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      N6‐methyladenosine regulatory machinery in plants: composition, function and evolution

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          Summary

          N6‐methyladenosine (m6A) RNA methylation, one of the most pivotal internal modifications of RNA, is a conserved post‐transcriptional mechanism to enrich and regulate genetic information in eukaryotes. The scope and function of this modification in plants has been an intense focus of study, especially in model plant systems. The characterization of plant m6A writers, erasers and readers, as well as the elucidation of their functions, is currently one of the most fascinating hotspots in plant biology research. The functional analysis of m6A in plants will be booming in the foreseeable future, which could contribute to crop genetic improvement through epitranscriptome manipulation. In this review, we systematically analysed and summarized recent advances in the understanding of the structure and composition of plant m6A regulatory machinery, and the biological functions of m6A in plant growth, development and stress response. Finally, our analysis showed that the evolutionary relationships between m6A modification components were highly conserved across the plant kingdom.

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          Pfam: clans, web tools and services

          Robert D. Finn, Jaina Mistry, Benjamin Schuster-Böckler … (2005)
          Pfam is a database of protein families that currently contains 7973 entries (release 18.0). A recent development in Pfam has enabled the grouping of related families into clans. Pfam clans are described in detail, together with the new associated web pages. Improvements to the range of Pfam web tools and the first set of Pfam web services that allow programmatic access to the database and associated tools are also presented. Pfam is available on the web in the UK (), the USA (), France () and Sweden ().
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            Rethinking m6A Readers, Writers, and Erasers.

            Kate Meyer, Samie R. Jaffrey (2017)
            In recent years, m6A has emerged as an abundant and dynamically regulated modification throughout the transcriptome. Recent technological advances have enabled the transcriptome-wide identification of m6A residues, which in turn has provided important insights into the biology and regulation of this pervasive regulatory mark. Also central to our current understanding of m6A are the discovery and characterization of m6A readers, writers, and erasers. Over the last few years, studies into the function of these proteins have led to important discoveries about the regulation and function of m6A. However, during this time our understanding of these proteins has also evolved considerably, sometimes leading to the reversal of early concepts regarding the reading, writing and erasing of m6A. In this review, we summarize recent advances in m6A research, and we highlight how these new findings have reshaped our understanding of how m6A is regulated in the transcriptome.
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              nhmmer: DNA homology search with profile HMMs

              Travis Wheeler, Sean R. Eddy (2013)
              Summary: Sequence database searches are an essential part of molecular biology, providing information about the function and evolutionary history of proteins, RNA molecules and DNA sequence elements. We present a tool for DNA/DNA sequence comparison that is built on the HMMER framework, which applies probabilistic inference methods based on hidden Markov models to the problem of homology search. This tool, called nhmmer, enables improved detection of remote DNA homologs, and has been used in combination with Dfam and RepeatMasker to improve annotation of transposable elements in the human genome. Availability: nhmmer is a part of the new HMMER3.1 release. Source code and documentation can be downloaded from http://hmmer.org. HMMER3.1 is freely licensed under the GNU GPLv3 and should be portable to any POSIX-compliant operating system, including Linux and Mac OS/X. Contact: wheelert@janelia.hhmi.org
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                Author and article information

                Contributors
                Song Weining:
                ORCID: https://orcid.org/0000-0003-2052-3880
                sweining2002@yahoo.com
                Journal
                Journal ID (nlm-ta): Plant Biotechnol J
                Journal ID (iso-abbrev): Plant Biotechnol. J
                Journal ID (doi): 10.1111/(ISSN)1467-7652
                Journal ID (publisher-id): PBI
                Title: Plant Biotechnology Journal
                Publisher: John Wiley and Sons Inc. (Hoboken )
                ISSN (Print): 1467-7644
                ISSN (Electronic): 1467-7652
                Publication date (Electronic): 21 May 2019
                Publication date (Print): July 2019
                Volume: 17
                Issue: 7 ( doiID: 10.1111/pbi.2019.17.issue-7 )
                Pages: 1194-1208
                Affiliations
                [ 1 ] College of Life Sciences State Key Laboratory of Crop Stress Biology in Arid Areas Northwest A&F University Yangling Shaanxi China
                [ 2 ] College of Horticulture and Forestry Sciences Huazhong Agricultural University Wuhan Hubei China
                Author notes
                [*] [* ] Correspondence (Tel 86 29 87082984; fax 86 29 87082203; email sweining2002@ 123456yahoo.com )
                [†]

                These authors contributed equally to this work.

                Author information
                https://orcid.org/0000-0002-4787-7550
                https://orcid.org/0000-0003-2052-3880
                Article
                Publisher ID: PBI13149
                DOI: 10.1111/pbi.13149
                PMC ID: 6576107
                PubMed ID: 31070865
                SO-VID: 7dfa5560-9f00-49d1-af18-45605b3909a0
                Copyright © © 2019 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
                License:

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 02 February 2019
                Date revision received : 28 April 2019
                Date accepted : 01 May 2019
                Page count
                Figures: 5, Tables: 1, Pages: 15, Words: 11606
                Funding
                Funded by: National Natural Science Foundation of China
                Award ID: 31771778
                Award ID: 31801355
                Funded by: State's Key Project of Research and Development Plan of China
                Award ID: 2016YFD0100302
                Categories
                Subject: Review
                Subject: Review
                Custom metadata
                source-schema-version-number 2.0
                component-id pbi13149
                cover-date July 2019
                details-of-publishers-convertor Converter:WILEY_ML3GV2_TO_NLMPMC version:5.6.4 mode:remove_FC converted:17.06.2019

                ScienceOpen disciplines: Biotechnology
                Keywords: m6a,plant,epitranscriptome,rna modification,regulatory machinery
                Data availability:
                ScienceOpen disciplines: Biotechnology
                Keywords: m6a, plant, epitranscriptome, rna modification, regulatory machinery

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