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1. Molecular mechanisms involved in functional macroevolution of plant transcription factors

Author:
Romani, Facundo; Moreno, Javier E.
Source:
Thenew phytologist 2021 v.230 no.4 pp. 1345-1353
ISSN:
0028-646X
Subject:
transcription (genetics),   etc   ; evolution; genes;     Show all 3 Subjects
Abstract:
... Transcription factors (TFs) are key components of the transcriptional regulation machinery. In plants, they accompanied the evolution from unicellular aquatic algae to complex flowering plants that dominate the land environment. The adaptations of the body plan and physiological responses required changes in the biological functions of TFs. Some ancestral gene regulatory networks are highly conser ...
DOI:
10.1111/nph.17161

2. Cis-regulatory code for determining the action of Foxd as both an activator and a repressor in ascidian embryos

Author:
Tokuhiro, Shinichi; Satou, Yutaka
Source:
Developmental biology 2021 v.476 pp. 11-17
ISSN:
0012-1606
Subject:
transcription (genetics),   etc   ; ; Ciona; embryogenesis; invertebrates;     Show all 5 Subjects
Abstract:
... In early embryos of Ciona, an invertebrate chordate, the animal-vegetal axis is established by the combinatorial actions of maternal factors. One target of these maternal factors, Foxd, is specifically expressed in the vegetal hemisphere and stabilizes the animal-vegetal axis by activating vegetal hemisphere-specific genes and repressing animal hemisphere-specific genes. This dual functionality is ...
DOI:
10.1016/j.ydbio.2021.03.010

3. Fast-acting chemical tools to delineate causality in transcriptional control

Author:
Jaeger, Martin G.; Winter, Georg E.
Source:
Molecular cell 2021 v.81 no.8 pp. 1617-1630
ISSN:
1097-2765
Subject:
transcription (genetics),   etc   ; active sites; genes;     Show all 3 Subjects
Abstract:
... Multi-dimensional omics profiling continues to illuminate the complexity of cellular processes. Because of difficult mechanistic interpretation of phenotypes induced by slow perturbation, fast experimental setups are increasingly used to dissect causal interactions directly in cells. Here we review a growing body of studies that leverage rapid pharmacological perturbation to delineate causality in ...
DOI:
10.1016/j.molcel.2021.02.015

4. Calycindaphines A–J, Daphniphyllum alkaloids from the roots of Daphniphyllum calycinum

Author:
Yang, Ji; Liu, Xin; Fu, Jing; Lyu, Hao-Yuan; Bai, Li-Ping; Jiang, Zhi-Hong; Zhu, Guo-Yuan
Source:
RSC advances 2021 v.11 no.16 pp. 9057-9066
ISSN:
2046-2069
Subject:
transcription (genetics),   etc   ; Daphniphyllum; alkaloids; spectroscopy;     Show all 4 Subjects
Abstract:
... Ten new Daphniphyllum alkaloids, calycindaphines A–J (1–10), together with seventeen known alkaloids were isolated from the roots of Daphniphyllum calycinum. Their structures were established by extensive spectroscopic methods and compared with data from literature. Compound 1 is a novel alkaloid with a new rearrangement C₂₂ skeleton with the 5/8/7/5/5 ring system. Compound 2 represents the second ...
DOI:
10.1039/d1ra00107h

5. Plant cell totipotency: Insights into cellular reprogramming

Author:
Su, Ying Hua; Tang, Li Ping; Zhao, Xiang Yu; Zhang, Xian Sheng
Source:
Journal of integrative plant biology 2021 v.63 no.1 pp. 228-243
ISSN:
1672-9072
Subject:
transcription (genetics),   etc   ; somatic embryogenesis; totipotency;     Show all 3 Subjects
Abstract:
... Plant cells have a powerful capacity in their propagation to adapt to environmental change, given that a single plant cell can give rise to a whole plant via somatic embryogenesis without the need for fertilization. The reprogramming of somatic cells into totipotent cells is a critical step in somatic embryogenesis. This process can be induced by stimuli such as plant hormones, transcriptional reg ...
DOI:
10.1111/jipb.12972

