Doug Higgs

Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs

BackgroundMammalian transcriptomes contain thousands of long noncoding RNAs (lncRNAs). Some lncRNAs originate from intragenic enhancers which, when active, behave as alternative promoters producing transcripts that are processed using the canonical signals of their host gene. We have followed up this observation by analyzing intergenic lncRNAs to determine the extent to which they might also originate from intergenic enhancers.ResultsWe integrated high-resolution maps of transcriptional initiation and transcription to annotate a conservative set of intergenic lncRNAs expressed in mouse erythroblasts. We subclassified intergenic lncRNAs according to chromatin status at transcriptional initiation regions, defined by relative levels of histone H3K4 mono- and trimethylation. These transcripts are almost evenly divided between those arising from enhancer-associated (elncRNA) or promoter-associated (plncRNA) elements. These two classes of 5′ capped and polyadenylated RNA transcripts are indistinguishable with regard to their length, number of exons or transcriptional orientation relative to their closest neighboring gene. Nevertheless, elncRNAs are more tissue-restricted, less highly expressed and less well conserved during evolution. Of considerable interest, we found that expression of elncRNAs, but not plncRNAs, is associated with enhanced expression of neighboring protein-coding genes during erythropoiesis.ConclusionsWe have determined globally the sites of initiation of intergenic lncRNAs in erythroid cells, allowing us to distinguish two similarly abundant classes of transcripts. Different correlations between the levels of elncRNAs, plncRNAs and expression of neighboring genes suggest that functional lncRNAs from the two classes may play contrasting roles in regulating the transcript abundance of local or distal loci.

A newly defined X linked mental retardation syndrome associated with alpha thalassaemia.

In 1981 three northern European families were described in which a severely mentally retarded son also had haemoglobin H (Hb H) disease. These findings were of interest because Hb H disease, a relatively severe manifestation of a thalassaemia, is rare in northern Europeans although it is frequently seen in Mediterranean and Oriental racial groups in which it is not known to be associated with an increased frequency of mental retardation. Furthermore, whereas the common forms of Hb H disease are always inherited in a mendelian fashion, in these northern European families this appeared not to be so. Hb H disease occurs when a greater than 50% reduction in synthesis of the a globin chains of adult haemoglobin (Hb A, a212) results in the accumulation of excess 1 globin chains which form 14 tetramers (Hb H). The common mendelian forms of HbH disease result from mutations of both allelic a globin complexes, most commonly owing to deletions or less frequently to small rearrangements or point mutations. The a globin complex is located close to the telomere of the short arm of chromosome 16, within band 16pl3.3. By 1990, a total of 13 subjects with a thalassaemia and mental retardation (ATR) had been identified and two distinct syndromes were delineated.34 Eight patients had large (1 to 2 megabases) deletions of the tip of chromosome 16p; the clinical features of this so called ATR-16 syndrome were rather variable, in

Localisation of human alpha globin to 16p13.3----pter.

A female child with alpha thalassaemia trait, moderate mental retardation, and dysmorphic features has inherited an abnormal chromosome 16 complement as a result of the unbalanced segregation of a maternal balanced translocation. Cytogenetic analysis indicates that the patient is monosomic for 16p13.3----pter and trisomic for 10q26.13----qter. DNA studies show that the patient has not inherited either maternal alpha globin allele. This accounts for the alpha thalassaemia trait in the child and places the human alpha globin complex in band 16p13.3----pter.

X linked alpha thalassaemia/mental retardation: spectrum of clinical features in three related males.

We describe three males (two brothers and a cousin) who have the X linked alpha thalassaemia/mental retardation (ATR-X) syndrome. The diagnosis, originally suspected in the brothers because of similarity in dysmorphic features to previous cases, was confirmed haematologically in the surviving brother. The cousin has less typical dysmorphism and a virtually normal routine blood count, but haemoglobin H inclusions were found in his red blood cells showing that he has the same condition. This report expands the clinical phenotype of the ATR-X syndrome and emphasises that a normal blood count does not exclude the diagnosis.

G gamma beta + type of hereditary persistence of fetal haemoglobin in association with Hb C.

This report describes a Negro family with the G gamma beta + type of hereditary persistence of fetal haemoglobin. Family members with levels of haemoglobin F of 17 to 23% had normal red cell indices, balanced globin chain synthesis, and a pancellular distribution of the fetal haemoglobin, showing that these subjects have a form of HPFH. The production of Hb A and C in addition to the large amount of Hb F in one family member showed that there was an active beta A gene in cis to the HPFH determinant, while structural analysis of the Hb F revealed the presence of only G gamma chains. The criteria for the diagnosis of G gamma beta + HPFH, and the relevance of such conditions to the control of globin gene expression, are discussed.

The non-deletion type of alpha thalassaemia/mental retardation: a recognisable dysmorphic syndrome with X linked inheritance.

