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1. A hitchhiker's guide to single-cell transcriptomics and data analysis pipelines

Author:
Nayak, Richa; Hasija, Yasha
Source:
Genomics 2021 v.113 no.2 pp. 606-619
ISSN:
0888-7543
Subject:
transcriptomics,   etc   ; cell biology; genomics;     Show all 3 Subjects
Abstract:
... Single-cell transcriptomics (SCT) is a tour de force in the era of big omics data that has led to the accumulation of massive cellular transcription data at an astounding resolution of single cells. It provides valuable insights into cells previously unachieved by bulk cell analysis and is proving crucial in uncovering cellular heterogeneity, identifying rare cell populations, distinct cell-lineag ...
DOI:
10.1016/j.ygeno.2021.01.007

2. FGF primes angioblast formation by inducing ETV2 and LMO2 via FGFR1/BRAF/MEK/ERK

Author:
Chen, Peng-Chieh; Hsueh, Ya-Wen; Lee, Yi-Hsuan; Tsai, Hung-Wen; Tsai, Kuen-Jer; Chiang, Po-Min
Source:
Cellular and molecular life sciences 2021 v.78 no.5 pp. 2199-2212
ISSN:
1420-682X
Subject:
transcriptomics,   etc   ; mesoderm; protein synthesis;     Show all 3 Subjects
Abstract:
... It is critical to specify a signal that directly drives the transition that occurs between cell states. However, such inferences are often confounded by indirect intercellular communications or secondary transcriptomic changes due to primary transcription factors. Although FGF is known for its importance during mesoderm-to-endothelium differentiation, its specific role and signaling mechanisms are ...
DOI:
10.1007/s00018-020-03630-8

3. leapR: An R Package for Multiomic Pathway Analysis

Author:
Danna, Vincent; Mitchell, Hugh; Anderson, Lindsey; Godinez, Iobani; Gosline, Sara J. C.; Teeguarden, Justin; McDermott, Jason E.
Source:
Journal of proteome research 2021 v.20 no.4 pp. 2116-2121
ISSN:
1535-3907
Subject:
transcriptomics,   etc   ; genomics; metabolomics; proteome; proteomics; research;     Show all 6 Subjects
Abstract:
... A generalized goal of many high-throughput data studies is to identify functional mechanisms that underlie observed biological phenomena, whether they be disease outcomes or metabolic output. Increasingly, studies that rely on multiple sources of high-throughput data (genomic, transcriptomic, proteomic, metabolomic) are faced with a challenge of summarizing the data to generate testable hypotheses ...
DOI:
10.1021/acs.jproteome.0c00963

4. Hedgehog signaling regulates regenerative patterning and growth in Harmonia axyridis leg

Author:
Zhou, Hang; Ma, Zhongzheng; Wang, Zhiqi; Yan, Shuo; Wang, Dan; Shen, Jie
Source:
Cellular and molecular life sciences 2021 v.78 no.5 pp. 2185-2197
ISSN:
1420-682X
Subject:
transcriptomics,   etc   ; Erinaceidae; Harmonia axyridis; animals; genes;     Show all 5 Subjects
Abstract:
... Appendage regeneration has been widely studied in many species. Compared to other animal models, Harmonia axyridis has the advantage of a short life cycle, is easily reared, has strong regeneration capacity and contains systemic RNAi, making it a model organism for research on appendage regeneration. Here, we performed transcriptome analysis, followed by gene functional assays to reveal the molecu ...
DOI:
10.1007/s00018-020-03631-7

