The genome sequence of (Chiroptera, Phyllostomidae, Stenodermatinae; Olfers, 1818).

We present a genome assembly from an individual male (Chordata; Mammalia; Chiroptera; Phyllostomidae). The genome sequence is 2.15 in span.

The genome sequence of (Chiroptera, Phyllostomidae, Glossophaginae; Merriam, 1898).

We present a genome assembly from an individual female (Chordata; Mammalia; Chiroptera; Phyllostomidae). The genome sequence is 2.13 in span.

The genome sequence of González-Ruiz, Ramírez-Pulido and Arroyo-Cabrales, 2011 (Chiroptera, Molossidae).

We present a genome assembly from an individual female (Chordata; Mammalia; Chiroptera; Molossidae). The genome sequence is 2.490 Gb in span.

The genome sequence of (Chiroptera, Emballonuridae, Rhynchonycteris).

We present a reference genome assembly from an individual male (Chordata; Mammalia; Chiroptera; Emballonuridae). The genome sequence is 2.46 Gb in span.

Alzheimer's disease rewires gene coexpression networks coupling different brain regions.

Connectome studies have shown how Alzheimer's disease (AD) disrupts functional and structural connectivity among brain regions. But the molecular basis of such disruptions is less studied, with most genomic/transcriptomic studies performing within-brain-region analyses. To inspect how AD rewires the correlation structure among genes in different brain regions, we performed an Inter-brain-region Differential Correlation (Inter-DC) analysis of RNA-seq data from Mount Sinai Brain Bank on four brain regions (frontal pole, superior temporal gyrus, parahippocampal gyrus and inferior frontal gyrus, comprising 264 AD and 372 control human post-mortem samples).

The genome sequence of (Chiroptera, Molossidae; Miller, 1902).

We present a genome assembly from an individual male (Chordata; Mammalia; Chiroptera; Molossidae). The genome sequence is 2.41 gigabases in span.

iCOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data.

Despite the tremendous increase in omics data generated by modern sequencing technologies, their analysis can be tricky and often requires substantial expertise in bioinformatics. To address this concern, we have developed a user-friendly pipeline to analyze (cancer) genomic data that takes in raw sequencing data (FASTQ format) as input and outputs insightful statistics. Our iCOMIC toolkit pipeline featuring many independent workflows is embedded in the popular Snakemake workflow management system.

CBP Regulates Recruitment and Release of Promoter-Proximal RNA Polymerase II.

Transcription activation involves RNA polymerase II (Pol II) recruitment and release from the promoter into productive elongation, but how specific chromatin regulators control these steps is unclear. Here, we identify a novel activity of the histone acetyltransferase p300/CREB-binding protein (CBP) in regulating promoter-proximal paused Pol II. We find that Drosophila CBP inhibition results in "dribbling" of Pol II from the pause site to positions further downstream but impedes transcription through the +1 nucleosome genome-wide.

Erratum to: CBP binding outside of promoters and enhancers in Drosophila melanogaster.

[This corrects the article DOI: 10.1186/s13072-015-0042-4.].

CBP binding outside of promoters and enhancers in Drosophila melanogaster.

Background: CREB-binding protein (CBP, also known as nejire) is a transcriptional co-activator that is conserved in metazoans. CBP plays an important role in embryonic development and cell differentiation and mutations in CBP can lead to various diseases in humans. In addition, CBP and the related p300 protein have successfully been used to predict enhancers in both humans and flies when they occur with monomethylation of histone H3 on lysine 4 (H3K4me1).

Non-coding roX RNAs prevent the binding of the MSL-complex to heterochromatic regions.

Long non-coding RNAs contribute to dosage compensation in both mammals and Drosophila by inducing changes in the chromatin structure of the X-chromosome. In Drosophila melanogaster, roX1 and roX2 are long non-coding RNAs that together with proteins form the male-specific lethal (MSL) complex, which coats the entire male X-chromosome and mediates dosage compensation by increasing its transcriptional output. Studies on polytene chromosomes have demonstrated that when both roX1 and roX2 are absent, the MSL-complex becomes less abundant on the male X-chromosome and is relocated to the chromocenter and the 4th chromosome.

Male X-linked genes in Drosophila melanogaster are compensated independently of the Male-Specific Lethal complex.

Background: In organisms where the two sexes have unequal numbers of X-chromosomes, the expression of X-linked genes needs to be balanced not only between the two sexes, but also between X and the autosomes. In Drosophila melanogaster, the Male-Specific Lethal (MSL) complex is believed to produce a 2-fold increase in expression of genes on the male X, thus restoring this balance.

Results: Here we show that almost all the genes on the male X are effectively compensated.

HP1a recruitment to promoters is independent of H3K9 methylation in Drosophila melanogaster.

