CAGE-TSSchip: promoter-based expression profiling using the 5'-leading label of capped transcripts

A novel approach that combines CAGE expression analysis with oligonucleotide array technology allows for the accurate and sensitive detection of promoter-based transcriptional activity

Embryonic LTR retrotransposons supply promoter modules to somatic tissues

Long terminal repeat (LTR) retrotransposons are widely distributed across the human genome. They have accumulated through retroviral integration into germline DNA and are latent genetic modules. Active LTR promoters are observed in germline cells; however, little is known about the mechanisms underlying their active transcription in somatic tissues. Here, by integrating our previous transcriptome data set with publicly available data sets, we show that the LTR families MLT2A1 and MLT2A2 are primarily expressed in human four-cell and eight-cell embryos and are also activated in some adult somatic tissues, particularly pineal gland. Three MLT2A elements function as the promoters and first exons of the protein-coding genes ABCE1, COL5A1, and GALNT13 specifically in the pineal gland of humans but not in that of macaques, suggesting that the exaptation of these LTRs as promoters occurred during recent primate evolution. This analysis provides insight into the possible transition from germline insertion to somatic expression of LTR retrotransposons.Peer reviewe

CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis

Cap-analysis gene expression (CAGE) Basic and Analysis Databases store an original resource produced by CAGE, which measures expression levels of transcription starting sites by sequencing large amounts of transcript 5′ ends, termed CAGE tags. Millions of human and mouse high-quality CAGE tags derived from different conditions in >20 tissues consisting of >250 RNA samples are essential for identification of novel promoters and promoter characterization in the aspect of expression profile. CAGE Basic Database is a primary database of the CAGE resource, RNA samples, CAGE libraries, CAGE clone and tag sequences and so on. CAGE Analysis Database stores promoter related information, such as counts of related transcripts, CpG islands and conserved genome region. It also provides expression profiles at base pair and promoter levels. Both databases are based on the same framework, CAGE tag starting sites, tag clusters for defining promoters and transcriptional units (TUs). Their associations and TU attributes are available to find promoters of interest. These databases were provided for Functional Annotation Of Mouse 3 (FANTOM3), an international collaboration research project focusing on expanding the transcriptome and subsequent analyses. Now access is free for all users through the World Wide Web at

Generation of RNA sequencing libraries for transcriptome analysis of globin-rich tissues of the domestic dog

Publisher Copyright: © 2021 The AuthorsWe have developed a protocol for barcoded cDNA libraries of 48 samples to study gene expression across tissues in the domestic dog, Canis familiaris, by modifying the Single-Cell Tagged Reverse Transcription (STRT) protocol (Islam et al., 2012, 2014). The cDNA reads represent mRNA 5′ ends, enabling the study of transcription start sites (TSS). Our modifications include longer UMIs for molecular counting and Globin-Lock® to deplete globin mRNAs that are abundant in blood and blood-rich tissues dominating all reads.Peer reviewe

Dynamic usage of transcription start sites within core promoters

BACKGROUND: Mammalian promoters do not initiate transcription at single, well defined base pairs, but rather at multiple, alternative start sites spread across a region. We previously characterized the static structures of transcription start site usage within promoters at the base pair level, based on large-scale sequencing of transcript 5' ends. RESULTS: In the present study we begin to explore the internal dynamics of mammalian promoters, and demonstrate that start site selection within many mouse core promoters varies among tissues. We also show that this dynamic usage of start sites is associated with CpG islands, broad and multimodal promoter structures, and imprinting. CONCLUSION: Our results reveal a new level of biologic complexity within promoters - fine-scale regulation of transcription starting events at the base pair level. These events are likely to be related to epigenetic transcriptional regulation

La5Ti2Cu1-xAgxS5O7 photocathodes operating at positive potentials during photoelectrochemical hydrogen evolution under irradiation of up to 710 nm

