Oryza sativa - Gene Expression Nebulas

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Molecular bases for differential aging programs between flag and second leaves during grain-filling in rice. Lee S, Jeong H, Lee S, Lee J, Kim SJ, Park JW, Woo HR, Lim PO, An G, Nam HG, Hwang D. Sci Rep. 2017-08-18; 7 (1) PMID: 28821707 DOI: 10.1038/s41598-017-07035-9
Comparative transcriptome analysis of transporters, phytohormone and lipid metabolism pathways in response to arsenic stress in rice (Oryza sativa). Yu LJ, Luo YF, Liao B, Xie LJ, Chen L, Xiao S, Li JT, Hu SN, Shu WS. New Phytol. 2012-04-27; 195 (1) PMID: 22537016 DOI: 10.1111/j.1469-8137.2012.04154.x
Spatio-temporal transcript profiling of rice roots and shoots in response to phosphate starvation and recovery. Secco D, Jabnoune M, Walker H, Shou H, Wu P, Poirier Y, Whelan J. Plant Cell. 2013-11-18; 25 (11) PMID: 24249833 DOI: 10.1105/tpc.113.117325
Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality. Hu L, Li N, Xu C, Zhong S, Lin X, Yang J, Zhou T, Yuliang A, Wu Y, Chen YR, Cao X, Zemach A, Rustgi S, von Wettstein D, Liu B. Proc Natl Acad Sci U S A. 2014-07-07; 111 (29) PMID: 25002488 DOI: 10.1073/pnas.1410761111
Rice germline-specific Argonaute MEL1 protein binds to phasiRNAs generated from more than 700 lincRNAs. Komiya R, Ohyanagi H, Niihama M, Watanabe T, Nakano M, Kurata N, Nonomura K. Plant J. 2014-04-15; 78 (3) PMID: 24635777 DOI: 10.1111/tpj.12483
Dynamics and functional interplay of histone lysine butyrylation, crotonylation, and acetylation in rice under starvation and submergence. Lu Y, Xu Q, Liu Y, Yu Y, Cheng ZY, Zhao Y, Zhou DX. Genome Biol. 2018-09-25; 19 (1) PMID: 30253806 DOI: 10.1186/s13059-018-1533-y
Rice SUB1A constrains remodelling of the transcriptome and metabolome during submergence to facilitate post-submergence recovery. Locke AM, Barding GA, Sathnur S, Larive CK, Bailey-Serres J. Plant Cell Environ. 2017-11-27; 41 (4) PMID: 29094353 DOI: 10.1111/pce.13094
Retrogenes in rice (Oryza sativa L. ssp. japonica) exhibit correlated expression with their source genes. Sakai H, Mizuno H, Kawahara Y, Wakimoto H, Ikawa H, Kawahigashi H, Kanamori H, Matsumoto T, Itoh T, Gaut BS. Genome Biol Evol. 2011-10-31; 3 PMID: 22042334 DOI: 10.1093/gbe/evr111
A transcription activator-like effector from Xanthomonas oryzae pv. oryzicola elicits dose-dependent resistance in rice. Hummel AW, Wilkins KE, Wang L, Cernadas RA, Bogdanove AJ. Mol Plant Pathol. 2016-04-21; 18 (1) PMID: 26821568 DOI: 10.1111/mpp.12377
Loss of function mutations in the rice chromomethylase OsCMT3a cause a burst of transposition. Cheng C, Tarutani Y, Miyao A, Ito T, Yamazaki M, Sakai H, Fukai E, Hirochika H. Plant J. 2015-09-01; 83 (6) PMID: 26243209 DOI: 10.1111/tpj.12952
Rice pyramided line IRBB67 (Xa4/Xa7) homeostasis under combined stress of high temperature and bacterial blight. Dossa GS, Quibod I, Atienza-Grande G, Oliva R, Maiss E, Vera Cruz C, Wydra K. Sci Rep. 2020-01-20; 10 (1) PMID: 31959799 DOI: 10.1038/s41598-020-57499-5
*A Core Regulatory Pathway Controlling Rice Tiller Angle Mediated by the LAZY1-Dependent Asymmetric Distribution of Auxin.* Zhang N, Yu H, Yu H, Cai Y, Huang L, Xu C, Xiong G, Meng X, Wang J, Chen H, Liu G, Jing Y, Yuan Y, Liang Y, Li S, Smith SM, Li J, Wang Y. Plant Cell. 2018-06-18; 30 (7) PMID: 29915152 DOI: 10.1105/tpc.18.00063
