diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml new file mode 100644 index 00000000..a1a30659 --- /dev/null +++ b/.github/workflows/test.yaml @@ -0,0 +1,20 @@ +name: Tests + +on: + push: + branches: + - '**' + pull_request: + branches: + - '**' + +jobs: + + build: + + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v3 + - name: test XML parsing + run: perl t/pubmed_xml.t diff --git a/data/pubmed_37189341.xml b/data/pubmed_37189341.xml new file mode 100644 index 00000000..170e11f1 --- /dev/null +++ b/data/pubmed_37189341.xml @@ -0,0 +1,676 @@ + + + + + + 37189341 + + 2023 + 05 + 17 + + + 2023 + 05 + 30 + +
+ + 2218-273X + + 13 + 4 + + 2023 + Mar + 25 + + + Biomolecules + Biomolecules + + Regulation of the SUV39H Family Methyltransferases: Insights from Fission Yeast. + 593 + 10.3390/biom13040593 + + Histones, which make up nucleosomes, undergo various post-translational modifications, such as acetylation, methylation, phosphorylation, and ubiquitylation. In particular, histone methylation serves different cellular functions depending on the location of the amino acid residue undergoing modification, and is tightly regulated by the antagonistic action of histone methyltransferases and demethylases. The SUV39H family of histone methyltransferases (HMTases) are evolutionarily conserved from fission yeast to humans and play an important role in the formation of higher-order chromatin structures called heterochromatin. The SUV39H family HMTases catalyzes the methylation of histone H3 lysine 9 (H3K9), and this modification serves as a binding site for heterochromatin protein 1 (HP1) to form a higher-order chromatin structure. While the regulatory mechanism of this family of enzymes has been extensively studied in various model organisms, Clr4, a fission yeast homologue, has made an important contribution. In this review, we focus on the regulatory mechanisms of the SUV39H family of proteins, in particular, the molecular mechanisms revealed by the studies of the fission yeast Clr4, and discuss their generality in comparison to other HMTases. + + + + Nakamura + Rinko + R + 0000-0001-5248-3540 + + Division of Chromatin Regulation, National Institute for Basic Biology, Okazaki 444-8585, Japan. + + + Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Okazaki 444-8585, Japan. + + + + Nakayama + Jun-Ichi + JI + 0000-0002-5597-8239 + + Division of Chromatin Regulation, National Institute for Basic Biology, Okazaki 444-8585, Japan. + + + Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Okazaki 444-8585, Japan. + + + + eng + + Journal Article + Review + Research Support, Non-U.S. Gov't + + + 2023 + 03 + 25 + +
+ + Switzerland + Biomolecules + 101596414 + 2218-273X + + + + EC 2.1.1.43 + Histone-Lysine N-Methyltransferase + + + 0 + Histones + + + EC 2.1.1.- + Histone Methyltransferases + + + 0 + Chromatin + + + 0 + Heterochromatin + + + 0 + Cell Cycle Proteins + + + EC 2.1.1.43 + clr4 protein, S pombe + + + 0 + Schizosaccharomyces pombe Proteins + + + IM + + + Humans + + + Schizosaccharomyces + genetics + metabolism + + + Histone-Lysine N-Methyltransferase + genetics + metabolism + + + Histones + metabolism + + + Histone Methyltransferases + metabolism + + + Chromatin + metabolism + + + Heterochromatin + metabolism + + + Cell Cycle Proteins + metabolism + + + Schizosaccharomyces pombe Proteins + genetics + metabolism + + + + Clr4 + SET domain + SUV39H + autoregulation + chromodomain + fission yeast + histone methylation + histone methyltransferases + ubiquitylation + + The authors declare no conflict of interest. + + + + + 2023 + 2 + 27 + + + 2023 + 3 + 22 + + + 2023 + 3 + 22 + + + 2023 + 5 + 17 + 6 + 42 + + + 2023 + 5 + 16 + 6 + 42 + + + 2023 + 5 + 16 + 1 + 8 + + + epublish + + 37189341 + PMC10135481 + 10.3390/biom13040593 + biom13040593 + + + + Strahl B.D., Allis C.D. 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Cell. 2017;68:350–360.e7. doi: 10.1016/j.molcel.2017.09.037. + + 10.1016/j.molcel.2017.09.037 + 29053958 + + + + + + diff --git a/t/pubmed_xml.t b/t/pubmed_xml.t new file mode 100644 index 00000000..ac711b9d --- /dev/null +++ b/t/pubmed_xml.t @@ -0,0 +1,37 @@ +use strict; +use warnings; +use Test::More tests => 2; + +use Storable qw(thaw); + +BEGIN { + unshift @INC, 't', 'lib'; +} + +use GDBM_File; +use PomBase::TestUtil; +use PomBase::Chado::PubmedUtil; + +my $test_util = PomBase::TestUtil->new(); +my $config = $test_util->config(); + +local $/ = undef; + +open my $f, '<', 'data/pubmed_37189341.xml' or die; + +my $xml = <$f>; + +unlink '/tmp/pubmed_cache.gdbm'; + +tie my %pubmed_cache, 'GDBM_File', '/tmp/pubmed_cache.gdbm', &GDBM_WRCREAT, 0640; + +my $pubmed_util = PomBase::Chado::PubmedUtil->new(chado => $test_util->chado(), + config => $config, + pubmed_cache => \%pubmed_cache); +$pubmed_util->parse_pubmed_xml($xml); + +ok(exists $pubmed_cache{'PMID:37189341'}); + +my $pub_details = thaw($pubmed_cache{'PMID:37189341'}); + +is($pub_details->{publication_date}, '25 Mar 2023');