                         SEQUENCE LISTING

<110>  The BROAD INSTITUTE, INC.
       Baylor College of Medicine
       Lieberman Aiden, Erez
       Lander, Eric S.
       Rao, Suhas
       Huang, Su-Chen
       Sanborn, Adrian L.
       Durand, Neva C.
       Huntley, Miriam
       Jewett, Andrew
 
<120>  Methods and Compositions for Altering Function and Structure of 
       Chromatin Loops and/or Domains

<130>  BROD-0552WP

<140>  PCT/US2016/047644
<141>  2016-08-18

<150>  US 62/206,606
<151>  2015-08-18

<150>  US 62/239,135
<151>  2015-10-08

<160>  45    

<170>  PatentIn version 3.5

<210>  1
<211>  31
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  synthetic oligonucleotide


<220>
<221>  misc_feature
<222>  (16)..(16)
<223>  n is a, c, g, or t

<400>  1
tcgcgcccat aactcnctga gggtccgcct t                                      31


<210>  2
<211>  31
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  synthetic oligonucleotide


<220>
<221>  misc_feature
<222>  (16)..(16)
<223>  n is a, c, g, or t

<400>  2
atcgcaccag cgtgtncact gcggctcctc a                                      31


<210>  3
<211>  31
<212>  DNA
<213>  Artificial Seqeunce

<220>
<223>  synthetic oligonucleotide


<220>
<221>  misc_feature
<222>  (16)..(16)
<223>  n is a, c, g, or t

<400>  3
cctcgcctat cccatncact accggggtct g                                      31


<210>  4
<211>  21
<212>  DNA
<213>  Artificial sequence

<220>
<223>  synthetic primer

<400>  4
ctgggatcgc gcccataact c                                                 21


<210>  5
<211>  21
<212>  DNA
<213>  Artificial sequence

<220>
<223>  synthetic primer

<400>  5
ctgggaatcg caccagcgtg t                                                 21


<210>  6
<211>  21
<212>  DNA
<213>  Artificial sequence

<220>
<223>  synthetic primer

<400>  6
ctgggacctc gcctatccca t                                                 21


<210>  7
<211>  21
<212>  DNA
<213>  Artificial sequence

<220>
<223>  synthetic primer

<400>  7
cgtggaaagg cggaccctca g                                                 21


<210>  8
<211>  21
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  synthetic primer

<400>  8
cgtggatgag gagccgcagt g                                                 21


<210>  9
<211>  21
<212>  DNA
<213>  Artificial sequence

<220>
<223>  synthetic primer

<400>  9
cgtggacaga ccccggtagt g                                                 21


<210>  10
<211>  41
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  synthetic primer

<400>  10
ggattctaat acgactcact atagggtcgc gcccataact c                           41


<210>  11
<211>  41
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  synthetic primer

<400>  11
ggattctaat acgactcact atagggatcg caccagcgtg t                           41


<210>  12
<211>  40
<212>  DNA
<213>  Artificial sequence

<220>
<223>  synthetic primer

<400>  12
ggattctaat acgactcact atagggcctc gcctatccca                             40


<210>  13
<211>  14
<212>  DNA
<213>  Artificial Sequece

<220>
<223>  synthetic


<220>
<221>  misc_feature
<222>  (6)..(6)
<223>  n is a, c, g, or t

<220>
<221>  misc_feature
<222>  (9)..(9)
<223>  n is a, c, g, or t

<400>  13
ccgcgnggng gcag                                                         14


<210>  14
<211>  288
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  N-terminal capping region

<400>  14

Met Asp Pro Ile Arg Ser Arg Thr Pro Ser Pro Ala Arg Glu Leu Leu 
1               5                   10                  15      


Ser Gly Pro Gln Pro Asp Gly Val Gln Pro Thr Ala Asp Arg Gly Val 
            20                  25                  30          


Ser Pro Pro Ala Gly Gly Pro Leu Asp Gly Leu Pro Ala Arg Arg Thr 
        35                  40                  45              


Met Ser Arg Thr Arg Leu Pro Ser Pro Pro Ala Pro Ser Pro Ala Phe 
    50                  55                  60                  


Ser Ala Asp Ser Phe Ser Asp Leu Leu Arg Gln Phe Asp Pro Ser Leu 
65                  70                  75                  80  


Phe Asn Thr Ser Leu Phe Asp Ser Leu Pro Pro Phe Gly Ala His His 
                85                  90                  95      


Thr Glu Ala Ala Thr Gly Glu Trp Asp Glu Val Gln Ser Gly Leu Arg 
            100                 105                 110         


Ala Ala Asp Ala Pro Pro Pro Thr Met Arg Val Ala Val Thr Ala Ala 
        115                 120                 125             


