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Citation for Study 16883

Citation title: "Histone chaperones in Arabidopsis and rice: genome-wide identification, phylogeny, architecture and transcriptional regulation".

Study name: "Histone chaperones in Arabidopsis and rice: genome-wide identification, phylogeny, architecture and transcriptional regulation".

This study is part of submission 16883 (Status: Published).

Citation

Tripathi A.K., Singh K., Pareek A., & Singla-pareek S.L. 2015. Histone chaperones in Arabidopsis and rice: genome-wide identification, phylogeny, architecture and transcriptional regulation. BMC Plant Biology, 15(42).

Authors

• Tripathi A.K.
• Singh K.
• Pareek A.
• Singla-pareek S.L.

Abstract

Background Histone chaperones modulate chromatin architecture and hence play a pivotal role in epigenetic regulation of gene expression. In contrast to their animal and yeast counterparts, not much is known about plant histone chaperones. To gain insights into their functions in plants, we sought to identify histone chaperones from two model plant species and investigated their phylogeny, domain architecture and transcriptional profiles to establish correlation between their expression patterns and potential role in stress physiology and plant development. Results Through comprehensive whole genome analyses of Arabidopsis and rice, we identified twenty-two and twenty-five genes encoding histone chaperones in these plants, respectively. These could be classified into seven different families, namely NAP, CAF1, SPT6, ASF1, HIRA, NASP, and FACT. Phylogenetic analyses of histone chaperones from diverse organisms including representative species from each of the major plant groups, yeast and human indicated functional divergence in NAP and CAF1C in plants. For the largest histone chaperone family, NAP, phylogenetic reconstruction suggested the presence of two distinct groups in plants, possibly with differing histone preferences. Further, to comment upon their physiological roles in plants, we analyzed their expression at different developmental stages, across various plant tissues, and under biotic and abiotic stress conditions using pre-existing microarray and qRT-PCR. We found tight transcriptional regulation of some histone chaperone genes during development in both Arabidopsis and rice, suggesting that they may play a role in genetic reprogramming associated with the developmental process. Besides, we found significant differential expression of a few histone chaperones under various biotic and abiotic stresses pointing towards their potential function in stress response. Conclusions Taken together, our findings shed light onto the possible evolutionary trajectory of plant histone chaperones and present novel prospects about their physiological roles. Considering that the developmental process and stress response require altered expression of a large array of genes, our results suggest that some plant histone chaperones may serve a regulatory role by controlling the expression of genes associated with these vital processes, possibly via modulating chromatin dynamics at the corresponding genetic loci.

Keywords

nucleosome, histone chaperones, rice, Arabidopsis, phylogeny, microarray, qRT-PCR, development, abiotic stress, biotic stress

External links

• DOI: 10.1186/s12870-015-0414-8
• Other URL: http://www.biomedcentral.com/1471-2229/15/42/

