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Article ; Online: Elucidating the biology of transcription factor-DNA interaction for accurate identification of cis-regulatory elements.

Hajheidari, Mohsen / Huang, Shao-Shan Carol

2022 Volume 68, Page(s) 102232

Abstract: Transcription factors (TFs) play a critical role in determining cell fate decisions by integrating developmental and environmental signals through binding to specific cis-regulatory modules and regulating spatio-temporal specificity of gene expression ... ...

Abstract	Transcription factors (TFs) play a critical role in determining cell fate decisions by integrating developmental and environmental signals through binding to specific cis-regulatory modules and regulating spatio-temporal specificity of gene expression patterns. Precise identification of functional TF binding sites in time and space not only will revolutionize our understanding of regulatory networks governing cell fate decisions but is also instrumental to uncover how genetic variations cause morphological diversity or disease. In this review, we discuss recent advances in mapping TF binding sites and characterizing the various parameters underlying the complexity of binding site recognition by TFs.
MeSH term(s)	Binding Sites ; Biology ; DNA/metabolism ; Protein Binding ; Transcription Factors/genetics ; Transcription Factors/metabolism
Chemical Substances	Transcription Factors ; DNA (9007-49-2)
Language	English
Publishing date	2022-06-06
Publishing country	England
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1418472-2
ISSN	1879-0356 ; 1369-5266
ISSN (online)	1879-0356
ISSN	1369-5266
DOI	10.1016/j.pbi.2022.102232
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Article: Elucidating the biology of transcription factor–DNA interaction for accurate identification of cis-regulatory elements

Hajheidari, Mohsen / Huang, Shao-shan Carol

Current opinion in plant biology. 2022 Aug., v. 68

2022

Abstract	Transcription factors (TFs) play a critical role in determining cell fate decisions by integrating developmental and environmental signals through binding to specific cis-regulatory modules and regulating spatio-temporal specificity of gene expression patterns. Precise identification of functional TF binding sites in time and space not only will revolutionize our understanding of regulatory networks governing cell fate decisions but is also instrumental to uncover how genetic variations cause morphological diversity or disease. In this review, we discuss recent advances in mapping TF binding sites and characterizing the various parameters underlying the complexity of binding site recognition by TFs.
Keywords	attitudes and opinions ; binding sites ; gene expression regulation ; genetic variation ; plant biology ; regulatory sequences ; space and time ; transcription factors ; wills
Language	English
Dates of publication	2022-08
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	1418472-2
ISSN	1879-0356 ; 1369-5266
ISSN (online)	1879-0356
ISSN	1369-5266
DOI	10.1016/j.pbi.2022.102232
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Article: Chromatin Evolution-Key Innovations Underpinning Morphological Complexity.

Hajheidari, Mohsen / Koncz, Csaba / Bucher, Marcel

Frontiers in plant science

2019 Volume 10, Page(s) 454

Abstract: The history of life consists of a series of major evolutionary transitions, including emergence and radiation of complex multicellular eukaryotes from unicellular ancestors. The cells of multicellular organisms, with few exceptions, contain the same ... ...

Abstract	The history of life consists of a series of major evolutionary transitions, including emergence and radiation of complex multicellular eukaryotes from unicellular ancestors. The cells of multicellular organisms, with few exceptions, contain the same genome, however, their organs are composed of a variety of cell types that differ in both structure and function. This variation is largely due to the transcriptional activity of different sets of genes in different cell types. This indicates that complex transcriptional regulation played a key role in the evolution of complexity in eukaryotes. In this review, we summarize how gene duplication and subsequent evolutionary innovations, including the structural evolution of nucleosomes and chromatin-related factors, contributed to the complexity of the transcriptional system and provided a basis for morphological diversity.
Language	English
Publishing date	2019-04-12
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2613694-6
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2019.00454
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Book ; Online ; Thesis: Functional analysis of CDKF;1

Hajheidari, Mohsen

a plant specific CAK-activating kinase

2010

Abstract: Zsfassung in dt. und engl. ... ...