Arg Pro Pro Arg Ala Lys Pro Ala Pro Arg Arg Arg Ala Ala Gln Pro 
    130                 135                 140                 


Ser Asp Ala Ser Pro Ala Ala Gln Val Asp Leu Arg Thr Leu Gly Tyr 
145                 150                 155                 160 


Ser Gln Gln Gln Gln Glu Lys Ile Lys Pro Lys Val Arg Ser Thr Val 
                165                 170                 175     


Ala Gln His His Glu Ala Leu Val Gly His Gly Phe Thr His Ala His 
            180                 185                 190         


Ile Val Ala Leu Ser Gln His Pro Ala Ala Leu Gly Thr Val Ala Val 
        195                 200                 205             


Lys Tyr Gln Asp Met Ile Ala Ala Leu Pro Glu Ala Thr His Glu Ala 
    210                 215                 220                 


Ile Val Gly Val Gly Lys Gln Trp Ser Gly Ala Arg Ala Leu Glu Ala 
225                 230                 235                 240 


Leu Leu Thr Val Ala Gly Glu Leu Arg Gly Pro Pro Leu Gln Leu Asp 
                245                 250                 255     


Thr Gly Gln Leu Leu Lys Ile Ala Lys Arg Gly Gly Val Thr Ala Val 
            260                 265                 270         


Glu Ala Val His Ala Trp Arg Asn Ala Leu Thr Gly Ala Pro Leu Asn 
        275                 280                 285             


<210>  15
<211>  183
<212>  PRT
<213>  Artificial Sequence

<220>
<223>  C-Terminal capping region

<400>  15

Arg Pro Ala Leu Glu Ser Ile Val Ala Gln Leu Ser Arg Pro Asp Pro 
1               5                   10                  15      


Ala Leu Ala Ala Leu Thr Asn Asp His Leu Val Ala Leu Ala Cys Leu 
            20                  25                  30          


Gly Gly Arg Pro Ala Leu Asp Ala Val Lys Lys Gly Leu Pro His Ala 
        35                  40                  45              


Pro Ala Leu Ile Lys Arg Thr Asn Arg Arg Ile Pro Glu Arg Thr Ser 
    50                  55                  60                  


His Arg Val Ala Asp His Ala Gln Val Val Arg Val Leu Gly Phe Phe 
65                  70                  75                  80  


Gln Cys His Ser His Pro Ala Gln Ala Phe Asp Asp Ala Met Thr Gln 
                85                  90                  95      


Phe Gly Met Ser Arg His Gly Leu Leu Gln Leu Phe Arg Arg Val Gly 
            100                 105                 110         


Val Thr Glu Leu Glu Ala Arg Ser Gly Thr Leu Pro Pro Ala Ser Gln 
        115                 120                 125             


Arg Trp Asp Arg Ile Leu Gln Ala Ser Gly Met Lys Arg Ala Lys Pro 
    130                 135                 140                 


Ser Pro Thr Ser Thr Gln Thr Pro Asp Gln Ala Ser Leu His Ala Phe 
145                 150                 155                 160 


Ala Asp Ser Leu Glu Arg Asp Leu Asp Ala Pro Ser Pro Met His Glu 
                165                 170                 175     


Gly Asp Gln Thr Arg Ala Ser 
            180             


<210>  16
<211>  14
<212>  DNA
<213>  Artificial Sequence

<220>
<223>  synthetic


<220>
<221>  misc_feature
<222>  (5)..(5)
<223>  n is a, c, g, or t

<400>  16
ccacnaggtg gcag                                                         14


<210>  17
<211>  23
<212>  DNA
<213>  Artificial sequence

<220>
<223>  mutant clone 001

<400>  17
tcacagctat ttccacaaga ggg                                               23


<210>  18
<211>  46
<212>  DNA
<213>  Artificial sequence

<220>
<223>  mutant clone 002

<400>  18
gcccgggagc tttcaggaca ggggctcacg gagcacttgc ccaggg                      46


<210>  19
<211>  46
<212>  DNA
<213>  Artificial sequence

<220>
<223>  mutant clone 003

<400>  19
ggaaaaccct ctggacccca gggagaagtc ctcccttgga cagggg                      46


<210>  20
<211>  46
<212>  DNA
<213>  Artificial sequence

<220>
<223>  mutant clone 004

<400>  20
ggaaaaccct ctggacccca gggagaagtc ctcccttgga cagggg                      46


<210>  21
<211>  46
<212>  DNA
<213>  Artificial sequence

<220>
<223>  mutant clone 005 - B forward inversion

<400>  21
ggaaaaccct ctggacccca gggagaagtc ctcccttgga cagggg                      46


