variations have been found in certain variables, such as lipid variables and body mass index. We hypothesize that this rhythm could influence the expected variation of the levels of biochemical variables in cases of body weight loss. Thus, the goal of this study was to observe whether the time of year in which bariatric surgery (BS) took place modulated the changes in several variables related to glucidic and lipid metabolism. Blood samples were obtained from 24 women and 10 men before BS and 1 and 3 months after BS. We calculated the percentage of variation that occurred for each individual and for each variable as a function of the time of the year. Data were adjusted to a 12-month period sinusoidal curve, with significance being set at p < 0.05. The results showed that almost all of the studied variables changed due to the BS according to a seasonal rhythm. Most of the variables showed a decrease that was most prominent in winter. In the cases of body mass index (BMI), adrenocorticotropin hormone (ACTH), and cortisol, the highest variation occurred in winter. Insulin and cholesterol in high-density lipoproteins (cHLD) variations were higher in springtime. Glucose variation showed a decrease after surgery with acrophase in summer-fall and plasminogen activator inhibitor-1 (PAI-1) and homeostatic model assessment-insulin resistance (HOMA-IR) in spring-summer. Ghrelin levels showed increases with a rhythm of variation with an acrophase in summer-fall. The seasonal rhythm found in this study fits nearly with the inverse of the endogenous circannual rhythm of the variables studied. The time of the year when the highest variation takes place is related to the circannual rhythm of the variable. The results agree with the manifestation of seasonal rhythm in human biochemical variables, which are reflected in the responses to weight loss after BS.     

Sequence complexity of histone H1 subtypes

H1 subtypes are involved in chromatin higher-order structure and gene regulation. H1 has a characteristic three-domain structure. We studied the length variation of the available H1 subtypes and showed that the length of the N-terminal and C-terminal domains was more variable than that of the central domain. The N-terminal and C-terminal domains were of low sequence complexity both at the nucleotide and at the amino acid level, whereas the globular domain was of high complexity. In most subtypes, low complexity was due only to cryptic simplicity, which reflects the clustering of a number of short and often imperfect sequence motifs. However, a subset of subtypes from eubacteria, plants, and invertebrates contained tandem repeats of short amino acid motifs (four to 12 residues), which could amount to a large proportion of the terminal domains. In addition, some other subtypes, such as those of Drosophila and mammalian H1t, were only marginally simple. The coexistence of these three kinds of subtypes suggests that the terminal domains could have originated in the amplification of short sequence motifs, which would then have evolved by point mutation and further slippage.     

Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut.

The human intestinal tract harbors a complex microbial ecosystem which plays a key role in nutrition and health. Although this microbiota has been studied in great detail by culture techniques, microscopic counts on human feces suggest that 60 to 80% of the observable bacteria cannot be cultivated. Using comparative analysis of cloned 16S rRNA gene (rDNA) sequences, we have investigated the bacterial diversity (both cultivated and noncultivated bacteria) within an adult-male fecal sample. The 284 clones obtained from 10-cycle PCR were classified into 82 molecular species (at least 98% similarity). Three phylogenetic groups contained 95% of the clones: the Bacteroides group, the Clostridium coccoides group, and the Clostridium leptum subgroup. The remaining clones were distributed among a variety of phylogenetic clusters. Only 24% of the molecular species recovered corresponded to described organisms (those whose sequences were available in public databases), and all of these were established members of the dominant human fecal flora (e.g., Bacteroides thetaiotaomicron, Fusobacterium prausnitzii, and Eubacterium rectale). However, the majority of generated rDNA sequences (76%) did not correspond to known organisms and clearly derived from hitherto unknown species within this human gut microflora.     

Forced desynchronization of dual circadian oscillators within the rat suprachiasmatic nucleus