6. YTHDF1-regulated expression of TEAD1 contributes to the maintenance of intestinal stem cells

Author:
Jiang, Dan; Hou, Jingyu; Qian, Yu; Gao, Yunyi; Gao, Xiangwei; Wei, Saisai
Source:
Biochemical and biophysical research communications 2021 v.557 pp. 85-89
ISSN:
0006-291X
Subject:
transcription (genetics),   etc   ; intestines; methyltransferases; organoids; research; ribosomes;     Show all 6 Subjects
Abstract:
... N6-methyladenosine (m⁶A) mRNA modification has been defined as a crucial regulator in various biological processes. Recent studies indicated an essential role of YTHDF1, an m⁶A reader, in the maintenance of intestinal stem cells (ISCs), while the detailed mechanism remains to be explored. By searching our m⁶A sequencing, RNA sequencing, and ribosome profiling data, we identified the transcriptiona ...
DOI:
10.1016/j.bbrc.2021.03.175

7. Transcriptional and epigenetic regulation of PD-1 expression

Author:
Chi, Zengde; Lu, Yan; Yang, Yinlong; Li, Bingqing; Lu, Peiyuan
Source:
Cellular and molecular life sciences 2021 v.78 no.7 pp. 3239-3246
ISSN:
1420-682X
Subject:
transcription (genetics),   etc   ; T-lymphocytes; autoimmunity; epigenetics; neoplasms;     Show all 5 Subjects
Abstract:
... Programmed cell death-1 (PD-1) is a co-inhibitory receptor that plays important roles in regulating T cell immunity and peripheral tolerance. PD-1 signaling prevents T cells from overactivation during acute infections, but it maintains T cell exhaustion during chronic infections. Tumor cells can exploit the PD-1 signaling pathway to evade antitumor immune responses. The PD-1 signaling pathway is a ...
DOI:
10.1007/s00018-020-03737-y

8. Adiponectin promotes myogenic differentiation via a Mef2C-AdipoR1 positive feedback loop

Author:
Yu, An; Zheng, Yu; Gong, Yuqing; Yu, Ruofan; Yang, Zaiqing; Chen, Xiaodong
Source:
Gene 2021 v.771 pp. 145380
ISSN:
0378-1119
Subject:
transcription (genetics),   etc   ; adiponectin; genes; metabolism; muscle development;     Show all 5 Subjects
Abstract:
... Adiponectin is an important hormone that regulates systemic metabolism, and it has been reported that globular adiponectin promotes myogenic differentiation. However, the mechanisms by which adiponectin promotes myogenic differentiation is not fully understood. In the present study, we show that adiponectin and its receptor 1 are significantly up-regulated during myogenic differentiation and that ...
DOI:
10.1016/j.gene.2020.145380

9. Cytokinin Signaling and De Novo Shoot Organogenesis

Author:
Hnatuszko-Konka, Katarzyna; Gerszberg, Aneta; Weremczuk-Jeżyna, Izabela; Grzegorczyk-Karolak, Izabela
Source:
Genes 2021 v.12 no.2
ISSN:
2073-4425
Subject:
transcription (genetics),   etc   ; cytokinins; epigenetics; organogenesis; plant hormones;     Show all 5 Subjects
Abstract:
... The ability to restore or replace injured tissues can be undoubtedly named among the most spectacular achievements of plant organisms. One of such regeneration pathways is organogenesis, the formation of individual organs from nonmeristematic tissue sections. The process can be triggered in vitro by incubation on medium supplemented with phytohormones. Cytokinins are a class of phytohormones demon ...
DOI:
10.3390/genes12020265

10. Soft repression: Subtle transcriptional regulation with global impact

Author:
Mitra, Anindita; Raicu, Ana‐Maria; Hickey, Stephanie L.; Pile, Lori A.; Arnosti, David N.
Source:
BioEssays 2021 v.43 no.2 pp. e2000231
ISSN:
0265-9247
Subject:
transcription (genetics),   etc   ; gene expression; gene expression regulation;     Show all 3 Subjects
Abstract:
... Pleiotropically acting eukaryotic corepressors such as retinoblastoma and SIN3 have been found to physically interact with many widely expressed “housekeeping” genes. Evidence suggests that their roles at these loci are not to provide binary on/off switches, as is observed at many highly cell‐type specific genes, but rather to serve as governors, directly modulating expression within certain bound ...
DOI:
10.1002/bies.202000231

