Arisa Oda

Stress‐induced lncRNAs evade nuclear degradation and enter the translational machinery

Long noncoding RNAs (lncRNAs) play important roles in the regulation of gene expression. In fission yeast, glucose starvation triggers a transcriptional cascade of polyadenylated lncRNAs in the upstream region of the fructose‐1,6‐bisphosphatase gene (fbp1+), which is correlated with stepwise chromatin remodeling and necessary for the massive induction of fbp1+ mRNA. Here, we show that these novel metabolic stress‐induced lncRNAs (mlonRNAs) are 5′‐capped, less stable than fbp1+ mRNA and sensitive to a certain extent to the nuclear exosome cofactor Rrp6. However, most mlonRNAs seem to escape nuclear degradation and are exported to the cytoplasm, where they localize to polysomes precisely during glucose starvation‐induced global translation inhibition. It is likely that ribosomes tend to accumulate in the upstream region of mlonRNAs. Although mlonRNAs contain an unusual amount of upstream AUGs (uAUGs) and small open reading frames (uORFs), they escape Upf1‐mediated targeting to the non‐sense‐mediated decay (NMD) pathway. The deletion of Upf1 had no effect on mlonRNA stability, but considerably destabilized fbp1+ mRNA, hinting toward a possible novel role of Upf1. Our findings suggest that the stability of mlonRNAs is distinctly regulated from mRNA and previously described noncoding transcripts.

Dynamic transition of transcription and chromatin landscape during fission yeast adaptation to glucose starvation

Shortage of glucose, the primary energy source for all organisms, is one of the most critical stresses influencing cell viability. Glucose starvation promptly induces changes in mRNA and noncoding RNA (ncRNA) transcription. We previously reported that glucose starvation induces long ncRNA (lncRNA) transcription in the 5′ segment of a fission yeast gluconeogenesis gene (fbp1+), which leads to stepwise chromatin alteration around the fbp1+ promoter and to subsequent robust gene activation. Here, we analyzed genomewide transcription by strand‐specific RNA sequencing, together with chromatin landscape by immunoprecipitation sequencing (ChIP‐seq). Clustering analysis showed that distinct mRNAs and ncRNAs are induced at the early, middle and later stages of cellular response to glucose starvation. The starvation‐induced transcription depends substantially on the stress‐responsive transcription factor Atf1. Using a new computer program that examines dynamic changes in expression patterns, we identified ncRNAs with similar behavior to the fbp1+ lncRNA. We confirmed that there are continuous lncRNAs associated with local reduction of histone density. Overlapping with the regions for transcription of these lncRNAs, antisense RNAs are antagonistically transcribed under glucose‐rich conditions. These results suggest that Atf1‐dependent integrated networks of mRNA and lncRNA govern drastic changes in cell physiology in response to glucose starvation.

Three-dimensional reconstruction of single-cell chromosome structure using recurrence plots

Single-cell analysis of the three-dimensional (3D) chromosome structure can reveal cell-to-cell variability in genome activities. Here, we propose to apply recurrence plots, a mathematical method of nonlinear time series analysis, to reconstruct the 3D chromosome structure of a single cell based on information of chromosomal contacts from genome-wide chromosome conformation capture (Hi-C) data. This recurrence plot-based reconstruction (RPR) method enables rapid reconstruction of a unique structure in single cells, even from incomplete Hi-C information.

Correlation of Meiotic DSB Formation and Transcription Initiation Around Fission Yeast Recombination Hotspots

Meiotic homologous recombination, a critical event for ensuring faithful chromosome segregation and creating genetic diversity, is initiated by programmed DNA double-strand breaks (DSBs) formed at recombination hotspots. Meiotic DSB formation is likely to be influenced by other DNA-templated processes including transcription, but how DSB formation and transcription interact with each other has not been understood well. In this study, we used fission yeast to investigate a possible interplay of these two events. A group of hotspots in fission yeast are associated with sequences similar to the cyclic AMP response element and activated by the ATF/CREB family transcription factor dimer Atf1-Pcr1. We first focused on one of those hotspots, ade6-3049, and Atf1. Our results showed that multiple transcripts, shorter than the ade6 full-length messenger RNA, emanate from a region surrounding the ade6-3049 hotspot. Interestingly, we found that the previously known recombination-activation region of Atf1 is also a transactivation domain, whose deletion affected DSB formation and short transcript production at ade6-3049. These results point to a possibility that the two events may be related to each other at ade6-3049. In fact, comparison of published maps of meiotic transcripts and hotspots suggested that hotspots are very often located close to meiotically transcribed regions. These observations therefore propose that meiotic DSB formation in fission yeast may be connected to transcription of surrounding regions.

Replication stress induces accumulation of FANCD2 at central region of large fragile genes

Abstract During mild replication stress provoked by low dose aphidicolin (APH) treatment, the key Fanconi anemia protein FANCD2 accumulates on common fragile sites, observed as sister foci, and protects genome stability. To gain further insights into FANCD2 function and its regulatory mechanisms, we examined the genome-wide chromatin localization of FANCD2 in this setting by ChIP-seq analysis. We found that FANCD2 mostly accumulates in the central regions of a set of large transcribed genes that were extensively overlapped with known CFS. Consistent with previous studies, we found that this FANCD2 retention is R-loop-dependent. However, FANCD2 monoubiquitination and RPA foci formation were still induced in cells depleted of R-loops. Interestingly, we detected increased Proximal Ligation Assay dots between FANCD2 and R-loops following APH treatment, which was suppressed by transcriptional inhibition. Collectively, our data suggested that R-loops are required to retain FANCD2 in chromatin at the middle intronic region of large genes, while the replication stress-induced upstream events leading to the FA pathway activation are not triggered by R-loops.

Transcriptomes and Raman spectra are linked linearly through a shared low-dimensional subspace

Raman spectroscopy is an imaging technique that can reflect whole-cell molecular compositions in vivo, and has been applied recently in cell biology to characterize different cell types and states. However, due to the complex molecular compositions and spectral overlaps, the interpretation of cellular Raman spectra have remained unclear. In this report, we compared cellular Raman spectra to transcriptomes of Schizosaccharomyces pombe and Escherichia coli, and provide firm evidence that they can be computationally connected and interpreted. Specifically, we find that the dimensions of high-dimensional Raman spectra and transcriptomes measured by RNA-seq can be effectively reduced and connected linearly through a shared low-dimensional subspace. Accordingly, we were able to reconstruct global gene expression profiles by applying the calculated transformation matrix to Raman spectra, and vice versa. Strikingly, highly expressed ncRNAs contributed to the Raman-transcriptome linear correspondence more significantly than mRNAs in S. pombe, which implies their major role in coordinating molecular compositions. This compatibility between whole-cell Raman spectra and transcriptomes marks an important and promising step towards establishing spectroscopic live-cell omics studies.