(Q26849461)

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Protein and DNA modifications: evolutionary imprints of bacterial biochemical diversification and geochemistry on the provenance of eukaryotic epigenetics

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Protein and DNA modifications: evolutionary imprints of bacterial biochemical diversification and geochemistry on the provenance of eukaryotic epigenetics (English)

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1

object named as

L. Aravind

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Maxwell Burroughs

2

object named as

A. M. Burroughs

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Lakshminarayan M. Iyer

4

object named as

L. M. Iyer

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object named as

D. Zhang

3

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author name string

A. M. Burroughs

2

1 reference

L. M. Iyer

4

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language of work or name

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publication date

1 July 2014

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Cold Spring Harbor Perspectives in Biology

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6

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7

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a016063

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Secreted protein kinases

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Novel transglutaminase-like peptidase and C2 domains elucidate the structure, biogenesis and evolution of the ciliary compartment

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Adenylylation control by intra- or intermolecular active-site obstruction in Fic proteins

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DNA rearrangements directed by non-coding RNAs in ciliates

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Genome-wide reprogramming in the mouse germ line entails the base excision repair pathway

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PML nuclear bodies

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REBASE--a database for DNA restriction and modification: enzymes, genes and genomes

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BBAP monoubiquitylates histone H4 at lysine 91 and selectively modulates the DNA damage response

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Dephosphorylation of the C-terminal tyrosyl residue of the DNA damage-related histone H2A.X is mediated by the protein phosphatase eyes absent

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Tyrosine dephosphorylation of H2AX modulates apoptosis and survival decisions

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WSTF regulates the H2A.X DNA damage response via a novel tyrosine kinase activity

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Base J: Discovery, Biosynthesis, and Possible Functions

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Structural and functional diversity of the microbial kinome

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A fresh look at the fossil evidence for early Archaean cellular life

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Protein arginine methyltransferase 6 specifically methylates the nonhistone chromatin protein HMGA1a

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EUKARYOTIC CYTOSINE METHYLTRANSFERASES

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Genome of bacteriophage P1

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Structure of factor-inhibiting hypoxia-inducible factor (HIF) reveals mechanism of oxidative modification of HIF-1 alpha

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Structure of factor-inhibiting hypoxia-inducible factor 1: An asparaginyl hydroxylase involved in the hypoxic response pathway

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Elongator is a histone H3 and H4 acetyltransferase important for normal histone acetylation levels in vivo

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Structure and ligand of a histone acetyltransferase bromodomain

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Histone deacetylases, acetoin utilization proteins and acetylpolyamine amidohydrolases are members of an ancient protein superfamily

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Biology of DNA restriction

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Dual recognition of phosphoserine and phosphotyrosine in histone variant H2A.X by DNA damage response protein MCPH1

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Structural basis for the recognition of phosphorylated histone h3 by the survivin subunit of the chromosomal passenger complex

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The structure of the FYR domain of transforming growth factor beta regulator 1

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Novel structural and functional mode of a knot essential for RNA binding activity of the Esa1 presumed chromodomain

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The structural basis of protein acetylation by the p300/CBP transcriptional coactivator

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7 April 2017

The ankyrin repeats of G9a and GLP histone methyltransferases are mono- and dimethyllysine binding modules

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A dimeric viral SET domain methyltransferase specific to Lys27 of histone H3

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7 April 2017

Structure and catalytic mechanism of a SET domain protein methyltransferase

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Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail

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7 April 2017

Chromatin modifications and their function

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PfSETvs methylation of histone H3K36 represses virulence genes in Plasmodium falciparum

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Cdc48 and Ufd3, new partners of the ubiquitin protease Ubp3, are required for ribophagy

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Comprehensive analysis of diverse ribonucleoprotein complexes.

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Histone demethylation by a family of JmjC domain-containing proteins

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A novel histone acetyltransferase is an integral subunit of elongating RNA polymerase II holoenzyme

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GCN5-related histone N-acetyltransferases belong to a diverse superfamily that includes the yeast SPT10 protein.

