erlenmyer-research
Research group/lab  |  P.I. Stefan Barakat, Ph.D., M.D., M.Sc

Barakat lab: Non-Coding Genome in Clinical Genetics

Our team focusses on deciphering the role of the non-coding genome in neurodevelopmental disorders and human embryonic stem cells

About our research group/lab

Our research

The non-coding genome

We know that most DNA sequences (~98%) in the human genome do not encode protein-coding genes. Yet, our understanding of those sequences and why they are important is still incomplete. An important group of non-coding genome elements are enhancers, which are crucial for the proper regulation of spatiotemporal gene expression. Although techniques such as ChIP-seq, chromatin accessibility assays, etc. can predict the identity of enhancers, predicting the activity of these sequences is still difficult. Understanding the non-coding genome is highly relevant, as many cases of genetic disorders are currently unexplained. A large fraction of this missing heritability is likely caused by aberrations in non-coding sequences.

New technologies to study the non-coding genome

Our newly-developed approach that combines chromatin immunoprecipitation with a massively parallel reporter assay allows generation of comprehensive, genome-wide enhancer activity maps for various cell types. This work has generated one of the largest resources of functionally validated enhancers in human embryonic stem cells existing to date, which will enable further knowledge-based studies to decipher the code underlying the gene regulation by non-coding sequences. Using these data, we discovered that only a small fraction of genomic regions bound by transcription factors or marked by histone modifications generally believed to be correlated to enhancers, show measurable enhancer activity in human embryonic stem cells. Active sites show a distinct protein binding profile and enrichment for sequences derived from transposable elements. Enhancer activity changes dramatically upon developmental transitions during differentiation, and only small constituents of “super-enhancers” are responsible for enhancer activity.   

Our current work 

We focus on deciphering the role of the non-coding genome in genetic disorders –particularly brain disorders. Using functional genomics and various other approaches, including induced pluripotent stem cells and cerebral organoids (“mini-brains”) and computational data mining, we are studying the enhancer landscape in cells representing neurodevelopment. We hypothesize that many genetic disorders of brain development are caused by alterations of non-coding elements, including enhancers. To directly test this hypothesis, we sequence enhancers identified through our genome-wide functional enhancer activity assays in patients. We are applying disease modelling for MCD neurodevelopmental disorder patients harboring identified mutations, using patient-specific induced pluripotent stem cells and differentiation to cerebral organoids, thereby simulating brain development in a dish. Our studies will help identify functional enhancer sequences in the non-coding genome, and will allow novel innovative approaches for patient diagnostics using functional genomics.
 
A novel research line focusses on identifying genetic causes of epileptic encephalopathy, a group of severe disorders presenting in early infancy with untreatable epilepsy and severe developmental delay. We recently discovered a new type of epileptic encephalopathy, caused by mutations in the UGP2 gene. This identified nucleotide sugar metabolism as an important pathway in this disease. We are working on methods to influence this pathway as possible future treatments.

Key Publications

Truncating mutations in YIF1B cause a progressive encephalopathy with various degrees of mixed movement disorder, microcephaly and epilepsy.
Mohammed AlMuhaizea, Rawan AlMass, Aljouhra AlHargan, Anoud AlBader, Eva Medico Salsench, Jude Howaidi, Jacie Ihinger, Peter Karachunski, Amber Begtrup, Monica Segura Castell, Peter Bauer, Aida Bertoli-Avella, Ibrahim H. Kaya, Jumanah AlSufayan, Laila AlQuait, Azizah Chedrawi, Stefan T. Arold, Dilek Colak, Tahsin Stefan Barakat , Namik Kaya. (2020). Acta Neuropathol. 2020 Jan 31.

