4 research outputs found
ChIPSummitDB:a ChIP-seq-based database of human transcription factor binding sites and the topological arrangements of the proteins bound to them.
ChIP-seq reveals genomic regions where proteins, e.g. transcription factors (TFs) interact with DNA. A substantial fraction of these regions, however, do not contain the cognate binding site for the TF of interest. This phenomenon might be explained by protein-protein interactions and co-precipitation of interacting gene regulatory elements. We uniformly processed 3727 human ChIP-seq data sets and determined the cistrome of 292 TFs, as well as the distances between the TF binding motif centers and the ChIP-seq peak summits. ChIPSummitDB enables the analysis of ChIP-seq data using multiple approaches. The 292 cistromes and corresponding ChIP-seq peak sets can be browsed in GenomeView. Overlapping SNPs can be inspected in dbSNPView. Most importantly, the MotifView and PairShiftView pages show the average distance between motif centers and overlapping ChIP-seq peak summits and distance distributions thereof, respectively. In addition to providing a comprehensive human TF binding site collection, the ChIPSummitDB database and web interface allows for the examination of the topological arrangement of TF complexes genome-wide. ChIPSummitDB is freely accessible at http://summit.med.unideb.hu/summitdb/. The database will be regularly updated and extended with the newly available human and mouse ChIP-seq data sets
Mapping and DNA sequence characterisation of the Ry(sto) locus conferring extreme virus resistance to potato cultivar 'White Lady'
Virus resistance genes carried by wild plant species are valuable resources for plant breeding. The Ry(sto) gene, conferring a broad spectrum of durable resistance, originated from Solanum stoloniferum and was introgressed into several commercial potato cultivars, including 'White Lady', by classical breeding. Ry(sto) was mapped to chromosome XII in potato, and markers used for marker-assisted selection in breeding programmes were identified. Nevertheless, there was no information on the identity of the Ry(sto) gene. To begin to reveal the identification of Ry(sto), fine-scale genetic mapping was performed which, in combination with chromosome walking, narrowed down the locus of the gene to approximately 1 Mb. DNA sequence analysis of the locus identified six full-length NBS-LRR-type (short NLR-type) putative resistance genes. Two of them, designated TMV2 and TMV3, were similar to a TMV resistance gene isolated from tobacco and to Y-1, which co-segregates with Ry(adg), the extreme virus resistance gene originated from Solanum andigena and localised to chromosome XI. Furthermore, TMV2 of 'White Lady' was found to be 95% identical at the genomic sequence level with the recently isolated Ry(sto) gene of the potato cultivar 'Alicja'. In addition to the markers identified earlier, this work generated five tightly linked new markers which can serve potato breeding efforts for extreme virus resistance
Dendritic Spikes Induce Ripples in Parvalbumin Interneurons during Hippocampal Sharp Waves
The red deer Cervus elaphus genome CerEla1.0: sequencing, annotating, genes, and chromosomes
We present here the de novo genome assembly CerEla1.0 for the
red deer, Cervus elaphus, an emblematic member of the natural
megafauna of the Northern Hemisphere. Humans spread the species
in the South. Today, the red deer is also a farm-bred animal
and is becoming a model animal in biomedical and population
studies. Stag DNA was sequenced at 74× coverage by Illumina
technology. The ALLPATHS-LG assembly of the reads resulted in
34.7 × 103 scaffolds, 26.1 × 103 of which were utilized in
Cer.Ela1.0. The assembly spans 3.4 Gbp. For building the red
deer pseudochromosomes, a pre-established genetic map was used
for main anchor points. A nearly complete co-linearity was
found between the mapmarker sequences of the deer genetic map
and the order and orientation of the orthologous sequences in
the syntenic bovine regions. Syntenies were also conserved at
the in-scaffold level. The cM distances corresponded to 1.34
Mbp uniformly along the deer genome. Chromosomal rearrangements
between deer and cattle were demonstrated. 2.8 × 106 SNPs, 365
× 103 indels and 19368 protein-coding genes were identified in
CerEla1.0, along with positions for centromerons. CerEla1.0
demonstrates the utilization of dual references, i.e., when a
target genome (here C. elaphus) already has a pre-established
genetic map, and is combined with the well-established whole
genome sequence of a closely related species (here Bos taurus).
Genome-wide association studies (GWAS) that CerEla1.0 (NCBI,
MKHE00000000) could serve for are discussed