Literature DB >> 31740812

Neurobiological functions of transcriptional enhancers.

Alex S Nord1,2, Anne E West3.   

Abstract

Transcriptional enhancers are regulatory DNA elements that underlie the specificity and dynamic patterns of gene expression. Over the past decade, large-scale functional genomics projects have driven transformative progress in our understanding of enhancers. These data have relevance for identifying mechanisms of gene regulation in the CNS, elucidating the function of non-coding regulatory sequences in neurobiology and linking sequence variation within enhancers to genetic risk for neurological and psychiatric disorders. However, the sheer volume and complexity of genomic data presents a challenge to interpreting enhancer function in normal and pathogenic neurobiological processes. Here, to advance the application of genome-scale enhancer data, we offer a primer on current models of enhancer function in the CNS, we review how enhancers regulate gene expression across the neuronal lifespan, and we suggest how emerging findings regarding the role of non-coding sequence variation offer opportunities for understanding brain disorders and developing new technologies for neuroscience.

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Mesh:

Year:  2019        PMID: 31740812      PMCID: PMC7049175          DOI: 10.1038/s41593-019-0538-5

Source DB:  PubMed          Journal:  Nat Neurosci        ISSN: 1097-6256            Impact factor:   24.884


  136 in total

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Authors:  Lingyun Song; Zhancheng Zhang; Linda L Grasfeder; Alan P Boyle; Paul G Giresi; Bum-Kyu Lee; Nathan C Sheffield; Stefan Gräf; Mikael Huss; Damian Keefe; Zheng Liu; Darin London; Ryan M McDaniell; Yoichiro Shibata; Kimberly A Showers; Jeremy M Simon; Teresa Vales; Tianyuan Wang; Deborah Winter; Zhuzhu Zhang; Neil D Clarke; Ewan Birney; Vishwanath R Iyer; Gregory E Crawford; Jason D Lieb; Terrence S Furey
Journal:  Genome Res       Date:  2011-07-12       Impact factor: 9.043

2.  Comprehensive single-cell transcriptional profiling of a multicellular organism.

Authors:  Junyue Cao; Jonathan S Packer; Vijay Ramani; Darren A Cusanovich; Chau Huynh; Riza Daza; Xiaojie Qiu; Choli Lee; Scott N Furlan; Frank J Steemers; Andrew Adey; Robert H Waterston; Cole Trapnell; Jay Shendure
Journal:  Science       Date:  2017-08-18       Impact factor: 47.728

3.  Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences.

Authors:  J Banerji; S Rusconi; W Schaffner
Journal:  Cell       Date:  1981-12       Impact factor: 41.582

Review 4.  The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas.

Authors:  Joseph R Ecker; Daniel H Geschwind; Arnold R Kriegstein; John Ngai; Pavel Osten; Damon Polioudakis; Aviv Regev; Nenad Sestan; Ian R Wickersham; Hongkui Zeng
Journal:  Neuron       Date:  2017-11-01       Impact factor: 17.173

Review 5.  Transcription factor-DNA binding: beyond binding site motifs.

Authors:  Sachi Inukai; Kian Hong Kock; Martha L Bulyk
Journal:  Curr Opin Genet Dev       Date:  2017-03-27       Impact factor: 5.578

6.  Joint profiling of chromatin accessibility and gene expression in thousands of single cells.

Authors:  Junyue Cao; Darren A Cusanovich; Vijay Ramani; Delasa Aghamirzaie; Hannah A Pliner; Andrew J Hill; Riza M Daza; Jose L McFaline-Figueroa; Jonathan S Packer; Lena Christiansen; Frank J Steemers; Andrew C Adey; Cole Trapnell; Jay Shendure
Journal:  Science       Date:  2018-08-30       Impact factor: 47.728

7.  Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors.

Authors:  Jie Wang; Jiali Zhuang; Sowmya Iyer; XinYing Lin; Troy W Whitfield; Melissa C Greven; Brian G Pierce; Xianjun Dong; Anshul Kundaje; Yong Cheng; Oliver J Rando; Ewan Birney; Richard M Myers; William S Noble; Michael Snyder; Zhiping Weng
Journal:  Genome Res       Date:  2012-09       Impact factor: 9.043

Review 8.  Defining functional DNA elements in the human genome.