The association of a thalassaemia and mental retardation (ATR), originally described in 1981,1 was further analysed in two papers published last year. Of 13 subjects ascertained because of their haematological abnormality, eight had deletions involving the tip of chromosome 16p, where the a globin genes lie (deletion cases)2; in the remaining five, the a globin genes appeared intact (nondeletion cases). Whereas the clinical features of the deletion cases were rather variable, the non-deletion cases showed a strikingly uniform phenotype comprising severe mental handicap, characteristic dysmorphic facies, genital abnormalities, and an unusual, mild form of haemoglobin H (Hb H) disease (a manifestation ofa thalassaemia). It was proposed that the nondeletion cases represented a distinct syndrome that probably mapped to the X chromosome3; however, in the absence of pedigrees containing multiple affected cases, the evidence for this was circumstantial. Two recent papers in this Journal4 s lend support to the conclusions of Wilkie et al3 and extend the delineation of the nondeletion ATR syndrome. Harvey et al4 described a severely retarded 21 year old male with similar haematological and dysmorphic features to the previous cases and a normal a globin genotype. A male sib who was severely retarded and said to have had a similar physical appearance had died some years previously. As pointed out by the authors, this was the first description of two affected males in a sibship and is compatible with X linked inheritance. Nearly simultaneous with the publication of Wilkie et al,3 Porteous and Burn described a 6 year old boy with an unknown retardation syndrome comprising dysmorphic facies, microcephaly, hypotonia, and small genitalia; his dead maternal uncle had shown similar clinical features, leading the authors to propose that this syndrome might be X linked. The striking similarity of their case to the non-deletion ATR syndrome prompted further haematological and molecular evaluation of the proband at the age of 7 years 3 months. The results were: haemoglobin (Hb) 10.3 g/dl, red cell count 4.55 x 1012/1, mean cell volume 73 fl, mean cell haemoglobin 23 pg, Hb electrophoresis, 2.7% Hb H; 14% of red cells contained Hb H inclusions after incubation with 1% brilliant cresyl blue, and the a globin genotype was aa/aa. These results prove that this boy has the non-deletion ATR syndrome; his uncle had been anaemic throughout life and had been treated with iron supplements, so it seems likely that he had the same condition. The boys parents had normal haematological indices. Porteous and Burn suggested that their case resembled two brothers previously thought to have an atypical form of the Coffin-Lowry syndrome and illustrated in Smiths recognizable patterns ofhuman malformation.6 Haematological evaluation of the surviving brother shows that he too has non-deletion ATR; a male cousin (his mothers sisters son), also mentally retarded, has the same condition. A fuller description of this family will appear in the next issue of the Journal. This recent work lends weight to the conclusions of Wilkie et aP in two respects. First, the non-deletion ATR syndrome shows a pattem of dysmorphic facial features and associated clinical abnormalities that is sufficiently characteristic to identify potential new cases; the diagnosis is then best confirmed by showing the presence ofHb H inclusions in the red cells. Second, the absence of male-tomale transmission in the three new pedigrees (comprising seven affected cases, all male) greatly strengthens the evidence that the non-deletion ATR syndrome is X linked. Accordingly, we propose that this syndrome3 is henceforth termed X linked a thalassaemia/mental retardation (ATR-X), to distinguish it from the separate syndrome associated with deletion of the a globin complex on chromosome 16 (ATR-16).

Sasquatch: predicting the impact of regulatory SNPs on transcription factor binding from cell- and tissue-specific DNase footprints.

In the era of genome-wide association studies (GWAS) and personalized medicine, predicting the impact of single nucleotide polymorphisms (SNPs) in regulatory elements is an important goal. Current approaches to determine the potential of regulatory SNPs depend on inadequate knowledge of cell-specific DNA binding motifs. Here, we present Sasquatch, a new computational approach that uses DNase footprint data to estimate and visualize the effects of noncoding variants on transcription factor binding. Sasquatch performs a comprehensive k-mer-based analysis of DNase footprints to determine any k-mers potential for protein binding in a specific cell type and how this may be changed by sequence variants. Therefore, Sasquatch uses an unbiased approach, independent of known transcription factor binding sites and motifs. Sasquatch only requires a single DNase-seq data set per cell type, from any genotype, and produces consistent predictions from data generated by different experimental procedures and at different sequence depths. Here we demonstrate the effectiveness of Sasquatch using previously validated functional SNPs and benchmark its performance against existing approaches. Sasquatch is available as a versatile webtool incorporating publicly available data, including the human ENCODE collection. Thus, Sasquatch provides a powerful tool and repository for prioritizing likely regulatory SNPs in the noncoding genome.

The worm has turned: unexpected similarities between the transcription of enhancers and promoters in the worm and mammalian genomes.

Our understanding of biological processes in humans is often based on examination of analogous processes in other organisms. The nematode worm Caenorhabditis elegans has been a particularly valuable model, leading to Nobel prize winning discoveries in development and genetics. Until recently, however, the worm has not been widely used as a model to study transcription due to the lack of a comprehensive catalogue of its RNA transcripts. A recent study by Chen et al. uses next‐generation sequencing to address this issue, mapping the transcription initiation sites in C. elegans and finding many unexpected similarities between the transcription of enhancers and promoters in the worm and mammalian genomes. As well as providing a valuable resource for researchers in the C. elegans community, these findings raise the possibility of using the worm as a model to investigate some key, current questions about transcriptional regulation that remain technically challenging in more complex organisms.