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manuscript.tex
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\documentclass[a4paper,10pt,oneside,onecolumn,article]{memoir}
\semiisopage
\checkandfixthelayout
\counterwithout{section}{chapter}
\setcounter{secnumdepth}{0}
\input{preamble}
\input{preamble-manuscript}
\title{The Human Canonical Core Histone Catalogue}
\author{David Miguel Susano Pinto\thanks{Centre for Chromosome
Biology, School of Natural Sciences, National University of
Ireland Galway, Galway, Ireland},
Andrew Flaus\thanksmark{1}\thanks{Corresponding author: Andrew Flaus
(\href{mailto:[email protected]}{[email protected]})}}
\makepagestyle{rxiv}
\makerunningwidth{rxiv}{\headwidth}
\makefootrule{rxiv}{\headwidth}{\normalrulethickness}{\footruleskip}
\makeoddfoot{rxiv}{}{}{\thepage}
\makeevenfoot{rxiv}{\thepage}{}{}
\makeheadposition{rxiv}{}{}{flushright}{flushleft}
\pagestyle{rxiv}
%% Shape the maketitle command. Remove the vertical space at the
%% start, and the whole date stuff.
\setlength{\droptitle}{-50pt}
\pretitle{\begin{flushleft}\huge\bfseries\scshape}
\posttitle{\end{flushleft}}
\preauthor{\begin{flushleft}\large}
\postauthor{\par\end{flushleft}}
\predate{}
\date{}
\postdate{}
\begin{document}
\maketitle
\begin{abstract}
\noindent
Core histone proteins H2A, H2B, H3, and H4 are encoded
by a large family of genes distributed across the human genome.
Canonical core histones contribute the majority of proteins to bulk chromatin packaging,
and are encoded in \NumberOfClusters{} clusters
by \TotalCoreCodingGenes{} coding genes comprising
\HTwoACodingGenes{} for H2A,
\HTwoBCodingGenes{} for H2B,
\HThreeCodingGenes{} for H3,
and \HFourCodingGenes{} for H4,
along with at least \TotalCorePseudoGenes{} total pseudogenes.
The canonical core histone genes display coding variation that gives rise to
\HTwoAUniqueProteins{} H2A, \HTwoBUniqueProteins{} H2B,
\HThreeUniqueProteins{} H3, and \HFourUniqueProteins{} H4 unique protein isoforms.
Although histone proteins are highly conserved overall,
these isoforms represent a surprising and seldom recognised variation
with amino acid identity as low as
\FPround{\result}{\HallMinPID}{0} \SI{\result}{\percent}
between canonical histone proteins of the same type.
The gene sequence and protein isoform diversity
also exceeds commonly used subtype designations such as H2A.1 and H3.1,
and exists in parallel with the well-known specialisation of variant histone proteins.
RNA sequencing of histone transcripts shows evidence for
differential expression of histone genes
but the functional significance of this variation has not yet been investigated.
To assist understanding of the implications of histone gene and protein diversity
we have catalogued the entire human canonical core
histone gene and protein complement.
In order to organise this information in a
robust, accessible, and accurate form,
we applied software build automation tools to
dynamically generate the canonical core histone repertoire
based on current genome annotations
and then to organise the information into a manuscript format.
Automatically generated values are shown with a light grey background.
Alongside recognition of the encoded protein diversity,
this has led to multiple corrections to human histone annotations,
reflecting the flux of the human genome as it is updated and
enriched in reference databases.
This dynamic manuscript approach is inspired by the aims of reproducible research and biocuration,
and can be readily adapted to other gene families.
\end{abstract}
\input{sections/intro.tex}
\input{sections/genes.tex}
\input{sections/transcripts.tex}
\input{sections/proteins.tex}
\input{sections/computation.tex}
\input{sections/conclusion.tex}
\input{sections/materialsmethods.tex}
\section{Acknowledgements}
We are grateful to the Perl community on the \url{irc.freenode.net}
channels \#perl and \#bioperl,
especially Altreus, mst, LeoNerd, and pyrimidine.
Invaluable support was also provided by the \TeX{} stackexchange community,
in particular David Carlisle.
DMSP acknowledges the support of the Portuguese Foundation for
Science and Technology (FCT).
\bibliography{references}
\newpage
\appendix
\input{sections/supplementary.tex}
\end{document}