Author's details	vorgelegt von Mohsen Hajheidari
Abstract	Zsfassung in dt. und engl. Sprache
Language	English
Size	Online-Ressource
Document type	Book ; Online ; Thesis
Thesis / German Habilitation thesis	Univ., Diss.--Köln, 2010
Database	Former special subject collection: coastal and deep sea fishing

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Article ; Online: Crop genetic diversity uncovers metabolites, elements, and gene networks predicted to be associated with high plant biomass yields in maize.

Hajheidari, Mohsen / Gerlach, Nina / Dorau, Kristof / Omidbakhshfard, M Amin / Pesch, Lina / Hofmann, Jörg / Hallab, Asis / Ponce-Soto, Gabriel Y / Kuhalskaya, Anastasiya / Medeiros, David B / Bourceret, Amélia / Usadel, Björn / Mayer, Jochen / Fernie, Alisdair / Mansfeldt, Tim / Sonnewald, Uwe / Bucher, Marcel

PNAS nexus

2022 Volume 1, Issue 3, Page(s) pgac068

Abstract: Rapid population growth and increasing demand for food, feed, and bioenergy in these times of unprecedented climate change require breeding for increased biomass production on the world's croplands. To accelerate breeding programs, knowledge of the ... ...

Abstract	Rapid population growth and increasing demand for food, feed, and bioenergy in these times of unprecedented climate change require breeding for increased biomass production on the world's croplands. To accelerate breeding programs, knowledge of the relationship between biomass features and underlying gene networks is needed to guide future breeding efforts. To this end, large-scale multiomics datasets were created with genetically diverse maize lines, all grown in long-term organic and conventional cropping systems. Analysis of the datasets, integrated using regression modeling and network analysis revealed key metabolites, elements, gene transcripts, and gene networks, whose contents during vegetative growth substantially influence the build-up of plant biomass in the reproductive phase. We found that S and P content in the source leaf and P content in the root during the vegetative stage contributed the most to predicting plant performance at the reproductive stage. In agreement with the Gene Ontology enrichment analysis, the
Language	English
Publishing date	2022-07-04
Publishing country	England
Document type	Journal Article
ISSN	2752-6542
ISSN (online)	2752-6542
DOI	10.1093/pnasnexus/pgac068
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Article ; Online: Emerging roles for RNA polymerase II CTD in Arabidopsis.

Hajheidari, Mohsen / Koncz, Csaba / Eick, Dirk

Trends in plant science

2013 Volume 18, Issue 11, Page(s) 633–643

Abstract: Post-translational modifications of the carboxy-terminal domain of the largest subunit of RNA polymerase II (RNAPII CTD) provide recognition marks to coordinate recruitment of numerous nuclear factors controlling transcription, cotranscriptional RNA ... ...

Abstract	Post-translational modifications of the carboxy-terminal domain of the largest subunit of RNA polymerase II (RNAPII CTD) provide recognition marks to coordinate recruitment of numerous nuclear factors controlling transcription, cotranscriptional RNA processing, chromatin remodeling, and RNA export. Compared with the progress in yeast and mammals, deciphering the regulatory roles of position-specific combinatorial CTD modifications, the so-called CTD code, is still at an early stage in plants. In this review, we discuss some of the recent advances in understanding of the molecular mechanisms controlling the deposition and recognition of RNAPII CTD marks in plants during the transcriptional cycle and highlight some intriguing differences between regulatory components characterized in yeast, mammals, and plants.
MeSH term(s)	Animals ; Arabidopsis/enzymology ; Arabidopsis/genetics ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Humans ; Mammals ; Models, Biological ; Phosphoprotein Phosphatases/genetics ; Phosphorylation ; Protein Kinases/genetics ; Protein Processing, Post-Translational ; Protein Structure, Tertiary ; RNA Polymerase II/genetics ; RNA Polymerase II/metabolism ; Saccharomyces cerevisiae/enzymology ; Saccharomyces cerevisiae/genetics ; Species Specificity ; Transcription, Genetic
Chemical Substances	Arabidopsis Proteins ; Protein Kinases (EC 2.7.-) ; carboxy-terminal domain kinase (EC 2.7.1.-) ; RNA Polymerase II (EC 2.7.7.-) ; Phosphoprotein Phosphatases (EC 3.1.3.16) ; carboxy-terminal domain phosphatase (EC 3.1.3.16)
Language	English
Publishing date	2013-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1305448-x
ISSN	1878-4372 ; 1360-1385
ISSN (online)	1878-4372
ISSN	1360-1385
DOI	10.1016/j.tplants.2013.07.001
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Article ; Online: Corrigendum: Coupled enhancer and coding sequence evolution of a homeobox gene shaped leaf diversity.

