Heterochromatin remodeling by CDK12 contributes to learning in Drosophila

Abstract

Dynamic regulation of chromatin structure is required to modulate the transcription of genes in eukaryotes. However, the factors that contribute to the plasticity of heterochromatin structure are elusive. Here, we report that cyclin-dependent kinase 12 (CDK12), a transcription elongation-associated RNA polymerase II (RNAPII) kinase, antagonizes heterochromatin enrichment in Drosophila chromosomes. Notably, loss of CDK12 induces the ectopic accumulation of heterochromatin protein 1 (HP1) on euchromatic arms, with a prominent enrichment on the X chromosome. Furthermore, ChIP and sequencing analysis reveals that the heterochromatin enrichment on the X chromosome mainly occurs within long genes involved in neuronal functions. Consequently, heterochromatin enrichment reduces the transcription of neuronal genes in the adult brain and results in a defect in Drosophila courtship learning. Taken together, these results define a previously unidentified role of CDK12 in controlling the epigenetic transition between euchromatin and heterochromatin and suggest a chromatin regulatory mechanism in neuronal behaviors.A ppropriate regulation of gene transcription is essential throughout the life of an organism. In eukaryotes, DNA and histone octamers are assembled into nucleosomes and further compacted into higher-order structures (1). Dynamic changes in the chromatin architecture affect gene transcription in many aspects of developmental and physiological processes, such as neural plasticity, memory formation, and cognition (2, 3). Eukaryotic genomes are composed of two basic forms, euchromatin and heterochromatin, which are originally characterized by their cytological chromatin packaging levels. Euchromatic regions are generally associated with a relatively open chromatin configuration and mainly contain transcriptionally active genes, whereas heterochromatin is highly compacted and less accessible to the transcriptional machinery (4). Drosophila heterochromatin is mainly localized at the pericentric and subtelomeric regions and enriched for methylation of histone H3 on Lys9 (H3K9me), which provides a docking site for heterochromatin protein 1 (HP1) (5, 6), a highly conserved protein involved in heterochromatin formation (7). Previous studies also show that HP1 and H3K9me associate with a subset of loci on euchromatic regions, and they presumably serve to fine tune the level of gene transcription (8-10). One significant question that comes up is how the chromatin structure is dynamically regulated to impact expression of genes in complex neuronal processes, such as learning and memory. Our earlier study on chromatin domain mapping of chromosome 4 suggests that heterochromatic domains may be regulated by the activities of RNA polymerase II (RNAPII) complexes, which form a "barrier" to prevent heterochromatin spreading and transcriptional gene silencing (11). However, the mechanism underlying such a mode of regulation and the consequence on reprogrammed transcription remain to be investigated. ResultsCyclin-Dependent Kinase 12 ...

Histone acetyltransferase CBP-related H3K23 acetylation contributes to courtship learning in Drosophila

“…As courtship learning was impaired in the H3K23A overexpression line, we next asked whether the expression of neuronal genes related to Drosophila learning were also affected in this line. To test this, an RT-qPCR assay was conducted to determine the expression levels of neuronal genes, including voltage-gated ion channels ( Sh , eag and para ), ligand-gated channels ( SK , Cngl and gfA ), phospholipase C ( norpA ), and phosphodiesterase ( dnc ) [ 32 – 40 ]. The expression of these candidate neuronal genes, except for eag and shakB , significantly decreased in the H3K23A overexpression line.…”

“…The methods were based on previous work by us and others [ 32 , 55 ]. Flies were raised at 25°C and 60–70% humidity in a 12-h/12-h light/dark cycle.…”

“…We performed immunofluorescence as previously described[ 32 ]. The salivary glands were dissected from third-instar larva and the brains were dissected from adult heads, respectively.…”

High-throughput assessment of context-dependent effects of chromatin proteins

“…Because H3K36 methylation is deposited co-transcriptionally [ 30 , 31 ], it is difficult to determine by correlative studies whether the histone mark, RNA Pol II or other factors inhibit HP1 action. One candidate is cyclin-dependent kinase 12 (CDK12), a transcription elongation-associated RNA Pol II kinase that was recently reported to antagonize heterochromatin in Drosophila [ 32 ]. We also found reduced silencing in regions bound by the H3S10 kinase JIL-1, in agreement with earlier observations [ 22 ].…”

Histone H3K27 methylation modulates the dynamics of FANCD2 on chromatin to facilitate NHEJ and genome stability

“…The cells were incubated with DAPI (1000×, Invitrogen) for 5 min at room temperature to visualize the nucleus. Slides were examined at 63× magnification using a fluorescence microscope (Leica) with a set parameter for each series of experiments (Pan et al, 2015). Image processing and analysis were performed using Image-Pro Plus software (Media Cybernetics).…”