Literature DB >> 22549952

HOT DNAs: a novel class of developmental enhancers.

Emma Farley1, Michael Levine.   

Abstract

Enhancers mediate localized patterns of gene expression during development. A common feature of "traditional" enhancers is the presence of clustered binding motifs for sequence-specific transcription factors (TFs). In this issue of Genes & Development, Kvon and colleagues (pp. 908-913) present new evidence that HOT (highly occupied transcription) DNAs direct specific patterns of gene expression, despite being depleted for TF-binding motifs.

Entities:  

Mesh：

Year:  2012        PMID： 22549952      PMCID： PMC3347785          DOI： 10.1101/gad.192583.112

Source DB:  PubMed          Journal:  Genes Dev        ISSN： 0890-9369            Impact factor:   11.361


  29 in total

1.  Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo.

Authors:  Michele Markstein; Peter Markstein; Vicky Markstein; Michael S Levine
Journal:  Proc Natl Acad Sci U S A       Date:  2001-12-18       Impact factor: 11.205

2.  Early and late periodic patterns of even skipped expression are controlled by distinct regulatory elements that respond to different spatial cues.

Authors:  T Goto; P Macdonald; T Maniatis
Journal:  Cell       Date:  1989-05-05       Impact factor: 41.582

3.  Regulation of a segmentation stripe by overlapping activators and repressors in the Drosophila embryo.

Authors:  D Stanojevic; S Small; M Levine
Journal:  Science       Date:  1991-11-29       Impact factor: 47.728

4.  Identification of functional elements and regulatory circuits by Drosophila modENCODE.

Authors:  Sushmita Roy; Jason Ernst; Peter V Kharchenko; Pouya Kheradpour; Nicolas Negre; Matthew L Eaton; Jane M Landolin; Christopher A Bristow; Lijia Ma; Michael F Lin; Stefan Washietl; Bradley I Arshinoff; Ferhat Ay; Patrick E Meyer; Nicolas Robine; Nicole L Washington; Luisa Di Stefano; Eugene Berezikov; Christopher D Brown; Rogerio Candeias; Joseph W Carlson; Adrian Carr; Irwin Jungreis; Daniel Marbach; Rachel Sealfon; Michael Y Tolstorukov; Sebastian Will; Artyom A Alekseyenko; Carlo Artieri; Benjamin W Booth; Angela N Brooks; Qi Dai; Carrie A Davis; Michael O Duff; Xin Feng; Andrey A Gorchakov; Tingting Gu; Jorja G Henikoff; Philipp Kapranov; Renhua Li; Heather K MacAlpine; John Malone; Aki Minoda; Jared Nordman; Katsutomo Okamura; Marc Perry; Sara K Powell; Nicole C Riddle; Akiko Sakai; Anastasia Samsonova; Jeremy E Sandler; Yuri B Schwartz; Noa Sher; Rebecca Spokony; David Sturgill; Marijke van Baren; Kenneth H Wan; Li Yang; Charles Yu; Elise Feingold; Peter Good; Mark Guyer; Rebecca Lowdon; Kami Ahmad; Justen Andrews; Bonnie Berger; Steven E Brenner; Michael R Brent; Lucy Cherbas; Sarah C R Elgin; Thomas R Gingeras; Robert Grossman; Roger A Hoskins; Thomas C Kaufman; William Kent; Mitzi I Kuroda; Terry Orr-Weaver; Norbert Perrimon; Vincenzo Pirrotta; James W Posakony; Bing Ren; Steven Russell; Peter Cherbas; Brenton R Graveley; Suzanna Lewis; Gos Micklem; Brian Oliver; Peter J Park; Susan E Celniker; Steven Henikoff; Gary H Karpen; Eric C Lai; David M MacAlpine; Lincoln D Stein; Kevin P White; Manolis Kellis
Journal:  Science       Date:  2010-12-22       Impact factor: 47.728

