Transcription-Austin最新文献_第2页

Minimization and complete loss of general transcription factor proteins in the intracellular parasite Encephalitozoon cuniculi. 细胞内寄生虫阴沟脑虫体内一般转录因子蛋白的最小化和完全丧失。

IF 3.6

Transcription-Austin Pub Date : 2024-06-01 Epub Date: 2024-05-09 DOI: 10.1080/21541264.2024.2350162

Alana E Belkevich, Andrew Y Khalil, Wayne A Decatur, Ryan J Palumbo, Bruce A Knutson

{"title":"Minimization and complete loss of general transcription factor proteins in the intracellular parasite Encephalitozoon cuniculi.","authors":"Alana E Belkevich, Andrew Y Khalil, Wayne A Decatur, Ryan J Palumbo, Bruce A Knutson","doi":"10.1080/21541264.2024.2350162","DOIUrl":"10.1080/21541264.2024.2350162","url":null,"abstract":"Genome compaction is a common evolutionary feature of parasites. The unicellular, obligate intracellular parasite Encephalitozoon cuniculi has one of smallest known eukaryotic genomes, and is nearly four times smaller than its distant fungi relative, the budding yeast Saccharomyces cerevisiae. Comparison of the proteins encoded by compacted genomes to those encoded by larger genomes can reveal the most highly conserved features of the encoded proteins. In this study, we identified the proteins comprising the RNA polymerases and their corresponding general transcription factors by using several bioinformatic approaches to compare the transcription machinery of E. cuniculi and S. cerevisiae. Surprisingly, our analyses revealed an overall reduction in the size of the proteins comprising transcription machinery of E. cuniculi, which includes the loss of entire regions or functional domains from proteins, as well as the loss of entire proteins and complexes. Unexpectedly, we found that the E. cuniculi ortholog of Rpc37 (a RNA Polymerase III subunit) more closely resembles the H. sapiens ortholog of Rpc37 than the S. cerevisiae ortholog of Rpc37, in both size and structure. Overall, our findings provide new insight into the minimal core eukaryotic transcription machinery and help define the most critical features of Pol components and general transcription factors.","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":" ","pages":"97-113"},"PeriodicalIF":3.6,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11810082/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140899858","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Negative feedback systems for modelling NF-κB transcription factor oscillatory activity. 用于模拟 NF-κB 转录因子振荡活动的负反馈系统。

IF 3.6

Transcription-Austin Pub Date : 2024-06-01 Epub Date: 2024-05-13 DOI: 10.1080/21541264.2024.2331887

Bonawentura Kochel

{"title":"Negative feedback systems for modelling NF-κB transcription factor oscillatory activity.","authors":"Bonawentura Kochel","doi":"10.1080/21541264.2024.2331887","DOIUrl":"10.1080/21541264.2024.2331887","url":null,"abstract":"Low-dimensional negative feedback systems (NFSs) were developed within a signal flow model to describe the oscillatory activities of NF-κB caused by interactions with its inhibitor IκBα. The NFSs were established as 3rd- and 4th-order linear systems containing unperturbed and perturbed negative feedback (NF) loops with constant or time-varying NF strengths and a feed-forward loop. NF-related analytical solutions to the NFSs representing the time courses of NF-κB and IκBα were determined and their exact mathematical relationship was found. The NFS's parameters were determined to fit the experimental time courses of NF-κB in TNF-α-stimulated embryonic fibroblasts, rela-/- embryonic fibroblasts reconstituted with RelA, C9L cells, GFP-p65 knock-in embryonic fibroblasts and embryogenic fibroblasts lacking Iκβ and IκBε, LPS-stimulated IC-21 macrophages treated or not with DCPA, and anti-IgM-stimulated DT40 B-lymphocytes. The unperturbed and perturbed NFSs describing the above biosystems generated isochronous and non-isochronous solutions, depending on a constant or time-varying NF strength, respectively. The oscillation period of the NF-coupled solutions, the phase difference between them and the time delays in the appearance of cytoplasmic IκBα after stimulation of NF-κB were determined. A significant divergence between the IκBα solutions to the NFSs and the IκBα experimental courses led to a rejection of the NF coupling between NF-κB and IκBα in the above biosystems. It was shown that neither the linearity nor the low dimensionality of the NFSs altered the NF relationship and the divergence between the IκBα solutions to the NFS and IκBα experimental time courses. Although the NF relationship between IκBα and NF-κB was not confirmed in all the experimental data analyzed, delayed negative feedback was found in some cases.","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":" ","pages":"65-96"},"PeriodicalIF":3.6,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11810101/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140913092","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Deciphering the dynamic code: DNA recognition by transcription factors in the ever-changing genome. 破译动态密码：转录因子在不断变化的基因组中识别 DNA。

IF 3.6

Transcription-Austin Pub Date : 2024-06-01 Epub Date: 2024-07-20 DOI: 10.1080/21541264.2024.2379161

Yumi Minyi Yao, Irina Miodownik, Michael P O'Hagan, Muhammad Jbara, Ariel Afek

引用次数: 0

Structure and function of bacterial transcription regulators of the SorC family. SorC 家族细菌转录调节器的结构和功能。

