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Literature DB >> 25569346

Genomic perspectives of transcriptional regulation in forebrain development.

Alex S Nord¹, Kartik Pattabiraman², Axel Visel³, John L R Rubenstein².

Abstract

The forebrain is the seat of higher-order brain functions, and many human neuropsychiatric disorders are due to genetic defects affecting forebrain development, making it imperative to understand the underlying genetic circuitry. Recent progress now makes it possible to begin fully elucidating the genomic regulatory mechanisms that control forebrain gene expression. Herein, we discuss the current knowledge of how transcription factors drive gene expression programs through their interactions with cis-acting genomic elements, such as enhancers; how analyses of chromatin and DNA modifications provide insights into gene expression states; and how these approaches yield insights into the evolution of the human brain.

Entities: CellLine Chemical Disease Gene Species

Mesh：

Substances：
Transcription Factors

Year: 2015 PMID： 25569346 PMCID： PMC4438709 DOI： 10.1016/j.neuron.2014.11.011

Source DB: PubMed Journal: Neuron ISSN： 0896-6273 Impact factor: 17.173

184 in total

1. Distinct cis-regulatory elements from the Dlx1/Dlx2 locus mark different progenitor cell populations in the ganglionic eminences and different subtypes of adult cortical interneurons.

Authors: Noël Ghanem; Man Yu; Jason Long; Gary Hatch; John L R Rubenstein; Marc Ekker
Journal: J Neurosci Date: 2007-05-09 Impact factor: 6.167

2. Super-enhancers in the control of cell identity and disease.

Authors: Denes Hnisz; Brian J Abraham; Tong Ihn Lee; Ashley Lau; Violaine Saint-André; Alla A Sigova; Heather A Hoke; Richard A Young
Journal: Cell Date: 2013-10-10 Impact factor: 41.582

3. Mutations in ARX Result in Several Defects Involving GABAergic Neurons.

Authors: Gaëlle Friocourt; John G Parnavelas
Journal: Front Cell Neurosci Date: 2010-03-11 Impact factor: 5.505

4. Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model.

Authors: Robin P Smith; Leila Taher; Rupali P Patwardhan; Mee J Kim; Fumitaka Inoue; Jay Shendure; Ivan Ovcharenko; Nadav Ahituv
Journal: Nat Genet Date: 2013-07-28 Impact factor: 38.330

5. Wnt and Bmp signalling cooperatively regulate graded Emx2 expression in the dorsal telencephalon.

Authors: Thomas Theil; Songül Aydin; Silke Koch; Lars Grotewold; Ulrich Rüther
Journal: Development Date: 2002-07 Impact factor: 6.868

6. Maturation-promoting activity of SATB1 in MGE-derived cortical interneurons.

Authors: Myrto Denaxa; Melanie Kalaitzidou; Anna Garefalaki; Angeliki Achimastou; Reena Lasrado; Tamara Maes; Vassilis Pachnis
Journal: Cell Rep Date: 2012-11-08 Impact factor: 9.423

7. Forces shaping the fastest evolving regions in the human genome.

Authors: Katherine S Pollard; Sofie R Salama; Bryan King; Andrew D Kern; Tim Dreszer; Sol Katzman; Adam Siepel; Jakob S Pedersen; Gill Bejerano; Robert Baertsch; Kate R Rosenbloom; Jim Kent; David Haussler
Journal: PLoS Genet Date: 2006-08-23 Impact factor: 5.917

8. Evolutionarily dynamic alternative splicing of GPR56 regulates regional cerebral cortical patterning.

Authors: Byoung-Il Bae; Ian Tietjen; Kutay D Atabay; Gilad D Evrony; Matthew B Johnson; Ebenezer Asare; Peter P Wang; Ayako Y Murayama; Kiho Im; Steven N Lisgo; Lynne Overman; Nenad Šestan; Bernard S Chang; A James Barkovich; P Ellen Grant; Meral Topçu; Jeffrey Politsky; Hideyuki Okano; Xianhua Piao; Christopher A Walsh
Journal: Science Date: 2014-02-14 Impact factor: 47.728