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S16883
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref24040,
  	 author = {Amit K.  Tripathi and Khushwant  Singh and Ashwani  Pareek and Sneh L. Singla-Pareek},
  	 title = {Histone chaperones in Arabidopsis and rice: genome-wide identification, phylogeny, architecture and transcriptional regulation},
  	 year = {2015},
  	 keywords = {nucleosome, histone chaperones, rice, Arabidopsis, phylogeny, microarray, qRT-PCR, development, abiotic stress, biotic stress },
  	 doi = {10.1186/s12870-015-0414-8},
  	 url = {http://www.biomedcentral.com/1471-2229/15/42/},
  	 pmid = {},
  	 journal = {BMC Plant Biology},
  	 volume = {15},
  	 number = {42},
  	 pages = {},
  	 abstract = {Background
  Histone chaperones modulate chromatin architecture and hence play a pivotal role in
  epigenetic regulation of gene expression. In contrast to their animal and yeast counterparts,
  not much is known about plant histone chaperones. To gain insights into their functions in
  plants, we sought to identify histone chaperones from two model plant species and
  investigated their phylogeny, domain architecture and transcriptional profiles to establish
  correlation between their expression patterns and potential role in stress physiology and plant
  development.
  Results
  Through comprehensive whole genome analyses of Arabidopsis and rice, we identified
  twenty-two and twenty-five genes encoding histone chaperones in these plants, respectively.
  These could be classified into seven different families, namely NAP, CAF1, SPT6, ASF1,
  HIRA, NASP, and FACT. Phylogenetic analyses of histone chaperones from diverse
  organisms including representative species from each of the major plant groups, yeast and
  human indicated functional divergence in NAP and CAF1C in plants. For the largest histone
  chaperone family, NAP, phylogenetic reconstruction suggested the presence of two distinct
  groups in plants, possibly with differing histone preferences. Further, to comment upon their
  physiological roles in plants, we analyzed their expression at different developmental stages,
  across various plant tissues, and under biotic and abiotic stress conditions using pre-existing microarray and qRT-PCR. We found tight transcriptional regulation of some histone
  chaperone genes during development in both Arabidopsis and rice, suggesting that they may
  play a role in genetic reprogramming associated with the developmental process. Besides, we
  found significant differential expression of a few histone chaperones under various biotic and
  abiotic stresses pointing towards their potential function in stress response.
  Conclusions
  Taken together, our findings shed light onto the possible evolutionary trajectory of plant
  histone chaperones and present novel prospects about their physiological roles. Considering
  that the developmental process and stress response require altered expression of a large array
  of genes, our results suggest that some plant histone chaperones may serve a regulatory role
  by controlling the expression of genes associated with these vital processes, possibly via
  modulating chromatin dynamics at the corresponding genetic loci.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 24040
  AU  - Tripathi,Amit K. 
  AU  - Singh,Khushwant 
  AU  - Pareek,Ashwani 
  AU  - Singla-Pareek,Sneh L.
  T1  - Histone chaperones in Arabidopsis and rice: genome-wide identification, phylogeny, architecture and transcriptional regulation
  PY  - 2015
  KW  - nucleosome
  KW  - histone chaperones
  KW  - rice
  KW  - Arabidopsis
  KW  - phylogeny
  KW  - microarray
  KW  - qRT-PCR
  KW  - development
  KW  - abiotic stress
  KW  - biotic stress 
  UR  - http://www.biomedcentral.com/1471-2229/15/42/
  N2  - Background
  Histone chaperones modulate chromatin architecture and hence play a pivotal role in
  epigenetic regulation of gene expression. In contrast to their animal and yeast counterparts,
  not much is known about plant histone chaperones. To gain insights into their functions in
  plants, we sought to identify histone chaperones from two model plant species and
  investigated their phylogeny, domain architecture and transcriptional profiles to establish
  correlation between their expression patterns and potential role in stress physiology and plant
  development.
  Results
  Through comprehensive whole genome analyses of Arabidopsis and rice, we identified
  twenty-two and twenty-five genes encoding histone chaperones in these plants, respectively.
  These could be classified into seven different families, namely NAP, CAF1, SPT6, ASF1,
  HIRA, NASP, and FACT. Phylogenetic analyses of histone chaperones from diverse
  organisms including representative species from each of the major plant groups, yeast and
  human indicated functional divergence in NAP and CAF1C in plants. For the largest histone
  chaperone family, NAP, phylogenetic reconstruction suggested the presence of two distinct
  groups in plants, possibly with differing histone preferences. Further, to comment upon their
  physiological roles in plants, we analyzed their expression at different developmental stages,
  across various plant tissues, and under biotic and abiotic stress conditions using pre-existing microarray and qRT-PCR. We found tight transcriptional regulation of some histone
  chaperone genes during development in both Arabidopsis and rice, suggesting that they may
  play a role in genetic reprogramming associated with the developmental process. Besides, we
  found significant differential expression of a few histone chaperones under various biotic and
  abiotic stresses pointing towards their potential function in stress response.
  Conclusions
  Taken together, our findings shed light onto the possible evolutionary trajectory of plant
  histone chaperones and present novel prospects about their physiological roles. Considering
  that the developmental process and stress response require altered expression of a large array
  of genes, our results suggest that some plant histone chaperones may serve a regulatory role
  by controlling the expression of genes associated with these vital processes, possibly via
  modulating chromatin dynamics at the corresponding genetic loci.
  L3  - 10.1186/s12870-015-0414-8
  JF  - BMC Plant Biology
  VL  - 15
  IS  - 42
  ER  -