Transcriptome Atlas by Long-Read RNA Sequencing: Contribution to a Reference Transcriptome

The recent emergence of long-read transcriptome sequencing has helped improve the overall accuracy of gene prediction compared with that by short-read RNA-Seq. In addition, the technology can offer a more comprehensive view of functional genomics in uncharacterized species with an efficient full-length unigene build and high-precision gene annotation, thus being efficient in developing transcriptome data resources from useful genetic pools. Hence, I will review the applications of long-read RNA isoform sequencing, including the relative merits of the technology, the improvement of the accuracy in gene prediction and gene annotation, and the full-length unigene builds in a new genome; the limitations of the technology will be also discussed. The review will be valuable in collecting data resources for functional genomic studies

Progress in Understanding and Sequencing the Genome of Brassica rapa

Brassica rapa, which is closely related to Arabidopsis thaliana, is an important crop and a model plant for studying genome evolution via polyploidization. We report the current understanding of the genome structure of B. rapa and efforts for the whole-genome sequencing of the species. The tribe Brassicaceae, which comprises ca. 240 species, descended from a common hexaploid ancestor with a basic genome similar to that of Arabidopsis. Chromosome rearrangements, including fusions and/or fissions, resulted in the present-day “diploid” Brassica species with variation in chromosome number and phenotype. Triplicated genomic segments of B. rapa are collinear to those of A. thaliana with InDels. The genome triplication has led to an approximately 1.7-fold increase in the B. rapa gene number compared to that of A. thaliana. Repetitive DNA of B. rapa has also been extensively amplified and has diverged from that of A. thaliana. For its whole-genome sequencing, the Brassica rapa Genome Sequencing Project (BrGSP) consortium has developed suitable genomic resources and constructed genetic and physical maps. Ten chromosomes of B. rapa are being allocated to BrGSP consortium participants, and each chromosome will be sequenced by a BAC-by-BAC approach. Genome sequencing of B. rapa will offer a new perspective for plant biology and evolution in the context of polyploidization

Functional elements demarcated by histone modifications in breast cancer cells

AbstractHistone modifications are regarded as one of markers to identify regulatory elements which are DNA segments modulating gene transcription. Aberrant changes of histone modification levels are frequently observed in cancer. We have employed ChIP-Seq to identify regulatory elements in human breast cancer cell line, MCF-7 by comparing histone modification patterns of H3K4me1, H3K4me3, and H3K9/14ac to those in normal mammary epithelial cell line, MCF-10A. The genome-wide analysis shows that H3K4me3 and H3K9/14ac are highly enriched at promoter regions and H3K4me1 has a relatively broad distribution over proximity of TSSs as well as other genomic regions. We identified that many differentially expressed genes in MCF-7 have divergent histone modification patterns. To understand the functional roles of distinctively histone-modified regions, we selected 35 genomic regions marked by at least one histone modification and located from 3 to 10kb upstream of TSS in both MCF-7 and MCF-10A and assessed their transcriptional activities. About 66% and 60% of selected regions in MCF-7 and MCF-10A, respectively, enhanced the transcriptional activity. Interestingly, most regions marked by H3K4me1 exhibited an enhancer activity. Regions with two or more kinds of histone modifications did show varying activities. In conclusion, our data reflects that comprehensive analysis of histone modification profiles under cell type-specific chromatin environment should provide a better chance for defining functional regulatory elements in the genome