5.  Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

Authors:  Mark B Gerstein; Zhi John Lu; Eric L Van Nostrand; Chao Cheng; Bradley I Arshinoff; Tao Liu; Kevin Y Yip; Rebecca Robilotto; Andreas Rechtsteiner; Kohta Ikegami; Pedro Alves; Aurelien Chateigner; Marc Perry; Mitzi Morris; Raymond K Auerbach; Xin Feng; Jing Leng; Anne Vielle; Wei Niu; Kahn Rhrissorrakrai; Ashish Agarwal; Roger P Alexander; Galt Barber; Cathleen M Brdlik; Jennifer Brennan; Jeremy Jean Brouillet; Adrian Carr; Ming-Sin Cheung; Hiram Clawson; Sergio Contrino; Luke O Dannenberg; Abby F Dernburg; Arshad Desai; Lindsay Dick; Andréa C Dosé; Jiang Du; Thea Egelhofer; Sevinc Ercan; Ghia Euskirchen; Brent Ewing; Elise A Feingold; Reto Gassmann; Peter J Good; Phil Green; Francois Gullier; Michelle Gutwein; Mark S Guyer; Lukas Habegger; Ting Han; Jorja G Henikoff; Stefan R Henz; Angie Hinrichs; Heather Holster; Tony Hyman; A Leo Iniguez; Judith Janette; Morten Jensen; Masaomi Kato; W James Kent; Ellen Kephart; Vishal Khivansara; Ekta Khurana; John K Kim; Paulina Kolasinska-Zwierz; Eric C Lai; Isabel Latorre; Amber Leahey; Suzanna Lewis; Paul Lloyd; Lucas Lochovsky; Rebecca F Lowdon; Yaniv Lubling; Rachel Lyne; Michael MacCoss; Sebastian D Mackowiak; Marco Mangone; Sheldon McKay; Desirea Mecenas; Gennifer Merrihew; David M Miller; Andrew Muroyama; John I Murray; Siew-Loon Ooi; Hoang Pham; Taryn Phippen; Elicia A Preston; Nikolaus Rajewsky; Gunnar Rätsch; Heidi Rosenbaum; Joel Rozowsky; Kim Rutherford; Peter Ruzanov; Mihail Sarov; Rajkumar Sasidharan; Andrea Sboner; Paul Scheid; Eran Segal; Hyunjin Shin; Chong Shou; Frank J Slack; Cindie Slightam; Richard Smith; William C Spencer; E O Stinson; Scott Taing; Teruaki Takasaki; Dionne Vafeados; Ksenia Voronina; Guilin Wang; Nicole L Washington; Christina M Whittle; Beijing Wu; Koon-Kiu Yan; Georg Zeller; Zheng Zha; Mei Zhong; Xingliang Zhou; Julie Ahringer; Susan Strome; Kristin C Gunsalus; Gos Micklem; X Shirley Liu; Valerie Reinke; Stuart K Kim; LaDeana W Hillier; Steven Henikoff; Fabio Piano; Michael Snyder; Lincoln Stein; Jason D Lieb; Robert H Waterston
Journal:  Science       Date:  2010-12-22       Impact factor: 47.728

6.  Transcriptional regulation of a pair-rule stripe in Drosophila.

Authors:  S Small; R Kraut; T Hoey; R Warrior; M Levine
Journal:  Genes Dev       Date:  1991-05       Impact factor: 11.361

7.  HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature.

Authors:  Evgeny Z Kvon; Gerald Stampfel; J Omar Yáñez-Cuna; Barry J Dickson; Alexander Stark
Journal:  Genes Dev       Date:  2012-04-12       Impact factor: 11.361

8.  Transcriptional regulatory code of a eukaryotic genome.

Authors:  Christopher T Harbison; D Benjamin Gordon; Tong Ihn Lee; Nicola J Rinaldi; Kenzie D Macisaac; Timothy W Danford; Nancy M Hannett; Jean-Bosco Tagne; David B Reynolds; Jane Yoo; Ezra G Jennings; Julia Zeitlinger; Dmitry K Pokholok; Manolis Kellis; P Alex Rolfe; Ken T Takusagawa; Eric S Lander; David K Gifford; Ernest Fraenkel; Richard A Young
Journal:  Nature       Date:  2004-09-02       Impact factor: 49.962

9.  Transcriptional regulatory networks in Saccharomyces cerevisiae.

Authors:  Tong Ihn Lee; Nicola J Rinaldi; François Robert; Duncan T Odom; Ziv Bar-Joseph; Georg K Gerber; Nancy M Hannett; Christopher T Harbison; Craig M Thompson; Itamar Simon; Julia Zeitlinger; Ezra G Jennings; Heather L Murray; D Benjamin Gordon; Bing Ren; John J Wyrick; Jean-Bosco Tagne; Thomas L Volkert; Ernest Fraenkel; David K Gifford; Richard A Young
Journal:  Science       Date:  2002-10-25       Impact factor: 47.728

10.  Autoregulatory and gap gene response elements of the even-skipped promoter of Drosophila.

Authors:  K Harding; T Hoey; R Warrior; M Levine
Journal:  EMBO J       Date:  1989-04       Impact factor: 11.598
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  4 in total

1.  Mammalian transcriptional hotspots are enriched for tissue specific enhancers near cell type specific highly expressed genes and are predicted to act as transcriptional activator hubs.

Authors:  Anagha Joshi
Journal:  BMC Bioinformatics       Date:  2014-12-30       Impact factor: 3.169

2.  The role of Dichaete in transcriptional regulation during Drosophila embryonic development.

Authors:  Jelena Aleksic; Enrico Ferrero; Bettina Fischer; Shih Pei Shen; Steven Russell
Journal:  BMC Genomics       Date:  2013-12-08       Impact factor: 3.969

3.  Genome-wide screens for in vivo Tinman binding sites identify cardiac enhancers with diverse functional architectures.

Authors:  Hong Jin; Robert Stojnic; Boris Adryan; Anil Ozdemir; Angelike Stathopoulos; Manfred Frasch
Journal:  PLoS Genet       Date:  2013-01-10       Impact factor: 5.917

4.  Absence of canonical marks of active chromatin in developmentally regulated genes.

Authors:  Sílvia Pérez-Lluch; Enrique Blanco; Hagen Tilgner; Joao Curado; Marina Ruiz-Romero; Montserrat Corominas; Roderic Guigó
Journal:  Nat Genet       Date:  2015-08-17       Impact factor: 38.330
  4 in total

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