5. Profiling of cis- and trans-acting factors supporting noncanonical splice site activation

Author:
Erkelenz, Steffen; Poschmann, Gereon; Ptok, Johannes; Müller, Lisa; Schaal, Heiner
Source:
RNA biology 2021 v.18 no.1 pp. 118-130
ISSN:
1555-8584
Subject:
transcriptomics,   etc   ; DNA damage; genome; humans; proteomics; spliceosomes;     Show all 6 Subjects
Abstract:
... Recently, by combining transcriptomics with functional splicing reporter assays we were able to identify GT > GC > TT as the three highest ranked dinucleotides of human 5ʹ splice sites (5’ss). Here, we have extended our investigations to the proteomic characterization of nuclear proteins that bind to canonical and noncanonical 5’ss. Surprisingly, we found that U1 snRNP binding to functional 5’ss s ...
DOI:
10.1080/15476286.2020.1798111

6. Reprogramming of m⁶A epitranscriptome is crucial for shaping of transcriptome and proteome in response to hypoxia

Author:
Wang, Yan-Jie; Yang, Bing; Lai, Qiao; Shi, Jun-Fang; Peng, Jiang-Yun; Zhang, Yin; Hu, Kai-Shun; Li, Ya-Qing; Peng, Jing-Wen; Yang, Zhi-Zhi; Li, Yao-Ting; Pan, Yue; Koeffler, H. Phillip; Liao, Jian-You; Yin, Dong
Source:
RNA biology 2021 v.18 no.1 pp. 131-143
ISSN:
1555-8584
Subject:
transcriptomics,   etc   ; energy; hypoxia; proteome; sequence analysis; transcriptome;     Show all 6 Subjects
Abstract:
... Hypoxia causes a series of responses supporting cells to survive in harsh environments. Substantial post-transcriptional and translational regulation during hypoxia has been observed. However, detailed regulatory mechanism in response to hypoxia is still far from complete. RNA m⁶A modification has been proven to govern the life cycle of RNAs. Here, we reported that total m⁶A level of mRNAs was dec ...
DOI:
10.1080/15476286.2020.1804697

7. CleanBSequences: an efficient curator of biological sequences in R

Author:
Pozzi, Florencia I.; Green, Gisela Y.; Barbona, Ivana G.; Rodríguez, Gustavo R.; Felitti, Silvina A.
Source:
Molecular genetics and genomics 2020 v.295 no.4 pp. 837-841
ISSN:
1617-4615
Subject:
transcriptomics,   etc   ; epigenetics; genomics;     Show all 3 Subjects
Abstract:
... This work presents a new method and tool to solve a common problem of molecular biologists and geneticists who use molecular markers in their scientific research and developments: curation of sequences. Omic studies conducted by molecular biologists and geneticists usually involve the use of molecular markers. AFLP, cDNA-AFLP, and MSAP are examples of markers that render information at the genomic ...
DOI:
10.1007/s00438-020-01671-z

8. tidybulk: an R tidy framework for modular transcriptomic data analysis

Author:
Mangiola, Stefano; Molania, Ramyar; Dong, Ruining; Doyle, Maria A.; Papenfuss, Anthony T.
Source:
Genome biology 2021 v.22 no.1 pp. 42
ISSN:
1474-760X
Subject:
transcriptomics,   etc   ; algorithms; data analysis; ecosystems; genome; learning; reproducibility; transcription (genetics);     Show all 8 Subjects
Abstract:
... Recently, efforts have been made toward the harmonization of transcriptomic data structures and workflows using the concept of data tidiness, to facilitate modularisation. We present tidybulk, a modular framework for bulk transcriptional analyses that introduces a tidy transcriptomic data structure paradigm and analysis grammar. Tidybulk covers a wide variety of analysis procedures and integrates ...
DOI:
10.1186/s13059-020-02233-7

9. Adrenal androgens, adrenarche, and zona reticularis: A human affair?

Author:
Dumontet, Typhanie; Martinez, Antoine
Source:
Molecular and cellular endocrinology 2021 v.528 pp. 111239
ISSN:
0303-7207
Subject:
transcriptomics,   etc   ; ; adrenal cortex; androgens; childhood; cortex; humans; mice; sexual maturity;     Show all 9 Subjects
Abstract:
... In humans, reticularis cells of the adrenal cortex fuel the production of androgen steroids, constituting the driver of numerous morphological changes during childhood. These steps are considered a precocious stage of sexual maturation and are grouped under the term “adrenarche”. This review describes the molecular and enzymatic characteristics of the zona reticularis, along with the possible sign ...
DOI:
10.1016/j.mce.2021.111239

