Systems Biology of Transcription Regulation
Transcription regulation is a complex process that can be considered and investigated from different perspectives. Traditionally and due to technical reasons (including the evolution of our understanding of the underlying processes) the main focus of the research was made on the regulation of expres...
I tiakina i:
| Ngā kaituhi matua: | , , |
|---|---|
| Hōputu: | Online |
| Reo: | Ingarihi |
| I whakaputaina: |
Frontiers Media SA
2021
|
| Ngā marau: | |
| Urunga tuihono: | 18354 |
| Ngā Tūtohu: |
Kāore He Tūtohu, Me noho koe te mea tuatahi ki te tūtohu i tēnei pūkete!
|
| _version_ | 1869529018350436352 |
|---|---|
| author | Joerg Linde Edgar Wingender Ekaterina Shelest |
| author_browse | Edgar Wingender Ekaterina Shelest Joerg Linde |
| author_facet | Joerg Linde Edgar Wingender Ekaterina Shelest |
| author_sort | Joerg Linde |
| collection | Directory of Open Access Books |
| description | Transcription regulation is a complex process that can be considered and investigated from different perspectives. Traditionally and due to technical reasons (including the evolution of our understanding of the underlying processes) the main focus of the research was made on the regulation of expression through transcription factors (TFs), the proteins directly binding to DNA. On the other hand, intensive research is going on in the field of chromatin structure, remodeling and its involvement in the regulation. Whatever direction we select, we can speak about several levels of regulation. For instance, concentrating on TFs, we should consider multiple regulatory layers, starting with signaling pathways and ending up with the TF binding sites in the promoters and other regulatory regions. However, it is obvious that the TF regulation, also including the upstream processes, represents a modest portion of all processes leading to gene expression. For more comprehensive description of the gene regulation, we need a systematic and holistic view, which brings us to the importance of systems biology approaches. Advances in methodology, especially in high-throughput methods, result in an ever-growing mass of data, which in many cases is still waiting for appropriate consideration. Moreover, the accumulation of data is going faster than the development of algorithms for their systematic evaluation. Data and methods integration is indispensable for the acquiring a systematic as well as a systemic view. In addition to the huge amount of molecular or genetic components of a biological system, the even larger number of their interactions constitutes the enormous complexity of processes occurring in a living cell (organ, organism). In systems biology, these interactions are represented by networks. Transcriptional or, more generally, gene regulatory networks are being generated from experimental ChIPseq data, by reverse engineering from transcriptomics data, or from computational predictions of transcription factor (TF) – target gene relations. While transcriptional networks are now available for many biological systems, mathematical models to simulate their dynamic behavior have been successfully developed for metabolic and, to some extent, for signaling networks, but relatively rarely for gene regulatory networks. Systems biology approaches provide new perspectives that raise new questions. Some of them address methodological problems, others arise from the newly obtained understanding of the data. These open questions and problems are also a subject of this Research Topic. |
| format | Online |
| id | doab-20.500.12854ir-60441 |
| institution | Directory of Open Access Books |
| language | eng |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Frontiers Media SA |
| publisherStr | Frontiers Media SA |
| record_format | ojs |
| spelling | doab-20.500.12854ir-604412024-04-05T12:35:12Z Systems Biology of Transcription Regulation Joerg Linde Edgar Wingender Ekaterina Shelest QH426-470 TA1-2040 TP248.13-248.65 QK1-989 Q1-390 Transcription Regulation network inreference Transcription Factors Systems Biology transcription networks thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAK Genetics (non-medical) Transcription regulation is a complex process that can be considered and investigated from different perspectives. Traditionally and due to technical reasons (including the evolution of our understanding of the underlying processes) the main focus of the research was made on the regulation of expression through transcription factors (TFs), the proteins directly binding to DNA. On the other hand, intensive research is going on in the field of chromatin structure, remodeling and its involvement in the regulation. Whatever direction we select, we can speak about several levels of regulation. For instance, concentrating on TFs, we should consider multiple regulatory layers, starting with signaling pathways and ending up with the TF binding sites in the promoters and other regulatory regions. However, it is obvious that the TF regulation, also including the upstream processes, represents a modest portion of all processes leading to gene expression. For more comprehensive description of the gene regulation, we need a systematic and holistic view, which brings us to the importance of systems biology approaches. Advances in methodology, especially in high-throughput methods, result in an ever-growing mass of data, which in many cases is still waiting for appropriate consideration. Moreover, the accumulation of data is going faster than the development of algorithms for their systematic evaluation. Data and methods integration is indispensable for the acquiring a systematic as well as a systemic view. In addition to the huge amount of molecular or genetic components of a biological system, the even larger number of their interactions constitutes the enormous complexity of processes occurring in a living cell (organ, organism). In systems biology, these interactions are represented by networks. Transcriptional or, more generally, gene regulatory networks are being generated from experimental ChIPseq data, by reverse engineering from transcriptomics data, or from computational predictions of transcription factor (TF) – target gene relations. While transcriptional networks are now available for many biological systems, mathematical models to simulate their dynamic behavior have been successfully developed for metabolic and, to some extent, for signaling networks, but relatively rarely for gene regulatory networks. Systems biology approaches provide new perspectives that raise new questions. Some of them address methodological problems, others arise from the newly obtained understanding of the data. These open questions and problems are also a subject of this Research Topic. 2021-02-12T05:09:59Z 2021-02-12T05:09:59Z 2016-01-19 14:05:46 2016 book 18354 16648714 9782889199679 https://directory.doabooks.org/handle/20.500.12854/60441 eng Frontiers Research Topics image/jpeg Attribution 4.0 International http://www.frontiersin.org/books/Systems_Biology_of_Transcription_Regulation/989 http://journal.frontiersin.org/researchtopic/3866/systems-biology-of-transcription-regulation Frontiers Media SA 10.3389/978-2-88919-967-9 10.3389/978-2-88919-967-9 bf5ce210-e72e-4860-ba9b-c305640ff3ae 9782889199679 189 open access |
| spellingShingle | QH426-470 TA1-2040 TP248.13-248.65 QK1-989 Q1-390 Transcription Regulation network inreference Transcription Factors Systems Biology transcription networks thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAK Genetics (non-medical) Joerg Linde Edgar Wingender Ekaterina Shelest Systems Biology of Transcription Regulation |
| title | Systems Biology of Transcription Regulation |
| title_full | Systems Biology of Transcription Regulation |
| title_fullStr | Systems Biology of Transcription Regulation |
| title_full_unstemmed | Systems Biology of Transcription Regulation |
| title_short | Systems Biology of Transcription Regulation |
| title_sort | systems biology of transcription regulation |
| topic | QH426-470 TA1-2040 TP248.13-248.65 QK1-989 Q1-390 Transcription Regulation network inreference Transcription Factors Systems Biology transcription networks thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAK Genetics (non-medical) |
| topic_facet | QH426-470 TA1-2040 TP248.13-248.65 QK1-989 Q1-390 Transcription Regulation network inreference Transcription Factors Systems Biology transcription networks thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAK Genetics (non-medical) |
| url | 18354 |
| work_keys_str_mv | AT joerglinde systemsbiologyoftranscriptionregulation AT edgarwingender systemsbiologyoftranscriptionregulation AT ekaterinashelest systemsbiologyoftranscriptionregulation |