The circadian clock in the suprachiasmatic nucleus of the hypothalamus (SCN) contains multiple autonomous single-cell circadian oscillators and their basic intracellular oscillatory mechanism is beginning to be identified. Less well understood is how individual SCN cells create an integrated tissue pacemaker that produces a coherent read-out to the rest of the organism. Intercellular coupling mechanisms must coordinate individual cellular periods to generate the averaged, genotype-specific circadian period of whole animals. To noninvasively dissociate this circadian oscillatory network in vivo, we (T.C. and A.D.-N.) have developed an experimental paradigm that exposes animals to exotic light-dark (LD) cycles with periods close to the limits of circadian entrainment. If individual oscillators with different periods are loosely coupled within the network, perhaps some of them would be synchronized to the external cycle while others remain unentrained. In fact, rats exposed to an artificially short 22 hr LD cycle express two stable circadian motor activity rhythms with different period lengths in individual animals. Our analysis of SCN gene expression under such conditions suggests that these two motor activity rhythms reflect the separate activities of two oscillators in the anatomically defined ventrolateral and dorsomedial SCN subdivisions. Our "forced desychronization" protocol has allowed the first stable separation of these two regional oscillators in vivo, correlating their activities to distinct behavioral outputs, and providing a powerful approach for understanding SCN tissue organization and signaling mechanisms in behaving animals.     

The preferential binding of histone H1 to DNA scaffold-associated regions is determined by its C-terminal domain

Histone H1 preferentially binds and aggregates scaffold-associated regions (SARs) via the numerous homopolymeric oligo(dA).oligo(dT) tracts present within these sequences. Here we show that the mammalian somatic subtypes H1a,b,c,d,e and H1° and the male germline-specific subtype H1t, all preferentially bind to the Drosophila histone SAR. Experiments with the isolated domains show that whilst the C-terminal domain maintains strong and preferential binding, the N-terminal and globular domains show weak binding and poor specificity for the SAR. The preferential binding of SAR by the H1 molecule thus appears to be determined by its highly basic C-terminal domain. Salmine, a typical fish protamine, which could have its evolutionary origin in histone H1, also shows preferential binding to the SAR. The interaction of distamycin, a minor groove binder with high affinity for homopolymeric oligo(dA).oligo(dT) tracts, abolishes preferential binding of the C-terminal domain of histone H1 and protamine to the SAR, suggesting the involvement of the DNA minor groove in the interaction.     

DNA-induced alpha-helical structure in the NH2-terminal domain of histone H1

It is important to establish the structural properties of linker histones to understand the role they play in chromatin higher order structure and gene regulation. Here, we use CD, NMR, and IR spectroscopy to study the conformation of the amino-terminal domain of histone H1 degrees, free in solution and bound to the DNA. The NH(2)-terminal domain has little structure in aqueous solution, but it acquires a substantial amount of alpha-helical structure in the presence of trifluoroethanol (TFE). As in other H1 subtypes, the basic residues of the NH(2)-terminal domain of histone H1 degrees are clustered in its COOH-terminal half. According to the NMR results, the helical region comprises the basic cluster (Lys(11)-Lys(20)) and extends until Asp(23). The fractional helicity of this region in 90% TFE is about 50%. His(24) together with Pro(25) constitute the joint between the NH(2)-terminal helix and helix I of the globular domain. Infrared spectroscopy shows that interaction with the DNA induces an amount of alpha-helical structure equivalent to that observed in TFE. As coulombic interactions are involved in complex formation, it is highly likely in the complexes with DNA that the minimal region with alpha-helical structure is that containing the basic cluster. In chromatin, the high positive charge density of the inducible NH(2)-terminal helical element may contribute to the binding stability of the globular domain.     

Differential kinetics of histone H1o accumulation in neuronal and glial cells from rat cerebral cortex during postnatal development

The accumulation of histone H1^o has been studied in neuronal and glial nuclei from rat cerebral cortex during postnatal development. In neurons H1^o represents ～2% of the H1 content at birth and remains unchanged until day 8. Beyond this point H1^o accumulates rapidly until day 18, where it levels off at 16% of H1. The midpoint of the transition is at day 14. In glial cells H1^o represents ～2.5% of the H1 at birth. It starts to accumulate between days 18 and 21; its concentration raises rapidly up to day 30 slowing down from then on. At day 300 (the farthest point examined) it represents 21% of H1. These results are discussed in relation to the events of the postnatal development of the cerebral cortex in the rat. It is concluded that H^o probably does not suppress cell proliferation.     

Changes in the proportions of histone H1° subtypes in brain cortical neurons

Histone H1° is found in tissues with little or no cellular proliferation and has been shown to accumulate during cellular terminal differentiation. Two subtypes of H1°, H1°a and H1°b, are present in any tissue where the protein has been detected. We report here the first evidence of an age-dependent change in the proportions of H1° subtypes. In rat cerebral cortex neurons the proportion of H1°a rises from 44% of total H1° at birth to about 80% at day 300. These results show that terminally differentiated neurons synthesize and exchange H1° at a significant rate.