Distinct MicroRNA Subcellular Size and Expression Patterns in Human Cancer Cells

Introduction. Small noncoding RNAs have important regulatory functions in different cell pathways. It is believed that most of them mainly play role in gene post-transcriptional regulation in the cytoplasm. Recent evidence suggests miRNA and siRNA activity in the nucleus. Here, we show distinct genome-wide sub-cellular localization distribution profiles of small noncoding RNAs in human breast cancer cells. Methods. We separated breast cancer cell nuclei from cytoplasm, and identified small RNA sequences using a high-throughput sequencing platform. To determine the relationship between miRNA sub-cellular distribution and cancer progression, we used microarray analysis to examine the miRNA expression levels in nucleus and cytoplasm of three human cell lines, one normal breast cell line and two breast cancer cell lines. Logistic regression and SVM were used for further analysis. Results. The sub-cellular distribution of small noncoding RNAs shows that numerous miRNAs and their isoforms (isomiR) not only locate to the cytoplasm but also appeare in the nucleus. Subsequent microarray analyses indicated that the miRNA nuclear-cytoplasmic-ratio is a significant characteristic of different cancer cell lines. Conclusions. Our results indicate that the sub-cellular distribution is important for miRNA function, and that the characterization of the small RNAs sub-cellular localizome may contribute to cancer research and diagnosis

Identification and Analysis of Intermediate Size Noncoding RNAs in the Human Fetal Brain

The involvement of noncoding RNAs (ncRNAs) in the development of the human brain remains largely unknown. Applying a cloning strategy for detection of intermediate size (50–500 nt) ncRNAs (is-ncRNAs) we have identified 82 novel transcripts in human fetal brain tissue. Most of the novel is-ncRNAs are not well conserved in vertebrates, and several transcripts were only found in primates. Northern blot and microarray analysis indicated considerable variation in expression across human fetal brain development stages and fetal tissues for both novel and known is-ncRNAs. Expression of several of the novel is-ncRNAs was conspicuously absent in one or two brain cancer cell lines, and transient overexpression of some transcripts in cancer cells significantly inhibited cell proliferation. Overall, our results suggest that is-ncRNAs play important roles in the development and tumorigenesis of human brain

In vivo analysis of Caenorhabditis elegans noncoding RNA promoter motifs

<p>Abstract</p> <p>Background</p> <p>Noncoding RNAs (ncRNAs) play important roles in a variety of cellular processes. Characterizing the transcriptional activity of ncRNA promoters is therefore a critical step toward understanding the complex cellular roles of ncRNAs.</p> <p>Results</p> <p>Here we present an <it>in vivo </it>transcriptional analysis of three <it>C. elegans </it>ncRNA upstream motifs (UM1-3). Transcriptional activity of all three motifs has been demonstrated, and mutational analysis revealed differential contributions of different parts of each motif. We showed that upstream motif 1 (UM1) can drive the expression of green fluorescent protein (GFP), and utilized this for detailed analysis of temporal and spatial expression patterns of 5 SL2 RNAs. Upstream motifs 2 and 3 do not drive GFP expression, and termination at consecutive T runs suggests transcription by RNA polymerase III. The UM2 sequence resembles the tRNA promoter, and is actually embedded within its own short-lived, primary transcript. This is a structure which is also found at a few plant and yeast loci, and may indicate an evolutionarily very old dicistronic transcription pattern in which a tRNA serves as a promoter for an adjacent snoRNA.</p> <p>Conclusion</p> <p>The study has demonstrated that the three upstream motifs UM1-3 have promoter activity. The UM1 sequence can drive expression of GFP, which allows for the use of UM1::GFP fusion constructs to study temporal-spatial expression patterns of UM1 ncRNA loci. The UM1 loci appear to act in concert with other upstream sequences, whereas the transcriptional activities of the UM2 and UM3 are confined to the motifs themselves.</p

Collaboration Helps Camera Overtake LiDAR in 3D Detection

Camera-only 3D detection provides an economical solution with a simple configuration for localizing objects in 3D space compared to LiDAR-based detection systems. However, a major challenge lies in precise depth estimation due to the lack of direct 3D measurements in the input. Many previous methods attempt to improve depth estimation through network designs, e.g., deformable layers and larger receptive fields. This work proposes an orthogonal direction, improving the camera-only 3D detection by introducing multi-agent collaborations. Our proposed collaborative camera-only 3D detection (CoCa3D) enables agents to share complementary information with each other through communication. Meanwhile, we optimize communication efficiency by selecting the most informative cues. The shared messages from multiple viewpoints disambiguate the single-agent estimated depth and complement the occluded and long-range regions in the single-agent view. We evaluate CoCa3D in one real-world dataset and two new simulation datasets. Results show that CoCa3D improves previous SOTA performances by 44.21% on DAIR-V2X, 30.60% on OPV2V+, 12.59% on CoPerception-UAVs+ for AP@70. Our preliminary results show a potential that with sufficient collaboration, the camera might overtake LiDAR in some practical scenarios. We released the dataset and code at https://siheng-chen.github.io/dataset/CoPerception+ and https://github.com/MediaBrain-SJTU/CoCa3D.Comment: Accepted by CVPR2

