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1. Parental and transgenerational impairments of thyroid endocrine system in zebrafish by 2,4,6-tribromophenol

Author:
Yuxi Zhou; Juanjuan Fu; Min Wang; Yongyong Guo; Lihua Yang; Jian Han; Bingsheng Zhou
Source:
Journal of environmental sciences (China) 2023 v.124 pp. 291-299
ISSN:
1001-0742
Subject:
transcription (genetics),   etc   ; Danio rerio; adults; bioaccumulation; brain; chemical analysis; flame retardants; histopathology; humans; liver; pollution; progeny; toxicity; China;     Show all 14 Subjects
Abstract:
... Many environmental contaminants could be transmitted from parents and generate impairments to their progeny. The 2,4,6-tribromophenol (TBP), a novel brominated flame retardant which has been frequently detected in various organisms, was supposed to be bioaccumulated and intergenerational transmitted in human beings. Previous studies revealed that TBP could disrupt thyroid endocrine system in zebra ...
DOI:
10.1016/j.jes.2021.09.022

2. Reference gene selection for transcriptional profiling by RT-qPCR in the 28-spotted larger potato ladybird

Author:
Yu-Xing Zhang; Qiao Tan; Chen-Hui Shen; Jian-Jian Wu; Yi-Kuan Wu; Wen-Ze Li; Lin Jin; Guo-Qing Li
Source:
Journal of Asia-Pacific entomology 2022 v.25 no.2 pp. 101900
ISSN:
1226-8615
Subject:
transcription (genetics),   etc   ; Henosepilachna vigintioctopunctata; entomology;     Show all 3 Subjects
Abstract:
... Henosepilachna vigintioctomaculata is one of the most serious defoliates attacking potatoes. However, studies on functional genes have greatly been limited due to the insufficiency of effective and stable endogenous references to normalize RT-qPCR data. In this report, nine housekeeping genes (RPL4, RPL6, RPL13, RPL32, RPS18, ACT, EF1α, GAPDH and α-TUB) involved in different biological processes w ...
DOI:
10.1016/j.aspen.2022.101900

3. The loud minority: Transcriptionally active HIV-1-infected cells survive, proliferate, and persist

Author:
Jack A. Collora; Ya-Chi Ho
Source:
Cell 2022 v.185 no.2 pp. 227-229
ISSN:
0092-8674
Subject:
transcription (genetics),   etc   ; HIV infections; chromatin; proviruses;     Show all 4 Subjects
Abstract:
... The shock-and-kill strategy reactivates HIV-1 latent reservoir for immune clearance. Einkauf et al. found that some HIV-1-infected cells that persist and proliferate have transcriptionally active HIV-1 in permissive chromatin. Silent proviruses in repressive chromatin resist reactivation. Understanding HIV-1-chromatin interactions and how transcriptionally active HIV-1-infected cells survive is a ...
DOI:
10.1016/j.cell.2021.12.038

4. YAP signaling in preovulatory granulosa cells is critical for the functioning of the EGF network during ovulation

Author:
Esdras Corrêa Dos Santos; Ariane Lalonde-Larue; Alfredo Quites Antoniazzi; Marcos Henrique Barreta; Christopher A. Price; Paulo Bayard Dias Gonçalves; Valério Marques Portela; Gustavo Zamberlam
Source:
Molecular and cellular endocrinology 2022 v.541 pp. 111524
ISSN:
0303-7207
Subject:
transcription (genetics),   etc   ; cows; ovulation; phosphorylation; ultrasonics;     Show all 5 Subjects
Abstract:
... Failure to ovulate is a major cause of infertility. The critical pathway that induces ovulation involves the EGF and MAPK phosphorylation, but studies in rodents have suggested that the Hippo activator, YAP, is also involved. It is unknown whether YAP-dependent transcriptional activity is important for the LH- or EGF-induced ovulatory cascade in monovulatory species such as the cow. Using a well-d ...
DOI:
10.1016/j.mce.2021.111524

5. Transcriptional and post-transcriptional control of epithelial-mesenchymal plasticity: why so many regulators?

Author:
Melodie Migault; Sunil Sapkota; Cameron P. Bracken
Source:
Cellular and molecular life sciences 2022 v.79 no.3 pp. 182
ISSN:
1420-682X
Subject:
transcription (genetics),   etc   ; adults; fibrosis; metastasis; microRNA; plasticity;     Show all 6 Subjects
Abstract:
... The dynamic transition between epithelial-like and mesenchymal-like cell states has been a focus for extensive investigation for decades, reflective of the importance of Epithelial-Mesenchymal Transition (EMT) through development, in the adult, and the contributing role EMT has to pathologies including metastasis and fibrosis. Not surprisingly, regulation of the complex genetic networks that under ...
DOI:
10.1007/s00018-022-04199-0