10. Direct conversion of adult human fibroblasts into functional endothelial cells using defined factors

Author:
Han, Jung-Kyu; Shin, Youngchul; Sohn, Min-Hwan; Choi, Saet-Byeol; Shin, Dasom; You, Youngrang; Shin, Jong-Yeon; Seo, Jeong-Sun; Kim, Hyo-Soo
Source:
Biomaterials 2021 v.272 pp. 120781
ISSN:
0142-9612
Subject:
transcriptomics,   etc   ; biocompatible materials; epigenetics; fibroblasts; humans; mice; transcriptome;     Show all 7 Subjects
Abstract:
... We aimed to directly convert adult human dermal fibroblasts (aHDFs) into functional endothelial cells (ECs). Lentiviral vectors encoding endothelial transcription factors (TFs) were constructed. We examined whether five TFs (FOXO1, ER71, KLF2, TAL1, and LMO2) used for the generation of mouse induced ECs (iECs) could convert the aHDFs into human iECs. Twenty-eight days after transduction with lenti ...
DOI:
10.1016/j.biomaterials.2021.120781

11. Eight new mitogenomes clarify the phylogenetic relationships of Stromboidea within the caenogastropod phylogenetic framework

Author:
Irwin, Alison R.; Strong, Ellen E.; Kano, Yasunori; Harper, Elizabeth M.; Williams, Suzanne T.
Source:
Molecular phylogenetics and evolution 2021 v.158 pp. 107081
ISSN:
1055-7903
Subject:
transcriptomics,   etc   ; Littorinimorpha; Strombidae; genomics; locomotion; mitochondrial genome; monophyly;     Show all 7 Subjects
Abstract:
... Members of the gastropod superfamily Stromboidea (Littorinimorpha) are characterised by their elaborate shell morphologies, distinctive mode of locomotion, and often large and colourful eyes. This iconic group comprises over 130 species, including many large and charismatic species. The family Strombidae is of particular interest, largely due to its commercial importance and wide distribution in t ...
DOI:
10.1016/j.ympev.2021.107081

12. Co-invalidation of Prnp and Sprn in FVB/N mice affects reproductive performances and highlight complex biological relationship between PrP and Shadoo

Author:
Castille, Johan; Passet, Bruno; Makhzami, Samira; Vilotte, Marthe; Moazami-Goudarzi, Katayoun; Truchet, Sandrine; Daniel-Carlier, Nathalie; Gaillard, Anne-Laure; Andréoletti, Olivier; Vaiman, Daniel; Beauvallet, Christian; Vaiman, Anne; Floriot, Sandrine; Calvel, Pierre; Mouillet-Richard, Sophie; Duchesne, Amandine; Béringue, Vincent; Vilotte, Jean-Luc
Source:
Biochemical and biophysical research communications 2021 v.551 pp. 1-6
ISSN:
0006-291X
Subject:
transcriptomics,   etc   ; antagonists; embryogenesis; genetic background; lactation; mice; phenotype; research;     Show all 8 Subjects
Abstract:
... Shadoo and PrP belongs to the same protein family, whose biological function remains poorly understood. Previous experiments reported potential functional redundancies or antagonisms between these two proteins, depending on the tissue analysed. While knockdown experiments suggested the requirement of Shadoo in the absence of PrP during early mouse embryogenesis, knockout ones, on the contrary, hig ...
DOI:
10.1016/j.bbrc.2021.03.013