Loss-of-function mutations in UDP-Glucose 6-Dehydrogenase cause recessive developmental epileptic encephalopathy.
Hengel H, Bosso-Lefèvre C, Grady G, Szenker-Ravi E, Li H, Pierce S, Lebigot E, Tan TT, Eio M, Narayanan G, Utami K, Yau M, Handal N, Deigendesch W, Keimer R, Marzouqa H, Gunay-Aygun M, Muriello M, Verhelst H, Weckhuysen S, Mahida S, Naidu S, Thomas T, Ying Lim J, Shien Tan E, Haye D, Willemsen M, Oegema R, Mitchell W, Pierson T, Andrews M, Willing M, Rodan L, Barakat TS, van Slegtenhorst M, Gavrilova R, Martinelli D, Gilboa T, Tamim A, Hashem M, AlSayed M, Abdulrahim M, Al-Owain M, Awaji A, Mahmoud A, Faqeih E, Al Asmar Ai, Algain S, Jad L,Aldhalaan H, Helbig I, Koolen D, Riess A, Kraegeloh-Mann I, Bauer P, Gulsuner S, Stamberger H, Ng A, Tang S, Tohari S, Keren B, Schultz-Rogers L, Klee E, Barresi S, Tartaglia M, Mor-Shaked H, Maddirevula S, Begtrup A, Telegraf Ai, Pfundt R, Schule R, Ciruna B, Bonnard C, Pouladi M, Stewart J, Claridge-Chang A, J Lefeber D, Alkuraya F, Mathuru A, Venkatesh B, Barycki J, Simpson M, Jamuar S, Schöls L and Reversade B. (2020). Nat Commun. 2020 Jan 30;11(1):595.

Loss of UGP2 in brain leads to a severe epileptic encephalopathy, emphasizing that bi-allelic isoform-specific start-loss mutations of essential genes can cause genetic diseases.
Perenthaler E, Nikoncuk A, Yousefi S, Berdowski WM, Alsagob M, Capo I, van der Linde HC, van den Berg P, Jacobs EH, Putar D, Ghazvini M, Aronica E, van IJcken WFJ, de Valk WG, Medici-van den Herik E, van Slegtenhorst M, Brick L, Kozenko M, Kohler JN, Bernstein JA, Monaghan KG, Begtrup A, Torene R, Al Futaisi A, Al Murshedi F, Mani R, Al Azri F, Kamsteeg EJ, Mojarrad M, Eslahi A, Khazaei Z, Darmiyan FM, Doosti M, Karimiani EG, Vandrovcova J, Zafar F, Rana N, Kandaswamy KK, Hertecant J, Bauer P, AlMuhaizea MA, Salih MA, Aldosary M, Almass R, Al-Quait L, Qubbaj W, Coskun S, Alahmadi KO, Hamad MHA, Alwadaee S, Awartani K, Dababo AM, Almohanna F, Colak D, Dehghani M, Mehrjardi MYV, Gunel M, Ercan-Sencicek AG, Passi GR, Cheema HA, Efthymiou S, Houlden H, Bertoli-Avella AM, Brooks AS, Retterer K, Maroofian R, Kaya N, van Ham TJ, Barakat TS. (2019). Acta Neuropathol. 2019 Dec 9.

De novo CLTC variants are associated with a variable phenotype from mild to severe intellectual disability, microcephaly, hypoplasia of the corpus callosum, and epilepsy.
Nabais Sá MJ, Venselaar H, Wiel L, Trimouille A, Lasseaux E, Naudion S, Lacombe D, Piton A, Vincent-Delorme C, Zweier C, Reis A, Trollmann R, Ruiz A, Gabau E, Vetro A, Guerrini R, Bakhtiari S, Kruer MC, Amor DJ, Cooper MS, Bijlsma EK, Barakat TS, van Dooren MF, van Slegtenhorst M, Pfundt R, Gilissen C, Willemsen MA, de Vries BBA, de Brouwer APM, Koolen DA. (2019). Genet Med. 2019 Nov 28.

Building Bridges Between the Clinic and the Laboratory: A Meeting Review – Brain Malformations: A Roadmap for Future Research.
Tamar Sapir, Tahsin Stefan Barakat, Mercedes F. Paredes, Tally Lerman-Sagie, Eleonora Aronica, Wlodzimierz Klonowski, Laurent Nguyen, Bruria Ben Zeev, Nadia Bahi-Buisson, Richard Leventer, Noa Rachmian and Orly Reiner. (2019). Front. Cell. Neurosci., 27 September 2019.

Beyond the Exome: The Non-coding Genome and Enhancers in Neurodevelopmental Disorders and Malformations of Cortical Development.
Elena Perenthaler, Soheil Yousefi, Eva Niggl and Tahsin Stefan Barakat. (2019). Front. Cell. Neurosci., 31 July 2019.

