Sequences Required for Paramutation of the Maize b Gene Map to a Region Containing the Promoter and Upstream Sequences

INVESTIGATIONS

Sequences Required for Paramutation of the Maize b Gene Map to a Region Containing the Promoter and Upstream Sequences

G. I. Patterson, K. M. Kubo, T. Shroyer and V. L. Chandler
Present address: Department of Molecular Biology, Wellman 8, Massachusetts General Hospital, Boston, MA 02114.

The b gene encodes a transcriptional regulator of the maize anthocyanin biosynthetic pathway. Certain b alleles participate in paramutation, an allele-specific interaction that heritably alters transcription. The moderately transcribed B' allele heritably reduces the transcription of the highly transcribed B-I allele in a B'/B-I heterozygote, such that the B-I allele becomes B'. To identify the cis-acting sequences required for paramutation, we used B' or B-I alleles to isolate intragenic recombinants with B-Peru, an allele that is insensitive to paramutation and has distinct tissue-specific regulation. Physical mapping of the recombinant alleles showed that most of the crossovers were in a small region near the 5' end of the b-transcribed region. Analysis of the recombinant alleles revealed that the ability to cause and respond to paramutation and the control of tissue-specific expression both localize to the 5' region of the gene. The 3' boundary of these functions lies just upstream of the translation initiation codon. The 5' boundary has been estimated to be no more than 0.1 cM further upstream (1-150 kb). Thus, sequences critical for paramutation lie upstream of the b coding sequences and may include transcriptional regulatory sequences.

This article has been cited by other articles:

F. Zhang and T. Peterson
Gene Conversion Between Direct Noncoding Repeats Promotes Genetic and Phenotypic Diversity at a Regulatory Locus of Zea mays (L.)
Genetics, October 1, 2006; 174(2): 753 - 762.
[Abstract] [Full Text] [PDF]

M. D. Yandeau-Nelson, B. J. Nikolau, and P. S. Schnable
Effects of trans-acting Genetic Modifiers on Meiotic Recombination Across the a1-sh2 Interval of Maize
Genetics, September 1, 2006; 174(1): 101 - 112.
[Abstract] [Full Text] [PDF]

H. Yan, W. Jin, K. Nagaki, S. Tian, S. Ouyang, C. R. Buell, P. B. Talbert, S. Henikoff, and J. Jiang
Transcription and Histone Modifications in the Recombination-Free Region Spanning a Rice Centromere
PLANT CELL, December 1, 2005; 17(12): 3227 - 3238.
[Abstract] [Full Text] [PDF]

M. D. Yandeau-Nelson, Q. Zhou, H. Yao, X. Xu, B. J. Nikolau, and P. S. Schnable
MuDR Transposase Increases the Frequency of Meiotic Crossovers in the Vicinity of a Mu Insertion in the Maize a1 Gene
Genetics, February 1, 2005; 169(2): 917 - 929.
[Abstract] [Full Text] [PDF]

L. Huang, S. A. Brooks, W. Li, J. P. Fellers, H. N. Trick, and B. S. Gill
Map-Based Cloning of Leaf Rust Resistance Gene Lr21 From the Large and Polyploid Genome of Bread Wheat
Genetics, June 1, 2003; 164(2): 655 - 664.
[Abstract] [Full Text] [PDF]

M. Stam, C. Belele, W. Ramakrishna, J. E. Dorweiler, J. L. Bennetzen, and V. L. Chandler
The Regulatory Regions Required for B' Paramutation and Expression Are Located Far Upstream of the Maize b1 Transcribed Sequences
Genetics, October 1, 2002; 162(2): 917 - 930.
[Abstract] [Full Text] [PDF]

M. Stam, C. Belele, J. E. Dorweiler, and V. L. Chandler
Differential chromatin structure within a tandem array 100 kb upstream of the maize b1 locus is associated with paramutation
Genes & Dev., August 1, 2002; 16(15): 1906 - 1918.
[Abstract] [Full Text] [PDF]

Y. Vigouroux, J. S. Jaqueth, Y. Matsuoka, O. S. Smith, W. D. Beavis, J. S. C. Smith, and J. Doebley
Rate and Pattern of Mutation at Microsatellite Loci in Maize
Mol. Biol. Evol., August 1, 2002; 19(8): 1251 - 1260.
[Abstract] [Full Text] [PDF]

H. K. Dooner
Extensive Interallelic Polymorphisms Drive Meiotic Recombination into a Crossover Pathway
PLANT CELL, May 1, 2002; 14(5): 1173 - 1183.
[Abstract] [Full Text] [PDF]

