RNA-Seq-Based Transcriptome Profiling of Early Nitrogen Deficiency Response in Cucumber Seedlings Provides New Insight into the Putative Nitrogen Regulatory Network

Psoriasis is an immune-mediated inflammatory skin disease with a complex etiology involving environmental and genetic factors. A better insight into related genomic alteration helps design precise therapies leading to better treatment outcome. Gene expression in psoriasis can provide relevant information about the altered expression of mRNA transcripts, thus giving new insights into the disease onset. Techniques for transcriptome analyses, such as microarray and RNA sequencing (RNA-seq), are relevant tools for the discovery of new biomarkers as well as new therapeutic targets. This review summarizes the findings related to the contribution of keratinocytes in the pathogenesis of psoriasis by an in-depth review of studies that have examined psoriatic transcriptomes in the past years. It also provides valuable information on reconstructed 3D psoriatic skin models using cells isolated from psoriatic patients for transcriptomic studies.

Download Full-text

(274) RNA-seq based transcriptome profiling of human and mouse dorsal root ganglia provides insight into potential new pain targets

Journal of Pain ◽

10.1016/j.jpain.2016.01.180 ◽

2016 ◽

Vol 17 (4) ◽

pp. S44

Author(s):

A. Torck ◽

J. Kim ◽

M. Zhang ◽

G. Dussor ◽

T. Price ◽

...

Keyword(s):

Dorsal Root Ganglia ◽

Dorsal Root ◽

Transcriptome Profiling ◽

Rna Seq ◽

Human And Mouse ◽

Insight Into

Download Full-text

Improved TGIRT-seq methods for comprehensive transcriptome profiling with decreased adapter dimer formation and bias correction

10.1101/474031 ◽

2018 ◽

Author(s):

Hengyi Xu ◽

Jun Yao ◽

Douglas C. Wu ◽

Alan M. Lambowitz

Keyword(s):

Rna Structure ◽

Transcriptome Profiling ◽

Rna Seq ◽

Structure Mapping ◽

Dimer Formation ◽

Biochemical Basis ◽

Reverse Transcriptases ◽

Small Ncrnas ◽

Rna Structure Mapping ◽

Insight Into

ABSTRACTThermostable group II intron reverse transcriptases (TGIRTs) with high fidelity and processivity have been used for a variety of RNA sequencing (RNA-seq) applications, including comprehensive profiling of whole-cell, exosomal, and human plasma RNAs; quantitative tRNA-seq based on the ability of TGIRT enzymes to give full-length reads of tRNAs and other structured small ncRNAs; high-throughput mapping of post-transcriptional modifications; and RNA structure mapping. Here, we improved TGIRT-seq methods for comprehensive transcriptome profiling by (i) rationally designing RNA-seq adapters that minimize adapter dimer formation, and (ii) developing biochemical and computational methods that remediate 5’- and 3’-end biases. These improvements, some of which may be applicable to other RNA-seq methods, increase the efficiency of TGIRT-seq library construction and improve coverage of very small RNAs, such as miRNAs. Our findings provide insight into the biochemical basis of 5’- and 3’-end biases in RNA-seq and suggest general approaches for remediating biases and decreasing adapter dimer formation.

Download Full-text

Faculty Opinions recommendation of RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718448277.793503061 ◽

2015 ◽

Author(s):

Mark Giembycz

Keyword(s):

Smooth Muscle ◽

Smooth Muscle Cells ◽

Airway Smooth Muscle ◽

Transcriptome Profiling ◽

Muscle Cells ◽

Airway Smooth Muscle Cells ◽

Rna Seq ◽

Responsive Gene

Download Full-text

Faculty Opinions recommendation of RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718448277.793496543 ◽

2014 ◽

Author(s):

Yassine Amrani

Keyword(s):

Smooth Muscle ◽

Smooth Muscle Cells ◽

Airway Smooth Muscle ◽

Transcriptome Profiling ◽

Muscle Cells ◽

Airway Smooth Muscle Cells ◽

Rna Seq ◽

Responsive Gene

Download Full-text

NKL Homeobox Gene VENTX Is Part of a Regulatory Network in Human Conventional Dendritic Cells

International Journal of Molecular Sciences ◽

10.3390/ijms22115902 ◽

2021 ◽

Vol 22 (11) ◽

pp. 5902

Author(s):

Stefan Nagel ◽

Claudia Pommerenke ◽

Corinna Meyer ◽

Hans G. Drexler

Keyword(s):

