Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2005 Oct;15(10):1441-6.
doi: 10.1101/gr.3362105.

Gene enrichment in maize with hypomethylated partial restriction (HMPR) libraries

John Emberton  1 , Jianxin Ma, Yinan Yuan, Phillip SanMiguel, Jeffrey L Bennetzen
Affiliations

Gene enrichment in maize with hypomethylated partial restriction (HMPR) libraries

John Emberton et al. Genome Res. 2005 Oct.

Abstract

A new technology was developed to assist gene-enrichment sequencing of any complex plant genome, employing maize as the test organism. Hypomethylated partial restriction (HMPR) libraries were constructed by using independent partial digestions with methylation-sensitive restriction enzymes HpaII (5'-CCGG-3') and HpyCH4IV (5'-ACGT-3'). Fragments of 1-4 kb were purified and cloned, followed by sequence analysis of >2000 clones from 10 separate libraries. Organellar clones comprised approximately 10% of each library but were useful in showing that no chimeric clones were generated and that digestion efficiencies were 10%-25% in different libraries. Four separate HMPR libraries, analyzed in detail, exhibited very similar degrees of gene enrichment and repeat depletion. Known gene homologies were found in approximately 25% of the HMPR clones, compared with <4% in clones from a fully random set of unfiltered maize shotgun sequences. This six- to sevenfold enrichment for genes compares favorably with the best previous gene enrichment techniques in maize, High Cot analysis and methylation filtration. Compared with High Cot and methylation filtration, HMPR is exceptional in depleting retrotransposons' content to the lowest level yet observed (<5%, compared with >70% for unfiltered maize sequences) and in providing an unmatched enrichment for the "unknown" sequences that contain promoters, introns, and other gene-adjacent regions.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Nuclear sequence composition of four HMPR libraries. Organellar sequences were removed from the data set prior to the analysis.
Figure 2.
Figure 2.
Nuclear sequence composition of hypomethylated partial restriction (HMPR), High Cot (HC), methylation filtration (MF) and unfiltered (UF) libraries. Organellar sequences were removed from the data set prior to the analysis.
See this image and copyright information in PMC

References

    1. Bennetzen, J.L. 2002a. Mechanisms and rates of genome expansion and contraction in flowering plants. Genetica 115: 29-36. - PubMed
    1. ———. 2002b. The rice genome: Opening the door to comparative plant biology. Science 296: 60-63. - PubMed
    1. Bennetzen, J.L., Schrick, K., Springer, P.S., Brown, W.E., and SanMiguel, P. 1994. Active maize genes are unmodified and flanked by diverse classes of modified, highly repetitive DNA. Genome 37: 565-576. - PubMed
    1. Bennetzen, J.L., Coleman, C., Liu, R., Ma, J., and Ramakrishna, W. 2004. Consistent over-estimation of gene number in complex plant genomes. Curr. Opin. Plant Biol. 7: 732-736. - PubMed
    1. Bennetzen, J.L., Liu, R., Ma, J., and Pontaroli, A. 2005. Maize genome structure and rearrangement. Maydica (in press).

WEB SITE REFERENCES

    1. http://www.tigr.org/tdb/tgi/maize/; the TIGR Maize Database - PMC - PubMed
    1. http://www.tigr.org/tdb/e2k1/plant.repeats/; the TIGR Plant Repeat Databases
    1. http://data.genomics.purdue.edu/~pmiguel/projects/retros/; Retrotransposon Database

Publication types

Associated data

LinkOut - more resources