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1. Transcriptional regulation of DC fate specification

Author:
Bosteels, Cédric; Scott, Charlotte L.
Source:
Molecular immunology 2020 v.121 pp. 38-46
ISSN:
0161-5890
Subject:
transcription (genetics),   etc   ; dendritic cells; macrophages;     Show all 3 Subjects
Abstract:
... Dendritic cells function in the immune system to instruct adaptive immune cells to respond accordingly to different threats. While conventional dendritic cells can be subdivided into two main subtypes, termed cDC1s and cDC2s, it is clear that further heterogeneity exists within these subtypes, particularly for cDC2s. Understanding the signals involved in specifying each of these lineages and subty ...
DOI:
10.1016/j.molimm.2020.02.021
PubMed:
32151907
PubMed Central:
PMC7187805

2. Exploring 3D chromatin contacts in gene regulation: The evolution of approaches for the identification of functional enhancer-promoter interaction

Author:
Xu, Hang; Zhang, Shijie; Yi, Xianfu; Plewczynski, Dariusz; Jun Li, Mulin
Source:
Computational and Structural Biotechnology Journal 2020
ISSN:
2001-0370
Subject:
transcription (genetics),   etc   ; chromatin; genes; prediction;     Show all 4 Subjects
Abstract:
... Mechanisms underlying gene regulation are key to understand how multicellular organisms with various cell types develop from the same genetic blueprint. Dynamic interactions between enhancers and genes are revealed to play central roles in controlling gene transcription, but the determinants to link functional enhancer-promoter pairs remain elusive. A major challenge is the lack of reliable approa ...
DOI:
10.1016/j.csbj.2020.02.013
PubMed:
32226593
PubMed Central:
PMC7090358

3. Metabolic regulation of epigenetic remodeling in immune cells

Author:
Britt, Emily C; John, Steven V; Locasale, Jason W; Fan, Jing
Source:
Current opinion in biotechnology 2020 v.63 pp. 111-117
ISSN:
0958-1669
Subject:
transcription (genetics),   etc   ; epigenetics; immune response; immunologic memory; systems biology;     Show all 5 Subjects
Abstract:
... Immune cells are capable of sensing various signals in the microenvironment and turning on specific immune functions in response. The appropriate transition of immune cells into diverse functional states, which is crucial for immunity, involves complex and well-regulated changes in transcriptional program. Accumulating evidence shows that epigenetic remodeling plays a central role in mediating the ...
DOI:
10.1016/j.copbio.2019.12.008

4. When is a transcription factor a NAP?

Author:
Dorman, Charles J; Schumacher, Maria A; Bush, Matthew J; Brennan, Richard G; Buttner, Mark J
Source:
Current opinion in microbiology 2020 v.55 pp. 26-33
ISSN:
1369-5274
Subject:
transcription (genetics),   etc   ; DNA; Streptomyces; binding sites; genes; transcription factors; transcriptome;     Show all 7 Subjects
Abstract:
... Proteins that regulate transcription often also play an architectural role in the genome. Thus, it has been difficult to define with precision the distinctions between transcription factors and nucleoid-associated proteins (NAPs). Anachronistic descriptions of NAPs as 'histone-like' implied an organizational function in a bacterial chromatin-like complex. Definitions based on protein abundance, re ...
DOI:
10.1016/j.mib.2020.01.019

5. A computational system for identifying operons based on RNA-seq data

Author:
Tjaden, Brian
Source:
Methods 2020 v.176 pp. 62-70
ISSN:
1046-2023
Subject:
transcription (genetics),   etc   ; biochemical pathways; databases; operon; probabilistic models; sequence analysis;     Show all 6 Subjects
Abstract:
... An operon is a set of neighboring genes in a genome that is transcribed as a single polycistronic message. Genes that are part of the same operon often have related functional roles or participate in the same metabolic pathways. The majority of all bacterial genes are co-transcribed with one or more other genes as part of a multi-gene operon. Thus, accurate identification of operons is important i ...
DOI:
10.1016/j.ymeth.2019.03.026
PubMed:
30953757
PubMed Central:
PMC6776731

6. H‐NS, IHF, and DnaA lead to changes in nucleoid organizations, replication initiation, and cell division

Author:
Huang, Tingting; Yuan, Hong; Fan, Lifei; Moregen, Morigen
Source:
Journal of basic microbiology 2020 v.60 no.2 pp. 136-148
ISSN:
0233-111X
Subject:
transcription (genetics),   etc   ; DNA; DNA replication; cell division; microbial physiology; proteins;     Show all 6 Subjects
Abstract:
... Histone‐like nucleoid‐structuring protein (H‐NS) and integration host factor (IHF) are major nucleoid‐associated proteins, and DnaA, a replication initiator, may also be related with nucleoid compaction. It has been shown that protein‐dependent DNA compaction is related with many aspects of bacterial physiology, including transcription, DNA replication, and site‐specific recombination. However, the ...
DOI:
10.1002/jobm.201900497