Vuolo, Francesco / Mentink, Remco A / Hajheidari, Mohsen / Bailey, C Donovan / Filatov, Dmitry A / Tsiantis, Miltos

Genes & development

2017 Volume 31, Issue 21, Page(s) 2199

Language	English
Publishing date	2017--01
Publishing country	United States
Document type	Journal Article ; Published Erratum
ZDB-ID	806684-x
ISSN	1549-5477 ; 0890-9369
ISSN (online)	1549-5477
ISSN	0890-9369
DOI	10.1101/gad.309179.117
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Article: Emerging roles for RNA polymerase II CTD in Arabidopsis

Hajheidari, Mohsen / Koncz, Csaba / Eick, Dirk

Trends in plant science. 2013 Nov., v. 18, no. 11

2013

Abstract	Post-translational modifications of the carboxy-terminal domain of the largest subunit of RNA polymerase II (RNAPII CTD) provide recognition marks to coordinate recruitment of numerous nuclear factors controlling transcription, cotranscriptional RNA processing, chromatin remodeling, and RNA export. Compared with the progress in yeast and mammals, deciphering the regulatory roles of position-specific combinatorial CTD modifications, the so-called CTD code, is still at an early stage in plants. In this review, we discuss some of the recent advances in understanding of the molecular mechanisms controlling the deposition and recognition of RNAPII CTD marks in plants during the transcriptional cycle and highlight some intriguing differences between regulatory components characterized in yeast, mammals, and plants.
Keywords	Arabidopsis ; DNA-directed RNA polymerase ; RNA ; chromatin ; mammals ; post-translational modification ; transcription (genetics) ; yeasts
Language	English
Dates of publication	2013-11
Size	p. 633-643.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	1305448-x
ISSN	1878-4372 ; 1360-1385
ISSN (online)	1878-4372
ISSN	1360-1385
DOI	10.1016/j.tplants.2013.07.001
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Article ; Online: Coupled enhancer and coding sequence evolution of a homeobox gene shaped leaf diversity.

Vuolo, Francesco / Mentink, Remco A / Hajheidari, Mohsen / Bailey, C Donovan / Filatov, Dmitry A / Tsiantis, Miltos

Genes & development

2016 Volume 30, Issue 21, Page(s) 2370–2375

Abstract: Here we investigate mechanisms underlying the diversification of biological forms using crucifer leaf shape as an example. We show that evolution of an enhancer element in the homeobox gene REDUCED COMPLEXITY (RCO) altered leaf shape by changing gene ... ...

Abstract	Here we investigate mechanisms underlying the diversification of biological forms using crucifer leaf shape as an example. We show that evolution of an enhancer element in the homeobox gene REDUCED COMPLEXITY (RCO) altered leaf shape by changing gene expression from the distal leaf blade to its base. A single amino acid substitution evolved together with this regulatory change, which reduced RCO protein stability, preventing pleiotropic effects caused by its altered gene expression. We detected hallmarks of positive selection in these evolved regulatory and coding sequence variants and showed that modulating RCO activity can improve plant physiological performance. Therefore, interplay between enhancer and coding sequence evolution created a potentially adaptive path for morphological evolution.
MeSH term(s)	Arabidopsis/anatomy & histology ; Arabidopsis/genetics ; Arabidopsis/physiology ; Cardamine/anatomy & histology ; Cardamine/classification ; Cardamine/genetics ; Enhancer Elements, Genetic/genetics ; Evolution, Molecular ; Gene Expression Profiling ; Genes, Plant/genetics ; Plant Leaves/anatomy & histology ; Plant Leaves/genetics
Language	English
Publishing date	2016-11-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	806684-x
ISSN	1549-5477 ; 0890-9369
ISSN (online)	1549-5477
ISSN	0890-9369
DOI	10.1101/gad.290684.116
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Article ; Online: CDKF;1 and CDKD protein kinases regulate phosphorylation of serine residues in the C-terminal domain of Arabidopsis RNA polymerase II.