11. Epidermal resident γδ T cell development and function in skin

Author:
Xu, Yingping; Dimitrion, Peter; Cvetkovski, Steven; Zhou, Li; Mi, Qing-Sheng
Source:
Cellular and molecular life sciences 2021 v.78 no.2 pp. 573-580
ISSN:
1420-682X
Subject:
transcription (genetics),   etc   ; T-lymphocytes; epigenetics; homeostasis;     Show all 4 Subjects
Abstract:
... Epidermal resident γδ T cells, or dendritic epidermal T cells (DETCs) in mice, are a unique and conserved population of γδ T cells enriched in the epidermis, where they serve as the regulators of immune responses and sense skin injury. Despite the great advances in the understanding of the development, homeostasis, and function of DETCs in the past decades, the origin and the underlying molecular ...
DOI:
10.1007/s00018-020-03613-9

12. High-Throughput Discovery and Characterization of Human Transcriptional Effectors

Author:
Tycko, Josh; DelRosso, Nicole; Hess, Gaelen T.; Aradhana,; Banerjee, Abhimanyu; Mukund, Aditya; Van, Mike V.; Ego, Braeden K.; Yao, David; Spees, Kaitlyn; Suzuki, Peter; Marinov, Georgi K.; Kundaje, Anshul; Bassik, Michael C.; Bintu, Lacramioara
Source:
Cell 2020 v.183 no.7 pp. 2020-2035.e16
ISSN:
0092-8674
Subject:
transcription (genetics),   etc   ; genes; humans;     Show all 3 Subjects
Abstract:
... Thousands of proteins localize to the nucleus; however, it remains unclear which contain transcriptional effectors. Here, we develop HT-recruit, a pooled assay where protein libraries are recruited to a reporter, and their transcriptional effects are measured by sequencing. Using this approach, we measure gene silencing and activation for thousands of domains. We find a relationship between repres ...
DOI:
10.1016/j.cell.2020.11.024

13. Developmental Transcriptional Enhancers: A Subtle Interplay between Accessibility and Activity: Considering Quantitative Accessibility Changes between Different Regulatory States of an Enhancer Deconvolutes the Complex Relationship between Accessibility and Activity

Author:
Bozek, Marta; Gompel, Nicolas
Source:
BioEssays 2020 v.42 no.4 pp. e1900188
ISSN:
0265-9247
Subject:
transcription (genetics),   etc   ; chromatin; models;     Show all 3 Subjects
Abstract:
... Measurements of open chromatin in specific cell types are widely used to infer the spatiotemporal activity of transcriptional enhancers. How reliable are these predictions? In this review, it is argued that the relationship between the accessibility and activity of an enhancer is insufficiently described by simply considering open versus closed chromatin, or active versus inactive enhancers. Inste ...
DOI:
10.1002/bies.201900188

14. 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:
transcription (genetics),   etc   ; algorithms; data analysis; ecosystems; genome; learning; reproducibility; transcriptomics;     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

15. Transcriptional and epigenetic control of hematopoietic stem cell fate decisions in vertebrates

Author:
Ding, Yanyan; Liu, Zhenxin; Liu, Feng
Source:
Developmental biology 2021 v.475 pp. 156-164
ISSN:
0012-1606
Subject:
transcription (genetics),   etc   ; adults; blood; chromatin; epigenetics; hematopoiesis; hematopoietic stem cells;     Show all 7 Subjects
Abstract:
... Hematopoietic stem cells (HSCs) are the foundation of adult hematopoiesis that produce all types of mature blood lineages. In vertebrates, HSC development is a stepwise process, coordinately regulated by chromatin architectures and a group of transcriptional and epigenetic regulators. A deeper understanding of the molecular mechanisms governing the generation, expansion, and function of HSCs holds ...
DOI:
10.1016/j.ydbio.2021.03.003

16. YAP1 and its fusion proteins in cancer initiation, progression and therapeutic resistance

Author:
Szulzewsky, Frank; Holland, Eric C.; Vasioukhin, Valeri
Source:
Developmental biology 2021 v.475 pp. 205-221
ISSN:
0012-1606
Subject:
transcription (genetics),   etc   ; homeostasis; humans; metastasis; microRNA; mutation; neoplasms; oncogenes; therapeutics;     Show all 9 Subjects
Abstract:
... YAP1 is a transcriptional co-activator whose activity is controlled by the Hippo signaling pathway. In addition to important functions in normal tissue homeostasis and regeneration, YAP1 has also prominent functions in cancer initiation, aggressiveness, metastasis, and therapy resistance. In this review we are discussing the molecular functions of YAP1 and its roles in cancer, with a focus on the ...
DOI:
10.1016/j.ydbio.2020.12.018

