Michael J Axtell

Michael J Axtell

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Michael J Axtell

Publications by authors named "Michael J Axtell"

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Convergent horizontal gene transfer and cross-talk of mobile nucleic acids in parasitic plants.

Nat Plants 2019 Sep 22;5(9):991-1001. Epub 2019 Jul 22.

Intercollege Graduate Program in Plant Biology, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.

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http://dx.doi.org/10.1038/s41477-019-0458-0DOI Listing
September 2019

Small RNA warfare: exploring origins and function of trans-species microRNAs from the parasitic plant Cuscuta.

Curr Opin Plant Biol 2019 Aug 28;50:76-81. Epub 2019 Apr 28.

Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA. Electronic address:

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http://dx.doi.org/10.1016/j.pbi.2019.03.014DOI Listing
August 2019

Molecular Dialog Between Parasitic Plants and Their Hosts.

Annu Rev Phytopathol 2019 Aug 21;57:279-299. Epub 2019 Jun 21.

School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061, USA; email:

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http://dx.doi.org/10.1146/annurev-phyto-082718-100043DOI Listing
August 2019

MicroRNAs in Plants: Key Findings from the Early Years.

Plant Cell 2019 Jun 29;31(6):1206-1207. Epub 2019 Apr 29.

The Pennsylvania State UniversityDepartment of Biology and Huck Institutes of the Life SciencesUniversity Park, Pennsylvania 16802

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http://www.plantcell.org/lookup/doi/10.1105/tpc.19.00310
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http://dx.doi.org/10.1105/tpc.19.00310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6588298PMC
June 2019

Second to None: Plant Secondary siRNAs as Defensive Agents against Phytophthora.

Authors:
Michael J Axtell

Cell Host Microbe 2019 01;25(1):7-9

Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chom.2018.12.007DOI Listing
January 2019

Several phased siRNA annotation methods can frequently misidentify 24 nucleotide siRNA-dominated loci.

Plant Direct 2018 Dec 17;2(12):e00101. Epub 2018 Dec 17.

Genetics Ph.D. Program Huck Institutes of the Life Sciences The Pennsylvania State University University Park Pennsylvania.

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http://dx.doi.org/10.1002/pld3.101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6508839PMC
December 2018

Analysis of RDR1/RDR2/RDR6-independent small RNAs in Arabidopsis thaliana improves MIRNA annotations and reveals unexplained types of short interfering RNA loci.

Plant J 2018 06 13;94(6):1051-1063. Epub 2018 May 13.

Genetics PhD Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.

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http://dx.doi.org/10.1111/tpj.13919DOI Listing
June 2018

Revisiting Criteria for Plant MicroRNA Annotation in the Era of Big Data.

Plant Cell 2018 02 17;30(2):272-284. Epub 2018 Jan 17.

Donald Danforth Plant Science Center, St. Louis, Missouri 63132

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http://dx.doi.org/10.1105/tpc.17.00851DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5868703PMC
February 2018

MicroRNAs from the parasitic plant Cuscuta campestris target host messenger RNAs.

Nature 2018 01;553(7686):82-85

Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1038/nature25027DOI Listing
January 2018

AGO4 is specifically required for heterochromatic siRNA accumulation at Pol V-dependent loci in Arabidopsis thaliana.

Plant J 2017 Apr 11;90(1):37-47. Epub 2017 Feb 11.

Intercollege Plant Biology Ph.D. Program, Huck Institutes of the Life Sciences, Penn State University, University Park, PA, 16802, USA.

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http://dx.doi.org/10.1111/tpj.13463DOI Listing
April 2017

Lost in translation? microRNAs at the rough ER.

Authors:
Michael J Axtell

Trends Plant Sci 2017 04 17;22(4):273-274. Epub 2017 Mar 17.

Department of Biology and Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802 USA. Electronic address:

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http://dx.doi.org/10.1016/j.tplants.2017.03.002DOI Listing
April 2017

Genome-wide analysis of single non-templated nucleotides in plant endogenous siRNAs and miRNAs.

Nucleic Acids Res 2016 09 20;44(15):7395-405. Epub 2016 May 20.

Intercollege Plant Biology PhD Program, Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA Department of Biology, Penn State University, University Park, PA 16802, USA

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http://dx.doi.org/10.1093/nar/gkw457DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5009732PMC
September 2016

Improved Placement of Multi-mapping Small RNAs.

G3 (Bethesda) 2016 07 7;6(7):2103-11. Epub 2016 Jul 7.