6. Function moves biomolecular condensates in phase space

Author:
Marina Feric; Tom Misteli
Source:
BioEssays 2022 v.44 no.5 pp. e2200001
ISSN:
0265-9247
Subject:
transcription (genetics),   etc   ; DNA; cell nucleus; condensates; mitochondria; separation;     Show all 6 Subjects
Abstract:
... Phase separation underlies the formation of biomolecular condensates. We hypothesize the cellular processes that occur within condensates shape their structural features. We use the example of transcription to discuss structure–function relationships in condensates. Various types of transcriptional condensates have been reported across the evolutionary spectrum in the cell nucleus as well as in mi ...
DOI:
10.1002/bies.202200001

7. Regulators regulated: Different layers of control for plasma membrane phosphoinositides in plants

Author:
Mareike Heilmann; Ingo Heilmann
Source:
Current opinion in plant biology 2022 v.67 pp. 102218
ISSN:
1369-5266
Subject:
transcription (genetics),   etc   ; biogenesis; cytoskeleton; plant tissues; plasma membrane;     Show all 5 Subjects
Abstract:
... The membranes of plant cells serve diverse physiological roles, which are defined largely by the localized and dynamic recruitment of proteins. Signaling lipids, such as phosphoinositides, can aid protein recruitment to the plasma membrane via specific recognition of their head groups and influence vesicular trafficking, cytoskeletal dynamics and other processes, with ramifications for plant tissu ...
DOI:
10.1016/j.pbi.2022.102218

8. Therapeutic targeting of chromatin: status and opportunities

Author:
Marton Siklos; Stefan Kubicek
Source:
FEBS journal 2022 v.289 no.5 pp. 1276-1301
ISSN:
1742-464X
Subject:
transcription (genetics),   etc   ; chromatin; epigenetics; fruits; genome; neoplasms; therapeutics;     Show all 7 Subjects
Abstract:
... The molecular characterization of mechanisms underlying transcriptional control and epigenetic inheritance since the 1990s has paved the way for the development of targeted therapies that modulate these pathways. In the past two decades, cancer genome sequencing approaches have uncovered a plethora of mutations in chromatin modifying enzymes across tumor types, and systematic genetic screens have ...
DOI:
10.1111/febs.15966

9. Total mRNA and primary human myoblasts’ in vitro cell cycle progression distinguishes between clones

Author:
Kirankumar B. Gudagudi; Niccolò Passerin d’Entrèves; Tracey Ollewagen; Kathryn H. Myburgh
Source:
Biochimie 2022 v.196 pp. 161-170
ISSN:
0300-9084
Subject:
transcription (genetics),   etc   ; cell lines; humans; interphase; myoblasts; transcriptome;     Show all 6 Subjects
Abstract:
... Satellite cells are generally quiescent in vivo. Once activated, progression through the cell cycle begins. Immortalised myoblasts from a single cell line are fairly homogenous in culture, but primary human myoblasts (PHMs) demonstrate heterogeneity. This phenomenon is poorly understood however may impact on PHM expansion. This study aimed to evaluate cell cycle transition from growth to synthesis ...
DOI:
10.1016/j.biochi.2022.01.010

10. Functional analysis of a PISTILLATA-like gene CcMADS20 involved in floral organs specification in citrus

Author:
Xiao-Jin Hou; Li-Xia Ye; Xiao-Yan Ai; Chun-Gen Hu; Zhong-Ping Cheng; Jin-Zhi Zhang
Source:
Plant science 2022 v.319 pp. 111263
ISSN:
0168-9452
Subject:
transcription (genetics),   etc   ; Arabidopsis; Citrus; phylogeny; sequence alignment; transcription factors;     Show all 6 Subjects
Abstract:
... PISTILLATA (PI), as a member of MADS-box transcription factor, plays an important role in petal and stamen specification in Arabidopsis. However, little is known about PI-like genes in citrus. To understand the molecular mechanism of PI during the developmental process of citrus flower, a PI-like gene CcMADS20 was isolated from Citrus Clemantina. Sequence alignment and phylogenetic analysis reveal ...
DOI:
10.1016/j.plantsci.2022.111263