Authors:  Manolis Kellis; Barbara Wold; Michael P Snyder; Bradley E Bernstein; Anshul Kundaje; Georgi K Marinov; Lucas D Ward; Ewan Birney; Gregory E Crawford; Job Dekker; Ian Dunham; Laura L Elnitski; Peggy J Farnham; Elise A Feingold; Mark Gerstein; Morgan C Giddings; David M Gilbert; Thomas R Gingeras; Eric D Green; Roderic Guigo; Tim Hubbard; Jim Kent; Jason D Lieb; Richard M Myers; Michael J Pazin; Bing Ren; John A Stamatoyannopoulos; Zhiping Weng; Kevin P White; Ross C Hardison
Journal:  Proc Natl Acad Sci U S A       Date:  2014-04-21       Impact factor: 12.779

9.  The cis-regulatory dynamics of embryonic development at single-cell resolution.

Authors:  Darren A Cusanovich; James P Reddington; David A Garfield; Riza M Daza; Delasa Aghamirzaie; Raquel Marco-Ferreres; Hannah A Pliner; Lena Christiansen; Xiaojie Qiu; Frank J Steemers; Cole Trapnell; Jay Shendure; Eileen E M Furlong
Journal:  Nature       Date:  2018-03-14       Impact factor: 49.962

10.  A systematic, large-scale comparison of transcription factor binding site models.

Authors:  Daniela Hombach; Jana Marie Schwarz; Peter N Robinson; Markus Schuelke; Dominik Seelow
Journal:  BMC Genomics       Date:  2016-05-21       Impact factor: 3.969

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  25 in total

1.  Whole Genome Analysis of Dizygotic Twins With Autism Reveals Prevalent Transposon Insertion Within Neuronal Regulatory Elements: Potential Implications for Disease Etiology and Clinical Assessment.

Authors:  Kaan Okay; Pelin Ünal Varış; Süha Miral; Athanasia Pavlopoulou; Yavuz Oktay; Gökhan Karakülah
Journal:  J Autism Dev Disord       Date:  2022-06-27

2.  Developmental and evolutionary dynamics of cis-regulatory elements in mouse cerebellar cells.

Authors:  Ioannis Sarropoulos; Mari Sepp; Stefan M Pfister; Henrik Kaessmann; Robert Frömel; Kevin Leiss; Nils Trost; Evgeny Leushkin; Konstantin Okonechnikov; Piyush Joshi; Peter Giere; Lena M Kutscher; Margarida Cardoso-Moreira
Journal:  Science       Date:  2021-07-29       Impact factor: 47.728

Review 3.  Current and Future Perspectives of Noncoding RNAs in Brain Function and Neuropsychiatric Disease.

Authors:  Evan J Kyzar; John Peyton Bohnsack; Subhash C Pandey
Journal:  Biol Psychiatry       Date:  2021-08-24       Impact factor: 13.382

4.  Temporal analysis of enhancers during mouse cerebellar development reveals dynamic and novel regulatory functions.

Authors:  Miguel Ramirez; Yuliya Badayeva; Joanna Yeung; Joshua Wu; Ayasha Abdalla-Wyse; Erin Yang; Brett Trost; Stephen W Scherer; Daniel Goldowitz
Journal:  Elife       Date:  2022-08-09       Impact factor: 8.713

5.  Cell-type specific transcriptional adaptations of nucleus accumbens interneurons to amphetamine.

Authors:  David A Gallegos; Melyssa Minto; Fang Liu; Mariah F Hazlett; S Aryana Yousefzadeh; Luke C Bartelt; Anne E West
Journal:  Mol Psychiatry       Date:  2022-02-16       Impact factor: 13.437

6.  Transcriptomic and epigenomic dynamics associated with development of human iPSC-derived GABAergic interneurons.

Authors:  George Andrew S Inglis; Ying Zhou; Dillon G Patterson; Christopher D Scharer; Yanfei Han; Jeremy M Boss; Zhexing Wen; Andrew Escayg
Journal:  Hum Mol Genet       Date:  2020-08-29       Impact factor: 6.150

Review 7.  Spatial Organization of Chromatin: Emergence of Chromatin Structure During Development.

Authors:  Rajarshi P Ghosh; Barbara J Meyer
Journal:  Annu Rev Cell Dev Biol       Date:  2021-07-06       Impact factor: 13.827

8.  Parallel functional testing identifies enhancers active in early postnatal mouse brain.

Authors:  Jason T Lambert; Linda Su-Feher; Karol Cichewicz; Tracy L Warren; Iva Zdilar; Yurong Wang; Kenneth J Lim; Jessica L Haigh; Sarah J Morse; Cesar P Canales; Tyler W Stradleigh; Erika Castillo Palacios; Viktoria Haghani; Spencer D Moss; Hannah Parolini; Diana Quintero; Diwash Shrestha; Daniel Vogt; Leah C Byrne; Alex S Nord
Journal:  Elife       Date:  2021-10-04       Impact factor: 8.140

9.  Chromatin Dynamics and Genetic Variation Combine to Regulate Innate Immune Memory.

Authors:  Jennifer Kim; Annie Vogel Ciernia
Journal:  J Clin Cell Immunol       Date:  2020-07-28

10.  Genes Bound by ΔFosB in Different Conditions With Recurrent Seizures Regulate Similar Neuronal Functions.

Authors:  Gabriel S Stephens; Chia-Hsuan Fu; Corey P St Romain; Yi Zheng; Justin J Botterill; Helen E Scharfman; Yin Liu; Jeannie Chin
Journal:  Front Neurosci       Date:  2020-05-28       Impact factor: 4.677

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