The eukaryotic genome is packaged into transcriptionally active euchromatin and silent heterochromatin, with most studies focused on the former encompassing the majority of protein‐coding genes. The recent development of various sequencing techniques has refined this classic dichromatic partition and has better illuminated the composition, establishment, and evolution of this genomic and epigenomic “dark matter” in the context of topologically associated domains and phase‐separated droplets. Heterochromatin includes genomic regions that can be densely stained by chemical dyes, which have been shown to be enriched for repetitive elements and epigenetic marks, including H3K9me2/3 and H3K27me3. Heterochromatin is usually replicated late, concentrated at the nuclear periphery or around nucleoli, and usually lacks highly expressed genes; and now it is considered to be as neither genetically inert nor developmentally static. Heterochromatin guards genome integrity against transposon activities and exerts important regulatory functions by targeting beyond its contained genes. Both its nucleotide sequences and regulatory proteins exhibit rapid coevolution between species. In addition, there are dynamic transitions between euchromatin and heterochromatin during developmental and evolutionary processes. We summarize here the ever‐changing characteristics of heterochromatin and propose models and principles for the evolutionary transitions of heterochromatin that have been mainly learned from studies of Drosophila and yeast. Finally, we highlight the role of sex chromosomes in studying heterochromatin evolution.

Previous evolutionary models of duplicate gene evolution have overlooked the pivotal role of genome architecture. Here, we show that proximity-based regulatory recruitment by distally duplicated genes is an efficient mechanism for modulating tissue-specific production of preexisting proteins. By leveraging genomic asymmetries, we performed a coexpression analysis on Drosophila melanogaster tissue data to show the generality of enhancer capture-divergence (ECD) as a significant evolutionary driver of asymmetric, distally duplicated genes. We use the recently evolved gene HP6 / Umbrea as an example of the ECD process. By assaying genome-wide chromosomal conformations in multiple Drosophila species, we show that HP6/Umbrea was inserted near a preexisting, long-distance three-dimensional genomic interaction. We then use this data to identify a newly found enhancer ( FLEE1 ), buried within the coding region of the highly conserved, essential gene MFS18 , that likely neofunctionalized HP6/Umbrea . Last, we demonstrate ancestral transcriptional coregulation of HP6/Umbrea ’s future insertion site, illustrating how enhancer capture provides a highly evolvable, one-step solution to Ohno’s dilemma.

Little is known about how the epigenomic states change during development and evolution in a 3D genome context. Here we use Drosophila pseudoobscura with complex turnover of sex chromosomes as a model to address this, by collecting massive epigenomic and Hi-C data from five developmental stages and three adult tissues. We reveal that over 60% of the genes and transposable elements (TE) exhibit at least one developmental transition of chromatin state. Transitions on specific but not housekeeping enhancers are associated with specific chromatin loops and topologically associated domain borders (TABs). While evolutionarily young TEs are generally silenced, old TEs more often have been domesticated as interacting TABs or specific enhancers. But on the recently evolved X chromosome, young TEs are instead often active and recruited as TABs, due to acquisition of dosage compensation. Overall we characterize how Drosophila epigenomic landscapes change during development and in response to chromosome evolution, and highlight the important roles of TEs in genome organization and regulation.

The epigenome and nuclear architectural mechanisms that regulate neuronal activity-induced transcriptional responses in cortical neurons remain incompletely understood. Previously, we have shown that the chromatin organizer SATB2 and the inner nuclear membrane protein LEMD2 form a chromatin tether at the nuclear lamina, and that activity-induced transcription is impaired in both Satb2 and Lemd2 loss-of-function models. Interaction of SATB2 and LEMD2 with subunits of the ESCRT-III complex indicates that the ESCRT-III complex could serve as an activity-dependent, dynamic component of this tether. Here, we study the activity-dependent subcellular localization and function of the ESCRT-III components CHMP7 and CHMP4B in primary cortical neurons. We find that increased neuronal activity correlates with the accumulation of co-localized CHMP7 and CHMP4B foci at the nuclear envelope. shRNA-mediated Chmp7 knockdown causes a reduction in the expression of activity-regulated genes and genes with highly specialized functions in synaptic organization and trans-synaptic signaling. Furthermore, the observed similarity in the global transcriptome responses in Satb2, Lemd2, and Chmp7 loss-of-function models points toward a previously unrecognized role of the SATB2–LEMD2–CHMP7 tether in linking chromatin architecture and nuclear envelope plasticity to activity-dependent gene regulation.

Previous evolutionary models of duplicate gene evolution have overlooked the pivotal role of genome architecture. Here, we show that proximity-based regulatory recruitment of distally duplicated genes (enhancer capture) is an efficient mechanism for modulating tissue-specific production of pre-existing proteins. By leveraging genomic asymmetries in synteny and function that distinguish new genes evolving under enhancer capture-divergence (ECD) from those evolving under previous models, we performed a co-expression analysis on Drosophila melanogaster tissue data to show the generality of ECD as a significant evolutionary driver of asymmetric, distally duplicated genes. We use the recently evolved gene HP6 / Umbrea , which duplicated <15 million years ago (mya), as an example of the ECD process. By assaying genome-wide chromosomal conformations in multiple Drosophila species, we show that HP6/Umbrea was inserted into a pre-existing, evolutionarily stable 3D genomic structure spanning over 125kb. We then utilize this data to identify a newly discovered enhancer (FLEE1), buried within the coding region of the highly conserved, essential gene MFS18 , that likely neo-functionalized HP6/Umbrea , thereby driving the new duplicate gene copy to fixation. Finally, we demonstrate ancestral transcriptional co-regulation of HP6/Umbrea ’s future insertion site using single-cell transcriptomics, illustrating how enhancer capture provides a highly evolvable, one-step solution to Ohno’s Dilemma. The intuitive molecular mechanism underpinning the ECD model unveils a novel and robust framework to understand the fixation and neofunctionalization of distally duplicated genes.

Chromatin states of genes and transposable elements (TEs) dictated by combinations of various histone modifications comprise key information for understanding the mechanisms of genome organization and regulation. However, little is known about the principles of their dynamic changes during development and evolution in a three-dimensional genome context. To address this, we study Drosophila pseudoobscura , a Drosophila model species that diverged from D. melanogaster about 25 million years ago. We collected 71 epigenomic datasets targeting 11 histone modification marks and 4 Hi-C datasets, and projected 15 chromatin states across four different developmental stages and two adult tissues. We estimate that before zygotic genome activation, 41% of the genome has already been deposited with histone modifications, while 20% of the rest genome switches from a ‘null’ state to an active/inactive chromatin state after the zygotic genome activation. Over two thirds of the genomic region exhibit at least one transition between different chromatin states during development. And such transitions on cis -regulatory regions are associated with tissue- or stage-specific formation of chromatin loops or topologically associated domain borders (TABs), as well as specific activation of gene expression. We further demonstrate that while evolutionarily young TEs are preferentially targeted by silencing histone modifications, old TEs are more frequently domesticated as TABs or specific enhancers that further contribute to the genome organization or local gene regulation. Interestingly, this trend is reversed on the newly evolved X chromosome in D. pseudoobscura , due to the acquisition of dosage compensation mechanism. Overall we characterize the developmental and evolutionary dynamics of Drosophila epigenomic states, and highlight the roles of certain TEs of different evolutionary ages in genome organization and regulation.