11. Metacell-2: a divide-and-conquer metacell algorithm for scalable scRNA-seq analysis

Author:
Oren Ben-Kiki; Akhiad Bercovich; Aviezer Lifshitz; Amos Tanay
Source:
Genome biology 2022 v.23 no.1 pp. 100
ISSN:
1474-760X
Subject:
transcription (genetics),   etc   ; algorithms; bone marrow; data collection; genome; humans;     Show all 6 Subjects
Abstract:
... Scaling scRNA-seq to profile millions of cells is crucial for constructing high-resolution maps of transcriptional manifolds. Current analysis strategies, in particular dimensionality reduction and two-phase clustering, offer only limited scaling and sensitivity to define such manifolds. We introduce Metacell-2, a recursive divide-and-conquer algorithm allowing efficient decomposition of scRNA-seq ...
DOI:
10.1186/s13059-022-02667-1

12. OmicsView: Omics data analysis through interactive visual analytics

Author:
Fergal Casey; Soumya Negi; Jing Zhu; Yu H. Sun; Maria Zavodszky; Derrick Cheng; Dongdong Lin; Sally John; Michelle A. Penny; David Sexton; Baohong Zhang
Source:
Computational and Structural Biotechnology Journal 2022 v.20 pp. 1277-1285
ISSN:
2001-0370
Subject:
transcription (genetics),   etc   ; biomarkers; biotechnology; data visualization; databases; exercise; humans;     Show all 7 Subjects
Abstract:
... With advances in NGS technologies, transcriptional profiling of human tissue across many diseases is becoming more routine, leading to the generation of petabytes of data deposited in public repositories. There is a need for bench scientists with little computational expertise to be able to access and mine this data to understand disease pathology, identify robust biomarkers of disease and the eff ...
DOI:
10.1016/j.csbj.2022.02.022

13. Plant RNA-mediated gene regulatory network

Author:
Behzad Hajieghrari; Naser Farrokhi
Source:
Genomics 2022 v.114 no.1 pp. 409-442
ISSN:
0888-7543
Subject:
transcription (genetics),   etc   ; gene expression; gene regulatory networks; genes; genomics;     Show all 5 Subjects
Abstract:
... Not all transcribed RNAs are protein-coding. Some non-coding RNAs (ncRNAs) seem to be non-functional and are resulted from spurious transcription. Many others have a significant function in the translation process. Gene expressions depend on complex networks of diverse gene regulatory pathways. Several ncRNAs, as major elements, regulate gene expression in a sequence-specific system either at the ...
DOI:
10.1016/j.ygeno.2021.12.020

14. TetR-Type Regulator Lp_2642 Positively Regulates Plantaricin EF Production Based on Genome-Wide Transcriptome Sequencing of Lactiplantibacillus plantarum 163

Author:
Deyin Zhao; Qian Wang; Fanqiang Meng; Fengxia Lu; Xiaomei Bie; Zhaoxin Lu; Yingjian Lu
Source:
Journal of agricultural and food chemistry 2022 v.70 no.14 pp. 4362-4372
ISSN:
1520-5118
Subject:
transcription (genetics),   etc   ; biosynthesis; chromosomes; food chemistry; plantaricins; plasmids; transcriptome;     Show all 7 Subjects
Abstract:
... Whole-genome and transcriptome sequences of Lactiplantibacillus plantarum 163 are provided. There was one circular chromosome and four circular plasmids, with sizes of 3,131,367; 56,674; 49,140; 43,628; and 36,387 bp, respectively, in L. plantarum 163. The regulator Lp_2642 was selected from the genome data, the overexpression of which increased the transcriptional levels of related genes in plant ...
DOI:
10.1021/acs.jafc.2c00206

15. Vitamin D Receptor (VDR) Gene Polymorphisms Modify the Response to Vitamin D Supplementation: A Systematic Review and Meta-Analysis

Author:
Ricardo Usategui-Martín; Daniel-Antonio De Luis-Román; José María Fernández-Gómez; Marta Ruiz-Mambrilla; José-Luis Pérez-Castrillón
Source:
Nutrients 2022 v.14 no.2 pp. -
ISSN:
2072-6643
Subject:
transcription (genetics),   etc   ; alleles; calcitriol; genotype; meta-analysis; systematic review;     Show all 6 Subjects
Abstract:
... The vitamin D receptor (VDR), a member of the nuclear receptor superfamily of transcriptional regulators, is crucial to calcitriol signalling. VDR is regulated by genetic and environmental factors and it is hypothesised that the response to vitamin D supplementation could be modulated by genetic variants in the VDR gene. The best studied polymorphisms in the VDR gene are Apal (rs7975232), BsmI (rs ...
DOI:
10.3390/nu14020360