C. F. Weil
Finding the crosswalks on DNA
PNAS, April 30, 2002; 99(9): 5763 - 5765.
[Full Text] [PDF]

D. Lisch, C. C. Carey, J. E. Dorweiler, and V. L. Chandler
A mutation that prevents paramutation in maize also reverses Mutator transposon methylation and silencing
PNAS, April 30, 2002; 99(9): 6130 - 6135.
[Abstract] [Full Text] [PDF]

H. Yao, Q. Zhou, J. Li, H. Smith, M. Yandeau, B. J. Nikolau, and P. S. Schnable
From the Cover: Molecular characterization of meiotic recombination across the 140-kb multigenic a1-sh2 interval of maize
PNAS, April 30, 2002; 99(9): 6157 - 6162.
[Abstract] [Full Text] [PDF]

H. Fu, Z. Zheng, and H. K. Dooner
Recombination rates between adjacent genic and retrotransposon regions in maize vary by 2 orders of magnitude
PNAS, January 22, 2002; 99(2): 1082 - 1087.
[Abstract] [Full Text] [PDF]

P. J. Yeadon, J. P. Rasmussen, and D. E. A. Catcheside
Recombination Events in Neurospora crassa May Cross a Translocation Breakpoint by a Template-Switching Mechanism
Genetics, October 1, 2001; 159(2): 571 - 579.
[Abstract] [Full Text] [PDF]

D. A. Selinger and V. L. Chandler
B-Bolivia, an Allele of the Maize b1 Gene with Variable Expression, Contains a High Copy Retrotransposon-Related Sequence Immediately Upstream
Plant Physiology, March 1, 2001; 125(3): 1363 - 1379.
[Abstract] [Full Text]

L. V. Sidorenko and T. Peterson
Transgene-Induced Silencing Identifies Sequences Involved in the Establishment of Paramutation of the Maize p1 Gene
PLANT CELL, February 1, 2001; 13(2): 319 - 335.
[Abstract] [Full Text]

J. E. Dorweiler, C. C. Carey, K. M. Kubo, J. B. Hollick, J. L. Kermicle, and V. L. Chandler
mediator of paramutation1 Is Required for Establishment and Maintenance of Paramutation at Multiple Maize Loci
PLANT CELL, November 1, 2000; 12(11): 2101 - 2118.
[Abstract] [Full Text]

J. B. Hollick, G. I. Patterson, I. M. Asmundsson, and V. L. Chandler
Paramutation Alters Regulatory Control of the Maize pl Locus
Genetics, April 1, 2000; 154(4): 1827 - 1838.
[Abstract] [Full Text]

J. D. Faris, K. M. Haen, and B. S. Gill
Saturation Mapping of a Gene-Rich Recombination Hot Spot Region in Wheat
Genetics, February 1, 2000; 154(2): 823 - 835.
[Abstract] [Full Text]

D. A. Selinger and V. L. Chandler
Major recent and independent changes in levels and patterns of expression have occurred at the b gene, a regulatory locus in maize
PNAS, December 21, 1999; 96(26): 15007 - 15012.
[Abstract] [Full Text] [PDF]

K. D. Livingstone, V. K. Lackney, J. R. Blauth, R. van Wijk, and M. K. Jahn
Genome Mapping in Capsicum and the Evolution of Genome Structure in the Solanaceae
Genetics, July 1, 1999; 152(3): 1183 - 1202.
[Abstract] [Full Text]

A. van Houwelingen, E. Souer, J. Mol, and R. Koes
Epigenetic Interactions among Three dTph1 Transposons in Two Homologous Chromosomes Activate a New Excision–Repair Mechanism in Petunia
PLANT CELL, July 1, 1999; 11(7): 1319 - 1336.
[Abstract] [Full Text]

W. Hu, M. C. P. Timmermans, and J. Messing
Interchromosomal Recombination in Zea mays
Genetics, November 1, 1998; 150(3): 1229 - 1237.
[Abstract] [Full Text]

J. B. Hollick and V. L. Chandler
Epigenetic Allelic States of a Maize Transcriptional Regulatory Locus Exhibit Overdominant Gene Action
Genetics, October 1, 1998; 150(2): 891 - 897.
[Abstract] [Full Text]

D. A. Selinger, D. Lisch, and V. L. Chandler
The Maize Regulatory Gene B-Peru Contains a DNA Rearrangement That Specifies Tissue-Specific Expression Through Both Positive and Negative Promoter Elements
Genetics, June 1, 1998; 149(2): 1125 - 1138.
[Abstract] [Full Text] [PDF]

E. L. Walker
Paramutation of the r1 Locus of Maize Is Associated With Increased Cytosine Methylation
Genetics, April 1, 1998; 148(4): 1973 - 1981.
[Abstract] [Full Text] [PDF]

Epigenetic Instability and Trans-Silencing Interactions Associated With an SPT::Ac T-DNA Locus in Tobacco
Genetics, January 1, 1998; 148(1): 457 - 470.