13. Biosynthesis of alkaloids in Amaryllidaceae plants: a review

Author:
Desgagné-Penix, Isabel
Source:
Phytochemistry reviews 2021 v.20 no.2 pp. 409-431
ISSN:
1568-7767
Subject:
transcriptomics,   etc   ; Amaryllidaceae; alkaloids; biosynthesis; cholinesterase inhibitors; markets; metabolites; phytochemicals;     Show all 8 Subjects
Abstract:
... Amaryllidaceae alkaloids are a group of specialized metabolites found predominantly in the Amaryllidaceae plant family. Approximately 600 naturally occurring Amaryllidaceae alkaloids have been identified, many of which possess a variety of potent biological and pharmacological properties. However, only the Amaryllidaceae alkaloid galanthamine, an acetylcholinesterase inhibitor used to treat sympto ...
DOI:
10.1007/s11101-020-09678-5

14. Comparative transcriptome analysis of canola carrying clubroot resistance from ‘Mendel’ or Rutabaga and the development of molecular markers

Author:
Summanwar, Aarohi; Farid, Mehdi; Basu, Urmila; Kav, Nat; Rahman, Habibur
Source:
Physiological and molecular plant pathology 2021 v.114 pp. 101640
ISSN:
0885-5765
Subject:
transcriptomics,   etc   ; canola; clubroot; genes; introgression; metabolism; plant pathology; rutabagas; trehalose;     Show all 9 Subjects
Abstract:
... Clubroot resistance has been introgressed into spring canola from various sources; however, the molecular basis of this using multiple resistances has not yet been investigated. We conducted a comparative transcriptomic study using resistance introgressed from rutabaga (RtR) and winter canola cv. ‘Mendel’ (MdR) and identified ~3500 upregulated genes of which 8–9% genes were involved in primary and ...
DOI:
10.1016/j.pmpp.2021.101640

15. Extensive transcription mis-regulation and membrane defects in AdipoR2-deficient cells challenged with saturated fatty acids

Author:
Ruiz, Mario; Palmgren, Henrik; Henricsson, Marcus; Devkota, Ranjan; Jaiswal, Himjyot; Maresca, Marcello; Bohlooly-Y, Mohammad; Peng, Xiao-Rong; Borén, Jan; Pilon, Marc
Source:
Biochimica et biophysica acta 2021 v.1866 no.4 pp. 158884
ISSN:
1388-1981
Subject:
transcriptomics,   etc   ; diet; homeostasis; humans; lipid metabolism; lipidomics; transcriptome;     Show all 7 Subjects
Abstract:
... How cells maintain vital membrane lipid homeostasis while obtaining most of their constituent fatty acids from a varied diet remains largely unknown. Here, we used transcriptomics, lipidomics, growth and respiration assays, and membrane property analyses in human HEK293 cells or human umbilical vein endothelial cells (HUVEC) to show that the function of AdipoR2 is to respond to membrane rigidifica ...
DOI:
10.1016/j.bbalip.2021.158884

16. Genome Sequence of the Bacteriophage CL31 and Interaction with the Host Strain Corynebacterium glutamicum ATCC 13032

Author:
Hünnefeld, Max; Viets, Ulrike; Sharma, Vikas; Wirtz, Astrid; Hardy, Aël; Frunzke, Julia
Source:
Viruses 2021 v.13 no.3
ISSN:
1999-4915
Subject:
transcriptomics,   etc   ; Corynebacterium glutamicum; adsorption; bacteriophages; biosynthesis; genomics; mycolic acids; proteome;     Show all 8 Subjects
Abstract:
... In this study, we provide a comprehensive analysis of the genomic features of the phage CL31 and the infection dynamics with the biotechnologically relevant host strain Corynebacterium glutamicum ATCC 13032. Genome sequencing and annotation of CL31 revealed a 45-kbp genome composed of 72 open reading frames, mimicking the GC content of its host strain (54.4%). An ANI-based distance matrix showed t ...
DOI:
10.3390/v13030495

