School of Biological and Chemical Sciences

Sex, Chromosomes, and Brain

Project description

The existence of sex chromosomes presents a challenge for genome function: some genes are represented in a single copy in one sex (XY in mammals, or ZW in birds), but two copies in the homogametic sex (XX, or ZZ). To control this imbalance in gene copy number, organisms have evolved various mechanisms of “dosage compensation” that usually involve long non-coding RNAs – for example, X-inactivation in female mammals (1). The mechanism for dosage compensation in birds is not yet known, however (2). Birds present some striking examples of chromosomally-based sex differences in brain and behaviour (e.g. (3), underscoring the broad impact of mechanisms for balancing the effective dosage of sex chromosome genes.

In this project, three mechanisms may be explored for their contribution to the balancing of gene expression in the two sexes of the zebra finch. One mechanism involves a Z-linked microRNA (mir-2954) which is NOT compensated (twice as much expression in ZZ males as in ZW females) and shows sex-specific responses in the brain to birdsong (4, 5). Data from a prior knock-down study using cultured cells (5) suggests that miR-2954 may suppress the expression of other Z genes in males, leading to effective dosage compensation (6).  Further experiments may explore the physical association of miR-2954 transcripts with sex-regulated genes in the nucleus.

A second mechanism involves the topological sequestration of dosage-compensated genes into a repressive nuclear domain, as has been observed with the mammalian X chromosome (1). If dosage-compensated genes are collected into a discrete topological domain, this should be detectable using the technique of chromatin conformation capture (“Hi-C”) (7, 8). A Hi-C dataset for male and female zebra finches is already available but unexplored; the goal of this project is to test for topological association of dosage-compensated genes, and for differences in this association in males (ZZ) and females (ZW).  

A third mechanism involves the expression of long non-coding RNAs (lncRNAs), perhaps analogous to the Xist RNA in mammals (1). No direct orthologue of Xist is present in birds, but we do have unpublished evidence of some striking sex-regulated lncRNAs. A mixture of computational analysis and direct visualization of lncRNAs in the nucleus may be used to test the role of candidate lncRNAs in dosage compensation.

Resources for this project include the bioinformatic tools expertise in the Clayton lab (with Dr Julia George), an active colony of zebra finches on the Mile End campus, and cell culture and microscopy facilities available both at Mile End and through our collaborator at the Blizard Institute, Dr Andrea Cerase.

See Clayton Lab website: 


  1. C.-K. Chen, M. Blanco, C. Jackson, E. Aznauryan, N. Ollikainen, C. Surka, A. Chow, A. Cerase, P. McDonel, M. Guttman, Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing. Science. 354, 468–472 (2016).
  2. Y. Itoh, K. Replogle, Y.-H. Kim, J. Wade, D. F. Clayton, A. P. Arnold, Sex bias and dosage compensation in the zebra finch versus chicken genomes: general and specialized patterns among birds. Genome Res. 20, 512–518 (2010).
  3. R. J. Agate, W. Grisham, J. Wade, S. Mann, J. Wingfield, C. Schanen, A. Palotie, A. P. Arnold, Neural, not gonadal, origin of brain sex differences in a gynandromorphic finch. Proc. Natl. Acad. Sci. U. S. A. 100, 4873–4878 (2003).
  4. P. H. Gunaratne, Y.-C. Lin, A. L. Benham, J. Drnevich, C. Coarfa, J. B. Tennakoon, C. J. Creighton, J. H. Kim, A. Milosavljevic, M. Watson, S. Griffiths-Jones, D. F. Clayton, Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrain. BMC Genomics. 12, 277 (2011).
  5. Y.-C. Lin, C. N. Balakrishnan, D. F. Clayton, Functional genomic analysis and neuroanatomical localization of miR-2954, a song-responsive sex-linked microRNA in the zebra finch. Front. Neurosci. 8, 409 (2014).
  6. M. Warnefors, K. Mössinger, J. Halbert, T. Studer, J. L. VandeBerg, I. Lindgren, A. Fallahshahroudi, P. Jensen, H. Kaessmann, Sex-biased microRNA expression in mammals and birds reveals underlying regulatory mechanisms and a role in dosage compensation. Genome Res. 27, 1961–1973 (2017).
  7. V. Fishman, N. Battulin, M. Nuriddinov, A. Maslova, A. Zlotina, A. Strunov, D. Chervyakova, A. Korablev, O. Serov, A. Krasikova, 3D organization of chicken genome demonstrates evolutionary conservation of topologically associated domains and highlights unique architecture of erythrocytes’ chromatin. Nucleic Acids Res. 47, 648–665 (2019).
  8. I. Mota-Gómez, D. G. Lupiáñez, A (3D-Nuclear) Space Odyssey: Making Sense of Hi-C Maps. Genes . 10 (2019), doi:10.3390/genes10060415.