Centromeric Transcription: A Conserved Swiss-Army Knife

Abstract

In most species, the centromere is comprised of repetitive DNA sequences, which rapidly evolve. Paradoxically, centromeres fulfill an essential function during mitosis, as they are the chromosomal sites wherein, through the kinetochore, the mitotic spindles bind. It is now generally accepted that centromeres are transcribed, and that such transcription is associated with a broad range of functions. More than a decade of work on this topic has shown that centromeric transcripts are found across the eukaryotic tree and associate with heterochromatin formation, chromatin structure, kinetochore structure, centromeric protein loading, and inner centromere signaling. In this review, we discuss the conservation of small and long non-coding centromeric RNAs, their associations with various centromeric functions, and their potential roles in disease.

Keywords: centromere; chromatin; epigenetics; non-coding RNAs; nucleosomes; transcription.

Figure 1

Cladogram showing which types of transcripts have been found in which species. The presence of centromeric small RNAs (<200 nt) and centromeric lncRNA (>200 nt) is shown behind each species described in Table 1. The colors yellow, blue, green, and red represent the Animalia, Fungi, Plantae, and Chromista kingdoms, respectively.

Figure 2

Biological functions of centromeric transcripts. The centromere-specific nucleosomes are distributed in a species-specific manner. For instance, in fission yeast, CENP-A^Cnp1 nucleosomes are restricted to the centromere core, whereas in humans CENP-A chromatin is interspersed with H3 chromatin at the centromere. Despite these different distribution patterns of CENP-A chromatin, centromeric transcription has been observed in a broad range of species. Centromeric transcripts are processed and are found as either lncRNAs or small RNAs. Through the argonaut/dicer machinery, centromeric small RNAs facilitate the pericentric heterochromatin formation. Centromeric chromatin structure can be modulated through DNA-RNA hybrids as well as through CENP-B, both of which associate with centromeric transcripts. Centromeric lncRNAs facilitate recruitment and loading of new CENP-A nucleosomes, whereas the kinetochore component CENP-C pulls down centromeric transcripts as well, contributing to kinetochore formation and structure. Finally, Aurora B signaling at the inner centromere is critical for faithful chromosome segregation, and centromeric transcription is important for this process.

Figure 3

Open questions about the functional consequences of centromeric transcription. (A) Even though two different types of RNAs are produced from the centromere, namely, lncRNAs and small RNAs, it remains unclear whether these two types of RNAs are produced sequentially or in parallel. (B) Both CENP-A and CENP-B associate with centromeric transcripts and both CENP-A loading and CENP-C loading have been linked to RNA–DNA triplex formation. Additionally, in maize, CENP-C binding to centromeric DNA is associated with small RNA, whereas in humans CENP-A loading has been tied to lncRNAs. It remains unclear whether the same transcript can recruit and stabilize both CENP-A and CENP-C at centromeric chromatin. (C) As CENP-A and CENP-C loading is cenRNA-dependent, one intriguing question is whether the kinetochore structure as a whole is dependent on the presence of centromeric transcripts. If so, which kinetochore components drive this dependence? (D) The localization and activity of CPC at the inner centromere are dependent on centromeric transcripts. It will be of great interest to understand how mitotic pulling forces modulate centromeric transcription, especially during the transition from metaphase to anaphase. (E) CENP-A nucleosomes have been found both at the centromere and ectopically. Especially in cancers, ectopic CENP-A accumulates. Little sequence conservation exists between ectopic CENP-A sites and the centromere. This leaves the possibility that specific secondary and tertiary RNA structures exist that are found similar to/in common between transcripts derived from the centromere and ectopic sites, allowing ectopic sites to hijack CENP-A recruitment. In addition, this might also provide critical insights into the evolution of centromere DNA from a functional perspective as a CENP-A recruitment motif. (F) Whereas various loci on the chromosome arms have been extensively studied using genetics tools such as LacO operons and MS2/PP7 stem-loops, the centromere has been recalcitrant to genetic manipulations because of its highly repetitive nature. In Arabidopsis thaliana, the A. lyrate Tal1 LTR retrotransposon specifically integrates into the A. thaliana centromere. This opens the door to finally genetically modify the centromere to be able to study transcription in an inducible and tractable manner, and recruit proteins of interest.