<210>  22
<211>  23
<212>  DNA
<213>  Artificial sequence

<220>
<223>  mutant clone 005 - B reverse insertion

<400>  22
cacctagata ctccaccagg ggg                                               23


<210>  23
<211>  46
<212>  DNA
<213>  Artificial sequence

<220>
<223>  mutant clone 006 - B forward inversion

<400>  23
ggaaaaccct ctggacccca gggagaagtc ctcccttgga cagggg                      46


<210>  24
<211>  23
<212>  DNA
<213>  Artificial sequence

<220>
<223>  mutant clone 006 - B reverse inversion

<400>  24
cacctagata ctccaccagg ggg                                               23


<210>  25
<211>  23
<212>  DNA
<213>  Artificial sequence

<220>
<223>  mutant clone 007

<400>  25
ccttgttagt taccagcaga ggg                                               23


<210>  26
<211>  23
<212>  DNA
<213>  Artificial sequence

<220>
<223>  mutant clone 008

<400>  26
ccttgttagt taccagcaga ggg                                               23


<210>  27
<211>  23
<212>  DNA
<213>  Artificial sequence

<220>
<223>  mutant clone 009

<400>  27
ccttgttagt taccagcaga ggg                                               23


<210>  28
<211>  23
<212>  DNA
<213>  Artificial sequence

<220>
<223>  mutant clone 010

<400>  28
ccttgttagt taccagcaga ggg                                               23


<210>  29
<211>  23
<212>  DNA
<213>  Artificial sequence

<220>
<223>  mutant clone 011

<400>  29
ttttaacttt tgccatcagg tgg                                               23


<210>  30
<211>  23
<212>  DNA
<213>  Artificial sequence

<220>
<223>  mutant clone 012

<400>  30
ccttgttagt taccagcaga ggg                                               23


<210>  31
<211>  23
<212>  DNA
<213>  Artificial sequence

<220>
<223>  mutant clone 013 - E forward

<400>  31
ccttgttagt taccagcaga ggg                                               23


<210>  32
<211>  23
<212>  DNA
<213>  Artificial sequence

<220>
<223>  mutant clone 13 - E reverse

<400>  32
ttttaacttt tgccatcagg tgg                                               23


<210>  33
<211>  23
<212>  DNA
<213>  Artificial sequence

<220>
<223>  mutant clone 014 - E forward

<400>  33
ccttgttagt taccagcaga ggg                                               23


<210>  34
<211>  23
<212>  DNA
<213>  Artificial sequence

<220>
<223>  mutant clone 014 - E reverse

<400>  34
ttttaacttt tgccatcagg tgg                                               23


<210>  35
<211>  23
<212>  DNA
<213>  Artificial sequence

<220>
<223>  mutant clone 015 - E forward

<400>  35
ccttgttagt taccagcaga ggg                                               23


<210>  36
<211>  23
<212>  DNA
<213>  Artificial sequence

<220>
<223>  mutant clone 015 - E reverse

<400>  36
ttttaacttt tgccatcagg tgg                                               23


<210>  37
<211>  23
<212>  DNA
<213>  Artificial sequence

<220>
<223>  mutant clone 016

<400>  37
ccttgttagt taccagcaga ggg                                               23


<210>  38
<211>  23
<212>  DNA
<213>  Artificial sequence

<220>
<223>  mutant clone 017

<400>  38
tctggtagtc tagggccacc tgg                                               23


<210>  39
<211>  46
<212>  DNA
<213>  Artificial sequence

<220>
<223>  mutant clone 018

<400>  39
cagcacagtt gaattcccag tggattcagt taagtttatt ccacgg                      46


<210>  40
<211>  19
<212>  DNA
<213>  Artificial sequence

<220>
<223>  synthetic oligonucleotides

<400>  40
caaccccaca gggagaact                                                    19


<210>  41
<211>  21
<212>  DNA
<213>  Artificial sequence

<220>
<223>  synthetic oligonucleotide

<400>  41
actttcattt tcaggtcaga c                                                 21


<210>  42
<211>  21
<212>  DNA
<213>  Artificial sequence

<220>
<223>  synthetic oligonucleotide

<400>  42
cttttcttct caggttacag t                                                 21


<210>  43
<211>  21
<212>  DNA
<213>  Artificial sequence

<220>
<223>  synthetic oligonucleotide

<400>  43
tcaatcacac aagggaaatg c                                                 21


<210>  44
<211>  22
<212>  DNA
<213>  Artificial sequence

<220>
<223>  synthetic oligonucleotide

<400>  44
caacagcaat ttcagtaagg tg                                                22


<210>  45
<211>  21
<212>  DNA
<213>  Artificial sequence

<220>
<223>  synthetic oligonucleotide

<400>  45
gatctggtca aaatcagaga t                                                 21