Hajheidari, Mohsen / Farrona, Sara / Huettel, Bruno / Koncz, Zsuzsa / Koncz, Csaba

The Plant cell

2012 Volume 24, Issue 4, Page(s) 1626–1642

Abstract: Phosphorylation of conserved Y₁S₂P₃T₄S₅P₆S₇ repeats in the C-terminal domain of largest subunit of RNA polymerase II (RNAPII CTD) plays a central role in the regulation of transcription and cotranscriptional RNA processing. Here, we show that Ser ... ...

Abstract	Phosphorylation of conserved Y₁S₂P₃T₄S₅P₆S₇ repeats in the C-terminal domain of largest subunit of RNA polymerase II (RNAPII CTD) plays a central role in the regulation of transcription and cotranscriptional RNA processing. Here, we show that Ser phosphorylation of Arabidopsis thaliana RNAPII CTD is governed by CYCLIN-DEPENDENT KINASE F;1 (CDKF;1), a unique plant-specific CTD S₇-kinase. CDKF;1 is required for in vivo activation of functionally redundant CYCLIN-DEPENDENT KINASE Ds (CDKDs), which are major CTD S₅-kinases that also phosphorylate in vitro the S₂ and S₇ CTD residues. Inactivation of CDKF;1 causes extreme dwarfism and sterility. Inhibition of CTD S₇-phosphorylation in germinating cdkf;1 seedlings is accompanied by 3'-polyadenylation defects of pre-microRNAs and transcripts encoding key regulators of small RNA biogenesis pathways. The cdkf;1 mutation also decreases the levels of both precursor and mature small RNAs without causing global downregulation of the protein-coding transcriptome and enhances the removal of introns that carry pre-microRNA stem-loops. A triple cdkd knockout mutant is not viable, but a combination of null and weak cdkd;3 alleles in a triple cdkd123* mutant permits semidwarf growth. Germinating cdkd123* seedlings show reduced CTD S₅-phosphorylation, accumulation of uncapped precursor microRNAs, and a parallel decrease in mature microRNA. During later development of cdkd123* seedlings, however, S₇-phosphorylation and unprocessed small RNA levels decline similarly as in the cdkf;1 mutant. Taken together, cotranscriptional processing and stability of a set of small RNAs and transcripts involved in their biogenesis are sensitive to changes in the phosphorylation of RNAPII CTD by CDKF;1 and CDKDs.
MeSH term(s)	Arabidopsis/enzymology ; Arabidopsis/genetics ; Arabidopsis/growth & development ; Arabidopsis Proteins/chemistry ; Arabidopsis Proteins/genetics ; Arabidopsis Proteins/metabolism ; Biosynthetic Pathways/genetics ; Cyclin-Dependent Kinases/metabolism ; Down-Regulation/genetics ; Gene Expression Regulation, Plant ; Genes, Plant/genetics ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Mutation/genetics ; Nucleic Acid Hybridization ; Phosphorylation ; Phosphoserine/metabolism ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases/metabolism ; RNA Caps/metabolism ; RNA Polymerase II/chemistry ; RNA Polymerase II/metabolism ; RNA Precursors/metabolism ; RNA Processing, Post-Transcriptional/genetics ; RNA Splicing/genetics ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; RNA, Plant/biosynthesis ; RNA, Plant/genetics ; RNA, Small Interfering/genetics ; RNA, Small Interfering/metabolism ; RNA, Untranslated/genetics ; Transcription, Genetic
Chemical Substances	Arabidopsis Proteins ; MicroRNAs ; RNA Caps ; RNA Precursors ; RNA, Messenger ; RNA, Plant ; RNA, Small Interfering ; RNA, Untranslated ; Phosphoserine (17885-08-4) ; Cak1at protein, Arabidopsis (EC 2.7.1.-) ; Protein-Serine-Threonine Kinases (EC 2.7.11.1) ; Cyclin-Dependent Kinases (EC 2.7.11.22) ; RNA Polymerase II (EC 2.7.7.-)
Language	English
Publishing date	2012-04-30
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	623171-8
ISSN	1532-298X ; 1040-4651
ISSN (online)	1532-298X
ISSN	1040-4651
DOI	10.1105/tpc.112.096834
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