Faculty Opinions recommendation of The transcriptional landscape of the yeast genome defined by RNA sequencing.

The TRS-mediated discontinuous transcription process is a hallmark of Arteriviruses. Precise assessment of the intricate subgenomic RNA (sg mRNA) populations is required to understand the kinetics of viral transcription. It is difficult to reconstruct and comprehensively quantify splicing events using short-read sequencing, making the identification of transcription-regulatory sequences (TRS) particularly problematic. Here, we applied long-read direct RNA sequencing to characterize the recombined RNA molecules produced in porcine alveolar macrophages during early passage infection of porcine reproductive and respiratory syndrome virus (PRRSV). Based on sequencing two PRRSV isolates, namely XM-2020 and GD, we revealed a high-resolution and diverse transcriptional landscape in PRRSV. The data revealed intriguing differences in subgenomic recombination types between the two PRRSVs while also demonstrating TRS-independent heterogeneous subpopulation not previously observed in Arteriviruses. We find that TRS usage is a regulated process and share the common preferred TRS in both strains. This study also identified a substantial number of TRS-mediated transcript variants, including alternative-sg mRNAs encoding the same annotated ORF, as well as putative sg mRNAs encoded nested internal ORFs, implying that the genetic information encoded in PRRSV may be more intensively expressed. Epigenetic modifications have emerged as an essential regulatory layer in gene expression. Here, we gained a deeper understanding of m5C modification in poly(A) RNA, elucidating a potential link between methylation and transcriptional regulation. Collectively, our findings provided meaningful insights for redefining the transcriptome complexity of PRRSV. This will assist in filling the research gaps and developing strategies for better control of the PRRS.

Download Full-text

CBX2-dependent transcriptional landscape: implications for human sex development and its defects

Scientific Reports ◽

10.1038/s41598-019-53006-7 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Patrick Sproll ◽

Wassim Eid ◽

Anna Biason-Lauber

Keyword(s):

Next Generation Sequencing ◽

Rna Sequencing ◽

Current Knowledge ◽

Next Generation ◽

Steroidogenic Factor 1 ◽

Sex Development ◽

New Genes ◽

Differences Of Sex Development ◽

Generation Sequencing ◽

Transcriptional Landscape

Abstract Sex development, a complex and indispensable process in all vertebrates, has still not been completely elucidated, although new genes involved in sex development are constantly being discovered and characterized. Chromobox Homolog 2 (CBX2) is one of these new additions and has been identified through a 46,XY girl with double heterozygous variants on CBX2.1, causing Differences of Sex Development (DSD). The mutated CBX2.1 failed to adequately regulate downstream targets important for sex development in humans, specifically steroidogenic factor 1 (NR5A1/SF1). To better place CBX2.1 in the human sex developmental cascade, we performed siRNA and CBX2.1 overexpression experiments and created a complete CRISPR/Cas9-CBX2 knockout in Sertoli-like cells. Furthermore, we deployed Next Generation Sequencing techniques, RNA-Sequencing and DamID-Sequencing, to identify new potential CBX2.1 downstream genes. The combination of these two next generation techniques enabled us to identify genes that are both bound and regulated by CBX2.1. This allowed us not only to expand our current knowledge about the influence of CBX2.1 in human sex development, but also to advance our insight in the mechanisms governing one of the most important decisions during embryonal development, the commitment to either female or male gonads.

Download Full-text

Breathing fresh air into respiratory research with single-cell RNA sequencing

European Respiratory Review ◽

10.1183/16000617.0060-2020 ◽

2020 ◽

Vol 29 (156) ◽

pp. 200060 ◽

Cited By ~ 2

Author(s):

Michael J. Alexander ◽

G.R. Scott Budinger ◽

Paul A. Reyfman

Keyword(s):

Single Cell ◽

Rna Sequencing ◽

Cellular Heterogeneity ◽

Unique Challenge ◽

Macrophage Population ◽

Single Cell Rna Sequencing ◽

Individual Contributions ◽

Respiratory Biology ◽

Transcriptional Landscape ◽

General Technical

The complex cellular heterogeneity of the lung poses a unique challenge to researchers in the field. While the use of bulk RNA sequencing has become a ubiquitous technology in systems biology, the technique necessarily averages out individual contributions to the overall transcriptional landscape of a tissue. Single-cell RNA sequencing (scRNA-seq) provides a robust, unbiased survey of the transcriptome comparable to bulk RNA sequencing while preserving information on cellular heterogeneity. In just a few years since this technology was developed, scRNA-seq has already been adopted widely in respiratory research and has contributed to impressive advancements such as the discoveries of the pulmonary ionocyte and of a profibrotic macrophage population in pulmonary fibrosis. In this review, we discuss general technical considerations when considering the use of scRNA-seq and examine how leading investigators have applied the technology to gain novel insights into respiratory biology, from development to disease. In addition, we discuss the evolution of single-cell technologies with a focus on spatial and multi-omics approaches that promise to drive continued innovation in respiratory research.

Download Full-text

Temporal specificity and heterogeneity of the fly immune cells’ transcriptional landscape

10.1101/2019.12.20.871301 ◽

2019 ◽

Cited By ~ 1

Author(s):

Pierre B. Cattenoz ◽

Rosy Sakr ◽

Alexia Pavlidaki ◽

Claude Delaporte ◽

Andrea Riba ◽

...