Exome Sequencing of a Primary Ovarian Insufficiency Cohort Reveals Common Molecular Etiologies for a Spectrum of Disease.
Jolly A, Bayram Y, Turan S, Aycan Z, Tos T, Abali ZY, Hacihamdioglu B, Coban Akdemir ZH, Hijazi H, Bas S, Atay Z, Guran T, Abali S, Bas F, Darendeliler F, Colombo R, Barakat TS, Rinne T1, White JJ, Yesil G, Gezdirici A, Gulec EY, Karaca E, Pehlivan D, Jhangiani SN, Muzny DM, Poyrazoglu S, Bereket A, Gibbs RA, Posey JE, Lupski JR. (2019). J Clin Endocrinol Metab. 2019 Aug 1;104(8):3049-3067.

The evolution of Great Apes has shaped the functional enhancers' landscape in human embryonic stem cells.
Glinsky G, Barakat TS. (2019). Stem Cell Res. 2019 May;37:101456.

REX1 is the critical target of RNF12 in imprinted X chromosome inactivation in mice.
Gontan C, Mira-Bontenbal H, Magaraki A, Dupont C, Barakat TS, Rentmeester E, Demmers J, Gribnau J. (2018). Nat Commun. 2018 Nov 12;9(1):4752.

Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells.
Tahsin Stefan Barakat, Florian Halbritter, Man Zhang, André F. Rendeiro, Elena Perenthaler, Christoph Bock, and Ian Chambers. (2018). Cell Stem Cell. 2018 Aug 2; 23(2): 276–288.e8.

Dynamics of gene silencing during X inactivation using allele-specific RNA-seq.
Marks H, Kerstens HH, Barakat TS, Splinter E, Dirks RA, van Mierlo G, Joshi O, Wang SY, Babak T, Albers CA, Kalkan T, Smith A, Jouneau A, de Laat W, Gribnau J, Stunnenberg HG. (2015). Genome Biol. 2015 Aug 3;16:149.

Stable X chromosome reactivation in female human induced pluripotent stem cells.
Barakat TS, Ghazvini M, de Hoon B, Li T, Eussen B, Douben H, van der Linden R, van der Stap N, Boter M, Laven JS, Galjaard RJ, Grootegoed JA, de Klein A, Gribnau J. (2015). Stem Cell Reports. 2015 Feb 10;4(2):199-208.

Generation of knockout alleles by RFLP based BAC targeting of polymorphic embryonic stem cells.
Tahsin Stefan Barakat and Joost Gribnau. (2015). Methods Mol Biol. 2015;1227:143-80.

Combined DNA-RNA fluorescent in situ hybridization (FISH) to study X chromosome inactivation in differentiated female mouse embryonic stem cells.
Barakat TS, Gribnau J. (2014). J Vis Exp. 2014 Jun 14;(88).

The trans-activator RNF12 and cis-acting elements effectuate X chromosome inactivation independent of X-pairing.
Barakat TS, Loos F, van Staveren S, Myronova E, Ghazvini M, Grootegoed JA, Gribnau J. (2014). Mol Cell. 2014 Mar 20;53(6):965-78.

Structural and numerical changes of chromosome X in patients with esophageal atresia.
Brosens E, de Jong EM, Barakat TS, Eussen BH, D'haene B, De Baere E, Verdin H4, Poddighe PJ, Galjaard RJ, Gribnau J, Brooks AS, Tibboel D, de Klein A. (2014). Eur J Hum Genet. 2014 Sep;22(9):1077-84.

The pluripotency factor-bound intron 1 of Xist is dispensable for X chromosome inactivation and reactivation in vitro and in vivo.
Minkovsky A, Barakat TS, Sellami N, Chin MH, Gunhanlar N, Gribnau J, Plath K. (2013). Cell Rep. 2013 Mar 28;3(3):905-18.

X chromosome inactivation in the cycle of life.
Barakat TS, Gribnau J. (2012). Development. 2012 Jun;139(12):2085-9.

RNF12 initiates X-chromosome inactivation by targeting REX1 for degradation.
Gontan C, Achame EM, Demmers J, Barakat TS, Rentmeester E, van IJcken W, Grootegoed JA, Gribnau J. (2012). Nature. 2012 Apr 29;485(7398):386-90.