Heterochromatin protein 1 (HP1) proteins, recognized readers of the heterochromatin mark methylation of histone H3 lysine 9 (H3K9me), are important regulators of heterochromatin-mediated gene silencing and chromosome structure. In Drosophila melanogaster three histone lysine methyl transferases (HKMTs) are associated with the methylation of H3K9: Su(var)3-9, Setdb1, and G9a. To probe the dependence of HP1a binding on H3K9me, its dependence on these three HKMTs, and the division of labor between the HKMTs, we have examined correlations between HP1a binding and H3K9me patterns in wild type and null mutants of these HKMTs.

Preferential genome targeting of the CBP co-activator by Rel and Smad proteins in early Drosophila melanogaster embryos.

CBP and the related p300 protein are widely used transcriptional co-activators in metazoans that interact with multiple transcription factors. Whether CBP/p300 occupies the genome equally with all factors or preferentially binds together with some factors is not known. We therefore compared Drosophila melanogaster CBP (nejire) ChIP-seq peaks with regions bound by 40 different transcription factors in early embryos, and we found high co-occupancy with the Rel-family protein Dorsal.

Sequence signatures involved in targeting the Male-Specific Lethal complex to X-chromosomal genes in Drosophila melanogaster.

Background: In Drosophila melanogaster, the dosage-compensation system that equalizes X-linked gene expression between males and females, thereby assuring that an appropriate balance is maintained between the expression of genes on the X chromosome(s) and the autosomes, is at least partially mediated by the Male-Specific Lethal (MSL) complex. This complex binds to genes with a preference for exons on the male X chromosome with a 3' bias, and it targets most expressed genes on the X chromosome. However, a number of genes are expressed but not targeted by the complex.

Normalization of high dimensional genomics data where the distribution of the altered variables is skewed.

Genome-wide analysis of gene expression or protein binding patterns using different array or sequencing based technologies is now routinely performed to compare different populations, such as treatment and reference groups. It is often necessary to normalize the data obtained to remove technical variation introduced in the course of conducting experimental work, but standard normalization techniques are not capable of eliminating technical bias in cases where the distribution of the truly altered variables is skewed, i.e.

RoBuST: an integrated genomics resource for the root and bulb crop families Apiaceae and Alliaceae.

Background: Root and bulb vegetables (RBV) include carrots, celeriac (root celery), parsnips (Apiaceae), onions, garlic, and leek (Alliaceae)--food crops grown globally and consumed worldwide. Few data analysis platforms are currently available where data collection, annotation and integration initiatives are focused on RBV plant groups. Scientists working on RBV include breeders, geneticists, taxonomists, plant pathologists, and plant physiologists who use genomic data for a wide range of activities including the development of molecular genetic maps, delineation of taxonomic relationships, and investigation of molecular aspects of gene expression in biochemical pathways and disease responses.

AspAlt: A tool for inter-database, inter-genomic and user-specific comparative analysis of alternative transcription and alternative splicing in 46 eukaryotes.

We have developed AspAlt-a web-based comparative analytical platform for exploring the variations in alternative transcription (AT) events and alternative splicing (AS) events in eukaryotes. AspAlt provides integrated access to 2.1 million AT-AS annotations from 1,58,876 multi-isoform genes and has the following user-friendly analytical features: (1) advanced graphical display to visualize and analyze AT-AS events in 46 eukaryotic genomes; (2) compare and identify the differences in AT-AS patterns among a group of genes specified by the user or among homologous gene groups; (3) inter-database comparative viewer to analyze the differences in the AT-AS annotations for the same gene among Ensembl, RefSeq and AceView databases; (4) dynamically classify and generate graphical plots of AT-AS events from mRNA annotations submitted by the user; and (5) download genomic AT-AS annotations of 46 eukaryotes in XML and tab-delimited formats.

ExDom: an integrated database for comparative analysis of the exon-intron structures of protein domains in eukaryotes.

We have developed ExDom, a unique database for the comparative analysis of the exon-intron structures of 96 680 protein domains from seven eukaryotic organisms (Homo sapiens, Mus musculus, Bos taurus, Rattus norvegicus, Danio rerio, Gallus gallus and Arabidopsis thaliana). ExDom provides integrated access to exon-domain data through a sophisticated web interface which has the following analytical capabilities: (i) intergenomic and intragenomic comparative analysis of exon-intron structure of domains; (ii) color-coded graphical display of the domain architecture of proteins correlated with their corresponding exon-intron structures; (iii) graphical analysis of multiple sequence alignments of amino acid and coding nucleotide sequences of homologous protein domains from seven organisms; (iv) comparative graphical display of exon distributions within the tertiary structures of protein domains; and (v) visualization of exon-intron structures of alternative transcripts of a gene correlated to variations in the domain architecture of corresponding protein isoforms. These novel analytical features are highly suited for detailed investigations on the exon-intron structure of domains and make ExDom a powerful tool for exploring several key questions concerning the function, origin and evolution of genes and proteins.