Identification of Key Genes for the Ultrahigh Yield of Rice Using Dynamic Cross-tissue Network Analysis. Hu J, Zeng T, Xia Q, Huang L, Zhang Y, Zhang C, Zeng Y, Liu H, Zhang S, Huang G, Wan W, Ding Y, Hu F, Yang C, Chen L, Wang W. Genomics Proteomics Bioinformatics. 2020-06-01; 18 (3) PMID: 32736037 DOI: 10.1016/j.gpb.2019.11.007
Genome-wide disruption of gene expression in allopolyploids but not hybrids of rice subspecies. Xu C, Bai Y, Lin X, Zhao N, Hu L, Gong Z, Wendel JF, Liu B. Mol Biol Evol. 2014-02-27; 31 (5) PMID: 24577842 DOI: 10.1093/molbev/msu085
Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements. Secco D, Wang C, Shou H, Schultz MD, Chiarenza S, Nussaume L, Ecker JR, Whelan J, Lister R. Elife. 2015-07-21; 4 PMID: 26196146 DOI: 10.7554/elife.09343
Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice. Zhang YC, Liao JY, Li ZY, Yu Y, Zhang JP, Li QF, Qu LH, Shu WS, Chen YQ. Genome Biol. 2014-12-03; 15 (12) PMID: 25517485 DOI: 10.1186/s13059-014-0512-1
Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation. Narsai R, Secco D, Schultz MD, Ecker JR, Lister R, Whelan J. Plant J. 2017-02-11; 89 (4) PMID: 27859855 DOI: 10.1111/tpj.13418
Stress-responsive regulation of long non-coding RNA polyadenylation in Oryza sativa. Yuan J, Li J, Yang Y, Tan C, Zhu Y, Hu L, Qi Y, Lu ZJ. Plant J. 2018-01-16; 93 (5) PMID: 29265542 DOI: 10.1111/tpj.13804
OsPRR37 confers an expanded regulation of the diurnal rhythms of the transcriptome and photoperiodic flowering pathways in rice. Liu C, Qu X, Zhou Y, Song G, Abiri N, Xiao Y, Liang F, Jiang D, Hu Z, Yang D. Plant Cell Environ. 2018-02-05; 41 (3) PMID: 29314052 DOI: 10.1111/pce.13135
Enhancing rice grain production by manipulating the naturally evolved cis-regulatory element-containing inverted repeat sequence of OsREM20. Wu X, Liang Y, Gao H, Wang J, Zhao Y, Hua L, Yuan Y, Wang A, Zhang X, Liu J, Zhou J, Meng X, Zhang D, Lin S, Huang X, Han B, Li J, Wang Y. Mol Plant. 2021-03-16; 14 (6) PMID: 33741527 DOI: 10.1016/j.molp.2021.03.016
Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa). Campbell MT, Du Q, Liu K, Sharma S, Zhang C, Walia H. BMC Genomics. 2020-06-08; 21 (1) PMID: 32513103 DOI: 10.1186/s12864-020-06786-6
Diversity in the complexity of phosphate starvation transcriptomes among rice cultivars based on RNA-Seq profiles. Oono Y, Kawahara Y, Yazawa T, Kanamori H, Kuramata M, Yamagata H, Hosokawa S, Minami H, Ishikawa S, Wu J, Antonio B, Handa H, Itoh T, Matsumoto T. Plant Mol Biol. 2013-07-16; 83 (6) PMID: 23857470 DOI: 10.1007/s11103-013-0106-4
TAL effectors and activation of predicted host targets distinguish Asian from African strains of the rice pathogen Xanthomonas oryzae pv. oryzicola while strict conservation suggests universal importance of five TAL effectors. Wilkins KE, Booher NJ, Wang L, Bogdanove AJ. Front Plant Sci. 2015-07-21; 6 PMID: 26257749 DOI: 10.3389/fpls.2015.00536
Network-based feature selection reveals substructures of gene modules responding to salt stress in rice. Du Q, Campbell M, Yu H, Liu K, Walia H, Zhang Q, Zhang C. Plant Direct. 2019-08-12; 3 (8) PMID: 31417977 DOI: 10.1002/pld3.154
Genome-wide transcriptome analysis reveals that cadmium stress signaling controls the expression of genes in drought stress signal pathways in rice. Oono Y, Yazawa T, Kawahara Y, Kanamori H, Kobayashi F, Sasaki H, Mori S, Wu J, Handa H, Itoh T, Matsumoto T. PLoS One. 2014-05-09; 9 (5) PMID: 24816929 DOI: 10.1371/journal.pone.0096946

