Computational Reconstruction of the Transcription Factor Regulatory Network Induced by Auxin in Arabidopsis thaliana L.

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Computational Reconstruction of the Transcription Factor Regulatory Network Induced by Auxin in Arabidopsis thaliana L. / Omelyanchuk, Nadya A.; Lavrekha, Viktoriya V.; Bogomolov, Anton G. et al.

In: Plants, Vol. 13, No. 14, 1905, 10.07.2024.

Research output: Contribution to journal › Article › peer-review

BibTeX

@article{d5401df102764f3d9da00a80e5b52c04,

title = "Computational Reconstruction of the Transcription Factor Regulatory Network Induced by Auxin in Arabidopsis thaliana L.",

abstract = "In plant hormone signaling, transcription factor regulatory networks (TFRNs), which link the master transcription factors to the biological processes under their control, remain insufficiently characterized despite their crucial function. Here, we identify a TFRN involved in the response to the key plant hormone auxin and define its impact on auxin-driven biological processes. To reconstruct the TFRN, we developed a three-step procedure, which is based on the integrated analysis of differentially expressed gene lists and a representative collection of transcription factor binding profiles. Its implementation is available as a part of the CisCross web server. With the new method, we distinguished two transcription factor subnetworks. The first operates before auxin treatment and is switched off upon hormone application, the second is switched on by the hormone. Moreover, we characterized the functioning of the auxin-regulated TFRN in control of chlorophyll and lignin biosynthesis, abscisic acid signaling, and ribosome biogenesis.",

keywords = "auxin, microarray, regulatory network, transcription factor, transcriptome",

author = "Omelyanchuk, {Nadya A.} and Lavrekha, {Viktoriya V.} and Bogomolov, {Anton G.} and Dolgikh, {Vladislav A.} and Sidorenko, {Aleksandra D.} and Zemlyanskaya, {Elena V.}",

note = "This research was funded by the Russian Science Foundation, grant number 20-14-00140.",

year = "2024",

month = jul,

day = "10",

doi = "10.3390/plants13141905",

language = "English",

volume = "13",

journal = "Plants",

issn = "2223-7747",

publisher = "Multidisciplinary Digital Publishing Institute (MDPI)",

number = "14",

}

RIS

TY - JOUR

T1 - Computational Reconstruction of the Transcription Factor Regulatory Network Induced by Auxin in Arabidopsis thaliana L.

AU - Omelyanchuk, Nadya A.

AU - Lavrekha, Viktoriya V.

AU - Bogomolov, Anton G.

AU - Dolgikh, Vladislav A.

AU - Sidorenko, Aleksandra D.

AU - Zemlyanskaya, Elena V.

N1 - This research was funded by the Russian Science Foundation, grant number 20-14-00140.

PY - 2024/7/10

Y1 - 2024/7/10

N2 - In plant hormone signaling, transcription factor regulatory networks (TFRNs), which link the master transcription factors to the biological processes under their control, remain insufficiently characterized despite their crucial function. Here, we identify a TFRN involved in the response to the key plant hormone auxin and define its impact on auxin-driven biological processes. To reconstruct the TFRN, we developed a three-step procedure, which is based on the integrated analysis of differentially expressed gene lists and a representative collection of transcription factor binding profiles. Its implementation is available as a part of the CisCross web server. With the new method, we distinguished two transcription factor subnetworks. The first operates before auxin treatment and is switched off upon hormone application, the second is switched on by the hormone. Moreover, we characterized the functioning of the auxin-regulated TFRN in control of chlorophyll and lignin biosynthesis, abscisic acid signaling, and ribosome biogenesis.

AB - In plant hormone signaling, transcription factor regulatory networks (TFRNs), which link the master transcription factors to the biological processes under their control, remain insufficiently characterized despite their crucial function. Here, we identify a TFRN involved in the response to the key plant hormone auxin and define its impact on auxin-driven biological processes. To reconstruct the TFRN, we developed a three-step procedure, which is based on the integrated analysis of differentially expressed gene lists and a representative collection of transcription factor binding profiles. Its implementation is available as a part of the CisCross web server. With the new method, we distinguished two transcription factor subnetworks. The first operates before auxin treatment and is switched off upon hormone application, the second is switched on by the hormone. Moreover, we characterized the functioning of the auxin-regulated TFRN in control of chlorophyll and lignin biosynthesis, abscisic acid signaling, and ribosome biogenesis.

KW - auxin

KW - microarray

KW - regulatory network

KW - transcription factor

KW - transcriptome

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85199560226&origin=inward&txGid=9e1e50794d3878490aaded948ab5a0a9

UR - https://www.mendeley.com/catalogue/68b07465-d7d9-399f-90cd-40c320264c90/

U2 - 10.3390/plants13141905

DO - 10.3390/plants13141905

M3 - Article

C2 - 39065433

VL - 13

JO - Plants

JF - Plants

SN - 2223-7747

IS - 14

M1 - 1905

ER -

ID: 60863056