A. Boulton, R. S. Myers, and R. J. Redfield
The hotspot conversion paradox and the evolution of meiotic recombination
PNAS, July 22, 1997; 94(15): 8058 - 8063.
[Abstract] [Full Text] [PDF]

H. Fu, Z. Zheng, and H. K. Dooner
Recombination rates between adjacent genic and retrotransposon regions in maize vary by 2 orders of magnitude
PNAS, January 22, 2002; 99(2): 1082 - 1087.
[Abstract] [Full Text] [PDF]

D. Lisch, C. C. Carey, J. E. Dorweiler, and V. L. Chandler
A mutation that prevents paramutation in maize also reverses Mutator transposon methylation and silencing
PNAS, April 30, 2002; 99(9): 6130 - 6135.
[Abstract] [Full Text] [PDF]

H. Yao, Q. Zhou, J. Li, H. Smith, M. Yandeau, B. J. Nikolau, and P. S. Schnable
From the Cover: Molecular characterization of meiotic recombination across the 140-kb multigenic a1-sh2 interval of maize
PNAS, April 30, 2002; 99(9): 6157 - 6162.
[Abstract] [Full Text] [PDF]

				M. D. Yandeau-Nelson, B. J. Nikolau, and P. S. Schnable Effects of trans-acting Genetic Modifiers on Meiotic Recombination Across the a1-sh2 Interval of Maize Genetics, September 1, 2006; 174(1): 101 - 112. [Abstract] [Full Text] [PDF]

				H. Yan, W. Jin, K. Nagaki, S. Tian, S. Ouyang, C. R. Buell, P. B. Talbert, S. Henikoff, and J. Jiang Transcription and Histone Modifications in the Recombination-Free Region Spanning a Rice Centromere PLANT CELL, December 1, 2005; 17(12): 3227 - 3238. [Abstract] [Full Text] [PDF]

				M. D. Yandeau-Nelson, Q. Zhou, H. Yao, X. Xu, B. J. Nikolau, and P. S. Schnable MuDR Transposase Increases the Frequency of Meiotic Crossovers in the Vicinity of a Mu Insertion in the Maize a1 Gene Genetics, February 1, 2005; 169(2): 917 - 929. [Abstract] [Full Text] [PDF]

				L. Huang, S. A. Brooks, W. Li, J. P. Fellers, H. N. Trick, and B. S. Gill Map-Based Cloning of Leaf Rust Resistance Gene Lr21 From the Large and Polyploid Genome of Bread Wheat Genetics, June 1, 2003; 164(2): 655 - 664. [Abstract] [Full Text] [PDF]

				M. Stam, C. Belele, W. Ramakrishna, J. E. Dorweiler, J. L. Bennetzen, and V. L. Chandler The Regulatory Regions Required for B' Paramutation and Expression Are Located Far Upstream of the Maize b1 Transcribed Sequences Genetics, October 1, 2002; 162(2): 917 - 930. [Abstract] [Full Text] [PDF]

				M. Stam, C. Belele, J. E. Dorweiler, and V. L. Chandler Differential chromatin structure within a tandem array 100 kb upstream of the maize b1 locus is associated with paramutation Genes & Dev., August 1, 2002; 16(15): 1906 - 1918. [Abstract] [Full Text] [PDF]

				Y. Vigouroux, J. S. Jaqueth, Y. Matsuoka, O. S. Smith, W. D. Beavis, J. S. C. Smith, and J. Doebley Rate and Pattern of Mutation at Microsatellite Loci in Maize Mol. Biol. Evol., August 1, 2002; 19(8): 1251 - 1260. [Abstract] [Full Text] [PDF]

				H. K. Dooner Extensive Interallelic Polymorphisms Drive Meiotic Recombination into a Crossover Pathway PLANT CELL, May 1, 2002; 14(5): 1173 - 1183. [Abstract] [Full Text] [PDF]

				C. F. Weil Finding the crosswalks on DNA PNAS, April 30, 2002; 99(9): 5763 - 5765. [Full Text] [PDF]

				D. Lisch, C. C. Carey, J. E. Dorweiler, and V. L. Chandler A mutation that prevents paramutation in maize also reverses Mutator transposon methylation and silencing PNAS, April 30, 2002; 99(9): 6130 - 6135. [Abstract] [Full Text] [PDF]