7. Single-Cell Transcriptomics: A High-Resolution Avenue for Plant Functional Genomics

Author:
Rich-Griffin, Charlotte; Stechemesser, Annika; Finch, Jessica; Lucas, Emma; Ott, Sascha; Schäfer, Patrick
Source:
Trends in plant science 2020 v.25 no.2 pp. 186-197
ISSN:
1360-1385
Subject:
transcription (genetics),   etc   ; data collection; genomics; sequence analysis; tissues; transcriptomics;     Show all 6 Subjects
Abstract:
... Plant function is the result of the concerted action of single cells in different tissues. Advances in RNA-seq technologies and tissue processing allow us now to capture transcriptional changes at single-cell resolution. The incredible potential of single-cell RNA-seq lies in the novel ability to study and exploit regulatory processes in complex tissues based on the behaviour of single cells. Impo ...
DOI:
10.1016/j.tplants.2019.10.008

8. Tuning chromosomal gene expression in Escherichia coli by combining single-stranded oligonucleotides mediated recombination and kil counter selection system

Author:
Chen, Wei; Chen, Ruyi; Wang, Hui; Li, Yujuan; Zhang, Yunyi; Li, Shanhu
Source:
Journal of biotechnology 2020 v.307 pp. 63-68
ISSN:
0168-1656
Subject:
transcription (genetics),   etc   ; Escherichia coli; gene expression; genes; metabolic engineering; oligonucleotides;     Show all 6 Subjects
Abstract:
... Extensively modulating gene expression to achieve optimal flux is a critical step in metabolic engineering. Gene expression is usually modulated at the transcriptional level by controlling the strength of a promoter. However, this type of modulation is often hampered by its inability to fully sample the complete continuum of transcriptional control. In Escherichia coli, this limitation can be solv ...
DOI:
10.1016/j.jbiotec.2019.10.014

9. The regulatory cascades of antibiotic production in Streptomyces

Author:
Xia, Haiyang; Zhan, Xinqiao; Mao, Xu-Ming; Li, Yong-Quan
Source:
World journal of microbiology & biotechnology 2020 v.36 no.1 pp. 13
ISSN:
0959-3993
Subject:
transcription (genetics),   etc   ; Streptomyces; antibiotics; biosynthesis; hormones; multigene family; receptors;     Show all 7 Subjects
Abstract:
... Streptomyces is famous for its capability to produce the most abundant antibiotics in all kingdoms. All Streptomyces antibiotics are natural products, whose biosynthesis from the so-called gene clusters are elaborately regulated by pyramidal transcriptional regulatory cascades. In the past decades, scientists have striven to unveil the regulatory mechanisms involved in antibiotic production in Str ...
DOI:
10.1007/s11274-019-2789-4

10. Challenges in detecting and quantifying intron retention from next generation sequencing data

Author:
Broseus, Lucile; Ritchie, William
Source:
Computational and Structural Biotechnology Journal 2020 v.18 pp. 501-508
ISSN:
2001-0370
Subject:
transcription (genetics),   etc   ; high-throughput nucleotide sequencing; introns; messenger RNA;     Show all 4 Subjects
Abstract:
... Intron retention (IR) occurs when an intron is transcribed into pre-mRNA and remains in the final mRNA. An increasing body of literature has demonstrated a major role for IR in numerous biological functions and in disease. Here we give an overview of the different computational approaches for detecting IR events from sequencing data. We show that these are based on different biological and computa ...
DOI:
10.1016/j.csbj.2020.02.010
PubMed:
32206209
PubMed Central:
PMC7078297

11. Modeling regulatory networks using machine learning for systems metabolic engineering

Author:
Kwon, Mun Su; Lee, Byung Tae; Lee, Sang Yup; Kim, Hyun Uk
Source:
Current opinion in biotechnology 2020 v.65 pp. 163-170
ISSN:
0958-1669
Subject:
transcription (genetics),   etc   ; artificial intelligence; biological production; computational methodology; data collection; metabolic engineering; models;     Show all 7 Subjects
Abstract:
... Systems metabolic engineering attempts to engineer a production host’s biological network to overproduce valuable chemicals and materials in a sustainable manner. In contrast to genome-scale metabolic models that are well established, regulatory network models have not been sufficiently considered in systems metabolic engineering despite their importance and recent notable advances. In this paper, ...
DOI:
10.1016/j.copbio.2020.02.014