Huck Institutes of the Life Sciences, Penn State University, Philadelphia 16802 Department of Biology, Penn State University, Philadelphia 16802

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http://dx.doi.org/10.1534/g3.116.030452DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4938663PMC
July 2016

Genome-Wide Characterization of Maize Small RNA Loci and Their Regulation in the required to maintain repression6-1 (rmr6-1) Mutant and Long-Term Abiotic Stresses.

Plant Physiol 2016 Mar 8;170(3):1535-48. Epub 2016 Jan 8.

Department of Agronomy, Animals, Food, Natural Resources and Environment, University of Padova, Agripolis Viale dell'Università 16, 35020 Legnaro PD Italy (A.L., C.F., S.F., S.V.); andDepartment of Biology and Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802 (A.L., M.J.A.)

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http://dx.doi.org/10.1104/pp.15.01205DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4775107PMC
March 2016

Quantitating plant microRNA-mediated target repression using a dual-luciferase transient expression system.

Methods Mol Biol 2015 ;1284:287-303

Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.

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http://dx.doi.org/10.1007/978-1-4939-2444-8_14DOI Listing
November 2015

Small RNA profiles of wild-type and silencing suppressor-deficient tomato spotted wilt virus infected Nicotiana benthamiana.

Virus Res 2015 Oct 3;208:30-8. Epub 2015 Jun 3.

Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, 10135 Torino, Italy. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S01681702150023
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http://dx.doi.org/10.1016/j.virusres.2015.05.021DOI Listing
October 2015

More than meets the eye? Factors that affect target selection by plant miRNAs and heterochromatic siRNAs.

Curr Opin Plant Biol 2015 Oct 31;27:118-24. Epub 2015 Jul 31.

Plant Biology Ph.D. Program, Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; Genetics Ph.D. Program, Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; Department of Biology, Penn State University, University Park, PA 16802, USA. Electronic address:

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http://dx.doi.org/10.1016/j.pbi.2015.06.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4732885PMC
October 2015

Comprehensive Annotation of Physcomitrella patens Small RNA Loci Reveals That the Heterochromatic Short Interfering RNA Pathway Is Largely Conserved in Land Plants.

Plant Cell 2015 Aug 24;27(8):2148-62. Epub 2015 Jul 24.

Plant Biology PhD Program, Penn State University, University Park, Pennsylvania 16802 Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802 Department of Biology, Penn State University, University Park, Pennsylvania 16802

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http://www.plantcell.org/lookup/doi/10.1105/tpc.15.00228
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http://dx.doi.org/10.1105/tpc.15.00228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4568501PMC
August 2015

Long-range genomic enrichment, sequencing, and assembly to determine unknown sequences flanking a known microRNA.

PLoS One 2013 20;8(12):e83721. Epub 2013 Dec 20.

Integrative Biosciences PhD Program in Bioinformatics and Genomics, Huck Institutes of the Life Sciences, and Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0083721PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3869802PMC
March 2015

Identification and annotation of small RNA genes using ShortStack.

Methods 2014 May 16;67(1):20-7. Epub 2013 Oct 16.

Plant Biology Ph.D. Program, Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; Department of Biology, Penn State University, University Park, PA 16802, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10462023130040
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http://dx.doi.org/10.1016/j.ymeth.2013.10.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3989477PMC
May 2014

A non-canonical plant microRNA target site.

Nucleic Acids Res 2014 Apr 21;42(8):5270-9. Epub 2014 Feb 21.

INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France, AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France and Department of Biology and Plant Biology Ph.D. Program, Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1093/nar/gku157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4005643PMC
April 2014

Seeing the forest for the trees: annotating small RNA producing genes in plants.

Curr Opin Plant Biol 2014 Apr 15;18:87-95. Epub 2014 Mar 15.

Department of Biology, Penn State University, University Park, PA 16802, USA; Plant Biology Intercollegiate Ph.D. Program, Penn State University, University Park, PA 16802, USA; Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA. Electronic address:

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http://dx.doi.org/10.1016/j.pbi.2014.02.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4001702PMC
April 2014

Analysis of complementarity requirements for plant microRNA targeting using a Nicotiana benthamiana quantitative transient assay.

Plant Cell 2014 Feb 7;26(2):741-53. Epub 2014 Feb 7.

Department of Biology, Pensylvania State University, University Park, Pensylvania 16802.

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http://dx.doi.org/10.1105/tpc.113.120972DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967037PMC
February 2014

Bidirectional processing of pri-miRNAs with branched terminal loops by Arabidopsis Dicer-like1.