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Archean microfossils: a reappraisal of early life on Earth

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PAD, a growing family of citrullinating enzymes: genes, features and involvement in disease

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Regulation of nucleosome dynamics by histone modifications

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Fluctuations in Precambrian atmospheric oxygenation recorded by chromium isotopes

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Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex

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The Sir2 family of protein deacetylases

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Structural and functional evidence for Bacillus subtilis PaiA as a novel N1-spermidine/spermine acetyltransferase

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7 April 2017

Origin of the nucleus and Ran-dependent transport to safeguard ribosome biogenesis in a chimeric cell

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7 April 2017

Evolution of eukaryotic transcription: insights from the genome of Giardia lamblia

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7 April 2017

JmjC-domain-containing proteins and histone demethylation

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7 April 2017

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7 April 2017

Histone methyltransferase activity of a Drosophila Polycomb group repressor complex

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7 April 2017

Promiscuity as a functional trait: intrinsically disordered regions as central players of interactomes

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28 September 2017

New mechanisms in memory storage: piRNAs and epigenetics

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28 September 2017

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28 September 2017

TETonic shift: biological roles of TET proteins in DNA demethylation and transcription

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28 September 2017

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28 September 2017

Memories from the polycomb group proteins.

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28 September 2017

Histone phosphorylation: a chromatin modification involved in diverse nuclear events

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28 September 2017

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28 September 2017

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28 September 2017

Genomics and epigenomics of the human glycome.

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28 September 2017

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28 September 2017

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28 September 2017

Histone ubiquitylation and chromatin dynamics

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28 September 2017

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28 September 2017

The maze of paramutation: a rough guide to the puzzling epigenetics of paramutation

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28 September 2017

Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems

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28 September 2017

Epigenetics of haematopoietic cell development

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28 September 2017

A history of TFIIH: two decades of molecular biology on a pivotal transcription/repair factor.

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28 September 2017

Natural history of the eukaryotic chromatin protein methylation system

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28 September 2017

Natural history of eukaryotic DNA methylation systems

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28 September 2017

Function and regulation of the Mediator complex

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28 September 2017

Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group.

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28 September 2017

LIF-independent JAK signalling to chromatin in embryonic stem cells uncovered from an adult stem cell disease

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28 September 2017

Evolutionary history of the poly(ADP-ribose) polymerase gene family in eukaryotes

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28 September 2017

Keeping it in the family: diverse histone recognition by conserved structural folds

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28 September 2017

Aminoglycoside modifying enzymes

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28 September 2017

ADP-ribosylation of arginine

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28 September 2017

Origin and evolution of peptide-modifying dioxygenases and identification of the wybutosine hydroxylase/hydroperoxidase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

RNAi-dependent formation of heterochromatin and its diverse functions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Amidoligases with ATP-grasp, glutamine synthetase-like and acetyltransferase-like domains: synthesis of novel metabolites and peptide modifications of proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Haspin: a newly discovered regulator of mitotic chromosome behavior.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Characterization of an endoplasmic reticulum-associated silaffin kinase from the diatom Thalassiosira pseudonana

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Recent advances in siderophore biosynthesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Reconstructing the ubiquitin network: cross-talk with other systems and identification of novel functions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Post-translational modifications of tubulin in the nervous system

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Minireview: protein arginine methylation of nonhistone proteins in transcriptional regulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

A comparison of BRCT domains involved in nonhomologous end-joining: introducing the solution structure of the BRCT domain of polymerase lambda.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Polyglutamylation: a fine-regulator of protein function? 'Protein Modifications: beyond the usual suspects' review series.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

MutL homologs in restriction-modification systems and the origin of eukaryotic MORC ATPases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

A code for lysine modifications of a silica biomineralizing silaffin protein

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Evolution and diversification of lamprey antigen receptors: evidence for involvement of an AID-APOBEC family cytosine deaminase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

