The histone chaperone SPT2 regulates chromatin structure and function in Metazoa.

Histone chaperones control nucleosome density and chromatin structure. In yeast, the H3-H4 chaperone Spt2 controls histone deposition at active genes but its roles in metazoan chromatin structure and organismal physiology are not known. Here we identify the Caenorhabditis elegans ortholog of SPT2 (CeSPT-2) and show that its ability to bind histones H3-H4 is important for germline development and transgenerational epigenetic gene silencing, and that spt-2 null mutants display signatures of a global stress response.

Widespread transposon co-option in the germline regulatory network.

The movement of selfish DNA elements can lead to widespread genomic alterations with potential to create novel functions. We show that transposon expansions in nematodes led to extensive rewiring of germline transcriptional regulation. We find that about one-third of germline-specific promoters have been co-opted from two related miniature inverted repeat transposable elements (TEs), CERP2 and CELE2.

Accessible Region Conformation Capture (ARC-C) gives high-resolution insights into genome architecture and regulation.

Nuclear organization and chromatin interactions are important for genome function, yet determining chromatin connections at high resolution remains a major challenge. To address this, we developed Accessible Region Conformation Capture (ARC-C), which profiles interactions between regulatory elements genome-wide without a capture step. Applied to , ARC-C identifies approximately 15,000 significant interactions between regulatory elements at 500-bp resolution.

DREAM represses distinct targets by cooperating with different THAP domain proteins.

The DREAM (dimerization partner [DP], retinoblastoma [Rb]-like, E2F, and MuvB) complex controls cellular quiescence by repressing cell-cycle and other genes, but its mechanism of action is unclear. Here, we demonstrate that two C. elegans THAP domain proteins, LIN-15B and LIN-36, co-localize with DREAM and function by different mechanisms for repression of distinct sets of targets.

periodicDNA: an R/Bioconductor package to investigate k-mer periodicity in DNA.

Periodic occurrences of oligonucleotide sequences can impact the physical properties of DNA. For example, DNA bendability is modulated by 10-bp periodic occurrences of WW (W = A/T) dinucleotides. We present periodicDNA, an R package to identify k-mer periodicity and generate continuous tracks of k-mer periodicity over genomic loci of interest, such as regulatory elements.