RNF12 controls embryonic stem cell fate and morphogenesis in zebrafish embryos by targeting Smad7 for degradation.
Zhang L, Huang H, Zhou F, Schimmel J, Pardo CG, Zhang T, Barakat TS, Sheppard KA, Mickanin C, Porter JA, Vertegaal AC, van Dam H, Gribnau J, Lu CX, ten Dijke P. Mol Cell. 2012 Jun 8;46(5):650-61.

Precise BAC targeting of genetically polymorphic mouse ES cells.
Barakat TS, Rentmeester E, Sleutels F, Grootegoed JA, Gribnau J. (2011). Nucleic Acids Res. 2011 Oct;39(18):e121.

RNF12 activates Xist and is essential for X chromosome inactivation.
Barakat TS, Gunhanlar N, Pardo CG, Achame EM, Ghazvini M, Boers R, Kenter A, Rentmeester E, Grootegoed JA, Gribnau. (2011). PLoS Genet. 2011 Jan 27;7(1):e1002001.

X chromosome inactivation and embryonic stem cells.
Barakat TS, Gribnau J. Adv Exp Med Biol. 2010;695:132-54.

A murine ESC-like state facilitates transgenesis and homologous recombination in human pluripotent stem cells.
Buecker C, Chen HH, Polo JM, Daheron L, Bu L, Barakat TS, Okwieka P, Porter A, Gribnau J, Hochedlinger K, Geijsen N. (2010). Cell Stem Cell. 2010 Jun 4;6(6):535-46.

X-changing information on X inactivation.
Barakat TS1, Jonkers I, Monkhorst K, Gribnau J. (2010). Exp Cell Res. 2010 Mar 10;316(5):679-87.

RNF12 is an X-Encoded dose-dependent activator of X chromosome inactivation.
Jonkers I, Barakat TS, Achame EM, Monkhorst K, Kenter A, Rentmeester E, Grosveld F, Grootegoed JA, Gribnau J. (2009). Cell. 2009 Nov 25;139(5):999-1011.

Books

Living with two X chromosomes: of mice and women : studies on the initiation mechanisms of X chromosome inactivation in stem cells and mouse models, and the role of RNF12 herein

Other publications

X-chromosome inactivation and its implications for human disease.
Joost Gribnau, Tahsin Stefan Barakat.

Can adrenaline safely be used in local anaesthesia involving distal extremities? A systematic review. Tahsin Stefan Barakat, Mariska de Pagter and Michel ten Have. (2015). Erasmus Journal of Medicine 4(2):15-19.

Collaborations

Collaboration within Erasmus MC

  • Grazia Mancini, Erasmus MC, Rotterdam
  • Department of Cell Biology, Erasmus MC, Rotterdam
  • Academic Center for Stem Cells & Organoids in personalized and Regenerative medicine (SCORE).

Collaboration outside of Erasmus MC

Funding & Grants

The Barakat lab is supported by grants from:

  • The Dutch Research Council (ZonMW Veni)
  • The Brain & Behavior Research Foundation (NARSAD Young investigator Award)
  • Erasmus MC Fellowship 2017
  • Erasmus MC Human Disease Model Award 2018
  • Erasmus MC MRACE Pilot Grant 2018

Previously, the principal investigator has been supported by:

  • MSCA-IF-2014-EF - Marie Skłodowska-Curie Individual  Fellowships (IF-EF) from the European Union
  • EMBO Long-Term Fellowship
  • Niels Stensen Fellowship
  • Human Frontiers Science Project Long-Term Fellowship (Gratefully declined in favor of EMBO/MSCA)
  • American Society of Human Genetics (ASHG) /Charles J. Epstein Trainee Award 2015 for Excellence in Human Genetics Research – Winner
  • Beverly Kerr McKinnel Award 2012, of the International Society for Differentiation (ISD), for outstanding research as a PhD student

Career opportunities

We are always looking for talented people at all career steps. If you are interested in our research, and would like to discuss possibilities, please feel free to contact the PI T.Barakat directly by sending a CV.

Our team

Group of Tahsin Stefan Barakat