Machine learning reveals the transcriptional regulatory network and circadian dynamics of Synechococcus elongatus PCC 7942

被引：1

作者：

Yuan, Yuan ^{[1
]}

Al Bulushi, Tahani ^{[1
]}

Sastry, Anand V. ^{[1
]}

Sancar, Cigdem ^{[2
]}

Szubin, Richard ^{[1
]}

Golden, Susan S. ^{[2
,3
]}

Palsson, Bernhard O. ^{[1
,4
,5
,6
]}

机构：

[1] Univ Calif San Diego, Shu Chien Gene Lay Dept Bioengn, La Jolla, CA 92093 USA

[2] Univ Calif San Diego, Ctr Circadian Biol, La Jolla, CA 92093 USA

[3] Univ Calif San Diego, Dept Mol Biol, La Jolla, CA 92093 USA

[4] Univ Calif San Diego, Bioinformat & Syst Biol Program, La Jolla, CA 92093 USA

[5] Univ Calif San Diego, Dept Pediat, La Jolla, CA 92093 USA

[6] Tech Univ Denmark, Novo Nordisk Fdn, Ctr Biosustainabil, DK-2800 Lyngby, Denmark

来源：

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA | 2024年 / 121卷 / 38期

关键词：

machine learning; transcriptional regulatory network; cyanobacteria; carbon fixation; circadian rhythm; GENE-EXPRESSION; CYANOBACTERIUM; CO2; LIGHT; MECHANISM; SEQUENCE; PLASMID; NTCA;

D O I：

10.1073/pnas.2410492121

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Synechococcus elongatus is an important cyanobacterium that serves as a versatile and robust model for studying circadian biology and photosynthetic metabolism. Its transcriptional regulatory network (TRN) is of fundamental interest, as it orchestrates the cell's adaptation to the environment, including its response to sunlight. Despite the previous characterization of constituent parts of the S. elongatus TRN, a comprehensive layout of its topology remains to be established. Here, we decomposed a compendium of 300 high-quality RNA sequencing datasets of the model strain PCC 7942 using independent component analysis. We obtained 57 independently modulated gene sets, or iModulons, that explain 67% of the variance in the transcriptional response and 1) accurately reflect the activity of known transcriptional regulations, 2) capture functional components of photosynthesis, 3) provide hypotheses for regulon structures and functional annotations of poorly characterized genes, and 4) describe the transcriptional shifts under dynamic light conditions. This transcriptome-wide analysis of S. elongatus provides a quantitative reconstruction of the TRN and presents a knowledge base that can guide future investigations. Our systems-level analysis also provides a global TRN structure for S. elongatus PCC 7942.

引用

页数：10

共 69 条

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