12. Kinetic affinity index informs the divisions of nitrate flux in aerobic denitrification

Author:
Ruan, Yunjie; Ma, Bin; Cai, Chen; Cai, Lei; Gu, Jun; Lu, Hui-Feng; Xu, Xiang-Yang; Zhang, Meng
Source:
Bioresource technology 2020 v.309 pp. 123345
ISSN:
0960-8524
Subject:
transcription (genetics),   etc   ; denitrification; denitrifying microorganisms; nitrate reduction; nitrates; nitrogen; nitrogen balance; phenotype; wastewater; wastewater treatment;     Show all 10 Subjects
Abstract:
... Aerobic denitrification is attracting increasing attention since its advantage of complete nitrogen removal in a single aerobic reactor with simplified configurations. This study investigated the nitrate kinetic affinity (half-saturation index, Kₘ) by an isolated aerobic denitrifier named P. balearica strain RAD-17. It turned out that strain RAD-17 had a high Kₘ of 162.5 mg-N/L and maximum nitrate ...
DOI:
10.1016/j.biortech.2020.123345

13. The HBx and HBc of hepatitis B virus can influence Id1 and Id3 by reducing their transcription and stability

Author:
Xia, Lulu; Wang, Shilie; Zhang, Hongpeng; Yang, Yuan; Wei, Jie; Shi, Yueyuan; Zou, Chunhong; Liu, Junye; Luo, Miao; Huang, Ailong; Wang, Deqiang
Source:
Virus research 2020 v.284 pp. 197973
ISSN:
0168-1702
Subject:
transcription (genetics),   etc   ; Hepatitis B virus; carcinogenesis; hepatitis B; hepatoma; signal transduction; viral proteins; viruses;     Show all 8 Subjects
Abstract:
... Hepatitis B virus (HBV) infection is closely related with the occurrence and development of hepatocellular carcinoma (HCC), in which Hepatitis B virus x protein (HBx) and core protein (HBc) play crucial roles. Additionally, inhibitors of differentiation (Id) proteins exhibited significant correlation with liver cancer development. Here, we identified that HBV dramatically inhibited the expression ...
DOI:
10.1016/j.virusres.2020.197973

14. RNA and protein-based nanodevices for mammalian post-transcriptional circuits

Author:
Kawasaki, Shunsuke; Ono, Hiroki; Hirosawa, Moe; Saito, Hirohide
Source:
Current opinion in biotechnology 2020 v.63 pp. 99-110
ISSN:
0958-1669
Subject:
transcription (genetics),   etc   ; RNA; biomedical research; gene regulatory networks; mammals; synthetic genes;     Show all 6 Subjects
Abstract:
... Mammalian synthetic gene circuits have promise in biological and medical research due to their capability of controlling cellular functions. Especially, post-transcriptional circuits are growing in interest because of features that include compatibility and superior safety. RNA-based molecular nanodevices are often a core component in these circuits. RNA nanodevices that act as translational contr ...
DOI:
10.1016/j.copbio.2019.11.019

15. Stories of Salicylic Acid: A Plant Defense Hormone

Author:
Ding, Pingtao; Ding, Yuli
Source:
Trends in plant science 2020 v.25 no.6 pp. 549-565
ISSN:
1360-1385
Subject:
transcription (genetics),   etc   ; biochemical pathways; biosynthesis; immunity; pathogens; phenylalanine ammonia-lyase; plant hormones; proteins; salicylic acid;     Show all 9 Subjects
Abstract:
... Salicylic acid (SA) is a key plant hormone required for establishing resistance to many pathogens. SA biosynthesis involves two main metabolic pathways with multiple steps: the isochorismate and the phenylalanine ammonia-lyase pathways. Transcriptional regulations of SA biosynthesis are important for fine-tuning SA level in plants. We highlight here recent discoveries on SA biosynthesis and transc ...
DOI:
10.1016/j.tplants.2020.01.004

16. Characterization of chromosome organization in the differentiation of acute myeloid leukemia cells by all-trans retinoic acid