IF 3.6

Transcription-Austin Pub Date : 2024-06-01 Epub Date: 2024-09-03 DOI: 10.1080/21541264.2024.2387895

Markéta Šoltysová, Pavlína Řezáčová

引用次数: 0

From silence to symphony: transcriptional repression and recovery in response to DNA damage. 从沉默到交响乐：DNA损伤时的转录抑制和恢复。

IF 3.6

Transcription-Austin Pub Date : 2024-06-01 Epub Date: 2024-10-01 DOI: 10.1080/21541264.2024.2406717

Kamal Ajit, Monika Gullerova

引用次数: 0

RNA polymerase collisions and their role in transcription. RNA 聚合酶碰撞及其在转录中的作用

IF 3.6

Transcription-Austin Pub Date : 2024-02-01 Epub Date: 2024-02-15 DOI: 10.1080/21541264.2024.2316972

Ling Wang

引用次数: 0

Bacterial phenotypic heterogeneity through the lens of single-cell RNA sequencing. 通过单细胞 RNA 测序透视细菌表型异质性。

IF 3.6

Transcription-Austin Pub Date : 2024-02-01 Epub Date: 2024-03-26 DOI: 10.1080/21541264.2024.2334110

Alex W Walls, Adam Z Rosenthal

{"title":"Bacterial phenotypic heterogeneity through the lens of single-cell RNA sequencing.","authors":"Alex W Walls, Adam Z Rosenthal","doi":"10.1080/21541264.2024.2334110","DOIUrl":"10.1080/21541264.2024.2334110","url":null,"abstract":"Bacterial transcription is not monolithic. Microbes exist in a wide variety of cell states that help them adapt to their environment, acquire and produce essential nutrients, and engage in both competition and cooperation with their neighbors. While we typically think of bacterial adaptation as a group behavior, where all cells respond in unison, there is often a mixture of phenotypic responses within a bacterial population, where distinct cell types arise. A primary phenomenon driving these distinct cell states is transcriptional heterogeneity. Given that bacterial mRNA transcripts are extremely short-lived compared to eukaryotes, their transcriptional state is closely associated with their physiology, and thus the transcriptome of a bacterial cell acts as a snapshot of the behavior of that bacterium. Therefore, the application of single-cell transcriptomics to microbial populations will provide novel insight into cellular differentiation and bacterial ecology. In this review, we provide an overview of transcriptional heterogeneity in microbial systems, discuss the findings already provided by single-cell approaches, and plot new avenues of inquiry in transcriptional regulation, cellular biology, and mechanisms of heterogeneity that are made possible when microbial communities are analyzed at single-cell resolution.","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":" ","pages":"48-62"},"PeriodicalIF":3.6,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11093040/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140294946","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Maintaining transcriptional homeostasis during cell cycle. 在细胞周期中维持转录平衡

IF 3.6

Transcription-Austin Pub Date : 2024-02-01 Epub Date: 2023-09-01 DOI: 10.1080/21541264.2023.2246868

Lucía Ramos-Alonso, Pierre Chymkowitch

引用次数: 0

An emerging paradigm in epigenetic marking: coordination of transcription and replication. 表观遗传标记的新范式：转录与复制的协调。

IF 3.6

Transcription-Austin Pub Date : 2024-02-01 Epub Date: 2024-02-20 DOI: 10.1080/21541264.2024.2316965

Tyler K Fenstermaker, Svetlana Petruk, Alexander Mazo

{"title":"An emerging paradigm in epigenetic marking: coordination of transcription and replication.","authors":"Tyler K Fenstermaker, Svetlana Petruk, Alexander Mazo","doi":"10.1080/21541264.2024.2316965","DOIUrl":"10.1080/21541264.2024.2316965","url":null,"abstract":"DNA replication and RNA transcription both utilize DNA as a template and therefore need to coordinate their activities. The predominant theory in the field is that in order for the replication fork to proceed, transcription machinery has to be evicted from DNA until replication is complete. If that does not occur, these machineries collide, and these collisions elicit various repair mechanisms which require displacement of one of the enzymes, often RNA polymerase, in order for replication to proceed. This model is also at the heart of the epigenetic bookmarking theory, which implies that displacement of RNA polymerase during replication requires gradual re-building of chromatin structure, which guides recruitment of transcriptional proteins and resumption of transcription. We discuss these theories but also bring to light newer data that suggest that these two processes may not be as detrimental to one another as previously thought. This includes findings suggesting that these processes can occur without fork collapse and that RNA polymerase may only be transiently displaced during DNA replication. We discuss potential mechanisms by which RNA polymerase may be retained at the replication fork and quickly rebind to DNA post-replication. These discoveries are important, not only as new evidence as to how these two processes are able to occur harmoniously but also because they have implications on how transcriptional programs are maintained through DNA replication. To this end, we also discuss the coordination of replication and transcription in light of revising the current epigenetic bookmarking theory of how the active gene status can be transmitted through S phase.","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":" ","pages":"22-37"},"PeriodicalIF":3.6,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11093037/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139913687","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction. 更正。

IF 3.6

Transcription-Austin Pub Date : 2024-02-01 Epub Date: 2024-03-21 DOI: 10.1080/21541264.2024.2333606

引用次数: 0