SUMOrganization of the nucleus

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Palmitoylation of ligands, receptors, and intracellular signaling molecules

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Crystal structure of human histone lysine-specific demethylase 1 (LSD1).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Comparative genomics and structural biology of the molecular innovations of eukaryotes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Genomic imprinting in plants and mammals: how life history constrains convergence

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Comprehensive multigene phylogenies of excavate protists reveal the evolutionary positions of "primitive" eukaryotes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Protein posttranslational modifications: the chemistry of proteome diversifications

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Archaeal chromatin proteins: different structures but common function?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Structural basis for the function of Clostridium difficile toxin B.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Kinomics: methods for deciphering the kinome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Structure of the conserved core of the yeast Dot1p, a nucleosomal histone H3 lysine 79 methyltransferase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

The PARP superfamily

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Histones and histone modifications

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

The many colours of chromodomains.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Cracking the histone code: one, two, three methyls, you're out!

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Epigenetic codes for heterochromatin formation and silencing: rounding up the usual suspects

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Reconstructing/deconstructing the earliest eukaryotes: how comparative genomics can help

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Histidine kinases and response regulator proteins in two-component signaling systems

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Structure of the yeast histone acetyltransferase Hat1: insights into substrate specificity and implications for the Gcn5-related N-acetyltransferase superfamily

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Metabolic symbiosis at the origin of eukaryotes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Hypermodified bases in DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 September 2017

Diversity of bacterial type II toxin-antitoxin systems: a comprehensive search and functional analysis of novel families

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

31 May 2018

Arginine deiminase has multiple regulatory roles in the biology of Giardia lamblia

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

31 May 2018

Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 November 2018

Mechanism and function of DHHC S-acyltransferases.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 November 2018

A Xanthomonas uridine 5'-monophosphate transferase inhibits plant immune kinases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 November 2018

Structure and Evolution of Ubiquitin and Ubiquitin-Related Domains

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 November 2018

Evolution of minerals.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 November 2018

WDR5, a complexed protein.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 November 2018

LSD1 demethylates histone and non-histone proteins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 November 2018

A nucleolar protein allows viability in the absence of the essential ER-residing molecular chaperone calnexin.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 November 2018

Production of the non-ribosomal peptide plipastatin in Bacillus subtilis regulated by three relevant gene blocks assembled in a single movable DNA segment.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 November 2018

Arginine methyltransferase Capsuleen is essential for methylation of spliceosomal Sm proteins and germ cell formation in Drosophila.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 November 2018

Genome-wide relationships between TAF1 and histone acetyltransferases in Saccharomyces cerevisiae

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 November 2018

Heterochromatin silencing and locus repositioning linked to regulation of virulence genes in Plasmodium falciparum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 November 2018

Structural analysis of the chromosome segregation protein Spo0J from Thermus thermophilus

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 November 2018

Precise nucleosome positioning and the TATA box dictate requirements for the histone H4 tail and the bromodomain factor Bdf1.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 November 2018

Structural basis for the mechanism and regulation of Sir2 enzymes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 November 2018

Self-assembly of highly phosphorylated silaffins and their function in biosilica morphogenesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4067991

28 November 2018

Bittersweet memories: linking metabolism to epigenetics through O-GlcNAcylation

1 reference

https://pubmed.ncbi.nlm.nih.gov/24984775

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Chromatin silencing protein and pachytene checkpoint regulator Dot1p has a methyltransferase fold

1 reference

https://pubmed.ncbi.nlm.nih.gov/24984775

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Intrinsically disordered proteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/24984775

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The real 'domains' of life

1 reference

https://pubmed.ncbi.nlm.nih.gov/24984775

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Yeast ribosomal/cytochrome c SET domain methyltransferase subfamily: identification of Rpl23ab methylation sites and recognition motifs

1 reference

https://pubmed.ncbi.nlm.nih.gov/24984775

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1101/CSHPERSPECT.A016063

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PMC publication ID

1 reference

PubMed publication ID

1 reference

ResearchGate publication ID

0 references

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