16. Driving Chromatin Organisation through N6-methyladenosine Modification of RNA: What Do We Know and What Lies Ahead?

Author:
Tommaso Selmi; Chiara Lanzuolo
Source:
Genes 2022 v.13 no.2 pp. -
ISSN:
2073-4425
Subject:
transcription (genetics),   etc   ; chromatin; gene expression; histone code; mammals; neurophysiology; transcriptome;     Show all 7 Subjects
Abstract:
... In recent years, there has been an increase in research efforts surrounding RNA modification thanks to key breakthroughs in NGS-based whole transcriptome mapping methods. More than 100 modifications have been reported in RNAs, and some have been mapped at single-nucleotide resolution in the mammalian transcriptome. This has opened new research avenues in fields such as neurobiology, developmental ...
DOI:
10.3390/genes13020340

17. Effect of G‐quadruplex loop mutations on the G‐quadruplex formation, protein binding and transcription of BmPOUM2 in Bombyx mori

Author:
Yanfei Chen; Kangkang Niu; Qisheng Song; Qili Feng
Source:
Archives of insect biochemistry and physiology 2022 v.110 no.1 pp. e21876
ISSN:
0739-4462
Subject:
transcription (genetics),   etc   ; Bombyx mori; insect biochemistry; mutation; physiology; transcription factors;     Show all 6 Subjects
Abstract:
... A G‐quadruplex (G4) was identified in the promoter of transcription factor BmPOUM2 in Bombyx mori. This G4 structure contains three loops and is bound by transcription factor BmLARK, facilitating the transcription of BmPOUM2. However, the relationship between the structure and function of the BmPOUM2 G4 remains to be clarified. In this study, loop mutants of the BmPOUM2 G4 structure were generated ...
DOI:
10.1002/arch.21876

18. Growth responses of seedlings under complete submergence in rice cultivars carrying both the submergence-tolerance gene SUB1A-1 and the floating genes SNORKELs

Author:
Shunsuke Oe; Daisuke Sasayama; Quanshu Luo; Hiroshi Fukayama; Tomoko Hatanaka; Tetsushi Azuma
Source:
Plant production science 2022 v.25 no.1 pp. 70-77
ISSN:
1349-1008
Subject:
transcription (genetics),   etc   ; Oryza sativa; cultivars; flooding tolerance; genes; rice; submergence;     Show all 7 Subjects
Abstract:
... We screened 80 Asian rice (Oryza sativa L.) cultivars for the presence of the submergence-tolerance gene SUB1A-1 and the floating genes SNORKEL1 (SK1) and SNORKEL2 (SK2), and found that the deepwater rice cultivar Baisbish (BSB) and the submergence-tolerant cultivar Flood Resistant 13A (FR13A) both possess the SUB1A-1 and the SK1/2. When BSB and FR13A seedlings were completely submerged, spindly g ...
DOI:
10.1080/1343943X.2021.1943465

19. Harnessing plasmid replication mechanism to enable dynamic control of gene copy in bacteria

Author:
Chenyi Li; Yusong Zou; Tian Jiang; Jianli Zhang; Yajun Yan
Source:
Metabolic engineering 2022 v.70 pp. 67-78
ISSN:
1096-7176
Subject:
transcription (genetics),   etc   ; biosynthesis; gene expression; genes; p-coumaric acid; plasmids;     Show all 6 Subjects
Abstract:
... Dynamic regulation has been proved efficient in controlling gene expression at transcriptional, translational, and post-translational level. However, the dynamic regulation at gene replication level has been rarely explored so far. In this study, we established dynamic regulation at gene copy level through engineering controllable plasmid replication to dynamically control the gene expression. Pro ...
DOI:
10.1016/j.ymben.2022.01.003

20. How long does the mRNA remains stable in untreated whole bovine blood?

Author:
Rodrigo Giglioti; Bianca Tainá Azevedo; Henrique Nunes de Oliveira; Luciana Morita Katiki; Anibal Eugênio Vercesi Filho; Márcia Cristina de Sena Oliveira; Cintia Hiromi Okino
Source:
Molecular biology reports 2022 v.49 no.1 pp. 789-795
ISSN:
0301-4851
Subject:
transcription (genetics),   etc   ; Holstein; blood; gene expression; messenger RNA; molecular biology;     Show all 6 Subjects
Abstract:
... BACKGROUND: High quality and quantity of messenger RNA (mRNA) are required for accuracy of gene expression studies and other RNA-based downstream applications. Since RNA is considered a labile macromolecular prone to degradation, which may result in falsely altered gene expression patterns, several commercial stabilizing reagents have been developed aiming to keep RNA stable for long period. Howev ...
DOI:
10.1007/s11033-021-06808-w