9. An encyclopedia of mouse DNA elements (Mouse ENCODE).

Authors: John A Stamatoyannopoulos; Michael Snyder; Ross Hardison; Bing Ren; Thomas Gingeras; David M Gilbert; Mark Groudine; Michael Bender; Rajinder Kaul; Theresa Canfield; Erica Giste; Audra Johnson; Mia Zhang; Gayathri Balasundaram; Rachel Byron; Vaughan Roach; Peter J Sabo; Richard Sandstrom; A Sandra Stehling; Robert E Thurman; Sherman M Weissman; Philip Cayting; Manoj Hariharan; Jin Lian; Yong Cheng; Stephen G Landt; Zhihai Ma; Barbara J Wold; Job Dekker; Gregory E Crawford; Cheryl A Keller; Weisheng Wu; Christopher Morrissey; Swathi A Kumar; Tejaswini Mishra; Deepti Jain; Marta Byrska-Bishop; Daniel Blankenberg; Bryan R Lajoie; Gaurav Jain; Amartya Sanyal; Kaun-Bei Chen; Olgert Denas; James Taylor; Gerd A Blobel; Mitchell J Weiss; Max Pimkin; Wulan Deng; Georgi K Marinov; Brian A Williams; Katherine I Fisher-Aylor; Gilberto Desalvo; Anthony Kiralusha; Diane Trout; Henry Amrhein; Ali Mortazavi; Lee Edsall; David McCleary; Samantha Kuan; Yin Shen; Feng Yue; Zhen Ye; Carrie A Davis; Chris Zaleski; Sonali Jha; Chenghai Xue; Alex Dobin; Wei Lin; Meagan Fastuca; Huaien Wang; Roderic Guigo; Sarah Djebali; Julien Lagarde; Tyrone Ryba; Takayo Sasaki; Venkat S Malladi; Melissa S Cline; Vanessa M Kirkup; Katrina Learned; Kate R Rosenbloom; W James Kent; Elise A Feingold; Peter J Good; Michael Pazin; Rebecca F Lowdon; Leslie B Adams
Journal: Genome Biol Date: 2012-08-13 Impact factor: 13.583

10. Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations.

Authors: Brian J O'Roak; Pelagia Deriziotis; Choli Lee; Laura Vives; Jerrod J Schwartz; Santhosh Girirajan; Emre Karakoc; Alexandra P Mackenzie; Sarah B Ng; Carl Baker; Mark J Rieder; Deborah A Nickerson; Raphael Bernier; Simon E Fisher; Jay Shendure; Evan E Eichler
Journal: Nat Genet Date: 2011-05-15 Impact factor: 38.330

81 in total

1. Genetic variants in 5-HTTLPR, BDNF, HTR1A, COMT, and FKBP5 and risk for treated depression after cancer diagnosis.

Authors: Nis P Suppli; Jens D Bukh; Terrie E Moffitt; Avshalom Caspi; Christoffer Johansen; Anne Tjønneland; Lars V Kessing; Susanne O Dalton
Journal: Depress Anxiety Date: 2017-06-07 Impact factor: 6.505

Review 2. Lost in Translation: Traversing the Complex Path from Genomics to Therapeutics in Autism Spectrum Disorder.

Authors: Nenad Sestan; Matthew W State
Journal: Neuron Date: 2018-10-24 Impact factor: 17.173

3. Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation.

Authors: Sebastian Preissl; Rongxin Fang; Hui Huang; Yuan Zhao; Ramya Raviram; David U Gorkin; Yanxiao Zhang; Brandon C Sos; Veena Afzal; Diane E Dickel; Samantha Kuan; Axel Visel; Len A Pennacchio; Kun Zhang; Bing Ren
Journal: Nat Neurosci Date: 2018-02-12 Impact factor: 24.884

Genomic perspectives of transcriptional regulation in forebrain development.

1. Distinct cis-regulatory elements from the Dlx1/Dlx2 locus mark different progenitor cell populations in the ganglionic eminences and different subtypes of adult cortical interneurons.

2. Super-enhancers in the control of cell identity and disease.

3. Mutations in ARX Result in Several Defects Involving GABAergic Neurons.

4. Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model.

5. Wnt and Bmp signalling cooperatively regulate graded Emx2 expression in the dorsal telencephalon.

6. Maturation-promoting activity of SATB1 in MGE-derived cortical interneurons.

7. Forces shaping the fastest evolving regions in the human genome.

8. Evolutionarily dynamic alternative splicing of GPR56 regulates regional cerebral cortical patterning.

9. An encyclopedia of mouse DNA elements (Mouse ENCODE).

10. Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations.

1. Genetic variants in 5-HTTLPR, BDNF, HTR1A, COMT, and FKBP5 and risk for treated depression after cancer diagnosis.

Review 2. Lost in Translation: Traversing the Complex Path from Genomics to Therapeutics in Autism Spectrum Disorder.

3. Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation.

Review 4. Signatures of sex: Sex differences in gene expression in the vertebrate brain.

5. Transcription Factor Motifs Associated with Anterior Insula Gene Expression Underlying Mood Disorder Phenotypes.

Review 6. Gene regulatory mechanisms underlying sex differences in brain development and psychiatric disease.

7. Transcriptional Architecture of Synaptic Communication Delineates GABAergic Neuron Identity.

8. The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis.

9. ARNT2 Tunes Activity-Dependent Gene Expression through NCoR2-Mediated Repression and NPAS4-Mediated Activation.

Review 10. Radial glia in the ventral telencephalon.