Dendritic Cells ◽

Transcription Factors ◽

Cell Lines ◽

Expression Profiling ◽

Regulatory Network ◽

Homeobox Gene ◽

Leukemia Cell Line ◽

Specific Gene ◽

Rna Seq ◽

And Function

Recently, we documented a hematopoietic NKL-code mapping physiological expression patterns of NKL homeobox genes in human myelopoiesis including monocytes and their derived dendritic cells (DCs). Here, we enlarge this map to include normal NKL homeobox gene expressions in progenitor-derived DCs. Analysis of public gene expression profiling and RNA-seq datasets containing plasmacytoid and conventional dendritic cells (pDC and cDC) demonstrated HHEX activity in both entities while cDCs additionally expressed VENTX. The consequent aim of our study was to examine regulation and function of VENTX in DCs. We compared profiling data of VENTX-positive cDC and monocytes with VENTX-negative pDC and common myeloid progenitor entities and revealed several differentially expressed genes encoding transcription factors and pathway components, representing potential VENTX regulators. Screening of RNA-seq data for 100 leukemia/lymphoma cell lines identified prominent VENTX expression in an acute myelomonocytic leukemia cell line, MUTZ-3 containing inv(3)(q21q26) and t(12;22)(p13;q11) and representing a model for DC differentiation studies. Furthermore, extended gene analyses indicated that MUTZ-3 is associated with the subtype cDC2. In addition to analysis of public chromatin immune-precipitation data, subsequent knockdown experiments and modulations of signaling pathways in MUTZ-3 and control cell lines confirmed identified candidate transcription factors CEBPB, ETV6, EVI1, GATA2, IRF2, MN1, SPIB, and SPI1 and the CSF-, NOTCH-, and TNFa-pathways as VENTX regulators. Live-cell imaging analyses of MUTZ-3 cells treated for VENTX knockdown excluded impacts on apoptosis or induced alteration of differentiation-associated cell morphology. In contrast, target gene analysis performed by expression profiling of knockdown-treated MUTZ-3 cells revealed VENTX-mediated activation of several cDC-specific genes including CSFR1, EGR2, and MIR10A and inhibition of pDC-specific genes like RUNX2. Taken together, we added NKL homeobox gene activities for progenitor-derived DCs to the NKL-code, showing that VENTX is expressed in cDCs but not in pDCs and forms part of a cDC-specific gene regulatory network operating in DC differentiation and function.

Download Full-text

Transcriptome profiling of Cysticercus Pisiformis provides insight into responses to host bile acids

Parasitology International ◽

10.1016/j.parint.2020.102246 ◽

2021 ◽

Vol 81 ◽

pp. 102246

Author(s):

Zhong-li Liu ◽

Shuai Wang ◽

Xue-peng Cai ◽

Qiao-ying Zeng

Keyword(s):

Bile Acids ◽

Transcriptome Profiling ◽

Insight Into

Download Full-text

Gene Expression and Carcass Traits Are Different between Different Quality Grade Groups in Red-Faced Hereford Steers

Animals ◽

10.3390/ani11071910 ◽

2021 ◽

Vol 11 (7) ◽

pp. 1910

Author(s):

Bailey Engle ◽

Molly Masters ◽

Jane Ann Boles ◽

Jennifer Thomson

Keyword(s):

Gene Expression ◽

Transcriptome Profiling ◽

Fat Deposition ◽

Lower Shear ◽

The Us ◽

Quality Grade ◽

Longissimus Lumborum ◽

Muscle Biochemistry ◽

Marbling Deposition ◽

Insight Into

Fat deposition is important to carcass value and some palatability characteristics. Carcasses with higher USDA quality grades produce more value for producers and processors in the US system and are more likely to have greater eating satisfaction. Using genomics to identify genes impacting marbling deposition provides insight into muscle biochemistry that may lead to ways to better predict fat deposition, especially marbling and thus quality grade. Hereford steers (16) were managed the same from birth through harvest after 270 days on feed. Samples were obtained for tenderness and transcriptome profiling. As expected, steaks from Choice carcasses had a lower shear force value than steaks from Select carcasses; however, steaks from Standard carcasses were not different from steaks from Choice carcasses. A significant number of differentially expressed (DE) genes was observed in the longissimus lumborum between Choice and Standard carcass RNA pools (1257 genes, p < 0.05), but not many DE genes were observed between Choice and Select RNA pools. Exploratory analysis of global muscle tissue transcriptome from Standard and Choice carcasses provided insight into muscle biochemistry, specifically the upregulation of extracellular matrix development and focal adhesion pathways and the downregulation of RNA processing and metabolism in Choice versus Standard. Additional research is needed to explore the function and timing of gene expression changes.

Download Full-text