Cis-NATs tend to be marked by euchromatic modifications, whereas trans-NATs tend to be marked by heterochromatic modifications.
In previous studies we demonstrated that either genetic mutations, or loss, of retinoic acid receptor alpha (RARα), can impair the integration of the retinoic acid (RA) signal at the chromatin of RA-responsive genes downstream of RARα, and can lead to aberrant repressive chromatin states marked by epigenetic modifications.
Genes associated with phagocytosis and antigen presentation were marked by H3K4me3 modifications.
But in the cis-NAT gene group, more than 35% TEs are marked by histone modifications from G1.
At distal regulatory regions that are marked by histone modifications and transcription factors, H3.3 steady-state levels are substantially higher in proximal regions compared to distal regions.
This indicates that those TEs, which are marked by histone modifications from G1 and are less methylated, may play an important role in systemic resistance.
Our results suggest that c9FTD/ALS can now be considered among the class of repeat disorders marked by chromatin modifications, such as myotonic dystrophy, SCA types 8 and 31, Friedreich ataxia, Fragile X and Fragile X-associated tremor/ataxia syndromes [ 6].
The bivalent domains are proposed to silence key developmental genes in ES cells while keeping them poised for later activation, and these developmental genes marked by bivalent modifications are dubbed as bivalent genes (14).
LINC01420 is a long noncoding RNA with enhancers marked by histone modifications in human umbilical vein endothelial cells (HUVEC and HSMMM based on HaploReg annotation [ 18] (Additional file 2: Table S2).
Our analysis indicates that there are clear differences between the chromatin states for cis-NAT, trans-NAT and non-NAT genes (Fig. 3B): cis-NAT genes tend to be targeted by histone marks from G1, whereas trans-NAT genes are mostly marked by histone modifications from G2.