Molecular bases for differential aging programs between flag and second leaves during grain-filling in rice.

Lee S, Jeong H, Lee S, Lee J, Kim SJ, Park JW, Woo HR, Lim PO, An G, Nam HG, Hwang D.

Sci Rep. 2017-08-18; 7 (1)

PMID: 28821707 DOI: 10.1038/s41598-017-07035-9

Comparative transcriptome analysis of transporters, phytohormone and lipid metabolism pathways in response to arsenic stress in rice (Oryza sativa).

Yu LJ, Luo YF, Liao B, Xie LJ, Chen L, Xiao S, Li JT, Hu SN, Shu WS.

New Phytol. 2012-04-27; 195 (1)

PMID: 22537016 DOI: 10.1111/j.1469-8137.2012.04154.x

Spatio-temporal transcript profiling of rice roots and shoots in response to phosphate starvation and recovery.

Secco D, Jabnoune M, Walker H, Shou H, Wu P, Poirier Y, Whelan J.

Plant Cell. 2013-11-18; 25 (11)

PMID: 24249833 DOI: 10.1105/tpc.113.117325

Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality.

Hu L, Li N, Xu C, Zhong S, Lin X, Yang J, Zhou T, Yuliang A, Wu Y, Chen YR, Cao X, Zemach A, Rustgi S, von Wettstein D, Liu B.

Proc Natl Acad Sci U S A. 2014-07-07; 111 (29)

PMID: 25002488 DOI: 10.1073/pnas.1410761111

Rice germline-specific Argonaute MEL1 protein binds to phasiRNAs generated from more than 700 lincRNAs.

Komiya R, Ohyanagi H, Niihama M, Watanabe T, Nakano M, Kurata N, Nonomura K.

Plant J. 2014-04-15; 78 (3)

PMID: 24635777 DOI: 10.1111/tpj.12483

Dynamics and functional interplay of histone lysine butyrylation, crotonylation, and acetylation in rice under starvation and submergence.

Lu Y, Xu Q, Liu Y, Yu Y, Cheng ZY, Zhao Y, Zhou DX.

Genome Biol. 2018-09-25; 19 (1)

PMID: 30253806 DOI: 10.1186/s13059-018-1533-y

Rice SUB1A constrains remodelling of the transcriptome and metabolome during submergence to facilitate post-submergence recovery.

Locke AM, Barding GA, Sathnur S, Larive CK, Bailey-Serres J.

Plant Cell Environ. 2017-11-27; 41 (4)

PMID: 29094353 DOI: 10.1111/pce.13094

Retrogenes in rice (Oryza sativa L. ssp. japonica) exhibit correlated expression with their source genes.

Sakai H, Mizuno H, Kawahara Y, Wakimoto H, Ikawa H, Kawahigashi H, Kanamori H, Matsumoto T, Itoh T, Gaut BS.

Genome Biol Evol. 2011-10-31; 3

PMID: 22042334 DOI: 10.1093/gbe/evr111

A transcription activator-like effector from Xanthomonas oryzae pv. oryzicola elicits dose-dependent resistance in rice.

Hummel AW, Wilkins KE, Wang L, Cernadas RA, Bogdanove AJ.

Mol Plant Pathol. 2016-04-21; 18 (1)

PMID: 26821568 DOI: 10.1111/mpp.12377

Loss of function mutations in the rice chromomethylase OsCMT3a cause a burst of transposition.

Cheng C, Tarutani Y, Miyao A, Ito T, Yamazaki M, Sakai H, Fukai E, Hirochika H.

Plant J. 2015-09-01; 83 (6)

PMID: 26243209 DOI: 10.1111/tpj.12952

Rice pyramided line IRBB67 (Xa4/Xa7) homeostasis under combined stress of high temperature and bacterial blight.

Dossa GS, Quibod I, Atienza-Grande G, Oliva R, Maiss E, Vera Cruz C, Wydra K.

Sci Rep. 2020-01-20; 10 (1)

PMID: 31959799 DOI: 10.1038/s41598-020-57499-5

A Core Regulatory Pathway Controlling Rice Tiller Angle Mediated by the LAZY1-Dependent Asymmetric Distribution of Auxin.

Zhang N, Yu H, Yu H, Cai Y, Huang L, Xu C, Xiong G, Meng X, Wang J, Chen H, Liu G, Jing Y, Yuan Y, Liang Y, Li S, Smith SM, Li J, Wang Y.

Plant Cell. 2018-06-18; 30 (7)

PMID: 29915152 DOI: 10.1105/tpc.18.00063

Identification of Key Genes for the Ultrahigh Yield of Rice Using Dynamic Cross-tissue Network Analysis.

