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Heterochromatin and the molecular mechanisms of ‘parent-of-origin’ effects in animals

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Abstract

Twenty five years ago it was proposed that conserved components of constitutive heterochromatin assemble heterochromatin-like complexes in euchromatin and this could provide a general mechanism for regulating heritable (cell-to-cell) changes in gene expressibility. As a special case, differences in the assembly of heterochromatin-like complexes on homologous chromosomes might also regulate the parent-of-origin-dependent gene expression observed in placental mammals. Here, the progress made in the intervening period with emphasis on the role of heterochromatin and heterochromatin-like complexes in parent-of-origin effects in animals is reviewed.

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Abbreviations

5hmC:

5-hydroxymethylcytosine

5mC:

5-methylcytosine

ADD:

ATRX-DNMT3-DNMT3L domain

ATRX:

Alpha Thalassemia/Mental Retardation Syndrome X-Linked

CAF-1:

chromatin assembly factor 1

CD:

chromodomain

CE:

controlling element

CF:

chromocenter formation

CGIs:

CpG islands

CSD:

chromo shadow domain

DamID:

DNA adenine methyltransferase identification

DAXX:

Death Domain associated protein

DNMT1:

maintenance DNA methyltransferase 1

DNMT3A:

de novo DNA methyltransferase 3A

DNMT3B:

de novo DNA methyltransferase 3B

DNMT3L:

DNA methyltransferase 3L

ES:

embryonic stem

G9a:

K9H3 HMTase

GLP:

G9a-like protein K9H3 HMTase

gDMRs:

germline differentially methylated regions

H3K9me2:

di-methylated lysine 9 on histone H3

H3K9me3:

tri-methylated lysine 9 on histone H3

H3S10P:

phosphorylation of serine 10 on histone H3

H4K20me3:

tri-methylated lysine 20 on histone H4

HMTases:

histone methyltransferases

HDACs:

histone deactylases

HR:

hinge region

HP1:

Heterochromatin Protein 1

ICR:

imprinting control region

IPS:

induced pluripotent stem cell

KAP1:

KRAB-associated protein 1

Kb:

kilobases

KRAB-ZNPs:

Krüppel-associated box (KRAB) domain zinc-finger proteins

KRAB-ZNF:

KRAB domain-zinc finger

LINE:

long interspersed elements

lncRNA:

long non-coding RNA

LTR:

long terminal repeat

Mb:

megabases

MEFs:

murine embryonic fibroblasts

MuERV-L:

murine endogenous retrovirus L

NOR:

nucleolar organizer region

Np95:

Nuclear protein 95

NuRD:

Nucleosome Remodelling histone Deacetylase

ORC:

origin of replication complex

PCHET2:

Plannococcus citri heterochromatin protein 2

PCNA:

proliferating cell nuclear antigen

PGCs:

primordial germ cells

PHD:

plant homeodomain

PEV:

position-effect variegation

pN:

pico-Newtons

PN:

pro-nuclear stage

PNBs:

peri-nucleolar bodies

PxVxL:

Proline/Any/Valine/Any/Leucine penta-peptide motif

RBCC:

Ring-finger B Box-Coiled Coil domain

reverse majSat:

reverse major satellite sequence

RNF12/RLIM:

Ring Finger protein LIM Domain interacting

RRR:

reprogramming resistant regions

SCNT:

somatic cell nuclear transfer

SETDB1:

SET Domain Bifurcated 1 K9H3 HMTase

siRNA:

small interfering RNA

SMARCAD1:

SWI/SNF-Related, Matrix-Associated Actin-Dependent Regulator of Chromatin, Subfamily A, Containing DEAD/H Box 1

SUMO2:

Small ubiquitin-related modifier 2

SUV39H1/2:

mammalian suvar K9H3 HMTase 1 and 2

Tet:

Ten-eleven translocation dioxygenase

UBE2i:

Ubiquitin conjugating enzyme 2i

Xp :

paternal X-chromosome

Xm :

maternal X chromosome

ZGA:

zygotic genome activation

Zscan4:

Zinc Finger and SCAN domain-containing 4.

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Acknowledgements

I thank Dr William Swaney for helpful discussions, especially with regards to early drafts of the figures. Ashley Clarke drew the figures. I also thank Dr Vladimir Shetyn for his kindness in obtaining many references when I needed them. I am indebted to Prof H Sharat Chandra for his hospitality while on sabbatical at the Centre for Human Genetics, Bengaluru, India, where the seed for this review was planted.

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  1. Fächerverbund Anatomie, Institut für Zell- und Neuro-biologie, Charite - Universitätsmedizin, 10117, Berlin, Germany

    Prim B Singh

  2. Department of Natural Sciences and Psychology, Liverpool John Moores University, Life Sciences Building, Byrom Street, Liverpool, L3 3AF, UK

    Prim B Singh

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Corresponding editor: SANJEEV KHOSLA

[Singh PB 2016 Heterochromatin and the molecular mechanisms of ‘parent-of-origin’ effects in animals. J. Biosci.]

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Singh, P.B. Heterochromatin and the molecular mechanisms of ‘parent-of-origin’ effects in animals. J Biosci 41, 759–786 (2016). https://doi.org/10.1007/s12038-016-9650-9

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