Research:

AlHaj Abed lab research focuses on the interplay between epigenetic states and parental genome packaging in the nucleus, with a particular interest in understanding the extent to which gene regulation is coordinated between maternal and paternal chromosomes.

We use allele-specific Hi-C, RNA-seq, ChIP-seq and super-resolution imaging (sequential OligoSTORM) i) to understand how parental genomes are organized to facilitate gene function, ii) to uncover what are the major factors and dynamics leading to changes in gene regulation and epigenetic states, and iii) to uncover genome organization in healthy and disease states, such as cancer, aneuploidy and wound healing. Allele-resolved Hi-C uncovers a genome-wide signature of chromosome interactions in embryos and diploid cell lines, while super-resolution imaging with OligoSTORM reveals high localization precision of chromosomal loci in 3D in the nucleus.

Keywords:

allele-specific approaches, genome organization, epigenetics, super-resolution imaging, trans-gene regulation

Ten most important publications

• MioS, an integrated imaging and computational strategy to model gene folding with nucleosome resolution, Neguembor, M. V.*, Pablo, J., Diana, B., Lema, R., Walther, J., Garate, X., Martin, L., Romero, P.AlHaj Abed, J., Gut, M., Blanc, J., Lakadamyali, M., Wu, C.t, Heath, I. B., Orozco, M., Dans, P. D., and Cosma, M. P., Nat Struct Mol Biol. (in press), 2022.
• Transcription-mediated supercoiling regulates genome folding and loop formation, Neguembor, M. V.*, Martin, L., Castells-García, A., Gómez-García, P. A., Vicario, C., AlHaj Abed, J., Granados, A., Sebastian-Perez, R., Sottile, F., Solon, J., Wu, C.t, Lakadamyali, M., and Cosma, M., P., Mol. Cell. 81(15):3065-3081.e12, 2021.
• The genome-wide, multi-layered architecture of chromosome pairing in early Drosophila embryos, Erceg, J., AlHaj Abed, J., Goloborodko, A.*, Lajoie, B. R., Fudenberg, G., Abdennur, N., Imakaev, M., McCole, R. B., Nguyen, S. C., Saylor, W., Joyce, E. F., Senaratne, N. T., Hannan, M. A., Nir, G., Dekker, J., Mirny, L. A., Wu, C. T., Nat Commun. 10(1):4486, 2019.
• Highly Structured Homolog Pairing Reflects Functional Organization of the Drosophila Genome, AlHaj Abed, J. , Erceg, J., Goloborodko, A.*, Nguyen, S. C., McCole, R. B., Saylor, W., Fudenberg, G., Lajoie, B. R., Dekker, J., Mirny, L. A., Wu, C. T, Nat Commun. 10(1):4485, 2019.
• Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling, Nir, G., Farabella, I., Estrada, C. P., Ebeling, C. G., Beliveau, B. J., Sasaki, H. M., Lee, S. H., Nguyen, S. C., McCole, R. B., Chattoraj, S., Erceg, J., AlHaj Abed, J., Martins, N. M. C., Nguyen, H. Q., Hannan, M., Russell, S., Durand, N., Rao, S. S. P., Kishi, J. Y., Soler-Vila, P., Di Pierro, M., Onuchic, J. N., Callahan, S., Schreiner, J., Jeff Stuckey, J., Yin, P., Lieberman, E., PLoS Genet. 14(12), 2018.
• De novo recruitment of Polycomb-group proteins in Drosophila embryos, AlHaj Abed, J.*, Ghotbi- Ravandi, E., Ye, P., Frolov, A., Benes, J., Jones, R. S., Development 145: dev165027, 2018. Mapping Polycomb Response Elements at the Drosophila melanogaster giant locus, AlHaj Abed, J.*, C. L. Cheng, C. R. Crowell, L. L. Madigan, E. Onwuegbuchu, S. Desai, J. Benes, R. S. Jones, G3. 3(12):2297- 2304, 2013.
• H3K36me3 key to Polycomb-mediated gene silencing in lineage specification, AlHaj Abed, J. and R.S. Jones, Nat Struct Mol Biol. 19(12):1214-5, 2012.