Hu J, Zeng T, Xia Q, Huang L, Zhang Y, Zhang C, Zeng Y, Liu H, Zhang S, Huang G, Wan W, Ding Y, Hu F, Yang C, Chen L, Wang W.

Genomics Proteomics Bioinformatics. 2020-06-01; 18 (3)

PMID: 32736037 DOI: 10.1016/j.gpb.2019.11.007

Genome-wide disruption of gene expression in allopolyploids but not hybrids of rice subspecies.

Xu C, Bai Y, Lin X, Zhao N, Hu L, Gong Z, Wendel JF, Liu B.

Mol Biol Evol. 2014-02-27; 31 (5)

PMID: 24577842 DOI: 10.1093/molbev/msu085

Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements.

Secco D, Wang C, Shou H, Schultz MD, Chiarenza S, Nussaume L, Ecker JR, Whelan J, Lister R.

Elife. 2015-07-21; 4

PMID: 26196146 DOI: 10.7554/elife.09343

Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice.

Zhang YC, Liao JY, Li ZY, Yu Y, Zhang JP, Li QF, Qu LH, Shu WS, Chen YQ.

Genome Biol. 2014-12-03; 15 (12)

PMID: 25517485 DOI: 10.1186/s13059-014-0512-1

Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation.

Narsai R, Secco D, Schultz MD, Ecker JR, Lister R, Whelan J.

Plant J. 2017-02-11; 89 (4)

PMID: 27859855 DOI: 10.1111/tpj.13418

Stress-responsive regulation of long non-coding RNA polyadenylation in Oryza sativa.

Yuan J, Li J, Yang Y, Tan C, Zhu Y, Hu L, Qi Y, Lu ZJ.

Plant J. 2018-01-16; 93 (5)

PMID: 29265542 DOI: 10.1111/tpj.13804

OsPRR37 confers an expanded regulation of the diurnal rhythms of the transcriptome and photoperiodic flowering pathways in rice.

Liu C, Qu X, Zhou Y, Song G, Abiri N, Xiao Y, Liang F, Jiang D, Hu Z, Yang D.

Plant Cell Environ. 2018-02-05; 41 (3)

PMID: 29314052 DOI: 10.1111/pce.13135

Enhancing rice grain production by manipulating the naturally evolved cis-regulatory element-containing inverted repeat sequence of OsREM20.

Wu X, Liang Y, Gao H, Wang J, Zhao Y, Hua L, Yuan Y, Wang A, Zhang X, Liu J, Zhou J, Meng X, Zhang D, Lin S, Huang X, Han B, Li J, Wang Y.

Mol Plant. 2021-03-16; 14 (6)

PMID: 33741527 DOI: 10.1016/j.molp.2021.03.016

Characterization of the transcriptional divergence between the subspecies of cultivated rice (Oryza sativa).

Campbell MT, Du Q, Liu K, Sharma S, Zhang C, Walia H.

BMC Genomics. 2020-06-08; 21 (1)

PMID: 32513103 DOI: 10.1186/s12864-020-06786-6

Diversity in the complexity of phosphate starvation transcriptomes among rice cultivars based on RNA-Seq profiles.

Oono Y, Kawahara Y, Yazawa T, Kanamori H, Kuramata M, Yamagata H, Hosokawa S, Minami H, Ishikawa S, Wu J, Antonio B, Handa H, Itoh T, Matsumoto T.

Plant Mol Biol. 2013-07-16; 83 (6)

PMID: 23857470 DOI: 10.1007/s11103-013-0106-4

TAL effectors and activation of predicted host targets distinguish Asian from African strains of the rice pathogen Xanthomonas oryzae pv. oryzicola while strict conservation suggests universal importance of five TAL effectors.

Wilkins KE, Booher NJ, Wang L, Bogdanove AJ.

Front Plant Sci. 2015-07-21; 6

PMID: 26257749 DOI: 10.3389/fpls.2015.00536

Network-based feature selection reveals substructures of gene modules responding to salt stress in rice.

Du Q, Campbell M, Yu H, Liu K, Walia H, Zhang Q, Zhang C.

Plant Direct. 2019-08-12; 3 (8)

PMID: 31417977 DOI: 10.1002/pld3.154

Genome-wide transcriptome analysis reveals that cadmium stress signaling controls the expression of genes in drought stress signal pathways in rice.

Oono Y, Yazawa T, Kawahara Y, Kanamori H, Kobayashi F, Sasaki H, Mori S, Wu J, Handa H, Itoh T, Matsumoto T.

PLoS One. 2014-05-09; 9 (5)

PMID: 24816929 DOI: 10.1371/journal.pone.0096946

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