Excess cost of non-remission among outpatients with major depressive disorder

Background: The purpose of this study was to assess the economic benefit of achieving remission among outpatients with major depressive disorder (MDD) who are currently employed in Korea. Methods: Cross-sectional observational study. A total of 337 outpatients with MDD with paid jobs were recruited from 14 psychiatric clinics in Korea and were then divided into three groups as follows: new visit group (n = 128), remitted group (n = 100) and non-remitted group (n = 109). The 17-item Hamilton Depression Rating Scale (HAM-D) was used to decide whether a patient should be assigned to the remitted or non-remitted group. Direct medical and non-medical costs were measured via interview with the subjects. The World Health Organization Health and Work Performance Questionnaire (HPQ) were applied in order to measure the lost productive time (LPT) and related productivity costs. Results: The three groups did not show a significant difference in direct medical cost. However, the difference between the remitted group and non-remitted group was statistically significant (25.49 ± 52.99 vs. 44.79 ± 126.55, χ2 = 12.99, p = 0.0015). The remitted group demonstrated a significant improvement in productivity (particularly presenteeism) when compared with the new visit group (Z = −3.29, p = 0.001). Although the non-remitted group received treatment at psychiatric clinics similar to the remitted group, it lost 33 more working hours per month, which is compatible to $332 per month. Conclusion: These results suggest the economic importance of achieving remission in treating depression

Ophthalmic Artery Obstruction and Cerebral Infarction Following Periocular Injection of Autologous Fat

We report a case of ophthalmic artery obstruction combined with brain infarction following periocular autologous fat injection. The patient, a 44-year-old woman, visited our hospital for decreased visual acuity in her left eye and dysarthria one hour after receiving an autologous fat injection in the periocular area. Her best corrected visual acuity for the concerned eye was no light perception. Also, a relative afferent pupillary defect was detected in this eye. The left fundus exhibited widespread retinal whitening with visible emboli in several retinal arterioles. Diffusion-weighted magnetic resonance imaging of the brain showed a hyperintense lesion at the left insular cortex. Therefore, we diagnosed ophthalmic artery obstruction and left middle cerebral artery infarction due to fat emboli. The patient was managed with immediate ocular massage, carbon dioxide, and oxygen therapy. Following treatment, dysarthria improved considerably but there was no improvement in visual acuity

Sequenced BAC anchored reference genetic map that reconciles the ten individual chromosomes of Brassica rapa

<p>Abstract</p> <p>Background</p> <p>In view of the immense value of <it>Brassica rapa </it>in the fields of agriculture and molecular biology, the multinational <it>Brassica rapa </it>Genome Sequencing Project (BrGSP) was launched in 2003 by five countries. The developing BrGSP has valuable resources for the community, including a reference genetic map and seed BAC sequences. Although the initial <it>B. rapa </it>linkage map served as a reference for the BrGSP, there was ambiguity in reconciling the linkage groups with the ten chromosomes of <it>B. rapa</it>. Consequently, the BrGSP assigned each of the linkage groups to the project members as chromosome substitutes for sequencing.</p> <p>Results</p> <p>We identified simple sequence repeat (SSR) motifs in the <it>B. rapa </it>genome with the sequences of seed BACs used for the BrGSP. By testing 749 amplicons containing SSR motifs, we identified polymorphisms that enabled the anchoring of 188 BACs onto the <it>B. rapa </it>reference linkage map consisting of 719 loci in the 10 linkage groups with an average distance of 1.6 cM between adjacent loci. The anchored BAC sequences enabled the identification of 30 blocks of conserved synteny, totaling 534.9 cM in length, between the genomes of <it>B. rapa </it>and <it>Arabidopsis thaliana</it>. Most of these were consistent with previously reported duplication and rearrangement events that differentiate these genomes. However, we were able to identify the collinear regions for seven additional previously uncharacterized sections of the A genome. Integration of the linkage map with the <it>B. rapa </it>cytogenetic map was accomplished by FISH with probes representing 20 BAC clones, along with probes for rDNA and centromeric repeat sequences. This integration enabled unambiguous alignment and orientation of the maps representing the 10 <it>B. rapa </it>chromosomes.</p> <p>Conclusion</p> <p>We developed a second generation reference linkage map for <it>B. rapa</it>, which was aligned unambiguously to the <it>B. rapa </it>cytogenetic map. Furthermore, using our data, we confirmed and extended the comparative genome analysis between <it>B. rapa </it>and <it>A. thaliana</it>. This work will serve as a basis for integrating the genetic, physical, and chromosome maps of the BrGSP, as well as for studies on polyploidization, speciation, and genome duplication in the genus <it>Brassica</it>.</p

Identification of the early and late responder genes during the generation of induced pluripotent stem cells from mouse fibroblasts

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