A photoelectrochemical (PEC) cell based on a series-connected photocathode and photoanode made of particulate semiconductors is a potentially scalable and inexpensive device for renewable solar hydrogen production via PEC water splitting without any external power supply. The realisation of such PEC devices hinges on the development of photoelectrodes that operate at a small applied voltage. In this study, solid solutions of La5Ti2CuS5O7 (LTC) and La5Ti2AgS5O7 (LTA) were synthesised, and their physical, optical, and PEC properties in the water splitting reaction were discussed. LTC and LTA formed a La5Ti2Cu1-xAgxS5O7 solid solution (LTC(1-x)A(x)) over the whole compositional range. The indirect bandgap energy of LTC(1-x)A(x) changed nonlinearly with respect to composition, attaining its minimum value (ca. 1.8 eV) at a composition of x approximate to 0.16. Photoelectrodes of Al-doped LTC(1-x)A(x) solid solution powder fabricated using the particle transfer method exhibited a photocathodic response regardless of the Ag content. 1% Al-LTC(0.9)A(0.1) photocathodes exhibited the best PEC properties in the hydrogen evolution reaction and yielded a hypothetical half-cell solar-to-hydrogen energy conversion efficiency of 0.25% at +0.6 V vs. RHE, three times higher than the previously reported 1% Sc-LTC. In addition, 1% Al-LTC(0.9)A(0.1) photocathodes were fairly stable at + 0.7 V vs. RHE without any protective modifications. Owing to the positive operational electrode potential of 1% Al-LTC(0.9)A(0.1), unassisted PEC water splitting was accomplished using series-connected photoelectrodes made of 1% Al-LTC(0.9)A(0.1) and BaTaO2N, particulate semiconductors with absorption edge wavelengths of 710 and 660 nm, respectively, at a Faradaic efficiency of unity and a solar-to-hydrogen energy conversion efficiency of approximately 0.1%.ArticleEnergy & Environmental Science.8(11):3354-3362(2015)journal articl

The Continued Absence of Functional Germline Stem Cells in Adult Ovaries

Ovaries are central to development, fertility, and reproduction of women. A particularly interesting feature of ovaries is their accelerated aging compared to other tissues, leading to loss of function far before other organs senesce. The limited pool of ovarian follicles is generated before birth and once exhausted, menopause will inevitably commence around the age of 50 years marking the end of fertility. Yet, there are reports suggesting the presence of germline stem cells and neo-oogenesis in adult human ovaries. These observations have fueled a long debate, created experimental fertility treatments, and opened business opportunities. Our recent analysis of cell types in the ovarian cortex of women of fertile age could not find evidence of germline stem cells. Like before, our work has been met with critique suggesting methodological shortcomings. We agree that excellence starts with methods and welcome discussion on the pros and cons of different protocols. In this commentary, we discuss the recent re-interpretation of our work.Peer reviewe

Reply : Revisiting Claims of the Continued Absence of Functional Germline Stem Cells in Adult Ovaries

Non peer reviewe

SkewC : Identifying cells with skewed gene body coverage in single-cell RNA sequencing data

The analysis and interpretation of single-cell RNA sequencing (scRNA-seq) experiments are compromised by the presence of poor-quality cells. For meaningful analyses, such poor-quality cells should be excluded as they introduce noise in the data. We introduce SkewC, a quality-assessment tool, to identify skewed cells in scRNA-seq experiments. The tool's methodology is based on the assessment of gene coverage for each cell, and its skewness as a quality measure; the gene body coverage is a unique characteristic for each protocol, and different protocols yield highly different coverage profiles. This tool is designed to avoid misclustering or false clusters by identifying, isolating, and removing cells with skewed gene body coverage profiles. SkewC is capable of processing any type of scRNA-seq dataset, regardless of the protocol. We envision SkewC as a distinctive QC method to be incorporated into scRNA-seq QC processing to preclude the possibility of scRNA-seq data misinterpretation.Peer reviewe