Keyword(s):

Rna Sequencing ◽

Immune Cells ◽

Humoral Response ◽

Cellular Processes ◽

Temporal Specificity ◽

Pathological Conditions ◽

Open Question ◽

Distinct Features ◽

Developing System ◽

Transcriptional Landscape

SummaryImmune cells provide defense against the non-self, however recent data suggest roles well beyond innate immunity, in processes as diverse as development, metabolism and tumor progression. Nevertheless, the heterogeneity of these cells remains an open question. Using bulk RNA sequencing we find that the Drosophila immune cells (hemocytes) display distinct features in the embryo, a closed and rapidly developing system, compared to the larva, which is exposed to environmental and metabolic challenges. Through single cell RNA sequencing we identify fourteen hemocyte clusters present in unchallenged larvae and associated with distinct cellular processes e.g. proliferation, phagocytosis, metabolic homeostasis and humoral response. Finally, we characterize the changes occurring in the hemocyte clusters upon wasp infestation that triggers the differentiation of a novel cell type, the lamellocyte. This first molecular atlas provides precious insights and paves the way to study the biology of the Drosophila immune cells in physiological and pathological conditions.

Download Full-text

Deep RNA Sequencing Reveals Complex Transcriptional Landscape of a Bat Adenovirus

Journal of Virology ◽

10.1128/jvi.02332-12 ◽

2012 ◽

Vol 87 (1) ◽

pp. 503-511 ◽

Cited By ~ 11

Author(s):

L. Wu ◽

P. Zhou ◽

X. Ge ◽

L.-F. Wang ◽

M. L. Baker ◽

...

Keyword(s):

Rna Sequencing ◽

Transcriptional Landscape

Download Full-text

Transcriptome analysis of thermophilic methylotrophic Bacillus methanolicus MGA3 using RNA-sequencing provides detailed insights into its previously uncharted transcriptional landscape

BMC Genomics ◽

10.1186/s12864-015-1239-4 ◽

2015 ◽

Vol 16 (1) ◽

pp. 73 ◽

Cited By ~ 32

Author(s):

Marta Irla ◽

Armin Neshat ◽

Trygve Brautaset ◽

Christian Rückert ◽

Jörn Kalinowski ◽

...

Keyword(s):

Rna Sequencing ◽

Transcriptome Analysis ◽

Bacillus Methanolicus ◽

Transcriptional Landscape

Download Full-text

A tour through the transcriptional landscape of platelets

Blood ◽

10.1182/blood-2014-04-512756 ◽

2014 ◽

Vol 124 (4) ◽

pp. 493-502 ◽

Cited By ~ 62

Author(s):

Sebastian Schubert ◽

Andrew S. Weyrich ◽

Jesse W. Rowley

Keyword(s):

Rna Sequencing ◽

Platelet Function ◽

Messenger Rna ◽

Next Generation ◽

Tour Guide ◽

It Impacts ◽

Health And Disease ◽

Transcriptional Landscape ◽

Shed Light

Abstract The RNA code found within a platelet and alterations of that code continue to shed light onto the mechanistic underpinnings of platelet function and dysfunction. It is now known that features of messenger RNA (mRNA) in platelets mirror those of nucleated cells. This review serves as a tour guide for readers interested in developing a greater understanding of platelet mRNA. The tour provides an in-depth and interactive examination of platelet mRNA, especially in the context of next-generation RNA sequencing. At the end of the expedition, the reader will have a better grasp of the topography of platelet mRNA and how it impacts platelet function in health and disease.

Download Full-text

RNA Sequencing Reveals Specific Transcriptomic Signatures Distinguishing Effects of the [SWI+] Prion and SWI1 Deletion in Yeast Saccharomyces cerevisiae

Genes ◽

10.3390/genes10030212 ◽

2019 ◽

Vol 10 (3) ◽

pp. 212 ◽

Cited By ~ 5

Author(s):

Yury V. Malovichko ◽

Kirill S. Antonets ◽

Anna R. Maslova ◽

Elena A. Andreeva ◽

Sergey G. Inge-Vechtomov ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Rna Sequencing ◽

Specific Pattern ◽

Point Of View ◽

Yeast Genome ◽

Loss Of Function ◽

Yeast Saccharomyces Cerevisiae ◽

The Media ◽

Functional Inactivation ◽

Chromosome I

Prions are infectious, self-perpetuating protein conformers. In mammals, pathological aggregation of the prion protein causes incurable neurodegenerative disorders, while in yeast Saccharomyces cerevisiae, prion formation may be neutral or even beneficial. According to the prevailing contemporary point of view, prion formation is considered to be a functional inactivation of the corresponding protein whose conformational state shifts from the functional monomeric one to the infectious aggregated one. The Swi1 protein forms the [SWI+] prion and belongs to the nucleosome remodeler complex SWI/SNF controlling the expression of a significant part of the yeast genome. In this work, we performed RNA sequencing of isogenic S. cerevisiae strains grown on the media containing galactose as the sole carbon source. These strains bore the [SWI+] prion or had its structural gene SWI1 deleted. The comparative analysis showed that [SWI+] affects genome expression significantly weaker as compared to the SWI1 deletion. Moreover, in contrast to [SWI+], the SWI1 deletion causes the general inhibition of translation-related genes expression and chromosome I disomy. At the same time, the [SWI+] prion exhibits a specific pattern of modulation of the metabolic pathways and some biological processes and functions, as well as the expression of several genes. Thus, the [SWI+] prion only partially corresponds to the loss-of-function of SWI1 and demonstrates several gain-of-function traits.

Download Full-text