Nat Struct Mol Biol 2013 Sep 11;20(9):1106-15. Epub 2013 Aug 11.

1] Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA. [2] Institute of Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas, USA. [3] College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.

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http://dx.doi.org/10.1038/nsmb.2646DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3766402PMC
September 2013

Classification and comparison of small RNAs from plants.

Authors:
Michael J Axtell

Annu Rev Plant Biol 2013 16;64:137-59. Epub 2013 Jan 16.

Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA.

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http://www.annualreviews.org/doi/10.1146/annurev-arplant-050
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http://dx.doi.org/10.1146/annurev-arplant-050312-120043DOI Listing
July 2013

ShortStack: comprehensive annotation and quantification of small RNA genes.

Authors:
Michael J Axtell

RNA 2013 Jun 22;19(6):740-51. Epub 2013 Apr 22.

Department of Biology, and Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802, USA.

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http://rnajournal.cshlp.org/cgi/doi/10.1261/rna.035279.112
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http://dx.doi.org/10.1261/rna.035279.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3683909PMC
June 2013

DICER-LIKE3 activity in Physcomitrella patens DICER-LIKE4 mutants causes severe developmental dysfunction and sterility.

Mol Plant 2012 Nov 17;5(6):1281-94. Epub 2012 Apr 17.

Plant Biotechnology, University of Freiburg, Schaenzlestraβe 1, D-79104 Freiburg, Germany.

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http://dx.doi.org/10.1093/mp/sss036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3506028PMC
November 2012

The helicase and RNaseIIIa domains of Arabidopsis Dicer-Like1 modulate catalytic parameters during microRNA biogenesis.

Plant Physiol 2012 Jun 3;159(2):748-58. Epub 2012 Apr 3.

Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://www.plantphysiol.org/cgi/doi/10.1104/pp.112.193508
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http://dx.doi.org/10.1104/pp.112.193508DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3406889PMC
June 2012

Vive la différence: biogenesis and evolution of microRNAs in plants and animals.

Genome Biol 2011 28;12(4):221. Epub 2011 Apr 28.

Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, PA 16802, USA.

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http://dx.doi.org/10.1186/gb-2011-12-4-221DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218855PMC
February 2012

The Selaginella genome identifies genetic changes associated with the evolution of vascular plants.

Authors:
Jo Ann Banks Tomoaki Nishiyama Mitsuyasu Hasebe John L Bowman Michael Gribskov Claude dePamphilis Victor A Albert Naoki Aono Tsuyoshi Aoyama Barbara A Ambrose Neil W Ashton Michael J Axtell Elizabeth Barker Michael S Barker Jeffrey L Bennetzen Nicholas D Bonawitz Clint Chapple Chaoyang Cheng Luiz Gustavo Guedes Correa Michael Dacre Jeremy DeBarry Ingo Dreyer Marek Elias Eric M Engstrom Mark Estelle Liang Feng Cédric Finet Sandra K Floyd Wolf B Frommer Tomomichi Fujita Lydia Gramzow Michael Gutensohn Jesper Harholt Mitsuru Hattori Alexander Heyl Tadayoshi Hirai Yuji Hiwatashi Masaki Ishikawa Mineko Iwata Kenneth G Karol Barbara Koehler Uener Kolukisaoglu Minoru Kubo Tetsuya Kurata Sylvie Lalonde Kejie Li Ying Li Amy Litt Eric Lyons Gerard Manning Takeshi Maruyama Todd P Michael Koji Mikami Saori Miyazaki Shin-ichi Morinaga Takashi Murata Bernd Mueller-Roeber David R Nelson Mari Obara Yasuko Oguri Richard G Olmstead Naoko Onodera Bent Larsen Petersen Birgit Pils Michael Prigge Stefan A Rensing Diego Mauricio Riaño-Pachón Alison W Roberts Yoshikatsu Sato Henrik Vibe Scheller Burkhard Schulz Christian Schulz Eugene V Shakirov Nakako Shibagaki Naoki Shinohara Dorothy E Shippen Iben Sørensen Ryo Sotooka Nagisa Sugimoto Mamoru Sugita Naomi Sumikawa Milos Tanurdzic Günter Theissen Peter Ulvskov Sachiko Wakazuki Jing-Ke Weng William W G T Willats Daniel Wipf Paul G Wolf Lixing Yang Andreas D Zimmer Qihui Zhu Therese Mitros Uffe Hellsten Dominique Loqué Robert Otillar Asaf Salamov Jeremy Schmutz Harris Shapiro Erika Lindquist Susan Lucas Daniel Rokhsar Igor V Grigoriev

Science 2011 May 5;332(6032):960-3. Epub 2011 May 5.

Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA.

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http://sites.psu.edu/axtell/wp-content/uploads/sites/21458/2
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http://www.sciencemag.org/cgi/doi/10.1126/science.1203810
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http://dx.doi.org/10.1126/science.1203810DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166216PMC
May 2011

Transcriptome-wide identification of microRNA targets in rice.

Plant J 2010 Jun 26;62(5):742-59. Epub 2010 Feb 26.

Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA.

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http://dx.doi.org/10.1111/j.1365-313X.2010.04187.xDOI Listing
June 2010

Arabidopsis lyrata small RNAs: transient MIRNA and small interfering RNA loci within the Arabidopsis genus.

Plant Cell 2010 Apr 20;22(4):1090-103. Epub 2010 Apr 20.

Integrative Biosciences PhD Program in Bioinformatics and Genomics, Huck Institutes of the Life Sciences, Pensylvania State University, University Park, Pensylvania 16802, USA.

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http://dx.doi.org/10.1105/tpc.110.073882DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2879747PMC
April 2010

A method to discover phased siRNA loci.

Authors:
Michael J Axtell

Methods Mol Biol 2010 ;592:59-70

Department of Biology, Pennsylvania State University, University Park, PA, USA.

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http://dx.doi.org/10.1007/978-1-60327-005-2_5DOI Listing
January 2010

RNA secondary structural determinants of miRNA precursor processing in Arabidopsis.

Curr Biol 2010 Jan;20(1):37-41

The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1016/j.cub.2009.10.076DOI Listing
January 2010

Sliced microRNA targets and precise loop-first processing of MIR319 hairpins revealed by analysis of the Physcomitrella patens degradome.

RNA 2009 Dec 22;15(12):2112-21. Epub 2009 Oct 22.

Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1261/rna.1774909DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779683PMC
December 2009

CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets.

Bioinformatics 2009 Jan 18;25(1):130-1. Epub 2008 Nov 18.

Department of Computer Science and Engineering and Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn604DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3202307PMC
January 2009

Evolution of microRNAs and their targets: are all microRNAs biologically relevant?

Authors:
Michael J Axtell

Biochim Biophys Acta 2008 Nov 10;1779(11):725-34. Epub 2008 Mar 10.

Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1016/j.bbagrm.2008.02.007DOI Listing
November 2008

Evolution of plant microRNAs and their targets.

Trends Plant Sci 2008 Jul 22;13(7):343-9. Epub 2008 May 22.

Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S136013850800137
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http://dx.doi.org/10.1016/j.tplants.2008.03.009DOI Listing
July 2008

Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome.

Curr Biol 2008 May 8;18(10):758-762. Epub 2008 May 8.

Cell and Developmental Biology Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802; Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2008.04.042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2583427PMC
May 2008

Common functions for diverse small RNAs of land plants.

Plant Cell 2007 Jun 29;19(6):1750-69. Epub 2007 Jun 29.

Department of Biology and Huck Institutes of the Life Sciences, Pensylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1105/tpc.107.051706DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1955733PMC
June 2007

A two-hit trigger for siRNA biogenesis in plants.

Cell 2006 Nov;127(3):565-77

Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S009286740601292
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http://dx.doi.org/10.1016/j.cell.2006.09.032DOI Listing
November 2006

Antiquity of microRNAs and their targets in land plants.

Plant Cell 2005 Jun 22;17(6):1658-73. Epub 2005 Apr 22.

Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1105/tpc.105.032185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1143068PMC
June 2005

Genetic and molecular evidence that the Pseudomonas syringae type III effector protein AvrRpt2 is a cysteine protease.

Mol Microbiol 2003 Sep;49(6):1537-46

University of California, Berkeley, Department of Plant and Microbial Biology, 111 Koshland Hall, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1046/j.1365-2958.2003.03666.xDOI Listing
September 2003

Initiation of RPS2-specified disease resistance in Arabidopsis is coupled to the AvrRpt2-directed elimination of RIN4.

Cell 2003 Feb;112(3):369-77

Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1016/s0092-8674(03)00036-9DOI Listing
February 2003

NPK1, an MEKK1-like mitogen-activated protein kinase kinase kinase, regulates innate immunity and development in plants.

Dev Cell 2002 Aug;3(2):291-7

Department of Plant and Microbial Biology, University of California, Berkeley, 94720, USA.

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August 2002