				H. Yao, Q. Zhou, J. Li, H. Smith, M. Yandeau, B. J. Nikolau, and P. S. Schnable From the Cover: Molecular characterization of meiotic recombination across the 140-kb multigenic a1-sh2 interval of maize PNAS, April 30, 2002; 99(9): 6157 - 6162. [Abstract] [Full Text] [PDF]

				H. Fu, Z. Zheng, and H. K. Dooner Recombination rates between adjacent genic and retrotransposon regions in maize vary by 2 orders of magnitude PNAS, January 22, 2002; 99(2): 1082 - 1087. [Abstract] [Full Text] [PDF]

				P. J. Yeadon, J. P. Rasmussen, and D. E. A. Catcheside Recombination Events in Neurospora crassa May Cross a Translocation Breakpoint by a Template-Switching Mechanism Genetics, October 1, 2001; 159(2): 571 - 579. [Abstract] [Full Text] [PDF]

				D. A. Selinger and V. L. Chandler B-Bolivia, an Allele of the Maize b1 Gene with Variable Expression, Contains a High Copy Retrotransposon-Related Sequence Immediately Upstream Plant Physiology, March 1, 2001; 125(3): 1363 - 1379. [Abstract] [Full Text]

				L. V. Sidorenko and T. Peterson Transgene-Induced Silencing Identifies Sequences Involved in the Establishment of Paramutation of the Maize p1 Gene PLANT CELL, February 1, 2001; 13(2): 319 - 335. [Abstract] [Full Text]

				J. E. Dorweiler, C. C. Carey, K. M. Kubo, J. B. Hollick, J. L. Kermicle, and V. L. Chandler mediator of paramutation1 Is Required for Establishment and Maintenance of Paramutation at Multiple Maize Loci PLANT CELL, November 1, 2000; 12(11): 2101 - 2118. [Abstract] [Full Text]

				J. B. Hollick, G. I. Patterson, I. M. Asmundsson, and V. L. Chandler Paramutation Alters Regulatory Control of the Maize pl Locus Genetics, April 1, 2000; 154(4): 1827 - 1838. [Abstract] [Full Text]

				J. D. Faris, K. M. Haen, and B. S. Gill Saturation Mapping of a Gene-Rich Recombination Hot Spot Region in Wheat Genetics, February 1, 2000; 154(2): 823 - 835. [Abstract] [Full Text]

				D. A. Selinger and V. L. Chandler Major recent and independent changes in levels and patterns of expression have occurred at the b gene, a regulatory locus in maize PNAS, December 21, 1999; 96(26): 15007 - 15012. [Abstract] [Full Text] [PDF]

				K. D. Livingstone, V. K. Lackney, J. R. Blauth, R. van Wijk, and M. K. Jahn Genome Mapping in Capsicum and the Evolution of Genome Structure in the Solanaceae Genetics, July 1, 1999; 152(3): 1183 - 1202. [Abstract] [Full Text]

				A. van Houwelingen, E. Souer, J. Mol, and R. Koes Epigenetic Interactions among Three dTph1 Transposons in Two Homologous Chromosomes Activate a New Excision–Repair Mechanism in Petunia PLANT CELL, July 1, 1999; 11(7): 1319 - 1336. [Abstract] [Full Text]

				W. Hu, M. C. P. Timmermans, and J. Messing Interchromosomal Recombination in Zea mays Genetics, November 1, 1998; 150(3): 1229 - 1237. [Abstract] [Full Text]

				J. B. Hollick and V. L. Chandler Epigenetic Allelic States of a Maize Transcriptional Regulatory Locus Exhibit Overdominant Gene Action Genetics, October 1, 1998; 150(2): 891 - 897. [Abstract] [Full Text]

				D. A. Selinger, D. Lisch, and V. L. Chandler The Maize Regulatory Gene B-Peru Contains a DNA Rearrangement That Specifies Tissue-Specific Expression Through Both Positive and Negative Promoter Elements Genetics, June 1, 1998; 149(2): 1125 - 1138. [Abstract] [Full Text] [PDF]

				E. L. Walker Paramutation of the r1 Locus of Maize Is Associated With Increased Cytosine Methylation Genetics, April 1, 1998; 148(4): 1973 - 1981. [Abstract] [Full Text] [PDF]

				Epigenetic Instability and Trans-Silencing Interactions Associated With an SPT::Ac T-DNA Locus in Tobacco Genetics, January 1, 1998; 148(1): 457 - 470.

				A. Boulton, R. S. Myers, and R. J. Redfield The hotspot conversion paradox and the evolution of meiotic recombination PNAS, July 22, 1997; 94(15): 8058 - 8063. [Abstract] [Full Text] [PDF]