Estimating the Quality of Reprogrammed Cells Using ES Cell Differentiation Expression Patterns

Somatic cells can be reprogrammed to a pluripotent state by over-expression of defined factors, and pluripotency has been confirmed by the tetraploid complementation assay. However, especially in human cells, estimating the quality of Induced Pluripotent Stem Cell(iPSC) is still difficult. Here, we present a novel supervised method for the assessment of the quality of iPSCs by estimating the gene expression profile using a 2-D “Differentiation-index coordinate”, which consists of two “developing lines” that reflects the directions of ES cell differentiation and the changes of cell states during differentiation. By applying a novel liner model to describe the differentiation trajectory, we transformed the ES cell differentiation time-course expression profiles to linear “developing lines”; and use these lines to construct the 2-D “Differentiation-index coordinate” of mouse and human. We compared the published gene expression profiles of iPSCs, ESCs and fibroblasts in mouse and human “Differentiation-index coordinate”. Moreover, we defined the Distance index to indicate the qualities of iPS cells, which based on the projection distance of iPSCs-ESCs and iPSCs-fibroblasts. The results indicated that the “Differentiation-index coordinate” can distinguish differentiation states of the different cells types. Furthermore, by applying this method to the analysis of expression profiles in the tetraploid complementation assay, we showed that the Distance index which reflected spatial distributions correlated the pluripotency of iPSCs. We also analyzed the significantly changed gene sets of “developing lines”. The results suggest that the method presented here is not only suitable for the estimation of the quality of iPS cells based on expression profiles, but also is a new approach to analyze time-resolved experimental data

Anomalous fractionation of mercury isotopes in the Late Archean atmosphere

This work was funded by a Natural Environment Research Council (NERC) Fellowship NE/H016805/2 and Standard Grant NE/J023485/2 (to A.L.Z.). R.Y. was funded by the Chinese Academy of Sciences through the Hundred Talent Plan. G.J.I. recognizes continued support from R. Summons under the auspices of the Simons Collaboration on the Origin of Life. We thank J. Kirschvink, J. Grotzinger, A. Knoll, and the Agouron Institute for organizing and funding the Agouron Drilling Project, and the Council for Geoscience in South Africa, specifically those at the National Core Library in Donkerhoek, for facilitating access to the core materials.Earth’s surface underwent a dramatic transition ~2.3 billion years ago when atmospheric oxygen first accumulated during the Great Oxidation Event, but the detailed composition of the reducing early atmosphere is not well known. Here we develop mercury (Hg) stable isotopes as a proxy for paleoatmospheric chemistry and use Hg isotope data from 2.5 billion-year-old sedimentary rocks to examine changes in the Late Archean atmosphere immediately prior to the Great Oxidation Event. These sediments preserve evidence of strong photochemical transformations of mercury in the absence of molecular oxygen. In addition, these geochemical records combined with previously published multi-proxy data support a vital role for methane in Earth’s early atmosphere.Publisher PDFPeer reviewe

A non-Gaussian factor analysis approach to transcription Network Component Analysis

Transcription factor activities (TFAs), rather than expression levels, control gene expression and provide valuable information for investigating TF-gene regulations. Network Component Analysis (NCA) is a model based method to deduce TFAs and TF-gene control strengths from microarray data and a priori TF-gene connectivity data. We modify NCA to model gene expression regulation by non-Gaussian Factor Analysis (NFA), which assumes TFAs independently comes from Gaussian mixture densities. We properly incorporate a priori connectivity and/or sparsity on the mixing matrix of NFA, and derive, under Bayesian Ying-Yang (BYY) learning framework, a BYY-NFA algorithm that can not only uncover the latent TFA profile similar to NCA, but also is capable of automatically shutting off unnecessary connections. Simulation study demonstrates the effectiveness of BYY-NFA, and a preliminary application to two real world data sets shows that BYY-NFA improves NCA for the case when TF-gene connectivity is not available or not reliable, and may provide a preliminary set of candidate TF-gene interactions or double check unreliable connections for experimental verification. ? 2012 IEEE.EI