-
Allison Gaudinier, Lifang Zhang,
John S Reece-Hoyes,
Mallorie Taylor-Teeples,
Li Pu,
Zhijie Liu,
Ghislain Breton,
Jose L Pruneda-Paz,
Dahae Kim,
Steve A Kay,
Albertha J M Walhout,
Doreen Ware,
Siobhan M Brady
[show abstract]
[hide abstract]
ABSTRACT: We present an Arabidopsis thaliana full-length transcription factor resource of 92% of root stele-expressed transcription factors and 74.5% of root-expressed transcription factors. We demonstrate its use with enhanced yeast one-hybrid (eY1H) screening for rapid, systematic mapping of plant transcription factor-promoter interactions. We identified 158 interactions with 13 stele-expressed promoters, many of which occur physically or are regulatory in planta.
Nature Methods 12/2011; 8(12):1053-5. · 19.28 Impact Factor
-
Siobhan M Brady, Lifang Zhang,
Molly Megraw,
Natalia J Martinez,
Eric Jiang,
Charles S Yi,
Weilin Liu,
Anna Zeng,
Mallorie Taylor-Teeples,
Dahae Kim,
Sebastian Ahnert,
Uwe Ohler,
Doreen Ware,
Albertha J M Walhout,
Philip N Benfey
[show abstract]
[hide abstract]
ABSTRACT: Tightly controlled gene expression is a hallmark of multicellular development and is accomplished by transcription factors (TFs) and microRNAs (miRNAs). Although many studies have focused on identifying downstream targets of these molecules, less is known about the factors that regulate their differential expression. We used data from high spatial resolution gene expression experiments and yeast one-hybrid (Y1H) and two-hybrid (Y2H) assays to delineate a subset of interactions occurring within a gene regulatory network (GRN) that determines tissue-specific TF and miRNA expression in plants. We find that upstream TFs are expressed in more diverse cell types than their targets and that promoters that are bound by a relatively large number of TFs correspond to key developmental regulators. The regulatory consequence of many TFs for their target was experimentally determined using genetic analysis. Remarkably, molecular phenotypes were identified for 65% of the TFs, but morphological phenotypes were associated with only 16%. This indicates that the GRN is robust, and that gene expression changes may be canalized or buffered.
Molecular Systems Biology 01/2011; 7:459. · 8.63 Impact Factor
-
Patrick S. Schnable,
Doreen Ware,
Robert S. Fulton,
Joshua C. Stein,
Fusheng Wei,
Shiran Pasternak,
Chengzhi Liang,
Jianwei Zhang,
Lucinda Fulton,
Tina A. Graves, [......],
Jiming Jiang,
Ning Jiang,
Gernot G. Presting,
Susan R. Wessler,
Srinivas Aluru,
Robert A. Martienssen,
Sandra W. Clifton,
W. Richard McCombie,
Rod A. Wing,
Richard K. Wilson
[show abstract]
[hide abstract]
ABSTRACT: We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for
biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of
the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were
responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions
of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven
gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state.
These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural
improvements of maize.
Science 11/2009; 326(5956):1112-1115. · 31.20 Impact Factor
-
Patrick S. Schnable,
Doreen Ware,
Robert S. Fulton,
Joshua C. Stein,
Fusheng Wei,
Shiran Pasternak,
Chengzhi Liang,
Jianwei Zhang,
Lucinda Fulton,
Tina A. Graves, [......],
Jiming Jiang,
Ning Jiang,
Gernot G. Presting,
Susan R. Wessler,
Srinivas Aluru,
Robert A. Martienssen,
Sandra W. Clifton,
W. Richard McCombie,
Rod A. Wing,
Richard K. Wilson
[show abstract]
[hide abstract]
ABSTRACT: We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for
biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of
the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were
responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions
of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven
gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state.
These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural
improvements of maize.
Science 11/2009; 326(5956):1112-1115. · 31.20 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: MicroRNAs (miRNAs) are small, non-coding RNAs that play essential roles in plant growth, development, and stress response. We conducted a genome-wide survey of maize miRNA genes, characterizing their structure, expression, and evolution. Computational approaches based on homology and secondary structure modeling identified 150 high-confidence genes within 26 miRNA families. For 25 families, expression was verified by deep-sequencing of small RNA libraries that were prepared from an assortment of maize tissues. PCR-RACE amplification of 68 miRNA transcript precursors, representing 18 families conserved across several plant species, showed that splice variation and the use of alternative transcriptional start and stop sites is common within this class of genes. Comparison of sequence variation data from diverse maize inbred lines versus teosinte accessions suggest that the mature miRNAs are under strong purifying selection while the flanking sequences evolve equivalently to other genes. Since maize is derived from an ancient tetraploid, the effect of whole-genome duplication on miRNA evolution was examined. We found that, like protein-coding genes, duplicated miRNA genes underwent extensive gene-loss, with approximately 35% of ancestral sites retained as duplicate homoeologous miRNA genes. This number is higher than that observed with protein-coding genes. A search for putative miRNA targets indicated bias towards genes in regulatory and metabolic pathways. As maize is one of the principal models for plant growth and development, this study will serve as a foundation for future research into the functional roles of miRNA genes.