17. Transcriptomic analysis reveals resistance mechanisms of Klebsiella michiganensis to copper toxicity under acidic conditions

Author:
Yan, Xiaoxue; Yang, Junlin; Wang, Qi; Lin, Shanshan
Source:
Ecotoxicology and environmental safety 2021 v.211 pp. 111919
ISSN:
0147-6513
Subject:
transcriptomics,   etc   ; Klebsiella; ecotoxicology; genomics; metabolism; pH; polymers; sulfur; toxicity;     Show all 9 Subjects
Abstract:
... The aim of this study was to elucidate the effect of pH on bacterial resistance mechanisms to copper (Cu) stress by genomic and transcriptomic analysis. Klebsiella michiganensis cells were exposed to 0.5 mM CuCl₂ at pH 4 and 5. Lower pH (pH < 4) strongly inhibited K. michiganensis growth, while Cu stress and higher pH (pH > 5) induced Cu precipitation in the medium. Transcriptomic analyses indicat ...
DOI:
10.1016/j.ecoenv.2021.111919

18. Сord blood hematopoietic stem cells ex vivo enhance the bipotential commitment of adipose mesenchymal stromal progenitors

Author:
Buravkova, L.B.; Ezdakova, M.I.; Andrianova, I.V.; Gornostaeva, A.N.; Bobyleva, P.I.; Andreeva, E.R.
Source:
Life sciences 2021 v.268 pp. 118970
ISSN:
0024-3205
Subject:
transcriptomics,   etc   ; ; alkaline phosphatase; blood; coculture; therapeutics; transcription (genetics);     Show all 7 Subjects
Abstract:
... Stroma-dependent ex vivo expansion of hematopoietic stem progenitor cells (HSPCs) is a valid approach for cell therapy needs. Our goal was to verify whether HSPCs can affect stromal cells to optimize their functions during ex vivo expansion.HSPCs from cord blood (cb) were cocultured with growth-arrested adipose mesenchymal stromal cells (MSCs). Commitment-related transcriptional and secretory prof ...
DOI:
10.1016/j.lfs.2020.118970

19. Epigenomic and transcriptomic analysis of chronic inflammatory diseases

Author:
Tam, Sabrina Ka Man; Leung, Danny Chi Yeu
Source:
Genes & genomics 2021 v.43 no.3 pp. 227-236
ISSN:
1976-9571
Subject:
transcriptomics,   etc   ; epigenetics; epigenome; etiology; gene expression; genomics; inflammation; transcription (genetics);     Show all 8 Subjects
Abstract:
... Chronic inflammatory diseases (CIDs) have complex pathologies that result from aberrant and persistent immune responses. However, the precise triggers and mechanisms remain elusive. An important aspect of CID research focuses on epigenetics modifications, which regulate gene expression and provide a dynamic transcriptional response to inflammation. In recent years, mounting evidence has demonstrat ...
DOI:
10.1007/s13258-021-01045-8

20. Mg deficiency interacts with the circadian clock and phytochromes pathways in Arabidopsis

Author:
Rivière, Quentin; Xiao, Qiying; Gutsch, Annelie; Defrance, Matthieu; Webb, Alex A. R.; Verbruggen, Nathalie
Source:
Annals of applied biology 2021 v.178 no.2 pp. 387-399
ISSN:
0003-4746
Subject:
transcriptomics,   etc   ; Arabidopsis thaliana; circadian clocks; magnesium; phytochrome; starvation;     Show all 6 Subjects
Abstract:
... Little is known about the relationship between nutrition and the circadian clock in plants. The first global transcriptomic study in plants of the response to magnesium deficiency (–Mg) revealed that the circadian clock was affected in the Arabidopsis thaliana model species. Interactions between the circadian clock and Mg status were here investigated in the light of recent knowledge. We highlight ...
DOI:
10.1111/aab.12659