17. Applicability of spatial transcriptional profiling to cancer research

Author:
Bassiouni, Rania; Gibbs, Lee D.; Craig, David W.; Carpten, John D.; McEachron, Troy A.
Source:
Molecular cell 2021 v.81 no.8 pp. 1631-1639
ISSN:
1097-2765
Subject:
transcription (genetics),   etc   ; architecture; assays; gene expression; information; landscapes; research;     Show all 7 Subjects
Abstract:
... Spatial transcriptional profiling provides gene expression information within the important anatomical context of tissue architecture. This approach is well suited to characterizing solid tumors, which develop within a complex landscape of malignant cells, immune cells, and stroma. In a single assay, spatial transcriptional profiling can interrogate the role of spatial relationships among these ce ...
DOI:
10.1016/j.molcel.2021.03.016

18. H3K27ac bookmarking promotes rapid post-mitotic activation of the pluripotent stem cell program without impacting 3D chromatin reorganization

Author:
Pelham-Webb, Bobbie; Polyzos, Alexander; Wojenski, Luke; Kloetgen, Andreas; Li, Jiexi; Di Giammartino, Dafne Campigli; Sakellaropoulos, Theodore; Tsirigos, Aristotelis; Core, Leighton; Apostolou, Effie
Source:
Molecular cell 2021 v.81 no.8 pp. 1732-1748.e8
ISSN:
1097-2765
Subject:
transcription (genetics),   etc   ; acetylation; chromatin; mice; mitosis; stem cells; topology;     Show all 7 Subjects
Abstract:
... During self-renewal, cell-type-defining features are drastically perturbed in mitosis and must be faithfully reestablished upon G1 entry, a process that remains largely elusive. Here, we characterized at a genome-wide scale the dynamic transcriptional and architectural resetting of mouse pluripotent stem cells (PSCs) upon mitotic exit. We captured distinct waves of transcriptional reactivation wit ...
DOI:
10.1016/j.molcel.2021.02.032

19. Contributions of Histone Variants in Nucleosome Structure and Function

Author:
Kurumizaka, Hitoshi; Kujirai, Tomoya; Takizawa, Yoshimasa
Source:
Journal of molecular biology 2021 v.433 no.6 pp. 166678
ISSN:
0022-2836
Subject:
transcription (genetics),   etc   ; DNA; epigenetics; eukaryotic cells; histones; nucleosomes;     Show all 6 Subjects
Abstract:
... Chromatin compacts genomic DNA in eukaryotes. The primary chromatin unit is the nucleosome core particle, composed of four pairs of the core histones, H2A, H2B, H3, and H4, and 145–147 base pairs of DNA. Since replication, recombination, repair, and transcription take place in chromatin, the structure and dynamics of the nucleosome must be versatile. These nucleosome characteristics underlie the e ...
DOI:
10.1016/j.jmb.2020.10.012

20. Single-cell transcriptional analysis reveals developmental stage-dependent changes in retinal progenitors in the murine early optic vesicle

Author:
Yamada, Ryuichi; Oguri, Akira; Fujiki, Katsunori; Shirahige, Katsuhiko; Takezoe, Hirotaka; Takahashi, Naoki; Kanai, Yoshiakira
Source:
Biochemical and biophysical research communications 2021 v.543 pp. 80-86
ISSN:
0006-291X
Subject:
transcription (genetics),   etc   ; ; epithelium; mice; research; retina; sequence analysis;     Show all 7 Subjects
Abstract:
... The optic vesicle in the developing embryonic eye contains a multitude of neuroepithelial progenitors that subsequently differentiate into functionally distinct domains of the optic cup, such as the neural retina, pigment epithelium, and optic stalk. To investigate cell-type diversity across early optic vesicles before regionalization of the optic cup, we performed single-cell RNA-sequencing (scRN ...
DOI:
10.1016/j.bbrc.2021.01.043