PLoS Genetics 11/2009; 5(11):e1000716. · 8.69 Impact Factor
-
Fusheng Wei,
Joshua C Stein,
Chengzhi Liang,
Jianwei Zhang,
Robert S Fulton,
Regina S Baucom,
Emanuele De Paoli,
Shiguo Zhou,
Lixing Yang,
Yujun Han, [......],
Blake C Meyers,
Jeffrey L Bennetzen,
Robert A Martienssen,
W Richard McCombie,
Srinivas Aluru,
Sandra W Clifton,
Patrick S Schnable,
Doreen Ware,
Richard K Wilson,
Rod A Wing
[show abstract]
[hide abstract]
ABSTRACT: Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of transposable elements (TEs) that are mostly nested within each other, of which most families are low-copy. We identified 544 gene models using multiple levels of evidence, as well as five miRNA genes. Gene fragments, many captured by TEs, are prevalent within this region. Elimination of gene redundancy from a tetraploid maize ancestor that originated a few million years ago is responsible in this region for most disruptions of synteny with sorghum and rice. Consistent with other sub-genomic analyses in maize, small RNA mapping showed that many small RNAs match TEs and that most TEs match small RNAs. These results, performed on approximately 1% of the maize genome, demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets. Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses.
PLoS Genetics 11/2009; 5(11):e1000728. · 8.69 Impact Factor
-
Patrick S Schnable,
Doreen Ware,
Robert S Fulton,
Joshua C Stein,
Fusheng Wei,
Shiran Pasternak,
Chengzhi Liang,
Jianwei Zhang,
Lucinda Fulton,
Tina A Graves, [......],
Jiming Jiang,
Ning Jiang,
Gernot G Presting,
Susan R Wessler,
Srinivas Aluru,
Robert A Martienssen,
Sandra W Clifton,
W Richard McCombie,
Rod A Wing,
Richard K Wilson
[show abstract]
[hide abstract]
ABSTRACT: We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.
Science 11/2009; 326(5956):1112-5. · 31.20 Impact Factor
-
Andrew H. Paterson,
John E. Bowers,
R|[eacute]|my Bruggmann,
Inna Dubchak,
Jane Grimwood,
Heidrun Gundlach,
Georg Haberer,
Uffe Hellsten,
Therese Mitros,
Alexander Poliakov, [......],
Stephen Kresovich,
Maureen C. McCann,
Ray Ming,
Daniel G. Peterson,
Mehboob-ur-Rahman,
Doreen Ware,
Peter Westhoff,
Klaus F. X. Mayer,
Joachim Messing,
Daniel S. Rokhsar
[show abstract]
[hide abstract]
ABSTRACT: Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the 730-megabase Sorghum bicolor (L.) Moench genome, placing 98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the 75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization 70 million years ago, most duplicated gene sets lost one member before the sorghum–rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.
Nature 01/2009; 457(7229):551-556. · 36.28 Impact Factor
-
Cheng Lu,
Dong-Hoon Jeong,
Karthik Kulkarni,
Manoj Pillay,
Kan Nobuta,
Rana German,
Shawn R Thatcher,
Christopher Maher, Lifang Zhang,
Doreen Ware,
Bin Liu,
Xiaofeng Cao,
Blake C Meyers,
Pamela J Green
[show abstract]
[hide abstract]
ABSTRACT: Small RNAs (21-24 nt) are involved in gene regulation through translation inhibition, mRNA cleavage, or directing chromatin modifications. In rice, currently approximately 240 microRNAs (miRNAs) have been annotated. We sequenced more than four million small RNAs from rice and identified another 24 miRNA genes. Among these, we found a unique class of miRNAs that derive from natural cis-antisense transcript pairs. This configuration generates miRNAs that can perfectly match their targets. We provide evidence that the miRNAs function by inducing mRNA cleavage in the middle of their complementary site. Their production requires Dicer-like 1 (DCL1) activity, which is essential for canonical miRNA biogenesis. All of the natural antisense miRNAs (nat-miRNAs) identified in this study have large introns in their precursors that appear critical for nat-miRNA evolution and for the formation of functional miRNA loci. These findings suggest that other natural cis-antisense loci with similar exon-intron arrangements could be another source of miRNA genes.
Proceedings of the National Academy of Sciences 04/2008; 105(12):4951-6. · 9.68 Impact Factor