Author:
Hu, Yanping; Zhao, Hongchao; Zhao, Yixun; Zheng, Jiawen; Guo, Yongjun; Ma, Jie
Source:
Life sciences 2020 v.249 pp. 117479
ISSN:
0024-3205
Subject:
transcription (genetics),   etc   ; chromosomes; epigenetics; myeloid leukemia; neoplasm cells; precipitin tests; retinoic acid; topology;     Show all 8 Subjects
Abstract:
... A concomitant change of nucleus shape and chromosome conformation often happens in all-trans retinoic acid (ATRA)-induced differentiation of acute myeloid leukemia cells. However, the relation between the 3D chromosome architecture and the genome-wide epigenetic pattern for transcriptional regulation is poorly understood. In this study, high-throughput chromosome conformation capture (Hi-C) and ch ...
DOI:
10.1016/j.lfs.2020.117479

17. BTB domain-containing protein 6 is involved in the development of locust wings during the nymph to adult transition

Author:
Zhao, Xiaoming; Zhang, Jing; Yang, Yang; Liu, Weimin; Zhang, Jianzhen
Source:
International journal of biological macromolecules 2020 v.150 pp. 965-973
ISSN:
0141-8130
Subject:
transcription (genetics),   etc   ; Locusta migratoria; ecdysone receptor; ecdysterone; genes; imagos; locusts; nymphs; phenotype; signal transduction; wings;     Show all 11 Subjects
Abstract:
... The development of insect wings is a complex process controlled by a series of genes, whereas the mechanism of wing development of orthoptera insects is less frequently reported. In the present study, a BTB domain-containing protein 6 (LmBTBD6) gene was identified from Locusta migratoria. Its encoded protein belongs to the BTB-BACK-PHR subfamily, and is highly conserved among insect species. LmBTB ...
DOI:
10.1016/j.ijbiomac.2019.10.267

18. Parallel Transcriptional Regulation of Artemisinin and Flavonoid Biosynthesis

Author:
Hassani, Danial; Fu, Xueqing; Shen, Qian; Khalid, Muhammad; Rose, Jocelyn K.C.; Tang, Kexuan
Source:
Trends in plant science 2020 v.25 no.5 pp. 466-476
ISSN:
1360-1385
Subject:
transcription (genetics),   etc   ; Artemisia annua; Plasmodium; artemisinin; biosynthesis; flavonoids; malaria; structural genes; synergism; transcription factors;     Show all 10 Subjects
Abstract:
... Plants regulate the synthesis of specialized compounds through the actions of individual transcription factors (TFs) or sets of TFs. One such compound, artemisinin from Artemisia annua, is widely used as a pharmacological product in the first-line treatment of malaria. However, the emergence of resistance to artemisinin in Plasmodium species, as well as its low production rates, have required inno ...
DOI:
10.1016/j.tplants.2020.01.001

19. Targeting cancer epigenetics with CRISPR-dCAS9: Principles and prospects

Author:
Rahman, Mohammad Mijanur; Tollefsbol, Trygve O.
Source:
Methods 2020
ISSN:
1046-2023
Subject:
transcription (genetics),   etc   ; CRISPR-Cas systems; cancer therapy; epigenetics; neoplasms; precision medicine; surgery;     Show all 7 Subjects
Abstract:
... Cancer therapeutics is an ever-evolving field due to incessant demands for effective and precise treatment options. Over the last few decades, cancer treatment strategies have shifted somewhat from surgery to targeted precision medicine. CRISPR-dCas9 is an emerging version of precision cancer therapy that has been adapted from the prokaryotic CRISPR-Cas system. Once ligated to epigenetic effectors ...
DOI:
10.1016/j.ymeth.2020.04.006

20. Transcriptome analysis of antennal cytochrome P450s and their transcriptional responses to plant and locust volatiles in Locusta migratoria

Author:
Wu, Haihua; Liu, Yongmei; Shi, Xuekai; Zhang, Xueyao; Ye, Changlü; Zhu, Kun Yan; Zhu, Fang; Zhang, Jianzhen; Ma, Enbo
Source:
International journal of biological macromolecules 2020 v.149 pp. 741-753
ISSN:
0141-8130
Subject:
transcription (genetics),   etc   ; Locusta migratoria; antennae; biosynthesis; cytochrome P-450; enzymes; mitochondria; odor compounds; phylogeny; transcriptomics;     Show all 10 Subjects
Abstract:
... Cytochrome P450 monooxygenases (P450s) constitute a large superfamily of heme-thiolate proteins that are involved in the biosynthesis or degradation of endogenous compounds and detoxification of exogenous chemicals. It has been reported that P450s could serve as odorant-degrading enzymes (ODEs) to inactivate odorants to avoid saturating the antennae. However, there is little information about P450 ...
DOI:
10.1016/j.ijbiomac.2020.01.309